[med-svn] [acacia] 07/09: New upstream version 1.53
Andreas Tille
tille at debian.org
Fri Dec 1 14:47:57 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository acacia.
commit 5f3d33c38201318783a9155f92eea9e310ddc845
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 1 15:42:42 2017 +0100
New upstream version 1.53
---
.classpath | 30 +
.metadata/.lock | 0
.metadata/.mylyn/repositories.xml.zip | Bin 0 -> 411 bytes
.metadata/.mylyn/tasks.xml.zip | Bin 0 -> 250 bytes
.../.root/.indexes/history.version | 1 +
.../.root/.indexes/properties.index | Bin 0 -> 57 bytes
.../.root/.indexes/properties.version | 1 +
.../org.eclipse.core.resources/.root/2.tree | Bin 0 -> 120 bytes
.../.safetable/org.eclipse.core.resources | Bin 0 -> 448 bytes
.../.settings/org.eclipse.core.resources.prefs | 3 +
.../org.eclipse.epp.usagedata.recording.prefs | 3 +
.../.settings/org.eclipse.jdt.ui.prefs | 15 +
.../.settings/org.eclipse.mylyn.context.core.prefs | 3 +
.../.settings/org.eclipse.mylyn.monitor.ui.prefs | 3 +
.../.settings/org.eclipse.team.cvs.ui.prefs | 3 +
.../.settings/org.eclipse.team.ui.prefs | 3 +
.../.settings/org.eclipse.ui.ide.prefs | 6 +
.../.settings/org.eclipse.ui.prefs | 3 +
.../.settings/org.eclipse.ui.workbench.prefs | 3 +
.../usagedata.csv | 210 +
.../org.eclipse.jdt.core/nonChainingJarsCache | Bin 0 -> 4 bytes
.../variablesAndContainers.dat | Bin 0 -> 96 bytes
.../org.eclipse.jdt.ui/OpenTypeHistory.xml | 2 +
.../QualifiedTypeNameHistory.xml | 2 +
.../org.eclipse.jdt.ui/dialog_settings.xml | 10 +
.../org.eclipse.ui.ide/dialog_settings.xml | 11 +
.../org.eclipse.ui.workbench/dialog_settings.xml | 3 +
.../org.eclipse.ui.workbench/workbench.xml | 238 +
.../org.eclipse.ui.workbench/workingsets.xml | 4 +
.metadata/version.ini | 1 +
.project | 17 +
README | 52 +
classmexer.jar | Bin 0 -> 4578 bytes
debian/README.source | 40 -
debian/acacia.desktop | 12 -
debian/acacia.docs | 1 -
debian/acacia.install | 4 -
debian/acacia.jlibs | 1 -
debian/bin/acacia | 10 -
debian/changelog | 18 -
debian/classpath.sh | 48 -
debian/compat | 1 -
debian/control | 40 -
debian/copyright | 25 -
debian/rules | 28 -
debian/source/format | 1 -
debian/upstream/metadata | 11 -
debian/watch | 5 -
jar-in-jar-loader.zip | Bin 0 -> 7269 bytes
script_exejar_gitbuild.xml | 44 +
script_exejar_gitbuild_workstation.xml | 41 +
src/data/.svn/entries | 198 +
src/data/.svn/text-base/MID_fivebase.csv.svn-base | 50 +
src/data/.svn/text-base/MID_tenbase.csv.svn-base | 14 +
src/data/.svn/text-base/NUC.4.4.svn-base | 25 +
src/data/.svn/text-base/QuinceProbs.csv.svn-base | 11 +
.../maldeEmpiricalDistributions.csv.svn-base | 140 +
src/data/100bpOneTouch_314_counts_complete.csv | 3073 +++++++++++
...00bpOneTouch_314_counts_complete_model_ones.csv | 33 +
...bpOneTouch_314_counts_complete_model_others.csv | 98 +
...bpOneTouch_314_counts_complete_model_zeroes.csv | 33 +
src/data/100bpOneTouch_316_counts_complete.csv | 3073 +++++++++++
...00bpOneTouch_316_counts_complete_model_ones.csv | 33 +
...bpOneTouch_316_counts_complete_model_others.csv | 98 +
...bpOneTouch_316_counts_complete_model_zeroes.csv | 33 +
src/data/200bpManual_314_counts_complete.csv | 5377 ++++++++++++++++++++
.../200bpManual_314_counts_complete_model_ones.csv | 33 +
...00bpManual_314_counts_complete_model_others.csv | 98 +
...00bpManual_314_counts_complete_model_zeroes.csv | 33 +
src/data/200bpManual_316_counts_complete.csv | 5377 ++++++++++++++++++++
.../200bpManual_316_counts_complete_model_ones.csv | 33 +
...00bpManual_316_counts_complete_model_others.csv | 98 +
...00bpManual_316_counts_complete_model_zeroes.csv | 33 +
src/data/200bpOneTouch_314_counts_complete.csv | 5377 ++++++++++++++++++++
...00bpOneTouch_314_counts_complete_model_ones.csv | 33 +
...bpOneTouch_314_counts_complete_model_others.csv | 98 +
...bpOneTouch_314_counts_complete_model_zeroes.csv | 33 +
src/data/200bpOneTouch_316_counts_complete.csv | 4993 ++++++++++++++++++
...00bpOneTouch_316_counts_complete_model_ones.csv | 33 +
...bpOneTouch_316_counts_complete_model_others.csv | 98 +
...bpOneTouch_316_counts_complete_model_zeroes.csv | 33 +
src/data/MID_fivebase.csv | 50 +
src/data/MID_tenbase.csv | 14 +
src/data/NUC.4.4 | 25 +
src/data/QuinceProbs.csv | 11 +
src/data/build_info.properties | 5 +
src/data/maldeEmpiricalDistributions.csv | 140 +
src/data/titanium_emp_nuc.csv | 140 +
src/images/.svn/entries | 232 +
src/images/.svn/prop-base/Acacia_logo.png.svn-base | 5 +
.../.svn/prop-base/Acacia_logo2.png.svn-base | 5 +
.../.svn/prop-base/acacia_logo_double.png.svn-base | 5 +
.../acacia_small_wattle_icon.png.svn-base | 5 +
.../.svn/prop-base/questionMarkGreen.png.svn-base | 5 +
src/images/.svn/prop-base/wattle.jpg.svn-base | 5 +
src/images/.svn/text-base/Acacia_logo.png.svn-base | Bin 0 -> 157428 bytes
.../.svn/text-base/Acacia_logo2.png.svn-base | Bin 0 -> 166565 bytes
.../.svn/text-base/acacia_logo_double.png.svn-base | Bin 0 -> 128722 bytes
.../acacia_small_wattle_icon.png.svn-base | Bin 0 -> 113733 bytes
.../.svn/text-base/questionMarkGreen.png.svn-base | Bin 0 -> 804 bytes
src/images/.svn/text-base/wattle.jpg.svn-base | Bin 0 -> 20414 bytes
src/images/Acacia_logo2.png | Bin 0 -> 166565 bytes
src/images/acacia_small_wattle_icon.png | Bin 0 -> 113733 bytes
src/images/questionMarkGreen.png | Bin 0 -> 804 bytes
src/pyromaniac/.metadata/.lock | 0
src/pyromaniac/.metadata/.mylyn/.tasks.xml.zip | Bin 0 -> 250 bytes
.../.metadata/.mylyn/repositories.xml.zip | Bin 0 -> 411 bytes
src/pyromaniac/.metadata/.mylyn/tasks.xml.zip | Bin 0 -> 250 bytes
.../.root/.indexes/history.version | 1 +
.../.root/.indexes/properties.index | Bin 0 -> 57 bytes
.../.root/.indexes/properties.version | 1 +
.../org.eclipse.core.resources/.root/2.tree | Bin 0 -> 121 bytes
.../.safetable/org.eclipse.core.resources | Bin 0 -> 448 bytes
.../.settings/org.eclipse.core.resources.prefs | 3 +
.../org.eclipse.epp.usagedata.recording.prefs | 3 +
.../.settings/org.eclipse.jdt.ui.prefs | 15 +
.../.settings/org.eclipse.mylyn.context.core.prefs | 3 +
.../.settings/org.eclipse.mylyn.monitor.ui.prefs | 3 +
.../.settings/org.eclipse.team.cvs.ui.prefs | 3 +
.../.settings/org.eclipse.team.ui.prefs | 3 +
.../.settings/org.eclipse.ui.ide.prefs | 6 +
.../.settings/org.eclipse.ui.prefs | 3 +
.../.settings/org.eclipse.ui.workbench.prefs | 3 +
.../usagedata.csv | 237 +
.../org.eclipse.jdt.core/nonChainingJarsCache | Bin 0 -> 4 bytes
.../variablesAndContainers.dat | Bin 0 -> 96 bytes
.../org.eclipse.jdt.ui/OpenTypeHistory.xml | 2 +
.../QualifiedTypeNameHistory.xml | 2 +
.../org.eclipse.jdt.ui/dialog_settings.xml | 10 +
.../org.eclipse.ui.ide/dialog_settings.xml | 11 +
.../org.eclipse.ui.workbench/dialog_settings.xml | 3 +
.../org.eclipse.ui.workbench/workbench.xml | 200 +
.../org.eclipse.ui.workbench/workingsets.xml | 4 +
src/pyromaniac/.metadata/version.ini | 1 +
src/pyromaniac/AcaciaConstants.java | 436 ++
src/pyromaniac/AcaciaEngine.java | 1570 ++++++
src/pyromaniac/AcaciaMain.java | 1075 ++++
.../Algorithm/BalzerOUCallFrequencyTable.java | 380 ++
src/pyromaniac/Algorithm/BigDecimalUtils.java | 380 ++
src/pyromaniac/Algorithm/BinomialTest.java | 120 +
src/pyromaniac/Algorithm/ClusterAligner.java | 60 +
src/pyromaniac/Algorithm/ClusterGenerator.java | 84 +
src/pyromaniac/Algorithm/CoarseAlignSplitter.java | 443 ++
src/pyromaniac/Algorithm/ConsensusGenerator.java | 61 +
.../Algorithm/ConsensusGeneratorLocalTests.java | 1034 ++++
src/pyromaniac/Algorithm/DivergentTagResult.java | 20 +
src/pyromaniac/Algorithm/HypothesisTest.java | 159 +
.../Algorithm/IonTorrentOUCallFrequencyTable.java | 561 ++
.../Algorithm/MultinomialOneSidedTest.java | 170 +
src/pyromaniac/Algorithm/OUFrequencyTable.java | 76 +
.../Algorithm/OligomerClusterGenerator.java | 429 ++
.../Algorithm/QuinceOUFrequencyTable.java | 281 +
.../Algorithm/RLEAlignmentIndelsOnly.java | 1475 ++++++
src/pyromaniac/Algorithm/SimpleClusterAligner.java | 456 ++
src/pyromaniac/DataCleaner.java | 366 ++
src/pyromaniac/DataStructures/DMCell.java | 28 +
src/pyromaniac/DataStructures/DistanceMatrix.java | 118 +
src/pyromaniac/DataStructures/FlowCycler.java | 166 +
src/pyromaniac/DataStructures/MIDPrimerCombo.java | 131 +
src/pyromaniac/DataStructures/MutableInteger.java | 86 +
src/pyromaniac/DataStructures/Pair.java | 74 +
src/pyromaniac/DataStructures/PatriciaTrie.java | 541 ++
src/pyromaniac/DataStructures/Pyrotag.java | 1187 +++++
src/pyromaniac/DataStructures/QualitySequence.java | 163 +
src/pyromaniac/DataStructures/Sequence.java | 181 +
src/pyromaniac/DataStructures/Triplet.java | 79 +
src/pyromaniac/ErrorCorrectionWorker.java | 235 +
src/pyromaniac/GUI/AcaciaGradientButton.java | 304 ++
src/pyromaniac/GUI/AcaciaMainFrame.java | 102 +
src/pyromaniac/GUI/CustomDialog.java | 118 +
src/pyromaniac/GUI/FeatureIcon.java | 66 +
src/pyromaniac/GUI/GridBagUtility.java | 152 +
src/pyromaniac/GUI/HelpButton.java | 172 +
src/pyromaniac/GUI/JoinIcon.java | 52 +
src/pyromaniac/GUI/LogTextPane.java | 210 +
src/pyromaniac/GUI/NonNumericFilter.java | 74 +
src/pyromaniac/GUI/SpringUtilities.java | 241 +
src/pyromaniac/GUI/TagInputPanel.java | 2266 +++++++++
src/pyromaniac/IO/AcaciaLogger.java | 354 ++
src/pyromaniac/IO/LogFileHandle.java | 94 +
src/pyromaniac/IO/LoggerOutput.java | 74 +
src/pyromaniac/IO/MIDReader.java | 166 +
src/pyromaniac/IO/MMFastaImporter.java | 501 ++
src/pyromaniac/IO/MMFastqImporter.java | 437 ++
src/pyromaniac/IO/QualityFile.java | 67 +
src/pyromaniac/IO/QualityFile454.java | 245 +
src/pyromaniac/IO/SeqReadingUtility.java | 480 ++
src/pyromaniac/IO/StandardOutputHandle.java | 83 +
src/pyromaniac/IO/TagImporter.java | 143 +
src/pyromaniac/RunCharacterisation.java | 282 +
src/pyromaniac/package.html | 7 +
191 files changed, 49883 insertions(+), 245 deletions(-)
diff --git a/.classpath b/.classpath
new file mode 100644
index 0000000..8e32835
--- /dev/null
+++ b/.classpath
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path="src"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib/ssj.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/blas.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib/colt.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/commons-cli-1.2/commons-cli-1.2.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib/tcode.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib/logger-1.6.4.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib/jcommon-1.0.13.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib/event-1.6.5.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib/interpreter-1.6.8.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/commons-math3-3.1.1/commons-math3-3.1.1.jar">
+ <attributes>
+ <attribute name="javadoc_location" value="file:/E:/Eclipse/workspace/3rd_party/commons-math-2.1/commons-math-2.1/docs/"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/biojava.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib/optimization.jar"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/hac"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/appframework-1.0.3.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/swing-layout-1.0.3.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/swing-worker-1.1.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/netbeans-7.4/platform/modules/org-netbeans-swing-outline.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/commons-io-2.4/commons-io-2.4.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/netbeans-7.4/platform/modules/org-openide-explorer.jar"/>
+ <classpathentry kind="lib" path="/home/bra427/netbeans-7.4/platform/modules/org-openide-nodes.jar"/>
+ <classpathentry kind="output" path="bin"/>
+</classpath>
diff --git a/.metadata/.lock b/.metadata/.lock
new file mode 100644
index 0000000..e69de29
diff --git a/.metadata/.mylyn/repositories.xml.zip b/.metadata/.mylyn/repositories.xml.zip
new file mode 100644
index 0000000..042fe9b
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diff --git a/.metadata/.mylyn/tasks.xml.zip b/.metadata/.mylyn/tasks.xml.zip
new file mode 100644
index 0000000..047edf0
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diff --git a/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version
new file mode 100644
index 0000000..25cb955
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version
@@ -0,0 +1 @@
+
\ No newline at end of file
diff --git a/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.index b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.index
new file mode 100644
index 0000000..9c245ea
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diff --git a/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version
new file mode 100644
index 0000000..6b2aaa7
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version
@@ -0,0 +1 @@
+
\ No newline at end of file
diff --git a/.metadata/.plugins/org.eclipse.core.resources/.root/2.tree b/.metadata/.plugins/org.eclipse.core.resources/.root/2.tree
new file mode 100644
index 0000000..44d690a
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diff --git a/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources b/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources
new file mode 100644
index 0000000..42d3f99
Binary files /dev/null and b/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources differ
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs
new file mode 100644
index 0000000..9798684
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs
@@ -0,0 +1,3 @@
+#Wed Apr 18 11:06:29 EST 2012
+version=1
+eclipse.preferences.version=1
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.epp.usagedata.recording.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.epp.usagedata.recording.prefs
new file mode 100644
index 0000000..5cf9618
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.epp.usagedata.recording.prefs
@@ -0,0 +1,3 @@
+#Wed Apr 18 11:06:25 EST 2012
+org.eclipse.epp.usagedata.recording.last-upload=1334711185449
+eclipse.preferences.version=1
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs
new file mode 100644
index 0000000..bda46dc
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs
@@ -0,0 +1,15 @@
+#Wed Apr 18 11:06:30 EST 2012
+useQuickDiffPrefPage=true
+proposalOrderMigrated=true
+tabWidthPropagated=true
+content_assist_proposals_background=255,255,255
+org.eclipse.jdt.ui.javadoclocations.migrated=true
+useAnnotationsPrefPage=true
+spelling_locale=en_GB
+org.eclipse.jface.textfont=1|Courier New|10.0|0|WINDOWS|1|0|0|0|0|0|0|0|0|1|0|0|0|0|Courier New;
+org.eclipse.jdt.ui.editor.tab.width=
+org.eclipse.jdt.ui.formatterprofiles.version=11
+spelling_locale_initialized=true
+eclipse.preferences.version=1
+content_assist_proposals_foreground=0,0,0
+fontPropagated=true
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs
new file mode 100644
index 0000000..1d12764
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs
@@ -0,0 +1,3 @@
+#Wed Apr 18 11:06:21 EST 2012
+eclipse.preferences.version=1
+mylyn.attention.migrated=true
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs
new file mode 100644
index 0000000..0bfb7ee
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs
@@ -0,0 +1,3 @@
+#Wed Apr 18 11:06:21 EST 2012
+org.eclipse.mylyn.monitor.activity.tracking.enabled.checked=true
+eclipse.preferences.version=1
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.cvs.ui.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.cvs.ui.prefs
new file mode 100644
index 0000000..1990069
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.cvs.ui.prefs
@@ -0,0 +1,3 @@
+#Wed Apr 18 11:06:30 EST 2012
+pref_first_startup=false
+eclipse.preferences.version=1
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.ui.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.ui.prefs
new file mode 100644
index 0000000..f819352
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.ui.prefs
@@ -0,0 +1,3 @@
+#Wed Apr 18 11:06:30 EST 2012
+eclipse.preferences.version=1
+org.eclipse.team.ui.first_time=false
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs
new file mode 100644
index 0000000..ca7dbab
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs
@@ -0,0 +1,6 @@
+#Wed Apr 18 11:06:30 EST 2012
+eclipse.preferences.version=1
+tipsAndTricks=true
+platformState=1307866151256
+quickStart=false
+PROBLEMS_FILTERS_MIGRATE=true
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.prefs
new file mode 100644
index 0000000..7f5c01c
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.prefs
@@ -0,0 +1,3 @@
+#Wed Apr 18 11:06:22 EST 2012
+eclipse.preferences.version=1
+showIntro=false
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs
new file mode 100644
index 0000000..9f12245
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs
@@ -0,0 +1,3 @@
+#Wed Apr 18 11:06:23 EST 2012
+eclipse.preferences.version=1
+ENABLED_DECORATORS=org.eclipse.egit.ui.internal.decorators.GitLightweightDecorator\:true,org.eclipse.jdt.ui.override.decorator\:true,org.eclipse.jdt.ui.interface.decorator\:false,org.eclipse.jdt.ui.buildpath.decorator\:true,org.eclipse.mylyn.context.ui.decorator.interest\:true,org.eclipse.mylyn.tasks.ui.decorators.task\:true,org.eclipse.mylyn.team.ui.changeset.decorator\:true,org.eclipse.team.cvs.ui.decorator\:true,org.eclipse.ui.LinkedResourceDecorator\:true,org.eclipse.ui.VirtualResour [...]
diff --git a/.metadata/.plugins/org.eclipse.epp.usagedata.recording/usagedata.csv b/.metadata/.plugins/org.eclipse.epp.usagedata.recording/usagedata.csv
new file mode 100644
index 0000000..4640523
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.epp.usagedata.recording/usagedata.csv
@@ -0,0 +1,210 @@
+what,kind,bundleId,bundleVersion,description,time
+activated,perspective,org.eclipse.jdt.ui,,"org.eclipse.jdt.ui.JavaPerspective",1334711184358
+started,bundle,org.eclipse.osgi,3.6.2.R36x_v20110210,"org.eclipse.osgi",1334711184359
+started,bundle,org.eclipse.equinox.simpleconfigurator,1.0.200.v20100503,"org.eclipse.equinox.simpleconfigurator",1334711184360
+started,bundle,com.ibm.icu,4.2.1.v20100412,"com.ibm.icu",1334711184361
+started,bundle,org.eclipse.core.contenttype,3.4.100.v20100505-1235,"org.eclipse.core.contenttype",1334711184361
+started,bundle,org.eclipse.core.databinding.observable,1.3.0.I20100601-0800,"org.eclipse.core.databinding.observable",1334711184363
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+stopped,bundle,org.eclipse.compare.win32,1.0.101.R36x_v20101103-0618,"org.eclipse.compare.win32",1334711222433
+stopped,bundle,org.eclipse.equinox.p2.ui.sdk,1.0.100.v20100513,"org.eclipse.equinox.p2.ui.sdk",1334711222434
+stopped,bundle,org.eclipse.mylyn.java.tasks,3.4.0.v20100608-0100-e3x,"org.eclipse.mylyn.java.tasks",1334711222435
+stopped,bundle,org.eclipse.mylyn.java.ui,3.4.0.v20100608-0100-e3x,"org.eclipse.mylyn.java.ui",1334711222436
+stopped,bundle,org.eclipse.jdt.junit,3.6.1.r361_v20100825-0800,"org.eclipse.jdt.junit",1334711222437
+stopped,bundle,org.eclipse.jdt.apt.ui,3.3.300.v20100513-0845,"org.eclipse.jdt.apt.ui",1334711222439
+stopped,bundle,org.eclipse.jdt.debug.ui,3.5.2.v20100928a_r362,"org.eclipse.jdt.debug.ui",1334711222441
+stopped,bundle,net.sf.jautodoc,1.9.0,"net.sf.jautodoc",1334711222442
+stopped,bundle,org.eclipse.jdt.ui,3.6.2.r362_v20110203,"org.eclipse.jdt.ui",1334711222443
+stopped,bundle,org.eclipse.wst.dtd.ui,1.0.500.v201004290328,"org.eclipse.wst.dtd.ui",1334711222444
diff --git a/.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache b/.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache
new file mode 100644
index 0000000..593f470
Binary files /dev/null and b/.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache differ
diff --git a/.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat b/.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat
new file mode 100644
index 0000000..3aea61c
Binary files /dev/null and b/.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat differ
diff --git a/.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml b/.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml
new file mode 100644
index 0000000..6cd9562
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml
@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<typeInfoHistroy/>
diff --git a/.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml b/.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml
new file mode 100644
index 0000000..8c365b7
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml
@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<qualifiedTypeNameHistroy/>
diff --git a/.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml b/.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml
new file mode 100644
index 0000000..4915323
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<section name="Workbench">
+ <section name="org.eclipse.jdt.internal.ui.packageview.PackageExplorerPart">
+ <item value="true" key="group_libraries"/>
+ <item value="false" key="linkWithEditor"/>
+ <item value="2" key="layout"/>
+ <item value="1" key="rootMode"/>
+ <item value="<?xml version="1.0" encoding="UTF-8"?>
<packageExplorer group_libraries="1" layout="2" linkWithEditor="0" rootMode="1" workingSetName="">
<customFilters userDefinedPatternsEnabled="false">
<xmlDefinedFilters>
<child filterId="org.eclipse.jdt.ui.PackageExplorer.LibraryFilter" isEnabled="false"/>
&# [...]
+ </section>
+</section>
diff --git a/.metadata/.plugins/org.eclipse.ui.ide/dialog_settings.xml b/.metadata/.plugins/org.eclipse.ui.ide/dialog_settings.xml
new file mode 100644
index 0000000..278942a
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.ui.ide/dialog_settings.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<section name="Workbench">
+ <section name="ChooseWorkspaceDialogSettings">
+ <item value="197" key="DIALOG_Y_ORIGIN"/>
+ <item value="202" key="DIALOG_X_ORIGIN"/>
+ </section>
+ <section name="WORKBENCH_SETTINGS">
+ <list key="ENABLED_TRANSFERS">
+ </list>
+ </section>
+</section>
diff --git a/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml b/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml
new file mode 100644
index 0000000..1ef2b05
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml
@@ -0,0 +1,3 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<section name="Workbench">
+</section>
diff --git a/.metadata/.plugins/org.eclipse.ui.workbench/workbench.xml b/.metadata/.plugins/org.eclipse.ui.workbench/workbench.xml
new file mode 100644
index 0000000..2a331f1
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.ui.workbench/workbench.xml
@@ -0,0 +1,238 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<workbench progressCount="21" version="2.0">
+<workbenchAdvisor/>
+<window height="768" width="1024" x="100" y="100">
+<fastViewData fastViewLocation="1024"/>
+<perspectiveBar>
+<itemSize x="160"/>
+</perspectiveBar>
+<coolbarLayout locked="0">
+<coolItem id="group.file" itemType="typeGroupMarker"/>
+<coolItem id="org.eclipse.ui.workbench.file" itemType="typeToolBarContribution" x="122" y="22"/>
+<coolItem id="additions" itemType="typeGroupMarker"/>
+<coolItem id="org.eclipse.debug.ui.launchActionSet" itemType="typeToolBarContribution" x="129" y="22"/>
+<coolItem id="org.eclipse.jdt.ui.JavaElementCreationActionSet" itemType="typeToolBarContribution" x="76" y="22"/>
+<coolItem id="org.eclipse.search.searchActionSet" itemType="typeToolBarContribution" x="99" y="22"/>
+<coolItem id="org.eclipse.wst.xml.ui.perspective.NewFileToolBar" itemType="typeToolBarContribution" x="-1" y="-1"/>
+<coolItem id="org.eclipse.wst.xml.ui.design.DesignToolBar" itemType="typeToolBarContribution" x="-1" y="-1"/>
+<coolItem id="group.nav" itemType="typeGroupMarker"/>
+<coolItem id="org.eclipse.ui.workbench.navigate" itemType="typeToolBarContribution" x="190" y="22"/>
+<coolItem id="group.editor" itemType="typeGroupMarker"/>
+<coolItem id="group.help" itemType="typeGroupMarker"/>
+<coolItem id="org.eclipse.ui.workbench.help" itemType="typeToolBarContribution" x="-1" y="-1"/>
+</coolbarLayout>
+<page aggregateWorkingSetId="Aggregate for window 1334711181803" focus="true" label="Workspace - Java">
+<editors>
+<editorArea activeWorkbook="DefaultEditorWorkbook">
+<info part="DefaultEditorWorkbook">
+<folder appearance="1" expanded="2">
+<presentation id="org.eclipse.ui.presentations.WorkbenchPresentationFactory"/>
+</folder>
+</info>
+</editorArea>
+</editors>
+<views>
+<view id="org.eclipse.ui.views.ProblemView" partName="Problems">
+<viewState PRIMARY_SORT_FIELD="org.eclipse.ui.ide.severityAndDescriptionField" categoryGroup="org.eclipse.ui.ide.severity" markerContentGenerator="org.eclipse.ui.ide.problemsGenerator" partName="Problems">
+<columnWidths org.eclipse.ui.ide.locationField="64" org.eclipse.ui.ide.markerType="94" org.eclipse.ui.ide.pathField="124" org.eclipse.ui.ide.resourceField="94" org.eclipse.ui.ide.severityAndDescriptionField="300"/>
+<visible IMemento.internal.id="org.eclipse.ui.ide.severityAndDescriptionField"/>
+<visible IMemento.internal.id="org.eclipse.ui.ide.resourceField"/>
+<visible IMemento.internal.id="org.eclipse.ui.ide.pathField"/>
+<visible IMemento.internal.id="org.eclipse.ui.ide.locationField"/>
+<visible IMemento.internal.id="org.eclipse.ui.ide.markerType"/>
+</viewState>
+</view>
+<view id="org.eclipse.jdt.ui.PackageExplorer" partName="Package Explorer">
+<viewState group_libraries="1" layout="2" linkWithEditor="0" rootMode="1" workingSetName="">
+<customFilters userDefinedPatternsEnabled="false">
+<xmlDefinedFilters>
+<child filterId="org.eclipse.jdt.ui.PackageExplorer.LibraryFilter" isEnabled="false"/>
+<child filterId="org.eclipse.jdt.ui.PackageExplorer.LocalTypesFilter" isEnabled="false"/>
+<child filterId="org.eclipse.jdt.ui.PackageExplorer.StaticsFilter" isEnabled="false"/>
+<child filterId="org.eclipse.jdt.ui.PackageExplorer.ClosedProjectsFilter" isEnabled="false"/>
+<child filterId="org.eclipse.jdt.ui.PackageExplorer.NonSharedProjectsFilter" isEnabled="false"/>
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+<child filterId="org.eclipse.jdt.ui.PackageExplorer.NonJavaProjectsFilter" isEnabled="false"/>
+<child filterId="org.eclipse.jdt.internal.ui.PackageExplorer.EmptyInnerPackageFilter" isEnabled="true"/>
+<child filterId="org.eclipse.jdt.ui.PackageExplorer.PackageDeclarationFilter" isEnabled="true"/>
+<child filterId="org.eclipse.jdt.internal.ui.PackageExplorer.EmptyPackageFilter" isEnabled="false"/>
+<child filterId="org.eclipse.jdt.ui.PackageExplorer.ImportDeclarationFilter" isEnabled="true"/>
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+<child filterId="org.eclipse.jdt.internal.ui.PackageExplorer.HideInnerClassFilesFilter" isEnabled="true"/>
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+<child filterId="org.eclipse.jdt.ui.PackageExplorer_patternFilterId_.*" isEnabled="true"/>
+<child filterId="org.eclipse.jdt.ui.PackageExplorer.EmptyLibraryContainerFilter" isEnabled="true"/>
+<child filterId="org.eclipse.jdt.ui.PackageExplorer.SyntheticMembersFilter" isEnabled="true"/>
+<child filterId="org.eclipse.mylyn.java.ui.MembersFilter" isEnabled="false"/>
+</xmlDefinedFilters>
+</customFilters>
+</viewState>
+</view>
+<view id="org.eclipse.mylyn.tasks.ui.views.tasks" partName="Task List">
+<viewState linkWithEditor="true" presentation="org.eclipse.mylyn.tasks.ui.categorized">
+<sorter groupBy="CATEGORY_QUERY">
+<sorter>
+<sort0 sortDirection="1" sortKey="PRIORITY"/>
+<sort1 sortDirection="1" sortKey="RANK"/>
+<sort2 sortDirection="1" sortKey="DATE_CREATED"/>
+<sort3 sortDirection="1" sortKey="NONE"/>
+<sort4 sortDirection="1" sortKey="NONE"/>
+<sort5 sortDirection="1" sortKey="NONE"/>
+<sort6 sortDirection="1" sortKey="NONE"/>
+<sort7 sortDirection="1" sortKey="NONE"/>
+</sorter>
+</sorter>
+<filteredTreeFindHistory/>
+</viewState>
+</view>
+<view id="org.eclipse.ui.views.ContentOutline" partName="Outline">
+<viewState/>
+</view>
+<view id="org.eclipse.jdt.ui.SourceView" partName="Declaration"/>
+<view id="org.eclipse.jdt.ui.JavadocView" partName="Javadoc"/>
+</views>
+<perspectives activePart="org.eclipse.jdt.ui.PackageExplorer" activePerspective="org.eclipse.jdt.ui.JavaPerspective">
+<perspective editorAreaTrimState="2" editorAreaVisible="1" fixed="0" version="0.016">
+<descriptor class="org.eclipse.jdt.internal.ui.JavaPerspectiveFactory" id="org.eclipse.jdt.ui.JavaPerspective" label="Java"/>
+<alwaysOnActionSet id="org.eclipse.mylyn.context.ui.actionSet"/>
+<alwaysOnActionSet id="org.eclipse.mylyn.doc.actionSet"/>
+<alwaysOnActionSet id="org.eclipse.mylyn.tasks.ui.navigation"/>
+<alwaysOnActionSet id="org.eclipse.ui.cheatsheets.actionSet"/>
+<alwaysOnActionSet id="org.eclipse.search.searchActionSet"/>
+<alwaysOnActionSet id="org.eclipse.ui.edit.text.actionSet.annotationNavigation"/>
+<alwaysOnActionSet id="org.eclipse.ui.edit.text.actionSet.navigation"/>
+<alwaysOnActionSet id="org.eclipse.ui.edit.text.actionSet.convertLineDelimitersTo"/>
+<alwaysOnActionSet id="org.eclipse.ui.externaltools.ExternalToolsSet"/>
+<alwaysOnActionSet id="org.eclipse.ui.actionSet.keyBindings"/>
+<alwaysOnActionSet id="org.eclipse.ui.actionSet.openFiles"/>
+<alwaysOnActionSet id="org.eclipse.debug.ui.launchActionSet"/>
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+<alwaysOnActionSet id="org.eclipse.debug.ui.breakpointActionSet"/>
+<alwaysOnActionSet id="org.eclipse.jdt.debug.ui.JDTDebugActionSet"/>
+<alwaysOnActionSet id="org.eclipse.jdt.junit.JUnitActionSet"/>
+<show_view_action id="org.eclipse.jdt.ui.PackageExplorer"/>
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+<show_view_action id="org.eclipse.ui.console.ConsoleView"/>
+<show_view_action id="org.eclipse.ui.views.ContentOutline"/>
+<show_view_action id="org.eclipse.ui.views.ProblemView"/>
+<show_view_action id="org.eclipse.ui.views.ResourceNavigator"/>
+<show_view_action id="org.eclipse.ui.views.TaskList"/>
+<show_view_action id="org.eclipse.ui.views.ProgressView"/>
+<show_view_action id="org.eclipse.ui.navigator.ProjectExplorer"/>
+<show_view_action id="org.eclipse.ui.texteditor.TemplatesView"/>
+<show_view_action id="org.eclipse.pde.runtime.LogView"/>
+<show_view_action id="org.eclipse.ant.ui.views.AntView"/>
+<show_view_action id="org.eclipse.mylyn.tasks.ui.views.tasks"/>
+<new_wizard_action id="org.eclipse.jdt.ui.wizards.JavaProjectWizard"/>
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+<new_wizard_action id="org.eclipse.jdt.ui.wizards.NewClassCreationWizard"/>
+<new_wizard_action id="org.eclipse.jdt.ui.wizards.NewInterfaceCreationWizard"/>
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+<new_wizard_action id="org.eclipse.jdt.ui.wizards.NewAnnotationCreationWizard"/>
+<new_wizard_action id="org.eclipse.jdt.ui.wizards.NewSourceFolderCreationWizard"/>
+<new_wizard_action id="org.eclipse.jdt.ui.wizards.NewSnippetFileCreationWizard"/>
+<new_wizard_action id="org.eclipse.jdt.ui.wizards.NewJavaWorkingSetWizard"/>
+<new_wizard_action id="org.eclipse.ui.wizards.new.folder"/>
+<new_wizard_action id="org.eclipse.ui.wizards.new.file"/>
+<new_wizard_action id="org.eclipse.ui.editors.wizards.UntitledTextFileWizard"/>
+<new_wizard_action id="org.eclipse.jdt.junit.wizards.NewTestCaseCreationWizard"/>
+<new_wizard_action id="org.eclipse.mylyn.tasks.ui.wizards.new.repository.task"/>
+<perspective_action id="org.eclipse.jdt.ui.JavaBrowsingPerspective"/>
+<perspective_action id="org.eclipse.debug.ui.DebugPerspective"/>
+<hide_toolbar_item_id id="org.eclipse.jdt.ui.actions.OpenProjectWizard"/>
+<hide_toolbar_item_id id="org.eclipse.ui.edit.text.toggleShowSelectedElementOnly"/>
+<view id="org.eclipse.jdt.ui.PackageExplorer"/>
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+<view id="org.eclipse.ui.views.ContentOutline"/>
+<view id="org.eclipse.mylyn.tasks.ui.views.tasks"/>
+<fastViewBars/>
+<layout>
+<mainWindow>
+<info folder="true" part="left">
+<folder activePageID="org.eclipse.jdt.ui.PackageExplorer" appearance="2" expanded="2">
+<page content="org.eclipse.jdt.ui.PackageExplorer" label="Package Explorer"/>
+<page content="org.eclipse.jdt.ui.TypeHierarchy" label="LabelNotFound"/>
+<page content="org.eclipse.ui.views.ResourceNavigator" label="LabelNotFound"/>
+<page content="org.eclipse.ui.navigator.ProjectExplorer" label="LabelNotFound"/>
+<page content="org.eclipse.jdt.junit.ResultView" label="LabelNotFound"/>
+<presentation id="org.eclipse.ui.presentations.WorkbenchPresentationFactory">
+<part id="0"/>
+</presentation>
+</folder>
+</info>
+<info folder="true" part="org.eclipse.ui.internal.ViewStack at 49e21540" ratio="0.75" ratioLeft="750" ratioRight="250" relationship="2" relative="left">
+<folder appearance="2" expanded="2">
+<page content="org.eclipse.help.ui.HelpView" label="LabelNotFound"/>
+<page content="org.eclipse.ui.internal.introview" label="LabelNotFound"/>
+<page content="org.eclipse.ui.cheatsheets.views.CheatSheetView" label="LabelNotFound"/>
+<presentation id="org.eclipse.ui.presentations.WorkbenchPresentationFactory"/>
+</folder>
+</info>
+<info part="org.eclipse.ui.editorss" ratio="0.25" ratioLeft="250" ratioRight="750" relationship="2" relative="left"/>
+<info folder="true" part="bottom" ratio="0.7496136" ratioLeft="485" ratioRight="162" relationship="4" relative="org.eclipse.ui.editorss">
+<folder activePageID="org.eclipse.ui.views.ProblemView" appearance="2" expanded="2">
+<page content="org.eclipse.ui.views.ProblemView" label="Problems"/>
+<page content="org.eclipse.jdt.ui.JavadocView" label="Javadoc"/>
+<page content="org.eclipse.jdt.ui.SourceView" label="Declaration"/>
+<page content="org.eclipse.search.ui.views.SearchView" label="LabelNotFound"/>
+<page content="org.eclipse.ui.console.ConsoleView" label="LabelNotFound"/>
+<page content="org.eclipse.ui.views.BookmarkView" label="LabelNotFound"/>
+<page content="org.eclipse.ui.views.ProgressView" label="LabelNotFound"/>
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+<part id="0"/>
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+<part id="2"/>
+</presentation>
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+</info>
+<info folder="true" part="org.eclipse.ui.internal.ViewStack at 2f26f304" ratio="0.7493333" ratioLeft="562" ratioRight="188" relationship="2" relative="org.eclipse.ui.editorss">
+<folder activePageID="org.eclipse.mylyn.tasks.ui.views.tasks" appearance="2" expanded="2">
+<page content="org.eclipse.mylyn.tasks.ui.views.tasks" label="Task List"/>
+<presentation id="org.eclipse.ui.presentations.WorkbenchPresentationFactory">
+<part id="0"/>
+</presentation>
+</folder>
+</info>
+<info folder="true" part="right" ratio="0.49896908" ratioLeft="242" ratioRight="243" relationship="4" relative="org.eclipse.ui.internal.ViewStack at 2f26f304">
+<folder activePageID="org.eclipse.ui.views.ContentOutline" appearance="2" expanded="2">
+<page content="org.eclipse.ui.views.ContentOutline" label="Outline"/>
+<page content="org.eclipse.ui.texteditor.TemplatesView" label="LabelNotFound"/>
+<page content="org.eclipse.ant.ui.views.AntView" label="LabelNotFound"/>
+<presentation id="org.eclipse.ui.presentations.WorkbenchPresentationFactory">
+<part id="0"/>
+</presentation>
+</folder>
+</info>
+<info part="org.eclipse.egit.ui.RepositoriesView" ratio="0.59969085" ratioLeft="388" ratioRight="259" relationship="4" relative="left"/>
+</mainWindow>
+</layout>
+</perspective>
+</perspectives>
+<workingSets/>
+<navigationHistory/>
+<input factoryID="org.eclipse.ui.internal.model.ResourceFactory" path="/" type="8"/>
+</page>
+<workbenchWindowAdvisor/>
+<actionBarAdvisor/>
+<trimLayout>
+<trimArea IMemento.internal.id="128">
+<trimItem IMemento.internal.id="org.eclipse.ui.internal.WorkbenchWindow.topBar"/>
+</trimArea>
+<trimArea IMemento.internal.id="1024">
+<trimItem IMemento.internal.id="org.eclise.ui.internal.FastViewBar"/>
+<trimItem IMemento.internal.id="org.eclipse.jface.action.StatusLineManager"/>
+<trimItem IMemento.internal.id="org.eclipse.ui.internal.progress.ProgressRegion"/>
+</trimArea>
+</trimLayout>
+</window>
+<mruList/>
+</workbench>
\ No newline at end of file
diff --git a/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml b/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml
new file mode 100644
index 0000000..7679cc6
--- /dev/null
+++ b/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<workingSetManager>
+<workingSet aggregate="true" factoryID="org.eclipse.ui.internal.WorkingSetFactory" id="1334711181805_0" label="Window Working Set" name="Aggregate for window 1334711181803"/>
+</workingSetManager>
\ No newline at end of file
diff --git a/.metadata/version.ini b/.metadata/version.ini
new file mode 100644
index 0000000..c51ff74
--- /dev/null
+++ b/.metadata/version.ini
@@ -0,0 +1 @@
+org.eclipse.core.runtime=1
\ No newline at end of file
diff --git a/.project b/.project
new file mode 100644
index 0000000..bcb4f62
--- /dev/null
+++ b/.project
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+<name>AcaciaGitProject</name>
+<comment></comment>
+<projects>
+</projects>
+<buildSpec>
+<buildCommand>
+<name>org.eclipse.jdt.core.javabuilder</name>
+<arguments>
+</arguments>
+</buildCommand>
+</buildSpec>
+<natures>
+<nature>org.eclipse.jdt.core.javanature</nature>
+</natures>
+</projectDescription>
\ No newline at end of file
diff --git a/README b/README
new file mode 100644
index 0000000..44cd85a
--- /dev/null
+++ b/README
@@ -0,0 +1,52 @@
+***(%%%%%)*\\**********************************************
+****(%%%) _/\\*********************************************
+******** _\\_ \\ ___**************************************
+******* / | \\\//** \/\''\*** _____ *
+****** / | /(%%%)**/ \ \** (, / | , *
+****** \ | /(%%%%%)*\ \ \* /---| _ _ _ _ *
+******* \ / (%%%%%)**\ \ |* ) / |_(__(_(_(___(_(_(_ *
+******** \/***(%%%)\\**\ | |*(_/ *
+********************\\**\ |/** *
+******************** \\**\/********************************
+***********************************************************
+
+
+
+SOFTWARE Acacia
+
+SOFTWARE 1.53-b0 (Release 1.53)
+
+
+
+Software by Lauren Bragg and Glenn Stone 2010-2014
+
+Contact: lauren.bragg at csiro.au
+
+
+
+INSTALLATION NOTES
+
+See associated documentation for running this program.
+
+This release consists of feature improvement and bug fixes (sorry -- no Ion Torrent correction yet, their new BAM format has some issues).
+
+
+NEW FEATURES
+
+#1 Can now perform hexamer clustering in Acacia without correction (using the "CLUSTER_ONLY=TRUE" flag). This allows you to run Acacia on each cluster separately, minimising the
+maximum memory required and allowing the processing to be distributed across threads and/or cluster nodes. If you need help distributing your run across threads, please contact Lauren.
+
+
+BUG FIXES
+
+#1 Acacia can now use input files larger than 2GB (thanks for spotting this, Henning Seedorf).
+
+#2 Addressed Bug (GitHub #3) -- buttons truncated in GUI
+
+
+
+
+KNOWN ISSUES (that will be addressed in a future release)
+
+#1 Not all parameters are available through the GUI interface, this will be amended in future versions of Acacia
+
diff --git a/classmexer.jar b/classmexer.jar
new file mode 100644
index 0000000..6528ab6
Binary files /dev/null and b/classmexer.jar differ
diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index 38f3b93..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,40 +0,0 @@
-Acacia ships as a single JAR with dependencies packaed inside using
-org/eclipse/jdt/internal/jarinjarloader. We will not be using this in Debian.
-
-Here's what's in the JAR and my notes;
-
- # biojava.jar (?version unknown?)
- # biojava-1.7.1-all.jar = libbiojava1.7 - already in Debian
- # classmexer-0_03.zip (a red herring? maybe only needed for testing)
- # colt.jar =
-http://acs.lbl.gov/software/colt/colt-download/releases/colt-1.2.0.tar.gz
-Already in Debian but non-free.
- # optimization.jar = http://www1.fpl.fs.fed.us/optimization.html (or
-the newer version??)
- # Blas.jar = http://www1.fpl.fs.fed.us/Blas_f77.html, but already in optimization.jar
- # tcode.jar = see ssj
- # jfreechart-1.0.10.jar - already in Debian
- # jcommon-1.0.13.jar - ditto
- # language-1.6.7.jar - in dsol
- # event-1.6.5.jar - in dsol
- # logger-1.6.4.jar - in dsol
- # interpreter-1.6.8.jar - in dsol
- # ssj.jar = http://www.iro.umontreal.ca/~simardr/ssj/ssj-source.html
- # needs Tcode and various jars, plus:
- http://statistik.wu-wien.ac.at/unuran/download.html
- which wants:
- http://statistik.wu-wien.ac.at/software/RngStreams/
- # commons-cli-1.2.jar = libcommons-cli-java
- # commons-math-2.1.jar = libcommons-math-java
-
-Also, SSJ might or might not need libdsol1-xml-java which in turn is a
-PITA....
-No, it seems to build without it.
-
-Acacia 1.52 source is on Sourceforge but otherwise the source is on GitHub.
-
-...
-
-I currently build ssj.jar without unuran jni support, which makes life simpler and doesn't
-seem to be needed to compile Acacia (not fully tested yet but will be). I may as
-well compile chrono support as this just needs standard system libs.
diff --git a/debian/acacia.desktop b/debian/acacia.desktop
deleted file mode 100644
index 9dd9d51..0000000
--- a/debian/acacia.desktop
+++ /dev/null
@@ -1,12 +0,0 @@
-[Desktop Entry]
-Version=1.0
-Type=Application
-Name=Acacia
-Comment=Correct errors in sequenced amplicons
-Exec=/usr/bin/acacia -u
-#Icon=/usr/share/pixmaps/acacia.png
-Icon=/usr/share/acacia/images/acacia_small_wattle_icon.png
-Terminal=false
-Categories=Science;Bioinformatics
-StartupNotify=true
-StartupWMClass=pyromaniac-AcaciaMain
diff --git a/debian/acacia.docs b/debian/acacia.docs
deleted file mode 100644
index ab1a32b..0000000
--- a/debian/acacia.docs
+++ /dev/null
@@ -1 +0,0 @@
-README*
diff --git a/debian/acacia.install b/debian/acacia.install
deleted file mode 100644
index 7e760f5..0000000
--- a/debian/acacia.install
+++ /dev/null
@@ -1,4 +0,0 @@
-src/data /usr/share/acacia
-src/images /usr/share/acacia
-debian/bin/* /usr/bin
-debian/*.desktop /usr/share/applications
diff --git a/debian/acacia.jlibs b/debian/acacia.jlibs
deleted file mode 100644
index 73dbbab..0000000
--- a/debian/acacia.jlibs
+++ /dev/null
@@ -1 +0,0 @@
-acacia.jar
diff --git a/debian/bin/acacia b/debian/bin/acacia
deleted file mode 100755
index 6b90578..0000000
--- a/debian/bin/acacia
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/sh
-
-# Note the Acacia JAR provided in the Debian package has been rebuilt from
-# source and is much smaller than the one found on the Acacia website as it
-# does not contain all the dependencies within itself.
-
-# However, it should still run normally as the Manifest is set to load all the
-# dependencies from the files provided on the system.
-
-java -jar /usr/share/java/acacia.jar "$@"
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 092208f..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,18 +0,0 @@
-acacia (1.53-0biolinux2) trusty; urgency=medium
-
- * Version bump to force rebuild against libcolt-free-java
-
- -- Tim Booth <tbooth at ceh.ac.uk> Thu, 09 Apr 2015 15:12:34 +0100
-
-acacia (1.53-0biolinux1.1) trusty; urgency=low
-
- * Rebuild for trusty
-
- -- Tim Booth <tbooth at ceh.ac.uk> Tue, 03 Jun 2014 12:03:22 +0100
-
-acacia (1.53-0biolinux1) precise; urgency=low
-
- * Initial release for Bio-Linux.
- * Started with 1.52 but realised the later code is on GitHub.
-
- -- Tim Booth <tbooth at ceh.ac.uk> Fri, 04 Apr 2014 11:00:31 +0100
diff --git a/debian/classpath.sh b/debian/classpath.sh
deleted file mode 100755
index 1577e04..0000000
--- a/debian/classpath.sh
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/bin/sh
-
-# Print the classpath. Simple.
-# Or else print a config for jh_manifest
-jars="
- biojava1.7
- ssj
- optimization
- colt
- dsol-logger
- dsol-event
- dsol-interpreter
- dsol-language
- commons-cli
- commons-math3
- hac
-"
-
-mainclass="pyromaniac.AcaciaMain"
-
-if [ "$1" = -m ] ; then # manifest mode
- echo "#Manifest generated by '$0 $@'"
- echo
- echo "usr/share/java/$2.jar:"
- echo " Main-Class: $mainclass"
- echo " Manifest-Version: 1.0"
-fi
-
-cp="$CLASSPATH"
-mcp=" /usr/share/acacia/"
-
-for c in $jars ; do
- if [ "${c##/}" = "$c" ] ; then
- f="/usr/share/java/$c.jar"
- ls "$f" > /dev/null
- cp="$cp:$f"
- mcp="$mcp $c.jar"
- else
- cp="$cp:$c"
- mcp="$mcp $c"
- fi
-done
-
-if [ "$1" = -m ] ; then
- echo " Class-Path:$mcp"
-else
- echo ${cp##:}
-fi
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index 758cb22..0000000
--- a/debian/control
+++ /dev/null
@@ -1,40 +0,0 @@
-Source: acacia
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
- Andreas Tille <tille at debian.org>
-Section: java
-Priority: optional
-Build-Depends: debhelper (>= 9),
- default-jdk,
- javahelper,
- libssj-java,
- libbiojava1.7-java,
- libhac-java,
- libcommons-cli-java,
- libcommons-math3-java,
- libcolt-free-java
-Standards-Version: 3.9.5
-Homepage: http://sourceforge.net/projects/acaciaerrorcorr/
-
-Package: acacia
-Architecture: all
-Depends: ${misc:Depends},
- ${java:Depends}
-Description: Error-corrector for pyrosequenced amplicon reads.
- Acacia is a java program developed to quickly and conservatively correct
- errors, whilst simultaneously de-replicating, amplicon sequences.
- .
- The main purpose of Acacia is to correct the over-call, under-call errors
- prevalent in Roche 454 GS-FLX data, and more recently, with the Titanium
- chemistry.
- Acacia will only ectively correct errors in amplicons - as it assumes that
- the 5' end of the sequences start at the same position, the MID, followed by
- the primer.
- Acacia uses empirically-derived models to identify homopolymer
- regions where there are more `errors' than expected by chance - these imply
- that the differences are due to population differences rather than
- error-induced polymorphisms.
- .
- Nat Methods. 2012 Apr 27;9(5):425-6. doi: 10.1038/nmeth.1990.
- Fast, accurate error-correction of amplicon pyrosequences using Acacia.
- Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 3851b12..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,25 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: acaciaerrorcorr
-Upstream-Contact: Lauren Bragg <lauren.bragg at csiro.au>
-Source: https://github.com/LBragg/Acacia
-
-Files: *
-Copyright: © 2011-2014 Lauren Bragg and Glenn Stone,
- CSIRO CMIS & University of Queensland
-License: GPL-3
- Acacia is free software: you can redistribute it and/or modify it under the
- terms of the GNU General Public License as published by the Free Software
- Foundation, either version 3 of the License, or (at your option) any later version.
- Acacia is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or
- FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
- License for more details.
- .
- On Debian systems, the full text of the GNU General Public
- License version 2 can be found in the file
- `/usr/share/common-licenses/GPL-3'.
-
-
-Files: debian/*
-Copyright: © 2014 Tim Booth <tbooth at ceh.ac.uk>
-License: GPL-3
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index f01ac48..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-%:
- dh $@ --with javahelper
-
-override_jh_manifest:
- debian/classpath.sh -m acacia > debian/acacia.manifest
- jh_manifest
-
-override_dh_auto_build:
- env CLASSPATH=`debian/classpath.sh` jh_build acacia.jar src/pyromaniac
-
-override_dh_auto_clean:
- find \( -name debian -prune \) -o -name '.?*' -prune -exec rm -rf '{}' ';'
- find -name '*.zip' -delete
- find -name '*.jar' -delete
-
-override_dh_clean:
- dh_clean
- #Remove auto-generated file
- rm -f debian/acacia.manifest
-
-override_dh_compress:
- dh_compress --exclude=.pdf
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
deleted file mode 100644
index c4c1a4c..0000000
--- a/debian/upstream/metadata
+++ /dev/null
@@ -1,11 +0,0 @@
-Reference:
- Author: Lauren Bragg and Glenn Stone and Michael Imelfort and Philip Hugenholtz and Gene W Tyson
- Title: "Fast, accurate error-correction of amplicon pyrosequences using Acacia"
- Journal: Nat Methods
- Year: 2012
- Volume: 9
- Number: 5
- Pages: 425-6
- DOI: 10.1038/nmeth.1990
- PMID: 22543370
- URL: http://www.nature.com/nmeth/journal/v9/n5/full/nmeth.1990.html
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index 10a2e7e..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,5 +0,0 @@
-version=3
-# There is a source dump on SF.net but actually the latest code is on GitHub
-#http://sf.net/acaciaerrorcorr/Acacia-([0-9.]+)_src.(?:tar.gz|.tar.bz2|.tgz)
-
-https://github.com/LBragg/Acacia/releases .*/archive/v?([0-9.]+).tar.gz
diff --git a/jar-in-jar-loader.zip b/jar-in-jar-loader.zip
new file mode 100644
index 0000000..6ee1217
Binary files /dev/null and b/jar-in-jar-loader.zip differ
diff --git a/script_exejar_gitbuild.xml b/script_exejar_gitbuild.xml
new file mode 100644
index 0000000..65775ce
--- /dev/null
+++ b/script_exejar_gitbuild.xml
@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<project default="create_run_jar" name="Create Runnable Jar for Project AcaciaGitProject with Jar-in-Jar Loader">
+ <!--this file was created by Eclipse Runnable JAR Export Wizard-->
+ <!--ANT 1.7 is required -->
+ <target name="create_run_jar">
+ <property file="src/data/build_info.properties"/>
+ <echo message="${build.number}"/>
+ <property name="version.number" value="${build.major.number}.${build.minor.number}.b${build.number}"/>
+ <jar destfile="E:\Coding_and_Data\Projects\AcaciaExcutablesGit\acacia-${version.number}.jar">
+ <manifest>
+ <attribute name="Built-By" value="Lauren Bragg"/>
+ <attribute name="Implementation-Version"
+ value="${version.num}-b${build.number}"/>
+ <attribute name="Built-Date" value="${TODAY}"/>
+ <attribute name="Main-Class" value="org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader"/>
+ <attribute name="Rsrc-Main-Class" value="pyromaniac.AcaciaMain"/>
+ <attribute name="Class-Path" value="."/>
+ <attribute name="Rsrc-Class-Path" value="./ biojava.jar biojava-1.7.1-all.jar classmexer-0_03.zip colt.jar optimization.jar Blas.jar tcode.jar jfreechart-1.0.10.jar jcommon-1.0.13.jar language-1.6.7.jar event-1.6.5.jar logger-1.6.4.jar interpreter-1.6.8.jar ssj.jar commons-cli-1.2.jar hac.jar commons-math-2.1.jar"/>
+ </manifest>
+ <zipfileset src="jar-in-jar-loader.zip"/>
+ <fileset dir="E:/GitRepo/AcaciaEclipse/Acacia/bin"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party" includes="biojava.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party" includes="biojava-1.7.1-all.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party" includes="classmexer-0_03.zip"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="colt.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="optimization.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="Blas.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="tcode.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="jfreechart-1.0.10.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="jcommon-1.0.13.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="language-1.6.7.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="event-1.6.5.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="logger-1.6.4.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="interpreter-1.6.8.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\ssj-20100908\ssj\lib" includes="ssj.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\commons-cli-1.2" includes="commons-cli-1.2.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\sape-hac-8b2a326" includes="hac.jar"/>
+ <zipfileset dir="E:\Work_Documents\Eclipse\workspace\3rd_party\commons-math-2.1\commons-math-2.1" includes="commons-math-2.1.jar"/>
+ </jar>
+ <propertyfile file="src/data/build_info.properties">
+ <entry key="build.number" type="int" operation="+" value="1" pattern="00"/>
+ </propertyfile>
+ </target>
+</project>
diff --git a/script_exejar_gitbuild_workstation.xml b/script_exejar_gitbuild_workstation.xml
new file mode 100644
index 0000000..c9e1840
--- /dev/null
+++ b/script_exejar_gitbuild_workstation.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<project default="create_run_jar" name="Create Runnable Jar for Project AcaciaGitProject with Jar-in-Jar Loader">
+ <!--this file was created by Eclipse Runnable JAR Export Wizard-->
+ <!--ANT 1.7 is required -->
+ <target name="create_run_jar">
+ <property file="src/data/build_info.properties"/>
+ <echo message="${build.number}"/>
+ <property name="version.number" value="${build.major.number}.${build.minor.number}.b${build.number}"/>
+ <jar destfile="/home/bra427/Projects/AcaciaJars/acacia-${version.number}.jar">
+ <manifest>
+ <attribute name="Built-By" value="Lauren Bragg"/>
+ <attribute name="Implementation-Version"
+ value="${version.num}-b${build.number}"/>
+ <attribute name="Built-Date" value="${TODAY}"/>
+ <attribute name="Main-Class" value="org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader"/>
+ <attribute name="Rsrc-Main-Class" value="pyromaniac.AcaciaMain"/>
+ <attribute name="Class-Path" value="."/>
+ <attribute name="Rsrc-Class-Path" value="./ bytecode.jar biojava.jar colt.jar optimization.jar Blas.jar tcode.jar jfreechart-1.0.10.jar jcommon-1.0.13.jar language-1.6.7.jar event-1.6.5.jar logger-1.6.4.jar interpreter-1.6.8.jar ssj.jar blas.jar commons-cli-1.2.jar commons-math3-3.1.1.jar"/>
+ </manifest>
+ <zipfileset src="jar-in-jar-loader.zip"/>
+ <fileset dir="/home/bra427/Projects/AcaciaDevelopment/Acacia/bin"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty" includes="bytecode.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty" includes="biojava.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="colt.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="optimization.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="Blas.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="tcode.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="jfreechart-1.0.10.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="jcommon-1.0.13.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="language-1.6.7.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="event-1.6.5.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="logger-1.6.4.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="interpreter-1.6.8.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/ssj/lib" includes="ssj.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty" includes="blas.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/commons-cli-1.2" includes="commons-cli-1.2.jar"/>
+ <zipfileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/commons-math3-3.1.1" includes="commons-math3-3.1.1.jar"/>
+ <fileset dir="/home/bra427/Projects/AcaciaDevelopment/ThirdParty/hac/bin"/>
+ </jar>
+ </target>
+</project>
diff --git a/src/data/.svn/entries b/src/data/.svn/entries
new file mode 100644
index 0000000..ed98a3b
--- /dev/null
+++ b/src/data/.svn/entries
@@ -0,0 +1,198 @@
+10
+
+dir
+34
+http://localhost:8080/Code_Repository/branches/acacia_dev_from_1.1/src/data
+http://localhost:8080/Code_Repository
+
+
+
+2011-02-22T22:33:26.697900Z
+31
+lauren
+
+
+
+
+
+
+
+
+
+
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+
+
+110287ce-512d-634d-87ac-25a96c5a541a
+
+MID_tenbase.csv
+file
+
+
+
+
+2011-01-27T22:38:35.241074Z
+e14dc1f2bd45a5fcdfd582137bce9848
+2011-02-22T22:33:26.697900Z
+31
+lauren
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+201
+
+QuinceProbs.csv
+file
+
+
+
+
+2010-01-08T00:32:41.237000Z
+7c438680f17beae09977393ca8aaa7b6
+2011-02-22T22:33:26.697900Z
+31
+lauren
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+395
+
+maldeEmpiricalDistributions.csv
+file
+
+
+
+
+2010-10-06T05:55:06.352157Z
+651a10dc9d62b77d16e12e325c118f37
+2011-02-22T22:33:26.697900Z
+31
+lauren
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+4522
+
+MID_fivebase.csv
+file
+
+
+
+
+2011-01-06T22:07:02.641661Z
+8c2c16270d47ca385a8c83b8a9064a28
+2011-02-22T22:33:26.697900Z
+31
+lauren
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+491
+
+NUC.4.4
+file
+
+
+
+
+2010-11-23T01:08:50.429000Z
+b89057d48792f4e18aa9b959d06d30c4
+2011-02-22T22:33:26.697900Z
+31
+lauren
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+1171
+
diff --git a/src/data/.svn/text-base/MID_fivebase.csv.svn-base b/src/data/.svn/text-base/MID_fivebase.csv.svn-base
new file mode 100644
index 0000000..325ebfc
--- /dev/null
+++ b/src/data/.svn/text-base/MID_fivebase.csv.svn-base
@@ -0,0 +1,50 @@
+1,CTACT
+2,CTCGC
+3,CGTAC
+4,TACGT
+5,TAGAG
+6,TCATC
+7,TCTAT
+8,TGCTG
+9,TGTAG
+10,ACGTC
+11,ACACG
+12,AGTGT
+13,AGCAC
+14,ATGCT
+15,ATATG
+16,CATGC
+17,CACAG
+18,CGATG
+19,TCTCG
+20,TCTGC
+21,TCGCT
+22,TCGTG
+23,TCGAC
+24,TCAGT
+25,TGCGC
+26,TGCAT
+27,TGTGT
+28,TGACT
+29,TACTC
+30,TATCT
+31,TATAC
+32,CTCTG
+33,CTCAT
+34,CTGCG
+35,CTGTC
+36,CGCTC
+37,CGCGT
+38,CGCAG
+39,CGTCT
+40,CGACG
+41,CGAGC
+42,CACAC
+43,CATCG
+44,CATGC
+45,CATAT
+46,CAGCT
+47,CAGTG
+48,ACTCT
+49,ACTAC
+50,ACGCG
diff --git a/src/data/.svn/text-base/MID_tenbase.csv.svn-base b/src/data/.svn/text-base/MID_tenbase.csv.svn-base
new file mode 100644
index 0000000..f268fc5
--- /dev/null
+++ b/src/data/.svn/text-base/MID_tenbase.csv.svn-base
@@ -0,0 +1,14 @@
+1,ACGAGTGCGT
+2,ACGCTCGACA
+3,AGACGCACTC
+4,AGCACTGTAG
+5,ATCAGACACG
+6,ATATCGCGAG
+7,CGTGTCTCTA
+8,CTCGCGTGTC
+9,TAGTATCAGC
+10,TCTCTATGCG
+11,TGATACGTCT
+12,TACTGAGCTA
+13,CATAGTAGTG
+14,CGAGAGATAC
diff --git a/src/data/.svn/text-base/NUC.4.4.svn-base b/src/data/.svn/text-base/NUC.4.4.svn-base
new file mode 100644
index 0000000..6fb12d2
--- /dev/null
+++ b/src/data/.svn/text-base/NUC.4.4.svn-base
@@ -0,0 +1,25 @@
+#
+# This matrix was created by Todd Lowe 12/10/92
+#
+# Uses ambiguous nucleotide codes, probabilities rounded to
+# nearest integer
+#
+# Lowest score = -4, Highest score = 5
+#
+ A T G C S W R Y K M B V H D N
+A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2
+T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2
+G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2
+C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2
+S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1
+W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1
+R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1
+Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1
+K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1
+M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1
+B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1
+V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1
+H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1
+D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1
+N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+
diff --git a/src/data/.svn/text-base/QuinceProbs.csv.svn-base b/src/data/.svn/text-base/QuinceProbs.csv.svn-base
new file mode 100644
index 0000000..89a4a75
--- /dev/null
+++ b/src/data/.svn/text-base/QuinceProbs.csv.svn-base
@@ -0,0 +1,11 @@
+TRUTH,P<,P=,P>
+0,0,0.999778204,0.000221796
+1,0.000321883,0.99946607,0.000212048
+2,0.000945431,0.998580713,0.000473855
+3,0.001607913,0.997984661,0.000407425
+4,0.003180412,0.993857994,0.002961594
+5,0.006680608,0.974554835,0.018764557
+6,0.024114593,0.951770815,0.024114593
+7,0.042847489,0.914305021,0.042847489
+8,0.064148049,0.871703903,0.064148048
+9,0.086291816,0.827416369,0.086291815
diff --git a/src/data/.svn/text-base/maldeEmpiricalDistributions.csv.svn-base b/src/data/.svn/text-base/maldeEmpiricalDistributions.csv.svn-base
new file mode 100644
index 0000000..105c785
--- /dev/null
+++ b/src/data/.svn/text-base/maldeEmpiricalDistributions.csv.svn-base
@@ -0,0 +1,140 @@
+1
+0,0,0.999390455,0.000609545
+1,0.000145949,0.998996373,0.000857678
+2,0.000392274,0.998185276,0.00142245
+3,0.004213332,0.991771547,0.004015122
+4,0.030886565,0.952239058,0.016874377
+5,0.084140353,0.901777229,0.014082418
+2
+0,0,0.999139916,0.000860084
+1,0.00017449,0.998657758,0.001167752
+2,0.000461348,0.997684968,0.001853684
+3,0.003575747,0.991487088,0.004937165
+4,0.026319297,0.954925079,0.018755625
+5,0.074565042,0.909553501,0.015881457
+3
+0,0,0.998956931,0.001043069
+1,0.000201955,0.998456178,0.001341867
+2,0.000476795,0.997589513,0.001933692
+3,0.003178747,0.991546588,0.005274666
+4,0.022085173,0.957619395,0.020295431
+5,0.061455511,0.922423336,0.016121154
+4
+0,0,0.998756868,0.001243132
+1,0.000230276,0.998270894,0.00149883
+2,0.000585859,0.997310392,0.00210375
+3,0.003165853,0.991050462,0.005783685
+4,0.01874524,0.9586526,0.02260216
+5,0.052501386,0.929792052,0.017706562
+5
+0,0,0.998770625,0.001229375
+1,0.000238894,0.998329684,0.001431422
+2,0.000645812,0.997240161,0.002114028
+3,0.003295719,0.99054823,0.006156051
+4,0.016369249,0.958878497,0.024752254
+5,0.042615984,0.936335633,0.021048383
+6
+0,0,0.998938842,0.001061158
+1,0.000253961,0.998464822,0.001281216
+2,0.000726126,0.997224806,0.002049068
+3,0.003287861,0.990287497,0.006424642
+4,0.014976614,0.956249172,0.028774215
+5,0.035664823,0.939623209,0.024711968
+7
+0,0,0.999049858,0.000950142
+1,0.000244308,0.998571518,0.001184174
+2,0.000824298,0.997112541,0.002063162
+3,0.00365503,0.98964353,0.006701441
+4,0.015926128,0.951790852,0.032283019
+5,0.030555888,0.940466971,0.028977141
+8
+0,0,0.999127246,0.000872754
+1,0.000284999,0.998531972,0.001183029
+2,0.001094545,0.996579821,0.002325634
+3,0.004576698,0.987579108,0.007844194
+4,0.017133658,0.943841634,0.039024708
+5,0.028870589,0.936737513,0.034391898
+9
+0,0,0.999125846,0.000874154
+1,0.000322675,0.998433007,0.001244318
+2,0.001525787,0.995697427,0.002776786
+3,0.00601209,0.984657256,0.009330655
+4,0.021465827,0.932634125,0.045900049
+5,0.032283149,0.927760282,0.039956568
+10
+0,0,0.999080976,0.000919024
+1,0.000416346,0.998111361,0.001472293
+2,0.002224252,0.993788882,0.003986866
+3,0.008227456,0.978342989,0.013429555
+4,0.027770739,0.909942873,0.062286388
+5,0.035340435,0.911465914,0.05319365
+11
+0,0,0.998313109,0.001686891
+1,0.000266413,0.997788035,0.001945552
+2,0.002945971,0.993208283,0.003845746
+3,0.011966694,0.976652696,0.01138061
+4,0.039827958,0.904402462,0.05576958
+5,0.053190752,0.890237586,0.056571663
+12
+0,0,0.998391992,0.001608008
+1,0.000277399,0.997666093,0.002056509
+2,0.003017329,0.992719375,0.004263295
+3,0.012053284,0.974764503,0.013182212
+4,0.038679136,0.896875753,0.064445111
+5,0.048357653,0.886346089,0.065296258
+13
+0,0,0.998253736,0.001746264
+1,0.000318978,0.997366457,0.002314565
+2,0.003788287,0.991466999,0.004744714
+3,0.015931561,0.969548937,0.014519502
+4,0.047374917,0.884792884,0.067832199
+5,0.057105893,0.870651062,0.072243045
+14
+0,0,0.997978346,0.002021654
+1,0.000392881,0.99667062,0.002936499
+2,0.005148699,0.988709377,0.006141924
+3,0.022727313,0.959362271,0.017910416
+4,0.060828486,0.864525465,0.074646049
+5,0.075042321,0.844159299,0.08079838
+15
+0,0,0.997654588,0.002345412
+1,0.000541349,0.995736607,0.003722044
+2,0.008584095,0.983042754,0.008373151
+3,0.041980702,0.934894878,0.02312442
+4,0.097740437,0.818806456,0.083453107
+5,0.119530774,0.794150822,0.086318404
+16
+0,0,0.994918406,0.005081594
+1,0.0003123,0.994717721,0.004969979
+2,0.018185936,0.975035289,0.006778775
+3,0.117446151,0.868630194,0.013923655
+4,0.233100496,0.716625616,0.050273888
+5,0.275266989,0.654266505,0.070466506
+17
+0,0,0.994407837,0.005592163
+1,0.000376288,0.99374061,0.005883102
+2,0.019530575,0.971874474,0.008594952
+3,0.119700878,0.862629596,0.017669526
+4,0.229554605,0.709237561,0.061207834
+5,0.270940877,0.649206126,0.079852998
+18
+0,0,0.993755352,0.006244648
+1,0.000471484,0.993038066,0.006490451
+2,0.022229208,0.968678509,0.009092283
+3,0.129764606,0.852271768,0.017963626
+4,0.249183526,0.692771968,0.058044507
+5,0.292177324,0.63605786,0.071764816
+19
+0,0,0.992457075,0.007542925
+1,0.000585145,0.992533909,0.006880946
+2,0.024875799,0.966246123,0.008878078
+3,0.139216031,0.842841629,0.01794234
+4,0.26707485,0.67927224,0.05365291
+5,0.312743518,0.622024991,0.065231491
+20
+0,0,0.980284687,0.019715313
+1,0.000636649,0.994161108,0.005202243
+2,0.021602178,0.972946099,0.005451723
+3,0.130532596,0.856044288,0.013423116
+4,0.264092148,0.693661551,0.042246301
+5,0.313498199,0.63911745,0.047384351
\ No newline at end of file
diff --git a/src/data/100bpOneTouch_314_counts_complete.csv b/src/data/100bpOneTouch_314_counts_complete.csv
new file mode 100644
index 0000000..5f51b8a
--- /dev/null
+++ b/src/data/100bpOneTouch_314_counts_complete.csv
@@ -0,0 +1,3073 @@
+"RefLen","Cycle","PIC","Under","At","Over"
+0,0,0,0,0.99870155108721,0.00129844891279041
+0,0,1,0,0.999262660042675,0.000737339957324834
+0,0,2,0,0.999777410764521,0.000222589235478798
+0,0,3,0,0.999327913484563,0.000672086515436709
+0,0,4,0,0.999243785637391,0.000756214362608865
+0,0,5,0,0.998904663226869,0.00109533677313134
+0,0,6,0,0.999574479766458,0.000425520233541699
+0,0,7,0,0.999304775144679,0.000695224855321253
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+0,0,10,0,0.999992607541786,7.39245821412994e-06
+0,0,11,0,0.999988881064453,1.11189355472369e-05
+0,0,12,0,0.99998857916211,1.14208378897718e-05
+0,0,13,0,0.999962767518956,3.72324810436551e-05
+0,0,14,0,0.999943276522589,5.6723477410966e-05
+0,0,15,0,0.999818637086961,0.000181362913039408
+0,0,16,0,0.999834028467191,0.000165971532808576
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+0,1,13,0,0.99942067843754,0.000579321562459963
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diff --git a/src/data/100bpOneTouch_314_counts_complete_model_ones.csv b/src/data/100bpOneTouch_314_counts_complete_model_ones.csv
new file mode 100644
index 0000000..dc96d12
--- /dev/null
+++ b/src/data/100bpOneTouch_314_counts_complete_model_ones.csv
@@ -0,0 +1,33 @@
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diff --git a/src/data/100bpOneTouch_314_counts_complete_model_others.csv b/src/data/100bpOneTouch_314_counts_complete_model_others.csv
new file mode 100644
index 0000000..8e509f8
--- /dev/null
+++ b/src/data/100bpOneTouch_314_counts_complete_model_others.csv
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diff --git a/src/data/100bpOneTouch_314_counts_complete_model_zeroes.csv b/src/data/100bpOneTouch_314_counts_complete_model_zeroes.csv
new file mode 100644
index 0000000..ca69a16
--- /dev/null
+++ b/src/data/100bpOneTouch_314_counts_complete_model_zeroes.csv
@@ -0,0 +1,33 @@
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diff --git a/src/data/100bpOneTouch_316_counts_complete.csv b/src/data/100bpOneTouch_316_counts_complete.csv
new file mode 100644
index 0000000..ad1c6dc
--- /dev/null
+++ b/src/data/100bpOneTouch_316_counts_complete.csv
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diff --git a/src/data/100bpOneTouch_316_counts_complete_model_ones.csv b/src/data/100bpOneTouch_316_counts_complete_model_ones.csv
new file mode 100644
index 0000000..57f0eff
--- /dev/null
+++ b/src/data/100bpOneTouch_316_counts_complete_model_ones.csv
@@ -0,0 +1,33 @@
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diff --git a/src/data/100bpOneTouch_316_counts_complete_model_others.csv b/src/data/100bpOneTouch_316_counts_complete_model_others.csv
new file mode 100644
index 0000000..b4a0b33
--- /dev/null
+++ b/src/data/100bpOneTouch_316_counts_complete_model_others.csv
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diff --git a/src/data/100bpOneTouch_316_counts_complete_model_zeroes.csv b/src/data/100bpOneTouch_316_counts_complete_model_zeroes.csv
new file mode 100644
index 0000000..1847560
--- /dev/null
+++ b/src/data/100bpOneTouch_316_counts_complete_model_zeroes.csv
@@ -0,0 +1,33 @@
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diff --git a/src/data/200bpManual_314_counts_complete.csv b/src/data/200bpManual_314_counts_complete.csv
new file mode 100644
index 0000000..23f1c60
--- /dev/null
+++ b/src/data/200bpManual_314_counts_complete.csv
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diff --git a/src/data/200bpManual_314_counts_complete_model_ones.csv b/src/data/200bpManual_314_counts_complete_model_ones.csv
new file mode 100644
index 0000000..8c491cc
--- /dev/null
+++ b/src/data/200bpManual_314_counts_complete_model_ones.csv
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diff --git a/src/data/200bpManual_314_counts_complete_model_others.csv b/src/data/200bpManual_314_counts_complete_model_others.csv
new file mode 100644
index 0000000..53ff766
--- /dev/null
+++ b/src/data/200bpManual_314_counts_complete_model_others.csv
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diff --git a/src/data/200bpManual_314_counts_complete_model_zeroes.csv b/src/data/200bpManual_314_counts_complete_model_zeroes.csv
new file mode 100644
index 0000000..1973908
--- /dev/null
+++ b/src/data/200bpManual_314_counts_complete_model_zeroes.csv
@@ -0,0 +1,33 @@
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diff --git a/src/data/200bpManual_316_counts_complete.csv b/src/data/200bpManual_316_counts_complete.csv
new file mode 100644
index 0000000..784cbf4
--- /dev/null
+++ b/src/data/200bpManual_316_counts_complete.csv
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diff --git a/src/data/200bpManual_316_counts_complete_model_ones.csv b/src/data/200bpManual_316_counts_complete_model_ones.csv
new file mode 100644
index 0000000..9a33a05
--- /dev/null
+++ b/src/data/200bpManual_316_counts_complete_model_ones.csv
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diff --git a/src/data/200bpManual_316_counts_complete_model_others.csv b/src/data/200bpManual_316_counts_complete_model_others.csv
new file mode 100644
index 0000000..0a27eca
--- /dev/null
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diff --git a/src/data/200bpManual_316_counts_complete_model_zeroes.csv b/src/data/200bpManual_316_counts_complete_model_zeroes.csv
new file mode 100644
index 0000000..e04145b
--- /dev/null
+++ b/src/data/200bpManual_316_counts_complete_model_zeroes.csv
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diff --git a/src/data/200bpOneTouch_314_counts_complete.csv b/src/data/200bpOneTouch_314_counts_complete.csv
new file mode 100644
index 0000000..4c115e4
--- /dev/null
+++ b/src/data/200bpOneTouch_314_counts_complete.csv
@@ -0,0 +1,5377 @@
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diff --git a/src/data/200bpOneTouch_314_counts_complete_model_ones.csv b/src/data/200bpOneTouch_314_counts_complete_model_ones.csv
new file mode 100644
index 0000000..f4ca669
--- /dev/null
+++ b/src/data/200bpOneTouch_314_counts_complete_model_ones.csv
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diff --git a/src/data/200bpOneTouch_314_counts_complete_model_others.csv b/src/data/200bpOneTouch_314_counts_complete_model_others.csv
new file mode 100644
index 0000000..c90cd66
--- /dev/null
+++ b/src/data/200bpOneTouch_314_counts_complete_model_others.csv
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diff --git a/src/data/200bpOneTouch_314_counts_complete_model_zeroes.csv b/src/data/200bpOneTouch_314_counts_complete_model_zeroes.csv
new file mode 100644
index 0000000..9b22221
--- /dev/null
+++ b/src/data/200bpOneTouch_314_counts_complete_model_zeroes.csv
@@ -0,0 +1,33 @@
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diff --git a/src/data/200bpOneTouch_316_counts_complete.csv b/src/data/200bpOneTouch_316_counts_complete.csv
new file mode 100644
index 0000000..eaa8b34
--- /dev/null
+++ b/src/data/200bpOneTouch_316_counts_complete.csv
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+11,12,26,0.521158168214632,0.425403495666655,0.0534383361187135
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diff --git a/src/data/200bpOneTouch_316_counts_complete_model_ones.csv b/src/data/200bpOneTouch_316_counts_complete_model_ones.csv
new file mode 100644
index 0000000..4a25e0e
--- /dev/null
+++ b/src/data/200bpOneTouch_316_counts_complete_model_ones.csv
@@ -0,0 +1,33 @@
+"(Intercept)",-9.0053054843301,-5.57848375349056
+"Cycle",0.278570295064458,0.311560427763238
+"PIC1",1.4095382530581,-0.473300371319766
+"PIC2",1.78110125170181,-1.80829379491639
+"PIC3",1.23769526983289,-1.6240191969811
+"PIC4",1.3403736637977,-0.552324038462309
+"PIC5",1.07381724726733,-0.420035910457381
+"PIC6",1.33520425850217,-1.36417613354913
+"PIC7",1.65119350370577,-1.60354781143568
+"PIC8",1.33935120243627,-0.496599450770905
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+"PIC18",1.71816868740047,-1.42156886745338
+"PIC19",1.45732758925186,-0.195692936523688
+"PIC20",1.57622685880725,-0.421939791187645
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+"PIC22",1.81815331055746,-1.3356586792456
+"PIC23",1.58944072382087,-0.122733465496846
+"PIC24",1.51005315792759,-0.348871445238174
+"PIC25",2.75324801885294,-1.74986079309138
+"PIC26",3.71255513184704,-1.86651401488077
+"PIC27",2.11104785245295,-0.412570581835993
+"PIC28",0.425963139139101,-0.477320233227297
+"PIC29",3.14030706585961,-1.49609380081567
+"PIC30",2.33109980037158,-1.46599727991499
+"PIC31",3.02132293103128,-1.88319927951543
diff --git a/src/data/200bpOneTouch_316_counts_complete_model_others.csv b/src/data/200bpOneTouch_316_counts_complete_model_others.csv
new file mode 100644
index 0000000..e996e70
--- /dev/null
+++ b/src/data/200bpOneTouch_316_counts_complete_model_others.csv
@@ -0,0 +1,98 @@
+"(Intercept)",-7.56454964370778,-6.61639242283797
+"RefLen",1.35833206999604,0.562073802896582
+"I(RefLen^2)",-0.0769069192614576,0.059102825809135
+"Cycle",0.226883989169024,0.407485329614459
+"PIC1",0.214290599610947,0.0488313889178967
+"PIC2",0.421208529877585,-0.342501231197424
+"PIC3",1.06126545515193,-1.30522762544812
+"PIC4",0.223083174414292,0.0234678929881037
+"PIC5",-0.0467516690344483,0.066605410709415
+"PIC6",0.199692280583622,-0.306188105701699
+"PIC7",1.22302198076557,-1.00114585262245
+"PIC8",0.322487693457742,-0.00982154370006477
+"PIC9",0.662460267639585,-0.267465247665271
+"PIC10",1.52601507837495,-1.2749381485469
+"PIC11",1.42688572953172,-1.67108053141564
+"PIC12",-0.91213182324114,0.739813631498705
+"PIC13",1.4692390550083,-0.951757773928218
+"PIC14",0.101376457584455,-0.0230337597318305
+"PIC15",0.746789556562231,-0.0230043897852542
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+"PIC19",0.198024573044406,0.0960007735745367
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+"Cycle:PIC1",0.0403661514463354,-0.0194994165851948
+"Cycle:PIC2",0.0573486035030734,-0.170041594696872
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+"RefLen:PIC22",-0.328099448132378,0.0398870291256898
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+"RefLen:PIC25",-0.296469491911154,0.108969776200582
+"RefLen:PIC26",-0.170556316087289,-0.142772231378809
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+"RefLen:PIC31",0.0029621687646094,-0.0330871779549432
diff --git a/src/data/200bpOneTouch_316_counts_complete_model_zeroes.csv b/src/data/200bpOneTouch_316_counts_complete_model_zeroes.csv
new file mode 100644
index 0000000..b050219
--- /dev/null
+++ b/src/data/200bpOneTouch_316_counts_complete_model_zeroes.csv
@@ -0,0 +1,33 @@
+"(Intercept)",-5.94161995908131
+"Cycle",0.35940056667315
+"PIC1",-0.658954548245633
+"PIC2",-1.81723423466241
+"PIC3",-1.35806054252917
+"PIC4",-0.463366818334649
+"PIC5",-0.310258034701994
+"PIC6",-1.21846874542018
+"PIC7",-1.37886480689424
+"PIC8",-0.250270885662802
+"PIC9",-1.93065301103321
+"PIC10",-3.37932628889794
+"PIC11",-2.61982173879037
+"PIC12",0.45545374033048
+"PIC13",-2.27802279717852
+"PIC14",-1.41779436500637
+"PIC15",-2.25213377265437
+"PIC16",0.254579086663464
+"PIC17",-2.02011334602329
+"PIC18",-1.39292991390901
+"PIC19",-0.212547898688851
+"PIC20",-0.280250423001568
+"PIC21",-0.981477433797104
+"PIC22",-1.19683739167556
+"PIC23",-0.0206773800532214
+"PIC24",-0.0432045025581233
+"PIC25",-1.62998672672519
+"PIC26",-3.32103061191097
+"PIC27",-1.0920639553631
+"PIC28",-0.192822048888317
+"PIC29",-2.00432717772546
+"PIC30",-1.32550162683581
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diff --git a/src/data/MID_fivebase.csv b/src/data/MID_fivebase.csv
new file mode 100644
index 0000000..325ebfc
--- /dev/null
+++ b/src/data/MID_fivebase.csv
@@ -0,0 +1,50 @@
+1,CTACT
+2,CTCGC
+3,CGTAC
+4,TACGT
+5,TAGAG
+6,TCATC
+7,TCTAT
+8,TGCTG
+9,TGTAG
+10,ACGTC
+11,ACACG
+12,AGTGT
+13,AGCAC
+14,ATGCT
+15,ATATG
+16,CATGC
+17,CACAG
+18,CGATG
+19,TCTCG
+20,TCTGC
+21,TCGCT
+22,TCGTG
+23,TCGAC
+24,TCAGT
+25,TGCGC
+26,TGCAT
+27,TGTGT
+28,TGACT
+29,TACTC
+30,TATCT
+31,TATAC
+32,CTCTG
+33,CTCAT
+34,CTGCG
+35,CTGTC
+36,CGCTC
+37,CGCGT
+38,CGCAG
+39,CGTCT
+40,CGACG
+41,CGAGC
+42,CACAC
+43,CATCG
+44,CATGC
+45,CATAT
+46,CAGCT
+47,CAGTG
+48,ACTCT
+49,ACTAC
+50,ACGCG
diff --git a/src/data/MID_tenbase.csv b/src/data/MID_tenbase.csv
new file mode 100644
index 0000000..f268fc5
--- /dev/null
+++ b/src/data/MID_tenbase.csv
@@ -0,0 +1,14 @@
+1,ACGAGTGCGT
+2,ACGCTCGACA
+3,AGACGCACTC
+4,AGCACTGTAG
+5,ATCAGACACG
+6,ATATCGCGAG
+7,CGTGTCTCTA
+8,CTCGCGTGTC
+9,TAGTATCAGC
+10,TCTCTATGCG
+11,TGATACGTCT
+12,TACTGAGCTA
+13,CATAGTAGTG
+14,CGAGAGATAC
diff --git a/src/data/NUC.4.4 b/src/data/NUC.4.4
new file mode 100644
index 0000000..6fb12d2
--- /dev/null
+++ b/src/data/NUC.4.4
@@ -0,0 +1,25 @@
+#
+# This matrix was created by Todd Lowe 12/10/92
+#
+# Uses ambiguous nucleotide codes, probabilities rounded to
+# nearest integer
+#
+# Lowest score = -4, Highest score = 5
+#
+ A T G C S W R Y K M B V H D N
+A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2
+T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2
+G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2
+C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2
+S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1
+W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1
+R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1
+Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1
+K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1
+M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1
+B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1
+V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1
+H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1
+D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1
+N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+
diff --git a/src/data/QuinceProbs.csv b/src/data/QuinceProbs.csv
new file mode 100644
index 0000000..89a4a75
--- /dev/null
+++ b/src/data/QuinceProbs.csv
@@ -0,0 +1,11 @@
+TRUTH,P<,P=,P>
+0,0,0.999778204,0.000221796
+1,0.000321883,0.99946607,0.000212048
+2,0.000945431,0.998580713,0.000473855
+3,0.001607913,0.997984661,0.000407425
+4,0.003180412,0.993857994,0.002961594
+5,0.006680608,0.974554835,0.018764557
+6,0.024114593,0.951770815,0.024114593
+7,0.042847489,0.914305021,0.042847489
+8,0.064148049,0.871703903,0.064148048
+9,0.086291816,0.827416369,0.086291815
diff --git a/src/data/build_info.properties b/src/data/build_info.properties
new file mode 100644
index 0000000..c000aeb
--- /dev/null
+++ b/src/data/build_info.properties
@@ -0,0 +1,5 @@
+#Thu, 20 Feb 2014 10:50:40 +1000
+#Thu Dec 20 08:47:19 EST 2012
+build.major.number=01
+build.number=0
+build.minor.number=53
diff --git a/src/data/maldeEmpiricalDistributions.csv b/src/data/maldeEmpiricalDistributions.csv
new file mode 100644
index 0000000..105c785
--- /dev/null
+++ b/src/data/maldeEmpiricalDistributions.csv
@@ -0,0 +1,140 @@
+1
+0,0,0.999390455,0.000609545
+1,0.000145949,0.998996373,0.000857678
+2,0.000392274,0.998185276,0.00142245
+3,0.004213332,0.991771547,0.004015122
+4,0.030886565,0.952239058,0.016874377
+5,0.084140353,0.901777229,0.014082418
+2
+0,0,0.999139916,0.000860084
+1,0.00017449,0.998657758,0.001167752
+2,0.000461348,0.997684968,0.001853684
+3,0.003575747,0.991487088,0.004937165
+4,0.026319297,0.954925079,0.018755625
+5,0.074565042,0.909553501,0.015881457
+3
+0,0,0.998956931,0.001043069
+1,0.000201955,0.998456178,0.001341867
+2,0.000476795,0.997589513,0.001933692
+3,0.003178747,0.991546588,0.005274666
+4,0.022085173,0.957619395,0.020295431
+5,0.061455511,0.922423336,0.016121154
+4
+0,0,0.998756868,0.001243132
+1,0.000230276,0.998270894,0.00149883
+2,0.000585859,0.997310392,0.00210375
+3,0.003165853,0.991050462,0.005783685
+4,0.01874524,0.9586526,0.02260216
+5,0.052501386,0.929792052,0.017706562
+5
+0,0,0.998770625,0.001229375
+1,0.000238894,0.998329684,0.001431422
+2,0.000645812,0.997240161,0.002114028
+3,0.003295719,0.99054823,0.006156051
+4,0.016369249,0.958878497,0.024752254
+5,0.042615984,0.936335633,0.021048383
+6
+0,0,0.998938842,0.001061158
+1,0.000253961,0.998464822,0.001281216
+2,0.000726126,0.997224806,0.002049068
+3,0.003287861,0.990287497,0.006424642
+4,0.014976614,0.956249172,0.028774215
+5,0.035664823,0.939623209,0.024711968
+7
+0,0,0.999049858,0.000950142
+1,0.000244308,0.998571518,0.001184174
+2,0.000824298,0.997112541,0.002063162
+3,0.00365503,0.98964353,0.006701441
+4,0.015926128,0.951790852,0.032283019
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diff --git a/src/pyromaniac/.metadata/.mylyn/tasks.xml.zip b/src/pyromaniac/.metadata/.mylyn/tasks.xml.zip
new file mode 100644
index 0000000..1c16106
Binary files /dev/null and b/src/pyromaniac/.metadata/.mylyn/tasks.xml.zip differ
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version
new file mode 100644
index 0000000..25cb955
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version
@@ -0,0 +1 @@
+
\ No newline at end of file
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.index b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.index
new file mode 100644
index 0000000..9c245ea
Binary files /dev/null and b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.index differ
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version
new file mode 100644
index 0000000..6b2aaa7
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version
@@ -0,0 +1 @@
+
\ No newline at end of file
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/2.tree b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/2.tree
new file mode 100644
index 0000000..3faa550
Binary files /dev/null and b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.root/2.tree differ
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources
new file mode 100644
index 0000000..12e21b3
Binary files /dev/null and b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources differ
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs
new file mode 100644
index 0000000..a1000eb
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs
@@ -0,0 +1,3 @@
+#Sun Jun 12 18:11:47 EST 2011
+version=1
+eclipse.preferences.version=1
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.epp.usagedata.recording.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.epp.usagedata.recording.prefs
new file mode 100644
index 0000000..2709777
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.epp.usagedata.recording.prefs
@@ -0,0 +1,3 @@
+#Sun Jun 12 18:10:54 EST 2011
+org.eclipse.epp.usagedata.recording.last-upload=1307866254356
+eclipse.preferences.version=1
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs
new file mode 100644
index 0000000..fd57bdb
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs
@@ -0,0 +1,15 @@
+#Sun Jun 12 18:11:47 EST 2011
+useQuickDiffPrefPage=true
+proposalOrderMigrated=true
+tabWidthPropagated=true
+content_assist_proposals_background=255,255,255
+org.eclipse.jdt.ui.javadoclocations.migrated=true
+useAnnotationsPrefPage=true
+spelling_locale=en_GB
+org.eclipse.jface.textfont=1|Courier New|10.0|0|WINDOWS|1|0|0|0|0|0|0|0|0|1|0|0|0|0|Courier New;
+org.eclipse.jdt.ui.editor.tab.width=
+org.eclipse.jdt.ui.formatterprofiles.version=11
+spelling_locale_initialized=true
+eclipse.preferences.version=1
+content_assist_proposals_foreground=0,0,0
+fontPropagated=true
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs
new file mode 100644
index 0000000..6f9f3ef
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs
@@ -0,0 +1,3 @@
+#Sun Jun 12 18:10:50 EST 2011
+eclipse.preferences.version=1
+mylyn.attention.migrated=true
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs
new file mode 100644
index 0000000..e487163
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs
@@ -0,0 +1,3 @@
+#Sun Jun 12 18:10:50 EST 2011
+org.eclipse.mylyn.monitor.activity.tracking.enabled.checked=true
+eclipse.preferences.version=1
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.cvs.ui.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.cvs.ui.prefs
new file mode 100644
index 0000000..629f9ca
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.cvs.ui.prefs
@@ -0,0 +1,3 @@
+#Sun Jun 12 18:11:47 EST 2011
+pref_first_startup=false
+eclipse.preferences.version=1
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.ui.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.ui.prefs
new file mode 100644
index 0000000..17a6848
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.ui.prefs
@@ -0,0 +1,3 @@
+#Sun Jun 12 18:11:47 EST 2011
+eclipse.preferences.version=1
+org.eclipse.team.ui.first_time=false
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs
new file mode 100644
index 0000000..affb366
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs
@@ -0,0 +1,6 @@
+#Sun Jun 12 18:11:47 EST 2011
+eclipse.preferences.version=1
+tipsAndTricks=true
+platformState=1307866151245
+quickStart=false
+PROBLEMS_FILTERS_MIGRATE=true
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.prefs
new file mode 100644
index 0000000..1f7b5bb
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.prefs
@@ -0,0 +1,3 @@
+#Sun Jun 12 18:10:50 EST 2011
+eclipse.preferences.version=1
+showIntro=false
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs
new file mode 100644
index 0000000..1bff601
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs
@@ -0,0 +1,3 @@
+#Sun Jun 12 18:10:52 EST 2011
+eclipse.preferences.version=1
+ENABLED_DECORATORS=org.eclipse.jdt.ui.override.decorator\:true,org.eclipse.jdt.ui.interface.decorator\:false,org.eclipse.jdt.ui.buildpath.decorator\:true,org.eclipse.mylyn.context.ui.decorator.interest\:true,org.eclipse.mylyn.tasks.ui.decorators.task\:true,org.eclipse.mylyn.team.ui.changeset.decorator\:true,org.eclipse.team.cvs.ui.decorator\:true,org.eclipse.ui.LinkedResourceDecorator\:true,org.eclipse.ui.VirtualResourceDecorator\:true,org.eclipse.ui.ContentTypeDecorator\:true,org.eclips [...]
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.epp.usagedata.recording/usagedata.csv b/src/pyromaniac/.metadata/.plugins/org.eclipse.epp.usagedata.recording/usagedata.csv
new file mode 100644
index 0000000..d67421b
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.epp.usagedata.recording/usagedata.csv
@@ -0,0 +1,237 @@
+what,kind,bundleId,bundleVersion,description,time
+activated,perspective,org.eclipse.jdt.ui,,"org.eclipse.jdt.ui.JavaPerspective",1307866253280
+started,bundle,org.eclipse.osgi,3.6.2.R36x_v20110210,"org.eclipse.osgi",1307866253280
+started,bundle,org.eclipse.equinox.simpleconfigurator,1.0.200.v20100503,"org.eclipse.equinox.simpleconfigurator",1307866253280
+started,bundle,com.ibm.icu,4.2.1.v20100412,"com.ibm.icu",1307866253295
+started,bundle,org.eclipse.core.contenttype,3.4.100.v20100505-1235,"org.eclipse.core.contenttype",1307866253295
+started,bundle,org.eclipse.core.databinding.observable,1.3.0.I20100601-0800,"org.eclipse.core.databinding.observable",1307866253295
+started,bundle,org.eclipse.core.expressions,3.4.200.v20100505,"org.eclipse.core.expressions",1307866253295
+started,bundle,org.eclipse.core.filebuffers,3.5.100.v20100520-0800,"org.eclipse.core.filebuffers",1307866253295
+started,bundle,org.eclipse.core.filesystem,1.3.1.R36x_v20100727-0745,"org.eclipse.core.filesystem",1307866253295
+started,bundle,org.eclipse.core.jobs,3.5.1.R36x_v20100824,"org.eclipse.core.jobs",1307866253295
+started,bundle,org.eclipse.core.net,1.2.100.I20100511-0800,"org.eclipse.core.net",1307866253295
+started,bundle,org.eclipse.core.resources,3.6.1.R36x_v20110131-1630,"org.eclipse.core.resources",1307866253295
+started,bundle,org.eclipse.core.runtime,3.6.0.v20100505,"org.eclipse.core.runtime",1307866253295
+started,bundle,org.eclipse.core.runtime.compatibility,3.2.100.v20100505,"org.eclipse.core.runtime.compatibility",1307866253295
+started,bundle,org.eclipse.core.runtime.compatibility.auth,3.2.200.v20100517,"org.eclipse.core.runtime.compatibility.auth",1307866253295
+started,bundle,org.eclipse.epp.usagedata.gathering,1.3.1.R201102081640,"org.eclipse.epp.usagedata.gathering",1307866253295
+started,bundle,org.eclipse.epp.usagedata.recording,1.3.1.R201102081640,"org.eclipse.epp.usagedata.recording",1307866253311
+started,bundle,org.eclipse.equinox.app,1.3.1.R36x_v20100803,"org.eclipse.equinox.app",1307866253311
+started,bundle,org.eclipse.equinox.common,3.6.0.v20100503,"org.eclipse.equinox.common",1307866253311
+started,bundle,org.eclipse.equinox.ds,1.2.1.R36x_v20100803,"org.eclipse.equinox.ds",1307866253311
+started,bundle,org.eclipse.equinox.event,1.2.0.v20100503,"org.eclipse.equinox.event",1307866253311
+started,bundle,org.eclipse.equinox.p2.core,2.0.3.R36x_v20110111,"org.eclipse.equinox.p2.core",1307866253311
+started,bundle,org.eclipse.equinox.p2.directorywatcher,1.0.203.R36x_v20101220,"org.eclipse.equinox.p2.directorywatcher",1307866253311
+started,bundle,org.eclipse.equinox.p2.engine,2.0.1.R36x_v20110201,"org.eclipse.equinox.p2.engine",1307866253311
+started,bundle,org.eclipse.equinox.p2.metadata,2.0.1.R36x_v20101202,"org.eclipse.equinox.p2.metadata",1307866253311
+started,bundle,org.eclipse.equinox.p2.metadata.repository,1.1.0.v20100513,"org.eclipse.equinox.p2.metadata.repository",1307866253311
+started,bundle,org.eclipse.equinox.p2.operations,2.0.0.v20100510,"org.eclipse.equinox.p2.operations",1307866253311
+started,bundle,org.eclipse.equinox.p2.reconciler.dropins,1.1.2.R36x_v20110114,"org.eclipse.equinox.p2.reconciler.dropins",1307866253311
+started,bundle,org.eclipse.equinox.p2.repository,2.0.2.R36x_v20110111-1500,"org.eclipse.equinox.p2.repository",1307866253311
+started,bundle,org.eclipse.equinox.p2.ui.sdk.scheduler,1.0.0.v20100507-1815,"org.eclipse.equinox.p2.ui.sdk.scheduler",1307866253311
+started,bundle,org.eclipse.equinox.p2.updatechecker,1.1.101.R36x_v20100823,"org.eclipse.equinox.p2.updatechecker",1307866253311
+started,bundle,org.eclipse.equinox.preferences,3.3.0.v20100503,"org.eclipse.equinox.preferences",1307866253311
+started,bundle,org.eclipse.equinox.registry,3.5.0.v20100503,"org.eclipse.equinox.registry",1307866253311
+started,bundle,org.eclipse.equinox.security,1.0.200.v20100503,"org.eclipse.equinox.security",1307866253311
+started,bundle,org.eclipse.equinox.util,1.0.200.v20100503,"org.eclipse.equinox.util",1307866253311
+started,bundle,org.eclipse.help,3.5.0.v20100524,"org.eclipse.help",1307866253311
+started,bundle,org.eclipse.jdt.core,3.6.2.v_A76_R36x,"org.eclipse.jdt.core",1307866253311
+started,bundle,org.eclipse.jdt.core.manipulation,1.3.0.v20100520-0800,"org.eclipse.jdt.core.manipulation",1307866253311
+started,bundle,org.eclipse.jdt.ui,3.6.2.r362_v20110203,"org.eclipse.jdt.ui",1307866253311
+started,bundle,org.eclipse.jface,3.6.2.M20110210-1200,"org.eclipse.jface",1307866253311
+started,bundle,org.eclipse.jsch.core,1.1.200.I20100505-1245,"org.eclipse.jsch.core",1307866253311
+started,bundle,org.eclipse.mylyn.bugzilla.core,3.4.2.v20100902-0100-e3x,"org.eclipse.mylyn.bugzilla.core",1307866253311
+started,bundle,org.eclipse.mylyn.bugzilla.ui,3.4.3.v20110131-0100-e3x,"org.eclipse.mylyn.bugzilla.ui",1307866253327
+started,bundle,org.eclipse.mylyn.commons.net,3.4.1.v20100625-2100-e3x,"org.eclipse.mylyn.commons.net",1307866253327
+started,bundle,org.eclipse.mylyn.commons.ui,3.4.0.v20100608-0100-e3x,"org.eclipse.mylyn.commons.ui",1307866253327
+started,bundle,org.eclipse.mylyn.context.core,3.4.1.v20100909-0100-e3x,"org.eclipse.mylyn.context.core",1307866253327
+started,bundle,org.eclipse.mylyn.context.ui,3.4.2.v20110131-0100-e3x,"org.eclipse.mylyn.context.ui",1307866253327
+started,bundle,org.eclipse.mylyn.monitor.ui,3.4.1.v20110131-0100-e3x,"org.eclipse.mylyn.monitor.ui",1307866253327
+started,bundle,org.eclipse.mylyn.tasks.ui,3.4.3.v20110131-0100-e3x,"org.eclipse.mylyn.tasks.ui",1307866253327
+started,bundle,org.eclipse.mylyn.team.ui,3.4.3.v20110131-0100-e3x,"org.eclipse.mylyn.team.ui",1307866253327
+started,bundle,org.eclipse.search,3.6.0.v20100520-0800,"org.eclipse.search",1307866253327
+started,bundle,org.eclipse.team.core,3.5.101.R36x_v20110203-1036,"org.eclipse.team.core",1307866253327
+started,bundle,org.eclipse.team.cvs.core,3.3.301.R36x_v20110119-0815,"org.eclipse.team.cvs.core",1307866253327
+started,bundle,org.eclipse.team.cvs.ui,3.3.302.R36x_v20110203-1036,"org.eclipse.team.cvs.ui",1307866253327
+started,bundle,org.eclipse.team.ui,3.5.102.R36x_v20110203-1036,"org.eclipse.team.ui",1307866253327
+started,bundle,org.eclipse.ui,3.6.2.M20110203-1100,"org.eclipse.ui",1307866253327
+started,bundle,org.eclipse.ui.console,3.5.0.v20100526,"org.eclipse.ui.console",1307866253327
+started,bundle,org.eclipse.ui.editors,3.6.1.r361_v20100825-0800,"org.eclipse.ui.editors",1307866253327
+started,bundle,org.eclipse.ui.forms,3.5.2.r36_v20100702,"org.eclipse.ui.forms",1307866253327
+started,bundle,org.eclipse.ui.ide,3.6.2.M20101201-0800,"org.eclipse.ui.ide",1307866253327
+started,bundle,org.eclipse.ui.intro,3.4.0.v20100427,"org.eclipse.ui.intro",1307866253327
+started,bundle,org.eclipse.ui.intro.universal,3.2.402.r36_v20100702,"org.eclipse.ui.intro.universal",1307866253327
+started,bundle,org.eclipse.ui.net,1.2.100.I20100505-1245,"org.eclipse.ui.net",1307866253327
+started,bundle,org.eclipse.ui.views,3.5.1.M20110202-0800,"org.eclipse.ui.views",1307866253327
+started,bundle,org.eclipse.ui.workbench,3.6.2.M20110210-1200,"org.eclipse.ui.workbench",1307866253327
+started,bundle,org.eclipse.ui.workbench.texteditor,3.6.1.r361_v20100714-0800,"org.eclipse.ui.workbench.texteditor",1307866253327
+started,bundle,org.eclipse.update.configurator,3.3.100.v20100512,"org.eclipse.update.configurator",1307866253327
+started,bundle,org.eclipse.update.core,3.2.402.R36x_v20100629,"org.eclipse.update.core",1307866253327
+started,bundle,org.eclipse.update.scheduler,3.2.300.v20100512,"org.eclipse.update.scheduler",1307866253327
+os,sysinfo,,,"win32",1307866253342
+arch,sysinfo,,,"x86_64",1307866253342
+ws,sysinfo,,,"win32",1307866253342
+locale,sysinfo,,,"en_AU",1307866253342
+processors,sysinfo,,,"8",1307866253342
+java.runtime.name,sysinfo,,,"Java(TM) SE Runtime Environment",1307866253342
+java.runtime.version,sysinfo,,,"1.6.0_26-b03",1307866253342
+java.specification.name,sysinfo,,,"Java Platform API Specification",1307866253342
+java.specification.vendor,sysinfo,,,"Sun Microsystems Inc.",1307866253342
+java.specification.version,sysinfo,,,"1.6",1307866253342
+java.vendor,sysinfo,,,"Sun Microsystems Inc.",1307866253342
+java.version,sysinfo,,,"1.6.0_26",1307866253342
+java.vm.info,sysinfo,,,"mixed mode",1307866253342
+java.vm.name,sysinfo,,,"Java HotSpot(TM) 64-Bit Server VM",1307866253342
+java.vm.specification.name,sysinfo,,,"Java Virtual Machine Specification",1307866253342
+java.vm.specification.vendor,sysinfo,,,"Sun Microsystems Inc.",1307866253342
+java.vm.specification.version,sysinfo,,,"1.0",1307866253342
+java.vm.vendor,sysinfo,,,"Sun Microsystems Inc.",1307866253342
+java.vm.version,sysinfo,,,"20.1-b02",1307866253342
+activated,view,org.eclipse.jdt.ui,3.6.2.r362_v20110203,"org.eclipse.jdt.ui.PackageExplorer",1307866254528
+activated,view,org.eclipse.jdt.ui,3.6.2.r362_v20110203,"org.eclipse.jdt.ui.PackageExplorer",1307866254543
+closed,view,org.eclipse.ui,3.6.2.M20110203-1100,"org.eclipse.ui.internal.introview",1307866254575
+deactivated,workbench,org.eclipse.ui.workbench,3.6.2.M20110210-1200,"",1307866269343
+activated,workbench,org.eclipse.ui.workbench,3.6.2.M20110210-1200,"",1307866271043
+executed,command,org.eclipse.ui.ide,3.6.2.M20101201-0800,"org.eclipse.ui.edit.text.openLocalFile",1307866271090
+activated,view,org.eclipse.ui.ide,3.6.2.M20101201-0800,"org.eclipse.ui.views.ProblemView",1307866300324
+closed,view,org.eclipse.jdt.ui,3.6.2.r362_v20110203,"org.eclipse.jdt.ui.PackageExplorer",1307866300340
+activated,view,org.eclipse.ui.views,3.5.1.M20110202-0800,"org.eclipse.ui.views.ContentOutline",1307866304630
+activated,view,org.eclipse.ui.ide,3.6.2.M20101201-0800,"org.eclipse.ui.views.ProblemView",1307866304630
+closed,view,org.eclipse.ui.views,3.5.1.M20110202-0800,"org.eclipse.ui.views.ContentOutline",1307866304661
+deactivated,workbench,org.eclipse.ui.workbench,3.6.2.M20110210-1200,"",1307866305893
+activated,workbench,org.eclipse.ui.workbench,3.6.2.M20110210-1200,"",1307866307063
+closed,workbench,org.eclipse.ui.workbench,3.6.2.M20110210-1200,"",1307866307126
+started,bundle,org.eclipse.compare.core,3.5.101.R36x_v20100929-0800,"org.eclipse.compare.core",1307866307360
+started,bundle,org.eclipse.compare,3.5.101.R36x_v20100929-0800,"org.eclipse.compare",1307866307360
+stopped,bundle,org.eclipse.mylyn.ide.ant,3.4.0.v20100608-0100-e3x,"org.eclipse.mylyn.ide.ant",1307866307485
+stopped,bundle,org.eclipse.ant.ui,3.5.0.v20100427,"org.eclipse.ant.ui",1307866307485
+stopped,bundle,org.eclipse.ant.launching,1.0.1.v20101020_r362,"org.eclipse.ant.launching",1307866307485
+stopped,bundle,org.eclipse.compare.win32,1.0.101.R36x_v20101103-0618,"org.eclipse.compare.win32",1307866307485
+stopped,bundle,org.eclipse.equinox.p2.ui.sdk,1.0.100.v20100513,"org.eclipse.equinox.p2.ui.sdk",1307866307485
+stopped,bundle,org.eclipse.mylyn.java.tasks,3.4.0.v20100608-0100-e3x,"org.eclipse.mylyn.java.tasks",1307866307485
+stopped,bundle,org.eclipse.mylyn.java.ui,3.4.0.v20100608-0100-e3x,"org.eclipse.mylyn.java.ui",1307866307485
+stopped,bundle,org.eclipse.jdt.junit,3.6.1.r361_v20100825-0800,"org.eclipse.jdt.junit",1307866307485
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diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache
new file mode 100644
index 0000000..593f470
Binary files /dev/null and b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache differ
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat
new file mode 100644
index 0000000..3aea61c
Binary files /dev/null and b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat differ
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml
new file mode 100644
index 0000000..6cd9562
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml
@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<typeInfoHistroy/>
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml
new file mode 100644
index 0000000..8c365b7
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml
@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<qualifiedTypeNameHistroy/>
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml
new file mode 100644
index 0000000..4915323
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<section name="Workbench">
+ <section name="org.eclipse.jdt.internal.ui.packageview.PackageExplorerPart">
+ <item value="true" key="group_libraries"/>
+ <item value="false" key="linkWithEditor"/>
+ <item value="2" key="layout"/>
+ <item value="1" key="rootMode"/>
+ <item value="<?xml version="1.0" encoding="UTF-8"?>
<packageExplorer group_libraries="1" layout="2" linkWithEditor="0" rootMode="1" workingSetName="">
<customFilters userDefinedPatternsEnabled="false">
<xmlDefinedFilters>
<child filterId="org.eclipse.jdt.ui.PackageExplorer.LibraryFilter" isEnabled="false"/>
&# [...]
+ </section>
+</section>
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.ide/dialog_settings.xml b/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.ide/dialog_settings.xml
new file mode 100644
index 0000000..558ae38
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.ide/dialog_settings.xml
@@ -0,0 +1,11 @@
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diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml b/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml
new file mode 100644
index 0000000..1ef2b05
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml
@@ -0,0 +1,3 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<section name="Workbench">
+</section>
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.workbench/workbench.xml b/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.workbench/workbench.xml
new file mode 100644
index 0000000..f668221
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.workbench/workbench.xml
@@ -0,0 +1,200 @@
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+<page content="org.eclipse.mylyn.tasks.ui.views.tasks" label="Task List"/>
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+</presentation>
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+</info>
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+</folder>
+</info>
+</mainWindow>
+</layout>
+</perspective>
+</perspectives>
+<workingSets/>
+<navigationHistory/>
+<input factoryID="org.eclipse.ui.internal.model.ResourceFactory" path="/" type="8"/>
+</page>
+<workbenchWindowAdvisor/>
+<actionBarAdvisor/>
+<trimLayout>
+<trimArea IMemento.internal.id="128">
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+</trimArea>
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+<trimItem IMemento.internal.id="org.eclise.ui.internal.FastViewBar"/>
+<trimItem IMemento.internal.id="org.eclipse.jface.action.StatusLineManager"/>
+<trimItem IMemento.internal.id="org.eclipse.ui.internal.progress.ProgressRegion"/>
+</trimArea>
+</trimLayout>
+</window>
+<mruList/>
+</workbench>
\ No newline at end of file
diff --git a/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml b/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml
new file mode 100644
index 0000000..06da518
--- /dev/null
+++ b/src/pyromaniac/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<workingSetManager>
+<workingSet aggregate="true" factoryID="org.eclipse.ui.internal.WorkingSetFactory" id="1307866250425_0" label="Window Working Set" name="Aggregate for window 1307866250425"/>
+</workingSetManager>
\ No newline at end of file
diff --git a/src/pyromaniac/.metadata/version.ini b/src/pyromaniac/.metadata/version.ini
new file mode 100644
index 0000000..c51ff74
--- /dev/null
+++ b/src/pyromaniac/.metadata/version.ini
@@ -0,0 +1 @@
+org.eclipse.core.runtime=1
\ No newline at end of file
diff --git a/src/pyromaniac/AcaciaConstants.java b/src/pyromaniac/AcaciaConstants.java
new file mode 100644
index 0000000..054647d
--- /dev/null
+++ b/src/pyromaniac/AcaciaConstants.java
@@ -0,0 +1,436 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac;
+
+import java.util.HashMap;
+
+import pyromaniac.DataStructures.MIDPrimerCombo;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class AcaciaConstants.
+ */
+public final class AcaciaConstants
+{
+
+ /** The Constant CONFIG_DELIMITER. */
+ public static final String CONFIG_DELIMITER = "=";
+
+ //hidden constants [from GUI or parameterisation]
+ /** The Constant CLUSTERING_OLIGO_LENGTH. */
+ public static final int CLUSTERING_OLIGO_LENGTH = 6;
+
+ /** The Constant MAXIMUM_BIN. */
+ public static final int MAXIMUM_BIN = 16; //maximum obs count.
+
+
+ //parameter names
+ /** The Constant OPT_FASTA. */
+ public static final String OPT_FASTA = "FASTA";
+
+ /** The Constant OPT_FASTA_LOC. */
+ public static final String OPT_FASTA_LOC = "FASTA_LOCATION";
+
+ /** The Constant OPT_QUAL_LOC. */
+ public static final String OPT_QUAL_LOC = "QUAL_LOCATION";
+
+ /** The Constant OPT_FASTQ. */
+ public static final String OPT_FASTQ = "FASTQ";
+
+ /** The Constant OPT_FASTQ_LOC. */
+ public static final String OPT_FASTQ_LOC = "FASTQ_LOCATION";
+
+ /** The Constant OPT_MID. */
+ public static final String OPT_MID = "MID_OPTION";
+
+ /** The Constant OPT_MID_FILE. */
+ public static final String OPT_MID_FILE = "MID_FILE";
+
+ /** The Constant OPT_TRIM_TO_LENGTH. */
+ public static final String OPT_TRIM_TO_LENGTH = "TRIM_TO_LENGTH";
+
+ /** The Constant OPT_OUTPUT_PREFIX. */
+ public static final String OPT_OUTPUT_PREFIX = "OUTPUT_PREFIX";
+
+ /** The Constant OPT_OUTPUT_DIR. */
+ public static final String OPT_OUTPUT_DIR = "OUTPUT_DIR";
+
+ /** The Constant OPT_LOAD_MIDS. */
+ public static final String OPT_LOAD_MIDS = "LOAD_MIDS";
+
+ /** The Constant OPT_ROCHE_5MID. */
+ public static final String OPT_ROCHE_5MID = "ROCHE_5MID";
+
+ /** The Constant OPT_ROCHE_10MID. */
+ public static final String OPT_ROCHE_10MID = "ROCHE_10MID";
+
+ /** The Constant OPT_NO_MID. */
+ public static final String OPT_NO_MID = "NO_MID";
+
+ /** The Constant OPT_SIGNIFICANCE_LEVEL. */
+ public static final String OPT_SIGNIFICANCE_LEVEL = "SIGNIFICANCE_LEVEL";
+
+ /** The Constant OPT_REPRESENTATIVE_SEQ. */
+ public static final String OPT_REPRESENTATIVE_SEQ = "REPRESENTATIVE_SEQUENCE";
+
+ /** The Constant OPT_MIN_AVG_QUALITY. */
+ public static final String OPT_MIN_AVG_QUALITY = "AVG_QUALITY_CUTOFF";
+
+ /** The Constant OPT_MODE_REPRESENTATIVE. */
+ public static final String OPT_MODE_REPRESENTATIVE = "Mode";
+
+ /** The Constant OPT_MAX_REPRESENTATIVE. */
+ public static final String OPT_MAX_REPRESENTATIVE = "Max";
+
+ /** The Constant OPT_MIN_REPRESENTATIVE. */
+ public static final String OPT_MIN_REPRESENTATIVE = "Min";
+
+ /** The Constant OPT_MEDIAN_REPRESENTATIVE. */
+ public static final String OPT_MEDIAN_REPRESENTATIVE = "Median";
+
+ /** The Constant OPT_SPLIT_ON_MID. */
+ public static final String OPT_SPLIT_ON_MID = "SPLIT_ON_MID";
+
+ /** The Constant OPT_MAX_STD_DEV_LENGTH. */
+ public static final String OPT_MAX_STD_DEV_LENGTH = "MAX_STD_DEV_LENGTH";
+
+ /** The Constant OPT_ERROR_MODEL. */
+ public static final String OPT_ERROR_MODEL = "ERROR_MODEL";
+
+ /** The Constant OPT_FLOWSIM_ERROR_MODEL. */
+ public static final String OPT_FLOWSIM_ERROR_MODEL = "Balzer";
+
+ /** The Constant OPT_PYRONOISE_ERROR_MODEL. */
+ public static final String OPT_PYRONOISE_ERROR_MODEL = "Quince";
+
+ /** The Constant OPT_FILTER_READS_WITH_N_BEFORE_POS. */
+ public static final String OPT_FILTER_READS_WITH_N_BEFORE_POS = "FILTER_N_BEFORE_POS";
+
+
+ /** The Constant OPT_ACACIA_TITANIUM_ERROR_MODEL. */
+ public static final String OPT_ACACIA_TITANIUM_ERROR_MODEL = "Acacia_Emp_Titanium";
+
+ /** The Constant OPT_FLOW_KEY. */
+ public static final String OPT_FLOW_KEY = "FLOW_KEY";
+
+ /** The Constant OPT_FLOW_CYCLE_STRING */
+ public static final String OPT_FLOW_CYCLE_STRING = "FLOW_CYCLE_STRING";
+
+
+ /** The Constant OPT_MAX_RECURSE_DEPTH. */
+ public static final String OPT_MAX_RECURSE_DEPTH = "MAX_RECURSE_DEPTH";
+
+ /** The Constant OPT_MAXIMUM_MANHATTAN_DIST. */
+ public static final String OPT_MAXIMUM_MANHATTAN_DIST = "MAXIMUM_MANHATTAN_DISTANCE";
+
+ /** The Constant OPT_TRUNCATE_CONSENSUS_TO_FLOW. */
+ public static final String OPT_TRUNCATE_READ_TO_FLOW = "TRUNCATE_READ_TO_FLOW";
+
+ /** The Constant OPT_MIN_FLOW_TRUNCATION. */
+ public static final String OPT_MIN_FLOW_TRUNCATION = "MIN_FLOW_TRUNCATION"; //paired with the percentage of reads covering blah
+
+ /** The Constant OPT_MIN_READ_REP_BEFORE_TRUNCATION. */
+ public static final String OPT_MIN_READ_REP_BEFORE_TRUNCATION = "MIN_READ_REP_BEFORE_TRUNCATION";
+
+ public static final String OPT_MAX_COMPLETE_LINKAGE_DIST = "MAX_COMPLETE_LINKAGE_DISTANCE";
+
+ public static final String OPT_CLEAN_DATA = "CLEAN_DATA";
+
+ //parameter default values
+ /** The Constant DEFAULT_OPT_FASTA. */
+ public static final String DEFAULT_OPT_FASTA = "TRUE";
+
+ /** The Constant DEFAULT_OPT_FASTQ. */
+ public static final String DEFAULT_OPT_FASTQ = "FALSE";
+
+ /** The Constant DEFAULT_OPT_TRIM_LENGTH. */
+ public static final String DEFAULT_OPT_TRIM_LENGTH = "";
+
+ /** The Constant DEFAULT_OPT_MID. */
+ public static final String DEFAULT_OPT_MID = OPT_NO_MID;
+
+ /** The Constant DEFAULT_ALLOW_LOOKAHEAD. */
+ public static final String DEFAULT_ALLOW_LOOKAHEAD = "FALSE";
+
+ /** The Constant DEFAULT_OPT_LOOKAHEAD. */
+ public static final String DEFAULT_OPT_LOOKAHEAD = "TRUE";
+
+ /** The Constant DEFAULT_OPT_SIGNIFICANCE_LEVEL. */
+ public static final String DEFAULT_OPT_SIGNIFICANCE_LEVEL = "-9";
+
+ /** The Constant DEFAULT_OPT_REPRESENTATIVE_SEQ. */
+ public static final String DEFAULT_OPT_REPRESENTATIVE_SEQ = OPT_MODE_REPRESENTATIVE;
+
+ /** The Constant DEFAULT_OPT_MIN_AVG_QUALITY. */
+ public static final String DEFAULT_OPT_MIN_AVG_QUALITY = "30";
+
+ /** The Constant DEFAULT_OPT_SPLIT_ON_MID. */
+ public static final String DEFAULT_OPT_SPLIT_ON_MID = "FALSE";
+
+ /** The Constant DEFAULT_OPT_MAX_STD_DEV_LENGTH. */
+ public static final String DEFAULT_OPT_MAX_STD_DEV_LENGTH = "2";
+
+ /** The Constant DEFAULT_OPT_ERROR_MODEL. */
+ public static final String DEFAULT_OPT_ERROR_MODEL = OPT_FLOWSIM_ERROR_MODEL;
+
+ /** The Constant DEFAULT_OPT_FLOW_KEY. */
+ public static final String DEFAULT_OPT_FLOW_KEY = "TCAG";
+
+ public static final String OPT_FLOW_CYCLE_454 = "TACG"; //double check this
+
+ public static final String OPT_FLOW_CYCLE_ION_TORRENT = "TACGTACGTCTGAGCATCGATCGATGTACAGC";
+
+ /** The Constant DEFAULT_OPT_FLOW_CYCLE_STRING */
+ public static final String DEFAULT_OPT_FLOW_CYCLE_STRING = OPT_FLOW_CYCLE_454;
+
+ /** The Constant DEFAULT_OPT_TRUNCATE_CONSENSUS_TO_FLOW. */
+ public static final String DEFAULT_OPT_TRUNCATE_READ_TO_FLOW= "";
+
+ /** The Constant DEFAULT_OPT_MIN_FLOW_TRUNCATION. */
+ public static final String DEFAULT_OPT_MIN_FLOW_TRUNCATION = "150"; //estimated flow.
+
+ /** The Constant DEFAULT_OPT_MIN_READ_REP_BEFORE_TRUNCATION. */
+ public static final String DEFAULT_OPT_MIN_READ_REP_BEFORE_TRUNCATION = "0.0"; //this is the default
+
+ /** The Constant DEFAULT_OPT_MAXIMUM_MANHATTAN_DIST. */
+ public static final String DEFAULT_OPT_MAXIMUM_MANHATTAN_DIST = "13";
+
+ /** The Constant DEFAULT_OPT_MAXIMUM_MANHATTAN_DIST_ALIGN. */
+ public static final String DEFAULT_OPT_MAXIMUM_MANHATTAN_DIST_ALIGN = "21";
+
+ /** The Constant DEFAULT_OPT_TRIM_COLLAPSED. */
+ public static final int DEFAULT_OPT_TRIM_COLLAPSED = 50;
+
+ /** The Constant DEFAULT_OPT_MAX_RECURSE_DEPTH. */
+ public static final String DEFAULT_OPT_MAX_RECURSE_DEPTH = "2";
+
+ /** The Constant DEFAULT_FILTER_N_BEFORE_POS. */
+ public static final String DEFAULT_FILTER_N_BEFORE_POS = "350";
+
+ public static final String DEFAULT_OPT_MAX_COMPLETE_LINKAGE_DIST = "0.25";
+
+ public static final String DEFAULT_OPT_CLEAN_DATA = "TRUE";
+
+ /** The Constant DEFAULT_FILE_LOC. */
+ public static final String DEFAULT_FILE_LOC;
+
+ /** The Constant DEFAULT_OPT_MID_LOC. */
+ public static final String DEFAULT_OPT_MID_LOC;
+
+ /** The Constant DEFAULT_OPT_OUTPUT_PREFIX. */
+ public static final String DEFAULT_OPT_OUTPUT_PREFIX;
+
+ /** The Constant PYRONOISE_PROBS_LOCATION. */
+ public static final String PYRONOISE_PROBS_LOCATION;
+
+ /** The Constant FLOWSIM_PROBS_LOCATION. */
+ public static final String FLOWSIM_PROBS_LOCATION;
+
+ /** The Constant FLOWSIM_PROBS_LOCATION. */
+ public static final String ACACIA_EMP_MODEL_TITANIUM_LOCATION;
+
+ //Ion Torrent is changing rapidly, maybe I should get the user to supply this...
+
+ public static final String IONTORRENT_314_100bp_PROBS_LOCATION;
+ public static final String IONTORRENT_314_100bp_ZERO_COEF;
+ public static final String IONTORRENT_314_100bp_ONE_COEF;
+ public static final String IONTORRENT_314_100bp_OTHER_COEF;
+
+ public static final String IONTORRENT_314_200bp_PROBS_LOCATION;
+ public static final String IONTORRENT_314_200bp_ZERO_COEF;
+ public static final String IONTORRENT_314_200bp_ONE_COEF;
+ public static final String IONTORRENT_314_200bp_OTHER_COEF;
+
+ public static final String IONTORRENT_314_200bpOneTouch_PROBS_LOCATION;
+ public static final String IONTORRENT_314_200bpOneTouch_ZERO_COEF;
+ public static final String IONTORRENT_314_200bpOneTouch_ONE_COEF;
+ public static final String IONTORRENT_314_200bpOneTouch_OTHER_COEF;
+
+ public static final String IONTORRENT_316_100bp_PROBS_LOCATION;
+ public static final String IONTORRENT_316_100bp_ZERO_COEF;
+ public static final String IONTORRENT_316_100bp_ONE_COEF;
+ public static final String IONTORRENT_316_100bp_OTHER_COEF;
+
+ public static final String IONTORRENT_316_200bp_PROBS_LOCATION;
+ public static final String IONTORRENT_316_200bp_ZERO_COEF;
+ public static final String IONTORRENT_316_200bp_ONE_COEF;
+ public static final String IONTORRENT_316_200bp_OTHER_COEF;
+
+ public static final String IONTORRENT_316_200bpOneTouch_PROBS_LOCATION;
+ public static final String IONTORRENT_316_200bpOneTouch_ZERO_COEF;
+ public static final String IONTORRENT_316_200bpOneTouch_ONE_COEF;
+ public static final String IONTORRENT_316_200bpOneTouch_OTHER_COEF;
+
+
+
+
+ //IO constants
+ /** The Constant STANDARD_OUT_NAME. */
+ public static final String STANDARD_OUT_NAME;
+
+ /** The Constant STANDARD_ERR_NAME. */
+ public static final String STANDARD_ERR_NAME;
+
+ /** The Constant STANDARD_DEBUG_NAME. */
+ public static final String STANDARD_DEBUG_NAME;
+
+
+ /** The Constant STATS_SUFFIX. */
+ public static final String STATS_SUFFIX = "stats";
+
+ /** The Constant SEQOUT_SUFFIX. */
+ public static final String SEQOUT_SUFFIX = "seqOut";
+
+ /** The Constant REFOUT_SUFFIX. */
+ public static final String REFOUT_SUFFIX = "refOut";
+
+ /** The Constant MAPOUT_SUFFIX. */
+ public static final String MAPOUT_SUFFIX = "mapOut";
+
+ /** The Constant HISTOUT_SUFFIX. */
+ public static final String HISTOUT_SUFFIX = "histOut";
+
+ /** The Constant STAT_OUT_FILE. */
+ public static final String STAT_OUT_FILE = "STATOUT";
+
+ /** The Constant SEQ_OUT_FILE. */
+ public static final String SEQ_OUT_FILE = "SEQOUT";
+
+ /** The Constant REF_OUT_FILE. */
+ public static final String REF_OUT_FILE = "REFOUT";
+
+ /** The Constant MAP_OUT_FILE. */
+ public static final String MAP_OUT_FILE = "MAPOUT";
+
+ /** The Constant HIST_OUT_FILE. */
+ public static final String HIST_OUT_FILE = "HISTOUT";
+
+ //GUI constants
+ /** The Constant MENU_STRING_EXIT. */
+ public static final String MENU_STRING_EXIT = "Quit";
+
+ /** The Constant MENU_PROGRAM_INFO. */
+ public static final String MENU_PROGRAM_INFO = "Program Info";
+
+
+ //Code Constants
+ /** The Constant SIGN_THRESHOLD_ZERO. */
+ public static final String SIGN_THRESHOLD_ZERO = "-Inf";
+
+ /** The Constant IUPAC_AMBIGUOUS_MAPPINGS. */
+ public static final HashMap <Character, char []> IUPAC_AMBIGUOUS_MAPPINGS = new HashMap<Character, char [] >();
+
+ /** The Constant NO_MID_GROUP. */
+ public static final MIDPrimerCombo NO_MID_GROUP = new MIDPrimerCombo("", "", "all_tags"); //changing it to Titanium to be like Denoiser
+
+
+ //should avoid the majority of introduced deletions observed in previous versions.
+ /** The Constant OPT_SIGNIFICANT_WHEN_TWO. */
+ public static final String OPT_SIGNIFICANT_WHEN_TWO = "ANY_DIFF_SIGNIFICANT_FOR_TWO_SEQS";
+
+
+ /** The Constant DEFAULT_OPT_SIGNIFICANT_WHEN_TWO. */
+ public static final String DEFAULT_OPT_SIGNIFICANT_WHEN_TWO = "TRUE";
+
+ /** These in-built ones are painful, and need to be replaced*/
+
+ //might even have to be broken down into 316 200bp 316 100bp, 314 100bp 314 200bp
+ public static final String OPT_ACACIA_IT_OT_100bp_316_MODEL = "ITO_100bp_316";
+ public static final String OPT_ACACIA_IT_OT_100bp_314_MODEL = "ITO_100bp_314";
+ public static final String OPT_ACACIA_IT_MAN_200bp_316_MODEL = "ITM_200bp_316";
+ public static final String OPT_ACACIA_IT_MAN_200bp_314_MODEL = "ITM_200bp_314";
+ public static final String OPT_ACACIA_IT_OT_200bp_316 = "ITO_200bp_316";
+ public static final String OPT_ACACIA_IT_OT_200bp_314 = "ITO_200bp_314";
+
+ public static final String IGNORE_PRIMER = "NoPrimer";
+
+ public static final String OPT_HEX_CLUSTER_ONLY = "CLUSTER_ONLY";
+ public static final String DEFAULT_OPT_HEX_CLUSTER_ONLY = "FALSE";
+
+
+
+ static
+ {
+ PYRONOISE_PROBS_LOCATION = "/data/QuinceProbs.csv";
+ FLOWSIM_PROBS_LOCATION = "/data/maldeEmpiricalDistributions.csv";
+ ACACIA_EMP_MODEL_TITANIUM_LOCATION = "/data/titanium_emp_nuc.csv";
+
+ IONTORRENT_314_100bp_PROBS_LOCATION = "/data/100bpOneTouch_314_counts_complete.csv";
+ IONTORRENT_314_100bp_ZERO_COEF = "/data/100bpOneTouch_314_counts_complete_model_zeroes.csv";
+ IONTORRENT_314_100bp_ONE_COEF = "/data/100bpOneTouch_314_counts_complete_model_ones.csv";
+ IONTORRENT_314_100bp_OTHER_COEF = "/data/100bpOneTouch_314_counts_complete_model_others.csv";
+
+ IONTORRENT_314_200bp_PROBS_LOCATION = "/data/200bpManual_314_counts_complete.csv";
+ IONTORRENT_314_200bp_ZERO_COEF = "/data/200bpManual_314_counts_complete_model_zeroes.csv";
+ IONTORRENT_314_200bp_ONE_COEF = "/data/200bpManual_314_counts_complete_model_ones.csv";
+ IONTORRENT_314_200bp_OTHER_COEF = "/data/200bpManual_314_counts_complete_model_others.csv";
+
+ IONTORRENT_314_200bpOneTouch_PROBS_LOCATION = "/data/200bpOneTouch_314_counts_complete.csv";
+ IONTORRENT_314_200bpOneTouch_ZERO_COEF = "/data/200bpOneTouch_314_counts_complete_model_zeroes.csv";
+ IONTORRENT_314_200bpOneTouch_ONE_COEF = "/data/200bpOneTouch_314_counts_complete_model_ones.csv";
+ IONTORRENT_314_200bpOneTouch_OTHER_COEF = "/data/200bpOneTouch_314_counts_complete_model_others.csv";
+
+ IONTORRENT_316_100bp_PROBS_LOCATION = "/data/100bpOneTouch_316_counts_complete.csv";
+ IONTORRENT_316_100bp_ZERO_COEF = "/data/100bpOneTouch_316_counts_complete_model_zeroes.csv";
+ IONTORRENT_316_100bp_ONE_COEF= "/data/100bpOneTouch_316_counts_complete_model_ones.csv";
+ IONTORRENT_316_100bp_OTHER_COEF = "/data/100bpOneTouch_316_counts_complete_model_others.csv";
+
+ IONTORRENT_316_200bp_PROBS_LOCATION = "/data/200bpManual_316_counts_complete.csv";
+ IONTORRENT_316_200bp_ZERO_COEF = "/data/200bpManual_316_counts_complete_model_zeroes.csv";
+ IONTORRENT_316_200bp_ONE_COEF = "/data/200bpManual_316_counts_complete_model_ones.csv";
+ IONTORRENT_316_200bp_OTHER_COEF = "/data/200bpManual_316_counts_complete_model_others.csv";
+
+ IONTORRENT_316_200bpOneTouch_PROBS_LOCATION = "/data/200bpOneTouch_316_counts_complete.csv";
+ IONTORRENT_316_200bpOneTouch_ZERO_COEF = "/data/200bpOneTouch_316_counts_complete_model_zeroes.csv";
+ IONTORRENT_316_200bpOneTouch_ONE_COEF = "/data/200bpOneTouch_316_counts_complete_model_ones.csv";
+ IONTORRENT_316_200bpOneTouch_OTHER_COEF = "/data/200bpOneTouch_316_counts_complete_model_others.csv";
+
+
+
+ IUPAC_AMBIGUOUS_MAPPINGS.put('R', new char [] {'A', 'G'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('Y', new char [] {'C', 'T'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('S', new char [] {'G', 'C'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('W', new char [] {'A', 'T'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('K', new char [] {'G', 'T'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('M', new char [] {'A', 'C'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('B', new char [] {'C', 'G', 'T'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('D', new char [] {'A', 'G', 'T'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('H', new char [] {'A', 'C', 'T'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('V', new char [] {'A', 'C', 'G'});
+ IUPAC_AMBIGUOUS_MAPPINGS.put('W', new char[] {'A', 'C', 'G', 'T'});
+
+ STANDARD_OUT_NAME = "acacia_standard_output.txt";
+ STANDARD_ERR_NAME = "acacia_standard_error.txt";
+ STANDARD_DEBUG_NAME = "acacia_standard_debug.txt";
+
+ DEFAULT_FILE_LOC = null;
+ DEFAULT_OPT_MID_LOC = null;
+ DEFAULT_OPT_OUTPUT_PREFIX = "acacia_out";
+ }
+
+ /**
+ * Instantiates a new acacia constants.
+ */
+ private AcaciaConstants()
+ {
+ //this prevents even the native class from
+ //calling this ctor as well :
+ throw new AssertionError();
+ }
+}
diff --git a/src/pyromaniac/AcaciaEngine.java b/src/pyromaniac/AcaciaEngine.java
new file mode 100644
index 0000000..fb2d4cc
--- /dev/null
+++ b/src/pyromaniac/AcaciaEngine.java
@@ -0,0 +1,1570 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.TreeMap;
+import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import pyromaniac.IO.AcaciaLogger;
+import pyromaniac.IO.LogFileHandle;
+import pyromaniac.IO.LoggerOutput;
+import pyromaniac.IO.MIDReader;
+import pyromaniac.IO.MMFastaImporter;
+import pyromaniac.IO.MMFastqImporter;
+import pyromaniac.IO.StandardOutputHandle;
+import pyromaniac.IO.TagImporter;
+import pyromaniac.Algorithm.ClusterGenerator;
+import pyromaniac.Algorithm.CoarseAlignSplitter;
+import pyromaniac.Algorithm.ConsensusGeneratorLocalTests;
+import pyromaniac.Algorithm.ConsensusGeneratorLocalTests.UnprocessedPyrotagResult;
+import pyromaniac.Algorithm.IonTorrentOUCallFrequencyTable;
+import pyromaniac.Algorithm.BalzerOUCallFrequencyTable;
+import pyromaniac.Algorithm.OUFrequencyTable;
+import pyromaniac.Algorithm.OligomerClusterGenerator;
+import pyromaniac.Algorithm.SimpleClusterAligner;
+import pyromaniac.Algorithm.RLEAlignmentIndelsOnly;
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.MIDPrimerCombo;
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.DataStructures.PatriciaTrie;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.DataStructures.MutableInteger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * This Singleton class runs the series of processes required to sort, MID-split, filter, trim and correct reads.
+ */
+public class AcaciaEngine
+{
+ //immutable.
+ /** The setting keys. */
+ private final String [] settingKeys;
+
+ /** The setting values. */
+ private final String [] settingValues;
+
+ /** The Constant BUILD_PROPERTIES_FILE. */
+ private static final String BUILD_PROPERTIES_FILE = "/data/build_info.properties";
+
+ /** The Constant BUILD_MAJOR_KEY. */
+ private static final String BUILD_MAJOR_KEY = "build.major.number";
+
+ /** The Constant BUILD_MINOR_KEY. */
+ private static final String BUILD_MINOR_KEY = "build.minor.number";
+
+ /** The Constant BUILD_REVISION_KEY. */
+ private static final String BUILD_REVISION_KEY = "build.number";
+
+ /**
+ * Gets the setting keys.
+ *
+ * @return the setting keys
+ */
+ public String[] getSettingKeys()
+ {
+ return settingKeys;
+ }
+
+ // Private constructor prevents instantiation from other classes
+ /**
+ * Instantiates a new acacia engine.
+ */
+ private AcaciaEngine()
+ {
+ String [] tmpSettingKeys =
+ {
+ AcaciaConstants.OPT_FASTA,
+ AcaciaConstants.OPT_FASTA_LOC,
+ AcaciaConstants.OPT_QUAL_LOC,
+ AcaciaConstants.OPT_FASTQ,
+ AcaciaConstants.OPT_FASTQ_LOC,
+ AcaciaConstants.OPT_MID,
+ AcaciaConstants.OPT_MID_FILE,
+ AcaciaConstants.OPT_TRIM_TO_LENGTH,
+ AcaciaConstants.OPT_OUTPUT_PREFIX,
+ AcaciaConstants.OPT_OUTPUT_DIR,
+ AcaciaConstants.OPT_MAXIMUM_MANHATTAN_DIST,
+ AcaciaConstants.OPT_SIGNIFICANCE_LEVEL,
+ AcaciaConstants.OPT_REPRESENTATIVE_SEQ,
+ AcaciaConstants.OPT_MIN_AVG_QUALITY,
+ AcaciaConstants.OPT_SPLIT_ON_MID,
+ AcaciaConstants.OPT_MAX_STD_DEV_LENGTH, //
+ AcaciaConstants.OPT_ERROR_MODEL,
+ AcaciaConstants.OPT_FLOW_KEY,
+ AcaciaConstants.OPT_MAX_RECURSE_DEPTH,
+ AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW,
+ AcaciaConstants.OPT_MIN_READ_REP_BEFORE_TRUNCATION,
+ AcaciaConstants.OPT_MIN_FLOW_TRUNCATION,
+ AcaciaConstants.OPT_FILTER_READS_WITH_N_BEFORE_POS,
+ AcaciaConstants.OPT_SIGNIFICANT_WHEN_TWO,
+ AcaciaConstants.OPT_FLOW_CYCLE_STRING,
+ AcaciaConstants.OPT_MAX_COMPLETE_LINKAGE_DIST,
+ AcaciaConstants.OPT_HEX_CLUSTER_ONLY,
+ AcaciaConstants.OPT_CLEAN_DATA
+ };
+
+ String [] tmpSettingValues =
+ {
+ AcaciaConstants.DEFAULT_OPT_FASTA,
+ AcaciaConstants.DEFAULT_FILE_LOC,
+ AcaciaConstants.DEFAULT_FILE_LOC,
+ AcaciaConstants.DEFAULT_OPT_FASTQ,
+ AcaciaConstants.DEFAULT_FILE_LOC,
+ AcaciaConstants.DEFAULT_OPT_MID,
+ AcaciaConstants.DEFAULT_OPT_MID_LOC,
+ AcaciaConstants.DEFAULT_OPT_TRIM_LENGTH,
+ AcaciaConstants.DEFAULT_OPT_OUTPUT_PREFIX,
+ AcaciaConstants.DEFAULT_FILE_LOC,
+ AcaciaConstants.DEFAULT_OPT_MAXIMUM_MANHATTAN_DIST,
+ AcaciaConstants.DEFAULT_OPT_SIGNIFICANCE_LEVEL,
+ AcaciaConstants.DEFAULT_OPT_REPRESENTATIVE_SEQ,
+ AcaciaConstants.DEFAULT_OPT_MIN_AVG_QUALITY,
+ AcaciaConstants.DEFAULT_OPT_SPLIT_ON_MID,
+ AcaciaConstants.DEFAULT_OPT_MAX_STD_DEV_LENGTH, //
+ AcaciaConstants.DEFAULT_OPT_ERROR_MODEL,
+ AcaciaConstants.DEFAULT_OPT_FLOW_KEY,
+ AcaciaConstants.DEFAULT_OPT_MAX_RECURSE_DEPTH,
+ AcaciaConstants.DEFAULT_OPT_TRUNCATE_READ_TO_FLOW,
+ AcaciaConstants.DEFAULT_OPT_MIN_READ_REP_BEFORE_TRUNCATION,
+ AcaciaConstants.DEFAULT_OPT_MIN_FLOW_TRUNCATION,
+ AcaciaConstants.DEFAULT_FILTER_N_BEFORE_POS,
+ AcaciaConstants.DEFAULT_OPT_SIGNIFICANT_WHEN_TWO,
+ AcaciaConstants.DEFAULT_OPT_FLOW_CYCLE_STRING,
+ AcaciaConstants.DEFAULT_OPT_MAX_COMPLETE_LINKAGE_DIST,
+ AcaciaConstants.DEFAULT_OPT_HEX_CLUSTER_ONLY,
+ AcaciaConstants.DEFAULT_OPT_CLEAN_DATA
+ };
+
+ settingKeys = tmpSettingKeys;
+ settingValues = tmpSettingValues;
+
+ }
+
+ //singleton pattern
+ /**
+ * Gets the singleton AcaciaEngine object.
+ *
+ * @return the AcaciaEngine object
+ */
+ public static AcaciaEngine getEngine()
+ {
+ return AcaciaUtilityHolder.getInstance();
+ }
+
+ //flow hash keeps a record of where each sequence is up to in the flow
+ //it is initially constructed during the _alignSequence phase, and marks the 'estimated' first flow position after the MID.
+ /**
+ * Clone flow hash.
+ *
+ * @param toClone the flow hash to deep clone
+ * @return a deep-cloned copy of the toClone hash-map
+ */
+ public HashMap <Pyrotag, Pair <Integer, Character>> cloneFlowHash(HashMap <Pyrotag, Pair <Integer, Character>> toClone)
+ {
+ HashMap <Pyrotag, Pair <Integer, Character>> clone = new HashMap <Pyrotag, Pair <Integer, Character>>();
+
+ for(Pyrotag p: toClone.keySet())
+ {
+ Pair <Integer, Character> oldPair = toClone.get(p);
+ Pair <Integer, Character> newPair = new Pair <Integer, Character>(oldPair.getFirst(), oldPair.getSecond());
+ clone.put(p,newPair);
+ }
+ return clone;
+ }
+
+ //initialises the output files. These consist of a stats file, a sequence output file, a reference output file, and a mapping file, which
+ //describes which sequences are represented by which reference sequence.
+ /**
+ * Initialises the output files (STATS, REFOUT, SEQOUT, MAPOUT, HISTOUT.
+ *
+ * @param settings the Acacia runtime settings
+ * @param mid the MID associated with these output files
+ * @return HashMap containing the key (output type), value (file handle) pairs
+ * @throws IOException Signal that an IO exception occurred in output file initialisation
+ */
+ private HashMap <String, BufferedWriter> initOutputFiles(HashMap <String, String> settings, MIDPrimerCombo mid) throws IOException
+ {
+ String outDir = settings.get(AcaciaConstants.OPT_OUTPUT_DIR);
+ String outputPrefix = settings.get(AcaciaConstants.OPT_OUTPUT_PREFIX);
+
+ String midStr = (mid != null)? mid.getDescriptor() : "mid_unspecified";
+
+ String statOut = outDir + getPlatformSpecificPathDivider() + outputPrefix + "_" + midStr + "." + AcaciaConstants.STATS_SUFFIX;
+ String seqOut = outDir + getPlatformSpecificPathDivider()+ outputPrefix + "_" + midStr + "." + AcaciaConstants.SEQOUT_SUFFIX;
+ String refOut = outDir + getPlatformSpecificPathDivider() + outputPrefix + "_" + midStr + "." + AcaciaConstants.REFOUT_SUFFIX;
+ String mapOut = outDir + getPlatformSpecificPathDivider() + outputPrefix + "_" + midStr + "." + AcaciaConstants.MAPOUT_SUFFIX;
+ String histOut = outDir + getPlatformSpecificPathDivider() + outputPrefix + "_" + midStr + "." + AcaciaConstants.HISTOUT_SUFFIX;
+
+ BufferedWriter statOutWriter = new BufferedWriter(new FileWriter(new File(statOut), false));
+ BufferedWriter seqOutWriter = new BufferedWriter(new FileWriter(new File (seqOut), false));
+ BufferedWriter refOutWriter = new BufferedWriter (new FileWriter (new File (refOut), false));
+ BufferedWriter mapOutWriter = new BufferedWriter (new FileWriter (new File (mapOut), false));
+ BufferedWriter histOutWriter = new BufferedWriter (new FileWriter (new File(histOut), false));
+
+ HashMap <String, BufferedWriter> outputHandles = new HashMap <String, BufferedWriter>();
+ outputHandles.put(AcaciaConstants.STAT_OUT_FILE, statOutWriter);
+ outputHandles.put(AcaciaConstants.SEQ_OUT_FILE, seqOutWriter);
+ outputHandles.put(AcaciaConstants.REF_OUT_FILE, refOutWriter);
+ outputHandles.put(AcaciaConstants.MAP_OUT_FILE, mapOutWriter);
+ outputHandles.put(AcaciaConstants.HIST_OUT_FILE, histOutWriter);
+ return outputHandles;
+ }
+
+ //close all the output handles, this does not include the DEBUG/PROGRESS/ERROR output files.
+
+ /**
+ * Closes the output file handles.
+ *
+ * @param outputHandles the output handles to close
+ * @throws IOException Signals that an I/O exception has occurred.
+ */
+ private void closeOutputFiles(HashMap <String, BufferedWriter> outputHandles) throws IOException
+ {
+ for(String output : outputHandles.keySet())
+ {
+ outputHandles.get(output).close();
+ }
+ }
+
+ //output singleton sequences.
+ /**
+ * Processes singleton reads, writes them to output file.
+ *
+ * @param singleton the singleton pyrotag
+ * @param settings the Acacia run settings
+ * @param outputHandles the output handles for this dataset
+ * @param representativeSeqs the collection of representative sequences so far
+ * @param logger the runtime logger
+ * @throws Exception Any exception that occurs during the processing and output of the singleton sequence
+ */
+ private void processSingleton(Pyrotag singleton, HashMap <String, String> settings, HashMap <String, BufferedWriter> outputHandles,
+ HashMap<Pyrotag, Integer> representativeSeqs, AcaciaLogger logger) throws Exception
+ {
+
+ this.outputSequence(settings, outputHandles.get(AcaciaConstants.SEQ_OUT_FILE), new String(singleton.getProcessedString()), singleton);
+ this.outputSequence(settings, outputHandles.get(AcaciaConstants.REF_OUT_FILE), new String(singleton.getProcessedString()), singleton);
+
+ String id = this.getOutputID(settings, singleton, false);
+ String toPrint = id + "\t" + id + System.getProperty("line.separator");
+ outputHandles.get(AcaciaConstants.MAP_OUT_FILE).write(toPrint);
+ representativeSeqs.put(singleton,1); //singleton representative
+ }
+
+
+
+ /**
+ * Gets the parameter MIN_READ_REP_BEFORE_TRUNCATION.
+ *
+ * @param settings the Acacia runtime settings
+ * @return Double the minimum read representation (coverage) before truncation of the consensus
+ */
+ public Double getMinReadRepTruncation(HashMap<String, String> settings)
+ {
+ if(settings.get(AcaciaConstants.OPT_MIN_READ_REP_BEFORE_TRUNCATION) != null)
+ {
+ return Double.parseDouble(settings.get(AcaciaConstants.OPT_MIN_READ_REP_BEFORE_TRUNCATION));
+ }
+
+ return null;
+ }
+
+ /**
+ * Gets the significance threshold.
+ *
+ * @param string The threshold value (String) from the command line /configuration file
+ * @return the double significance threshold
+ */
+ public double parseSignificanceThreshold(String string)
+ {
+ if(string.equals(AcaciaConstants.SIGN_THRESHOLD_ZERO))
+ {
+ return (double)0;
+ }
+ else
+ {
+ return Math.pow(10, Integer.parseInt(string));
+ }
+ }
+
+
+
+ //generates perfect clusterings based on prefix of reads, and filters out reads that are not satisfying thresholds (also does trimming).
+ /**
+ * Generates clusters based on perfect identity. Read trimming and filtering are also performed.
+ *
+ * @param settings the Acacia runtime settings
+ * @param logger the Acacia logger
+ * @param rc the RunCharacterisation object
+ * @param midsToUse the MIDs to use
+ * @param outputHandles the output handles for this run
+ * @param representativeSeqs the representative sequences so far
+ * @return HashMap containing the consensus prefix to read mapping, which describes the perfect identity clusters
+ * @throws Exception any exception that occurred during the generation of the perfect identity clusters
+ */
+ public HashMap <String, LinkedList <Pyrotag>> generatePerfectClusters(HashMap <String, String> settings, AcaciaLogger logger,
+ RunCharacterisation rc, LinkedList <MIDPrimerCombo> midsToUse, HashMap<String, BufferedWriter> outputHandles, HashMap<Pyrotag, Integer> representativeSeqs) throws Exception
+ {
+ HashMap <String, LinkedList <Pyrotag>> perfectClusters = new HashMap <String, LinkedList <Pyrotag>>();
+
+ int usableSeqs = 0;
+
+ HashMap <String, Integer> dereplicated = new HashMap<String, Integer>();
+
+ boolean verbose = false;
+
+ //another outfile
+ LinkedList <MIDPrimerCombo> midsToProcess = midsToUse;
+
+ if(midsToProcess.size() == 1 && midsToProcess.getFirst() == AcaciaConstants.NO_MID_GROUP)
+ {
+ midsToProcess = new LinkedList <MIDPrimerCombo>(rc.MIDToSequences.keySet());
+ }
+
+ for(MIDPrimerCombo midPrimer: midsToProcess)
+ {
+ //there were no tags for that MID
+ if(!rc.MIDToSequences.containsKey(midPrimer))
+ {
+ continue;
+ }
+
+ LinkedList <Pyrotag> seqs = rc.MIDToSequences.get(midPrimer);
+
+ for(Pyrotag p: seqs)
+ {
+
+ //trim to first N.
+ //note that if the first N occurs straight after the MID primer, the read will have length zero.
+ int firstN = p.firstOccurrenceOfAmbiguous(); //
+
+ if(firstN != Pyrotag.NO_N)
+ {
+ throw new Exception("Sequence containing N found in data: maybe you should run cleaning first.");
+ }
+
+
+
+ //dont touch the other things.
+ p.setInternalID(usableSeqs + 1);
+ usableSeqs++;
+
+ char [] trimmedSequence = p.getProcessedString();
+
+ if(! dereplicated.containsKey(new String(trimmedSequence)))
+ {
+ dereplicated.put(new String(trimmedSequence), 0);
+ }
+
+ dereplicated.put(new String(trimmedSequence), dereplicated.get(new String(trimmedSequence) + 1));
+
+ char [] trimmedCollapsed = Arrays.copyOf(p.getCollapsedRead(), AcaciaConstants.DEFAULT_OPT_TRIM_COLLAPSED);
+
+ String rle = new String(trimmedCollapsed);
+
+ if(!perfectClusters.containsKey(rle))
+ {
+ perfectClusters.put(rle, new LinkedList <Pyrotag>());
+ }
+ perfectClusters.get(rle).add(p);
+ }
+
+ if(usableSeqs == 0)
+ {
+ logger.writeLog("MID: " + midPrimer.getDescriptor() + " had no reads", AcaciaLogger.LOG_PROGRESS);
+ }
+ }
+
+ if(usableSeqs == 0)
+ {
+ logger.writeLog("No sequences satisified all filters", AcaciaLogger.LOG_PROGRESS);
+ return null;
+ }
+
+ return perfectClusters;
+ }
+
+
+
+ /**
+ * Run acacia.
+ *
+ * @param settings the Acacia runtime settings
+ * @param validTags the acceptable MID/primer prefixes which are valid for processing
+ * @param logger the Acacia logger
+ * @param worker the ErrorCorrectionWorker thread - running this method
+ * @param version the Acacia version
+ * @throws Exception any exception during the runAcacia method
+ */
+ public void runAcacia(HashMap <String, String> settings, LinkedList <MIDPrimerCombo> validTags, AcaciaLogger logger,
+ ErrorCorrectionWorker worker, String version, boolean runningFromGUI) throws Exception
+ {
+
+ this.initLogFiles(settings, logger, runningFromGUI, validTags);
+
+ if(worker != null && worker.isCancelled())
+ {
+ throw new InterruptedException("Job cancelled");
+ }
+
+
+ if(worker != null && worker.isCancelled())
+ {
+ System.out.println("Failed 3");
+ throw new InterruptedException("Job cancelled");
+ }
+
+ try
+ {
+ logger.writeLog("Analysing file...", AcaciaLogger.LOG_PROGRESS);
+
+ RunCharacterisation rc = null;
+ DataCleaner dc = DataCleaner.getDataCleaner();
+ rc = dc.initialiseRunCharacterisation(settings, logger, validTags);
+
+
+ //TODO: test this has not buggered up.
+ // get stats of tags in file.
+ if(worker != null && worker.isCancelled())
+ {
+ System.out.println("Failed 4");
+ throw new InterruptedException("Job cancelled");
+ }
+
+ FlowCycler fc = new FlowCycler(settings.get(AcaciaConstants.OPT_FLOW_CYCLE_STRING), logger);
+
+ //all tags to be processed must have a valid MID if mids were specified by the user.
+ LinkedList <MIDPrimerCombo> aggregateAs = new LinkedList <MIDPrimerCombo>();
+ //sets up the mids to use.
+ if(settings.get(AcaciaConstants.OPT_SPLIT_ON_MID).equals("FALSE"))
+ {
+ if(validTags.size() == 1)
+ {
+ aggregateAs.add(validTags.get(0));
+ }
+ else
+ {
+ aggregateAs.add(AcaciaConstants.NO_MID_GROUP);
+ }
+ }
+ else if(settings.get(AcaciaConstants.OPT_SPLIT_ON_MID).equals("TRUE"))
+ {
+ aggregateAs.addAll(validTags);
+ }
+
+ for(MIDPrimerCombo m: aggregateAs)
+ {
+ LinkedList <MIDPrimerCombo> midsToProcess = new LinkedList <MIDPrimerCombo>();
+ midsToProcess.add(m);
+
+ logger.writeLog("Processing MID " + m.getDescriptor() + ": " + rc.getTagCountForMIDs(midsToProcess) + " tags", AcaciaLogger.LOG_PROGRESS);
+
+ HashMap <String, BufferedWriter> outputHandles = this.initOutputFiles(settings, m);
+
+ if(settings.containsKey(AcaciaConstants.OPT_CLEAN_DATA) && Boolean.parseBoolean(settings.get(AcaciaConstants.OPT_CLEAN_DATA)))
+ {
+ dc.filterAndTrimReads(settings, logger, rc, validTags, outputHandles);
+ }
+
+ HashMap <Pyrotag, Integer> representativeSeqs = new HashMap <Pyrotag, Integer> ();
+
+ int numSeqsCorrected = 0;
+ HashMap <String, LinkedList <Pyrotag>> perfectClusters = generatePerfectClusters(settings, logger, rc, midsToProcess,
+ outputHandles, representativeSeqs);
+
+ if(perfectClusters == null)
+ {
+ continue;
+ }
+
+ if(aggregateAs.size() == 1)
+ rc = null; //no longer need it (save memory).
+
+ logger.writeLog("There are " + perfectClusters.size() + "RLE prefix clusters before hexamer recruiting", AcaciaLogger.LOG_PROGRESS);
+
+ ClusterGenerator clusterer = new OligomerClusterGenerator();
+
+ clusterer.initialise(perfectClusters, settings, logger, outputHandles);
+ clusterer.runClustering();
+
+ logger.writeLog("There are " + perfectClusters.size() + " after hexamer recruiting", AcaciaLogger.LOG_PROGRESS);
+
+ //at this point, do not care about the relationship between clusters...
+ String hexClustOnly = settings.get(AcaciaConstants.OPT_HEX_CLUSTER_ONLY).toUpperCase();
+
+ boolean outputClusterMemberships = Boolean.parseBoolean(hexClustOnly);
+ int clusterID = 0;
+
+ if(outputClusterMemberships)
+ {
+ logger.writeLog("Creating fasta files per sequence cluster...", AcaciaLogger.LOG_PROGRESS);
+ for(String clusterRep: perfectClusters.keySet())
+ {
+ String outDir = settings.get(AcaciaConstants.OPT_OUTPUT_DIR);
+ String outputPrefix = settings.get(AcaciaConstants.OPT_OUTPUT_PREFIX);
+ String midStr = (m != null)? m.getDescriptor() : "mid_unspecified";
+ String hexOut = outDir + getPlatformSpecificPathDivider() + outputPrefix + "_" + midStr + "_hexamer_cluster_" + clusterID +".fasta";
+ BufferedWriter hexOutBuff = new BufferedWriter (new FileWriter (new File(hexOut), false));
+
+ logger.writeLog("Outputting cluster of size: " + perfectClusters.get(clusterRep).size(), AcaciaLogger.LOG_PROGRESS);
+
+ for(Pyrotag p: perfectClusters.get(clusterRep))
+ {
+ outputSequence(settings, hexOutBuff, new String(p.getProcessedString()), p);
+ }
+ hexOutBuff.close();
+
+ clusterID++;
+ }
+ }
+ else
+ {
+ logger.writeLog("Performing error correction on clusters...", AcaciaLogger.LOG_PROGRESS);
+ for(String clusterRep: perfectClusters.keySet())
+ {
+ LinkedList <Pyrotag> clusterMembers = perfectClusters.get(clusterRep);
+
+ //alignment for the cluster
+ ArrayDeque <Pair <RLEAlignmentIndelsOnly, HashMap <Pyrotag, Pair <Integer, Character>>>> mainAlignRes =
+ new ArrayDeque <Pair <RLEAlignmentIndelsOnly, HashMap <Pyrotag, Pair <Integer, Character>>>>();
+
+ //maybe this adds the same sequence twice to singletons?
+ LinkedList <Pyrotag> singletons = new LinkedList <Pyrotag>();
+
+ //alignment only allows sequence to belong to one cluster.
+
+ if(perfectClusters.get(clusterRep).size() > 1)
+ {
+ logger.writeLog("Processing cluster of " + perfectClusters.get(clusterRep).size() + " reads...", AcaciaLogger.LOG_PROGRESS);
+ }
+
+ //run the alignment algorithm, it will populate the results collections.
+ SimpleClusterAligner.getInstance().generateAlignments(logger, settings, clusterMembers, clusterRep, outputHandles,
+ representativeSeqs, mainAlignRes, singletons);
+
+ while(mainAlignRes.size() > 0)
+ {
+ Pair <RLEAlignmentIndelsOnly, HashMap <Pyrotag, Pair <Integer, Character>>> alignRes = mainAlignRes.pop();
+ ///can I pass in the alignment singletons here... to see if they will align using a substitution only aligner?
+
+ //this was the way the consensus was generated in the original acacia
+ boolean originalConsensusGeneration = true; //TODO: new code requires testing
+
+ if(originalConsensusGeneration)
+ {
+ HashMap <Pyrotag, Pair <Integer,Character>> flowMapInner = cloneFlowHash(alignRes.getSecond());
+
+ numSeqsCorrected += generateConsensusAndOutput(logger, settings, outputHandles, alignRes.getFirst(), flowMapInner, representativeSeqs, fc);
+
+ }
+ else //new way, which attempts to partition the alignment if there are obvious deviations.
+ {
+ //don't want to do the full tests when there are obvious, highly significant deviations.
+ HashSet <HashSet <Pyrotag>> splitFurther = CoarseAlignSplitter.getInstance().scanAlignmentForObviousDeviations(logger, settings, outputHandles, alignRes, fc);
+
+ //System.out.println("After hierarchical clustering, we have " + splitFurther.size() + " sub-clusters");
+ LinkedList <RLEAlignmentIndelsOnly> result = alignRes.getFirst().splitNonConforming(splitFurther);
+
+ for(RLEAlignmentIndelsOnly subalign: result)
+ {
+ HashMap <Pyrotag, Pair <Integer,Character>> flowMapInner = cloneFlowHash(alignRes.getSecond());
+
+ numSeqsCorrected += generateConsensusAndOutput(logger, settings, outputHandles, subalign, flowMapInner, representativeSeqs, fc);
+ }
+ }
+
+ }
+
+ //ideally here... we have a set of consensus sequences, and a set of singletons...
+ for(Pyrotag solo: singletons)
+ {
+ this.processSingleton(solo, settings, outputHandles, representativeSeqs, logger);
+ }
+
+ clusterMembers = null;
+ mainAlignRes = null;
+ singletons = null;
+
+ }
+
+
+ logger.writeLog("Outputting final statistics...", AcaciaLogger.LOG_PROGRESS);
+
+ //do we want to keep all the representative seqs in memory... just for this? Could probably just store the ID for the pyrotag.
+ outputFinalStatsAndHist(numSeqsCorrected,settings,logger,outputHandles,representativeSeqs, version);
+ }
+ perfectClusters = null; //clean that up.
+ }
+ }
+ catch(OutOfMemoryError error)
+ {
+ logger.writeLog("Out of memory: " + Thread.currentThread().getName(), AcaciaLogger.LOG_DEBUG);
+ throw(error);
+ }
+ finally
+ {
+ logger.writeLog("Finished: " + Thread.currentThread().getName(), AcaciaLogger.LOG_PROGRESS);
+ }
+ }
+
+
+
+ /**
+ * Outputs the consensus sequences for all reads in the ThreadedAlignment.
+ *
+ * @param consensusClusterCollection the consensus cluster collection
+ * @param motherAlignment the mother alignment
+ * @param settings the Acacia settings
+ * @param logger the Acacia logger
+ * @param outputHandles the output handles for this run
+ * @param representativeSeqs the representative sequences generated so far
+ * @return the number of reads corrected in this cluster
+ * @throws Exception any exceptions that occurred during this method
+ */
+
+ private int outputCluster
+ (
+ Collection <HashSet <Pyrotag>> consensusClusterCollection,
+ RLEAlignmentIndelsOnly motherAlignment,
+ HashMap<String, String> settings, AcaciaLogger logger,
+ HashMap<String, BufferedWriter> outputHandles,
+ HashMap<Pyrotag, Integer> representativeSeqs
+ ) throws Exception
+ {
+ int counter = 0;
+ int numSeqsCorrected = 0;
+
+ for(HashSet <Pyrotag> clusterMembers: consensusClusterCollection)
+ {
+ //hash containing all the corrected sequences
+ HashMap <Pyrotag, String> correctedTags = new HashMap<Pyrotag, String>();
+
+ //its a singleton
+ if(clusterMembers.size() == 1)
+ {
+ //much cleaner
+ Pyrotag p = clusterMembers.iterator().next();
+ this.processSingleton(p, settings, outputHandles, representativeSeqs, logger);
+ continue;
+ }
+
+ //the longest consensus sequence, and which base in consensus the tag aligns up to.
+ Pair<String, HashMap<Pyrotag, MutableInteger>> longestConsensus = motherAlignment.getLongestConsensus(clusterMembers);
+
+ for(Pyrotag p: longestConsensus.getSecond().keySet())
+ {
+ //get the longest consensus
+ String substr = longestConsensus.getFirst().substring(0, longestConsensus.getSecond().get(p).value());
+
+ //if they are not identical... then the sequence was modified at least once
+ if(!substr.equals(new String(p.getProcessedString())))
+ {
+ numSeqsCorrected++;
+ }
+
+ //add p to the correct tags
+ correctedTags.put(p, substr);
+
+ //somehow this sequence gets two cluster memberships.
+ //we output the corrected tag...
+ outputSequence(settings, outputHandles.get(AcaciaConstants.SEQ_OUT_FILE),substr, p);
+ }
+
+ //afterwards, we identify who is the representative sequence for the corrected tags.
+ Pair <Pyrotag, String> representativeSeq = this.getRepresentativeSeq(correctedTags, settings);
+
+ int clusterSize = correctedTags.size();
+
+ if(representativeSeqs.containsKey(representativeSeq.getFirst()))
+ {
+ //we have one representative representing two clusters...
+ clusterSize += representativeSeqs.get(representativeSeq.getFirst());
+ }
+
+ representativeSeqs.put(representativeSeq.getFirst(), correctedTags.size());
+
+ //we output the representative sequence in the reference file
+ if(clusterSize == correctedTags.size()) //we've outputted this sequence before..
+ {
+ outputSequence(settings, outputHandles.get(AcaciaConstants.REF_OUT_FILE), representativeSeq.getSecond(), representativeSeq.getFirst());
+ }
+
+ String repID = this.getOutputID(settings, representativeSeq.getFirst(), false);
+
+ //we output all the mappings...
+ for(Pyrotag p: longestConsensus.getSecond().keySet()) //its possible that one read can map to multiple clusters, but they wont be output multiple times.
+ {
+ String memberID = this.getOutputID(settings,p, false);
+ outputHandles.get(AcaciaConstants.MAP_OUT_FILE).write(repID + "\t" + memberID + System.getProperty("line.separator"));
+ }
+
+ counter++;
+ }
+ return numSeqsCorrected;
+ }
+
+ /**
+ * Output final stats and hist.
+ *
+ * @param numSeqsCorrected the num seqs corrected
+ * @param settings the settings
+ * @param logger the logger
+ * @param outputHandles the output handles
+ * @param representativeSeqs the representative seqs
+ * @param version the version
+ * @throws Exception the exception
+ */
+ private void outputFinalStatsAndHist(int numSeqsCorrected,
+ HashMap<String, String> settings, AcaciaLogger logger,
+ HashMap<String, BufferedWriter> outputHandles,
+ HashMap<Pyrotag, Integer> representativeSeqs, String version) throws Exception
+ {
+ Comparator <Integer> c = new Comparator <Integer>(){
+
+ public int compare(Integer arg0, Integer arg1)
+ {
+ if(arg0 > arg1)
+ {
+ return -1;
+ }
+ else if(arg1 > arg0)
+ {
+ return 1;
+ }
+ return 0;
+ }
+ };
+
+ TreeMap <Integer, Integer> clusterSizeHist = new TreeMap <Integer, Integer>(c);
+ outputHandles.get(AcaciaConstants.HIST_OUT_FILE).write("CLUSTER_SIZE, FREQUENCY" + System.getProperty("line.separator"));
+
+ for(Pyrotag rep: representativeSeqs.keySet())
+ {
+ int clusterSize = representativeSeqs.get(rep);
+
+ if(! clusterSizeHist.containsKey(clusterSize))
+ {
+ clusterSizeHist.put(clusterSize, 1);
+ }
+ else
+ {
+ clusterSizeHist.put(clusterSize, clusterSizeHist.get(clusterSize) + 1);
+ }
+ }
+
+ for(int clusterSize: clusterSizeHist.keySet())
+ {
+ if(clusterSize == 1)
+ {
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# Singletons: " + clusterSizeHist.get(clusterSize) + System.getProperty("line.separator"));
+ }
+
+ outputHandles.get(AcaciaConstants.HIST_OUT_FILE).write(clusterSize + "," + clusterSizeHist.get(clusterSize) + System.getProperty("line.separator"));
+ }
+
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# Reference sequences: " + representativeSeqs.size() +System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# Sequences corrected: " + numSeqsCorrected + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("Acacia version: " + version);
+ this.closeOutputFiles(outputHandles);
+ }
+
+ /**
+ * Process and correct alignments.
+ *
+ * @param logger the logger
+ * @param settings the settings
+ * @param outputHandles the output handles
+ * @param motherAlign the mother align
+ * @param motherFlow the mother flow
+ * @param representativeSeqs the representative seqs
+ * @return the linked list
+ * @throws Exception the exception
+ */
+
+ //potentiall in this bit, a sequence is added to somewhere twice.
+ private int generateConsensusAndOutput
+ (
+ AcaciaLogger logger, HashMap<String, String> settings,
+ HashMap<String, BufferedWriter> outputHandles,
+ RLEAlignmentIndelsOnly motherAlign,
+ HashMap<Pyrotag, Pair<Integer, Character>> motherFlow,
+ HashMap<Pyrotag, Integer> representativeSeqs,
+ FlowCycler fc
+ //, HashSet <Pyrotag> singletons //to be added later -- these are guys thrown out during the alignment process.
+
+ ) throws Exception
+ {
+
+ int numCorrected = 0;
+ HashSet <Pyrotag> toProcess = motherAlign.getAllTags(); //grabs the results of the last run
+
+
+
+
+ //running over ThreadedAlignment... always clone the flow hash, in preparation for error correction later
+ HashMap <Pyrotag, Pair <Integer,Character>> flowMap = cloneFlowHash(motherFlow); //this cloning operation is unavoidable unless huge changes made.
+
+ LinkedList <HashSet <Pyrotag>> consensusClusters = new LinkedList<HashSet<Pyrotag>>();
+ //first is the consensus members, and the second is the other sets.
+ UnprocessedPyrotagResult failedFirst =
+ ConsensusGeneratorLocalTests.getInstance().generateConsensus(logger, settings, motherAlign, toProcess, consensusClusters, flowMap, fc, false);
+
+
+ if(failedFirst != null && failedFirst.getTags().size() > 0)
+ {
+ LinkedList <HashSet<Pyrotag>> clustersWhichVaryTogether = ConsensusGeneratorLocalTests.getInstance().generateClustersFromVaryTogether(logger, settings, consensusClusters, failedFirst, true);
+
+ for(HashSet <Pyrotag> nc : clustersWhichVaryTogether)
+ {
+ //try generating a consensus branch....
+ HashMap <Pyrotag, Pair <Integer,Character>> flowMapInner = cloneFlowHash(motherFlow);
+
+ //passing true to vary identically makes sure every seequence is processed this time.
+ UnprocessedPyrotagResult failedSecond = ConsensusGeneratorLocalTests.getInstance().generateConsensus(logger, settings, motherAlign, nc, consensusClusters, flowMapInner, fc, false);
+
+ //last resource is trie.
+ if(failedSecond != null && failedSecond.getTags().size() > 0)
+ {
+ PatriciaTrie trie = ConsensusGeneratorLocalTests.getInstance().generateTrieFromUnprocessedTags(logger, failedSecond.getTags());
+ HashSet <Pyrotag> recorded = new HashSet <Pyrotag>();
+
+ LinkedList <HashSet <Pyrotag>> trieClusters = new LinkedList <HashSet <Pyrotag>>();
+
+ //need to check that the trie is not maintaining reads in several clusters
+ for(HashSet <Pyrotag> set : trie)
+ {
+ HashSet <Pyrotag> toRemove = new HashSet <Pyrotag>();
+ for(Pyrotag inner: set)
+ {
+ if(recorded.contains(inner))
+ {
+ toRemove.add(inner);
+ }
+ recorded.add(inner);
+ }
+ set.removeAll(toRemove);
+
+ if(set.size() > 0)
+ {
+ trieClusters.add(set);
+ }
+ }
+ numCorrected += this.outputCluster(trieClusters, motherAlign, settings, logger, outputHandles, representativeSeqs);
+ }
+ }
+ }
+
+ numCorrected += this.outputCluster(consensusClusters, motherAlign, settings, logger, outputHandles, representativeSeqs);
+ return numCorrected;
+ }
+
+ public static OUFrequencyTable getErrorModel(AcaciaLogger logger, HashMap <String, String> settings) throws Exception
+ {
+ OUFrequencyTable table = null;
+
+ String errModel = settings.get(AcaciaConstants.OPT_ERROR_MODEL);
+
+ if(errModel.equals(AcaciaConstants.OPT_FLOWSIM_ERROR_MODEL))
+ {
+ table = new BalzerOUCallFrequencyTable(AcaciaConstants.FLOWSIM_PROBS_LOCATION);
+ }
+ else if (errModel.equals(AcaciaConstants.OPT_ACACIA_TITANIUM_ERROR_MODEL))
+ {
+ //this model is still be evaluated
+ table = new BalzerOUCallFrequencyTable(AcaciaConstants.ACACIA_EMP_MODEL_TITANIUM_LOCATION);
+ }
+ else if(errModel.equals(AcaciaConstants.OPT_ACACIA_IT_OT_100bp_314_MODEL))
+ {
+ table = new IonTorrentOUCallFrequencyTable(settings, logger, AcaciaConstants.IONTORRENT_314_100bp_PROBS_LOCATION,
+ AcaciaConstants.IONTORRENT_314_100bp_ZERO_COEF, AcaciaConstants.IONTORRENT_314_100bp_ONE_COEF,
+ AcaciaConstants.IONTORRENT_314_100bp_OTHER_COEF);
+ }
+ else if(errModel.equals(AcaciaConstants.OPT_ACACIA_IT_OT_100bp_316_MODEL))
+ {
+ table = new IonTorrentOUCallFrequencyTable(settings, logger, AcaciaConstants.IONTORRENT_316_100bp_PROBS_LOCATION,
+ AcaciaConstants.IONTORRENT_316_100bp_ZERO_COEF, AcaciaConstants.IONTORRENT_316_100bp_ONE_COEF,
+ AcaciaConstants.IONTORRENT_316_100bp_OTHER_COEF);
+ }
+ else if (errModel.equals(AcaciaConstants.OPT_ACACIA_IT_MAN_200bp_314_MODEL))
+ {
+ table = new IonTorrentOUCallFrequencyTable(settings, logger, AcaciaConstants.IONTORRENT_314_200bp_PROBS_LOCATION,
+ AcaciaConstants.IONTORRENT_314_200bp_ZERO_COEF, AcaciaConstants.IONTORRENT_314_200bp_ONE_COEF,
+ AcaciaConstants.IONTORRENT_314_200bp_OTHER_COEF);
+ }
+ else if(errModel.equals(AcaciaConstants.OPT_ACACIA_IT_MAN_200bp_316_MODEL))
+ {
+ table = new IonTorrentOUCallFrequencyTable(settings, logger, AcaciaConstants.IONTORRENT_316_200bp_PROBS_LOCATION,
+ AcaciaConstants.IONTORRENT_316_200bp_ZERO_COEF, AcaciaConstants.IONTORRENT_316_200bp_ONE_COEF,
+ AcaciaConstants.IONTORRENT_316_200bp_OTHER_COEF);
+ }
+ else if(errModel.equals(AcaciaConstants.OPT_ACACIA_IT_OT_200bp_314))
+ {
+ table = new IonTorrentOUCallFrequencyTable(settings, logger, AcaciaConstants.IONTORRENT_314_200bpOneTouch_PROBS_LOCATION,
+ AcaciaConstants.IONTORRENT_314_200bpOneTouch_ZERO_COEF, AcaciaConstants.IONTORRENT_314_200bpOneTouch_ONE_COEF,
+ AcaciaConstants.IONTORRENT_314_200bpOneTouch_OTHER_COEF);
+ }
+ else if (errModel.equals(AcaciaConstants.OPT_ACACIA_IT_OT_200bp_316))
+ {
+ table = new IonTorrentOUCallFrequencyTable(settings, logger, AcaciaConstants.IONTORRENT_316_200bpOneTouch_PROBS_LOCATION,
+ AcaciaConstants.IONTORRENT_316_200bpOneTouch_ZERO_COEF, AcaciaConstants.IONTORRENT_316_200bpOneTouch_ONE_COEF,
+ AcaciaConstants.IONTORRENT_316_200bpOneTouch_OTHER_COEF);
+ }
+ else //quince
+ {
+ table = new pyromaniac.Algorithm.QuinceOUFrequencyTable(AcaciaConstants.PYRONOISE_PROBS_LOCATION);
+ }
+ return table;
+ }
+
+
+ //inspect the file, characterise the reads.
+ /**
+ * Prepare file for clustering.
+ *
+ * @param logger the logger
+ * @param settings the settings
+ * @param validTags the valid tags
+ * @return the run characterisation
+ * @throws Exception the exception
+ */
+ private RunCharacterisation prepareFileForClustering(AcaciaLogger logger, HashMap <String, String> settings, LinkedList <MIDPrimerCombo> validTags) throws Exception
+ {
+ //this method needs to rename the sequences too.
+
+ HashMap <MIDPrimerCombo, LinkedList <Pyrotag>> MIDToSequences = new HashMap <MIDPrimerCombo, LinkedList <Pyrotag> >();
+ HashMap <MIDPrimerCombo, Integer> MIDseqLength = new HashMap <MIDPrimerCombo, Integer>();
+ HashMap <MIDPrimerCombo, Integer> MIDcollapsedSeqLength = new HashMap <MIDPrimerCombo, Integer>();
+ HashMap <MIDPrimerCombo, Double> MIDqualities = new HashMap <MIDPrimerCombo, Double>();
+
+
+ if(validTags.size() == 0)
+ validTags.add(AcaciaConstants.NO_MID_GROUP);
+
+ int fileIndex = 0;
+
+ logger.writeLog("Preparing sequence importer", AcaciaLogger.LOG_PROGRESS);
+ TagImporter importer = this.getTagImporter(settings, logger);
+
+ Pyrotag p = importer.getPyrotagAtIndex(fileIndex);
+
+ //loading only sequences which have valid MID.
+
+ int invalidMID = 0;
+ int validMID = 0;
+
+ while (p != null)
+ {
+ // System.out.println("P is " + p.getID());
+ // System.out.println("MID matching");
+ MIDPrimerCombo matching = p.whichMID(validTags);
+
+ if(matching == null)
+ {
+ fileIndex++;
+ p = importer.getPyrotagAtIndex(fileIndex);
+
+ //skipping over not matching MIDS.
+
+ invalidMID++;
+
+ continue;
+ }
+
+ validMID++;
+
+ // System.out.println("Set MID matching");
+ p.setMIDPrimerCombo(matching); //may already be initialised?
+
+ if(! MIDToSequences.containsKey(matching))
+ {
+ MIDToSequences.put(matching, new LinkedList <Pyrotag>());
+ }
+ MIDToSequences.get(matching).add(p);
+
+ if(! MIDseqLength.containsKey(matching))
+ {
+ MIDseqLength.put(matching, 0);
+ }
+
+ MIDseqLength.put(matching, MIDseqLength.get(matching) + p.getLength());
+
+ if(p.getQualities() != null)
+ {
+ if(! MIDqualities.containsKey(matching))
+ {
+ MIDqualities.put(matching, 0.0);
+ }
+
+ MIDqualities.put(matching, MIDqualities.get(matching) + p.getUntrimmedAvgQuality());
+ }
+
+ // System.out.println("Getting collapsed read");
+
+ char [] collapsedReadMinusMid = p.getCollapsedRead();
+
+ if(!MIDcollapsedSeqLength.containsKey(matching))
+ {
+ MIDcollapsedSeqLength.put(matching, 0);
+ }
+
+ MIDcollapsedSeqLength.put(matching, MIDcollapsedSeqLength.get(matching) + collapsedReadMinusMid.length);
+
+ fileIndex++;
+ p = importer.getPyrotagAtIndex(fileIndex);
+ }
+
+ RunCharacterisation rc = new RunCharacterisation(MIDToSequences, MIDseqLength, MIDcollapsedSeqLength, MIDqualities, validMID, invalidMID);
+ return rc;
+ }
+
+
+ //get Tag Importer
+ /**
+ * Gets the tag importer.
+ *
+ * @param settings the settings
+ * @param logger the logger
+ * @return the tag importer
+ */
+ public TagImporter getTagImporter(HashMap <String, String> settings, AcaciaLogger logger)
+ {
+ TagImporter importer;
+
+ if (settings.get(AcaciaConstants.OPT_FASTA).equals("TRUE"))
+ {
+ //System.out.println("Getting importer from " + settings.get(AcaciaConstants.OPT_FASTA_LOC));
+ String fastaFile = settings.get(AcaciaConstants.OPT_FASTA_LOC);
+ String qualFile = settings.get(AcaciaConstants.OPT_QUAL_LOC);
+
+ String flowCycle = settings.get(AcaciaConstants.OPT_FLOW_CYCLE_STRING);
+
+ importer = new MMFastaImporter(fastaFile, qualFile, flowCycle, logger);
+ return importer;
+ }
+ else if(settings.get(AcaciaConstants.OPT_FASTQ).equals("TRUE"))
+ {
+ // System.out.println("Getting importer from " + settings.get(AcaciaConstants.OPT_FASTQ_LOC));
+ String fastqFile = settings.get(AcaciaConstants.OPT_FASTQ_LOC);
+ String flowCycle = settings.get(AcaciaConstants.OPT_FLOW_CYCLE_STRING);
+
+ importer = new MMFastqImporter(fastqFile, flowCycle, logger);
+ return importer;
+ }
+ else
+ {
+ // System.out.println("Get tag importer returns null");
+ }
+
+ return null;
+ }
+
+ /**
+ * Checks if the trim length is defined.
+ *
+ * @param settings the Acacia runtime settings
+ * @return true if the trim length is defined, false otherwise
+ */
+ public boolean trimDefined(HashMap <String, String> settings)
+ {
+ String sTrimLength = settings.get(AcaciaConstants.OPT_TRIM_TO_LENGTH);
+ if (sTrimLength != null && !sTrimLength.equals("NONE"))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Gets the trim length.
+ *
+ * @param settings the Acacia settings
+ * @return the trim length
+ * @throws NumberFormatException Any formatting exception that occurs while parsing the trim length parameter
+ */
+ public int getTrim(HashMap <String, String> settings) throws NumberFormatException
+ {
+ String sTrimLength = settings.get(AcaciaConstants.OPT_TRIM_TO_LENGTH);
+ int trimLength = 0;
+ if (sTrimLength != null && !sTrimLength.equals(""))
+ {
+ trimLength = Integer.parseInt(sTrimLength);
+ return trimLength;
+ }
+ return -1; // fail
+ }
+
+
+ /**
+ * Output sequence.
+ *
+ * @param settings the settings
+ * @param out the out
+ * @param corrected the corrected
+ * @param original the original
+ * @throws Exception the exception
+ */
+ private void outputSequence(HashMap <String, String> settings, BufferedWriter out, String corrected, Pyrotag original) throws Exception
+ {
+ String outputID = getOutputID(settings, original, true);
+
+ //they use split libraries first, which will already have a name of X_[0-9]
+ //either re-use the name from split_libaries, or create my own.
+
+ //some MIDS were specified
+ out.write(">" + outputID + System.getProperty("line.separator"));
+ out.write(corrected + System.getProperty("line.separator"));
+ }
+
+ /**
+ * Gets the output id.
+ *
+ * @param settings the settings
+ * @param p the p
+ * @param withDesc the with desc
+ * @return the output id
+ */
+ private String getOutputID(HashMap <String, String> settings, Pyrotag p, boolean withDesc)
+ {
+ StringBuilder id = new StringBuilder();
+ if(! settings.get(AcaciaConstants.OPT_MID).equals(AcaciaConstants.OPT_NO_MID) && p.getMultiplexTag() != AcaciaConstants.NO_MID_GROUP)
+ {
+ id.append(p.getMultiplexTag().getDescriptor());
+ id.append("_" + p.getInternalID());
+
+ if(withDesc)
+ {
+ String newDesc = " " + p.getID() + " orig_bc=" + p.getMultiplexTag().getMID() + " new_bc=" + p.getMultiplexTag().getMID() + " bc_diffs=0";
+ id.append(newDesc);
+ }
+ }
+ else
+ {
+ //no mids were supplied, return with the original ID.
+ id.append(p.getID());
+
+ if(withDesc)
+ id.append(" " + p.getDescription());
+ }
+
+ return id.toString();
+ }
+
+
+ // returns the ID of the sequence which should be used as the reference
+ /**
+ * Gets the representative seq.
+ *
+ * @param tagsOfInterest tags to select a representative sequences from
+ * @param settings the Acacia runtime settings
+ * @return the representative sequence selected
+ */
+ private Pair<Pyrotag, String> getRepresentativeSeq(
+ HashMap<Pyrotag, String> tagsOfInterest, HashMap <String, String> settings)
+ {
+ String refOption = settings.get(AcaciaConstants.OPT_REPRESENTATIVE_SEQ);
+
+ HashMap<Integer, ArrayList<Pyrotag>> lengthToFreq = new HashMap<Integer, ArrayList<Pyrotag>>();
+
+ int max = -1;
+ Pyrotag maxP = null;
+
+ int min = 100;
+ Pyrotag minP = null;
+
+ int modeLength = -1;
+ int modeFreq = -1;
+
+ for (Pyrotag p : tagsOfInterest.keySet())
+ {
+ String corrected = tagsOfInterest.get(p);
+ int correctedLength = corrected.length();
+ if (!lengthToFreq.containsKey(correctedLength))
+ {
+ lengthToFreq.put(correctedLength, new ArrayList<Pyrotag>());
+ }
+
+ if (correctedLength < min)
+ {
+ min = correctedLength;
+ minP = p;
+ }
+
+ if (correctedLength > max)
+ {
+ max = correctedLength;
+ maxP = p;
+ }
+
+ ArrayList<Pyrotag> tags = lengthToFreq.get(correctedLength);
+ tags.add(p);
+
+ if (tags.size() > modeFreq)
+ {
+ modeFreq = tags.size();
+ modeLength = correctedLength;
+ }
+ }
+
+ if (refOption.equals(AcaciaConstants.OPT_MODE_REPRESENTATIVE))
+ {
+
+ Pyrotag first = lengthToFreq.get(modeLength).get(0);
+ return new Pair<Pyrotag, String>(first,tagsOfInterest.get(first));
+ }
+ else if (refOption.equals(AcaciaConstants.OPT_MAX_REPRESENTATIVE))
+ {
+ return new Pair<Pyrotag, String>(maxP, tagsOfInterest.get(maxP));
+ }
+ else if (refOption.equals(AcaciaConstants.OPT_MIN_REPRESENTATIVE)) // assume its refOption MIN
+ {
+ return new Pair<Pyrotag, String>(minP, tagsOfInterest.get(minP));
+ }
+ else //default is median representative
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Generates all possible MID sequences (expands ambiguous nucleotides).
+ *
+ * @param midString the mid string to generate the explicit
+ * @return String [] containing all the possible explicit sequences that are represented by the MID sequence
+ */
+ public String [] allPossibleVariants(String midString)
+ {
+ //first check whether there is any non nucleotide.
+ StringBuilder [] prefixes = new StringBuilder [] {new StringBuilder()};
+ String ambiguousNucleotide = "[^ATGC]";
+
+ // Compile and get a reference to a Pattern object.
+ Pattern pattern = Pattern.compile(ambiguousNucleotide);
+
+ // Get a matcher object - we cover this next.
+ Matcher matcher = pattern.matcher(midString);
+
+ int prevMatch = -1;
+
+ while(matcher.find())
+ {
+ int pos = matcher.start();
+ char ambiguous = midString.charAt(pos);
+ String gapSeq = midString.substring(prevMatch + 1, pos);
+ StringBuilder [] newPrefixes = new StringBuilder[prefixes.length * AcaciaConstants.IUPAC_AMBIGUOUS_MAPPINGS.get(ambiguous).length];
+ int arrayPos = 0;
+
+ for(Character possVal: AcaciaConstants.IUPAC_AMBIGUOUS_MAPPINGS.get(ambiguous))
+ {
+ for(StringBuilder orig: prefixes)
+ {
+ StringBuilder newBuilder = new StringBuilder(orig.toString());
+ newBuilder.append(gapSeq);
+ newBuilder.append(possVal);
+ newPrefixes[arrayPos] = newBuilder;
+ arrayPos++;
+ }
+ }
+ prefixes = newPrefixes;
+ prevMatch = pos;
+ }
+
+ String [] result = new String [prefixes.length];
+ String lastBit = midString.substring(prevMatch + 1, midString.length());
+
+
+ for(int i = 0; i < prefixes.length; i++)
+ {
+ StringBuilder b = prefixes[i];
+ if(prevMatch != midString.length() - 1)
+ {
+ b.append(lastBit);
+ result[i] = b.toString();
+ }
+ else
+ {
+ result[i] = b.toString();
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Gets the image url.
+ *
+ * @param fileName the image file to get a URL for
+ * @return the image url
+ * @throws Exception Any exception that occurred while getting the URL
+ */
+ public static URL getImageUrl(String fileName) throws Exception
+ {
+ // try to get the URL as a system resource
+ URL url = AcaciaUtilityHolder.getInstance().getClass().getResource(fileName);
+ if (url == null)
+ {
+ // try to get the URL directly from the filename
+ url = new URL("file:" + fileName);
+ }
+ return url;
+ }
+
+ /**
+ * Inits the log files.
+ *
+ * @param settings the Acacia runtime settings
+ * @param logger the Acacia logger
+ * @param runningFromGUI whether Acacia is running from the GUI
+ * @param validMIDS which MIDS to process during this run
+ * @throws Exception any exception that occurs during initialisation of the log files
+ */
+ public void initLogFiles(HashMap <String, String> settings, AcaciaLogger logger, boolean runningFromGUI, LinkedList<MIDPrimerCombo> validMIDS) throws Exception
+ {
+ String outDir = settings.get(AcaciaConstants.OPT_OUTPUT_DIR);
+
+ if(outDir.lastIndexOf(AcaciaEngine.getPlatformSpecificPathDivider()) != (outDir.length() - 1))
+ {
+ outDir = outDir + AcaciaEngine.getPlatformSpecificPathDivider();
+ }
+
+ String runPrefix = settings.get(AcaciaConstants.OPT_OUTPUT_PREFIX);
+
+ //String stdOutLoc = outDir + AcaciaMain.STANDARD_OUT_NAME;
+ //String stdErrLoc = outDir + AcaciaMain.STANDARD_ERR_NAME;
+ //String stdDebugLoc = outDir + AcaciaMain.STANDARD_DEBUG_NAME;
+
+ String stdOutLoc = outDir + runPrefix + "_" + AcaciaMain.STANDARD_OUT_SUFFIX;
+ String stdErrLoc = outDir + runPrefix + "_" + AcaciaMain.STANDARD_ERR_SUFFIX;
+ String stdDebugLoc = outDir + runPrefix + "_" + AcaciaMain.STANDARD_DEBUG_SUFFIX;
+
+ String runSettingsLoc = outDir + runPrefix + ".config";
+ String runSettingsMIDLoc = outDir + runPrefix + ".selectedMIDS";
+
+ BufferedWriter out = null, err = null, debug = null, config = null, midOut = null;
+
+
+ out = new BufferedWriter(new FileWriter(stdOutLoc));
+ err = new BufferedWriter(new FileWriter(stdErrLoc));
+ debug = new BufferedWriter(new FileWriter(stdDebugLoc));
+
+ //output the run settings as a record.
+ if(runningFromGUI)
+ {
+ config = new BufferedWriter(new FileWriter(runSettingsLoc));
+ midOut = new BufferedWriter(new FileWriter(runSettingsMIDLoc));
+ outputSettings(config, midOut, runSettingsMIDLoc, settings, validMIDS);
+ }
+
+ LogFileHandle stdOut = new LogFileHandle(out);
+ LogFileHandle stdErr = new LogFileHandle(err);
+ LogFileHandle stdDebug = new LogFileHandle(debug);
+ LoggerOutput console = new StandardOutputHandle();
+
+ logger.addOutput(console, AcaciaLogger.LOG_ALL);
+ logger.addOutput(stdOut, AcaciaLogger.LOG_PROGRESS);
+ logger.addOutput(stdErr, AcaciaLogger.LOG_ERROR);
+ logger.addOutput(stdDebug, AcaciaLogger.LOG_DEBUG);
+ }
+
+ /**
+ * Output settings.
+ *
+ * @param config the config
+ * @param selectedMIDs the selected mi ds
+ * @param selectedMIDsFileName the selected mi ds file name
+ * @param settings the settings
+ * @param validMIDS the valid mids
+ * @throws IOException Signals that an I/O exception has occurred.
+ */
+ private void outputSettings(BufferedWriter config, BufferedWriter selectedMIDs, String selectedMIDsFileName,
+ HashMap<String, String> settings, LinkedList<MIDPrimerCombo> validMIDS) throws IOException
+ {
+ TreeSet<String> keys = new TreeSet<String>(settings.keySet());
+
+ //need to sort alphabetically, sick of the inconsistency...
+ for(String setting: keys)
+ {
+ if(!(setting.equals(AcaciaConstants.OPT_MID) || setting.equals(AcaciaConstants.OPT_MID_FILE) || settings.get(setting) == null))
+ {
+ config.write(setting + AcaciaConstants.CONFIG_DELIMITER + settings.get(setting) + System.getProperty("line.separator"));
+ }
+ }
+
+
+ //now has a column for the primer sequence
+ if(validMIDS.size() == 0)
+ {
+ config.write(AcaciaConstants.OPT_MID + AcaciaConstants.CONFIG_DELIMITER + AcaciaConstants.OPT_NO_MID + System.getProperty("line.separator"));
+ config.write(AcaciaConstants.OPT_MID_FILE + AcaciaConstants.CONFIG_DELIMITER + System.getProperty("line.separator"));
+ }
+ else
+ {
+ config.write(AcaciaConstants.OPT_MID + AcaciaConstants.CONFIG_DELIMITER + AcaciaConstants.OPT_LOAD_MIDS + System.getProperty("line.separator"));
+ config.write(AcaciaConstants.OPT_MID_FILE + AcaciaConstants.CONFIG_DELIMITER + selectedMIDsFileName);
+
+ for(MIDPrimerCombo mid : validMIDS)
+ {
+ selectedMIDs.write(mid.getDescriptor() + "," + mid.getMID() + "," + mid.getPrimer() + System.getProperty("line.separator"));
+ }
+ }
+
+ config.close();
+ selectedMIDs.close();
+ }
+
+ //creates a hashmap containing the default settings
+ /**
+ * Gets the default settings.
+ *
+ * @return the default settings
+ */
+ public HashMap <String, String> getDefaultSettings()
+ {
+ HashMap <String, String> settings = new HashMap <String, String>();
+ for (int i = 0; i < settingKeys.length; i++) {
+ System.out.println("Loading " + settingKeys[i] + " to value "
+ + settingValues[i]);
+ settings.put(settingKeys[i], settingValues[i]);
+ }
+ return settings;
+ }
+
+ /**
+ * Load mids.
+ *
+ * @param filename the file containing the MIDs and descriptions
+ * @param logger the Acacia logger
+ * @return a list of MIDS found in the file
+ * @throws Exception any exception that occurred while loading the MIDS
+ */
+ public LinkedList <MIDPrimerCombo> loadMIDS(String filename, AcaciaLogger logger) throws Exception
+ {
+ if(filename == null)
+ {
+ return null;
+ }
+
+ MIDReader mReader = new MIDReader(filename);
+ LinkedList <MIDPrimerCombo> mids = mReader.loadMIDS();
+ return mids;
+ }
+
+ /**
+ * Gets the platform specific path divider.
+ *
+ * @return the platform specific path divider
+ */
+ public static String getPlatformSpecificPathDivider()
+ {
+ String pathSep = System.getProperty("file.separator");
+ return pathSep;
+ }
+
+ /**
+ * SingletonHolder is loaded on the first execution of Singleton.getInstance()
+ * or the first access to SingletonHolder.INSTANCE, not before.
+ */
+ private static class AcaciaUtilityHolder
+ {
+
+ /** The Constant INSTANCE. */
+ private static final AcaciaEngine INSTANCE = new AcaciaEngine();
+
+ /**
+ * Gets the single instance of AcaciaUtilityHolder.
+ *
+ * @return single instance of AcaciaUtilityHolder
+ */
+ public static AcaciaEngine getInstance()
+ {
+ return AcaciaUtilityHolder.INSTANCE;
+ }
+
+ }
+
+ /**
+ * Checks if a character is recognised as IUPAC.
+ *
+ * @param curr the character to check
+ * @return true, if is iUPAC
+ */
+ public boolean isIUPAC(char curr)
+ {
+ String valid = "ATGCatgc"; //for now, it is either upper case or lowercase....
+ if(valid.indexOf(curr) >= 0 || AcaciaConstants.IUPAC_AMBIGUOUS_MAPPINGS.containsKey(Character.toUpperCase(curr)))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Gets the Acacia executable version number.
+ *
+ * @return the version
+ * @throws Exception the exception
+ */
+ public static String getVersion() throws Exception
+ {
+ URL url = AcaciaEngine.getEngine().getClass().getResource(BUILD_PROPERTIES_FILE);
+
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
+ String major = null;
+ String minor = null;
+ String build = null;
+
+ String line = in.readLine();
+
+ while(line != null)
+ {
+ String [] keyValue = line.split("=");
+
+ if(keyValue[0].equals(BUILD_MAJOR_KEY))
+ {
+ major = keyValue[1];
+ }
+ else if (keyValue[0].equals(BUILD_MINOR_KEY))
+ {
+ minor = keyValue[1];
+ }
+ else if(keyValue[0].equals(BUILD_REVISION_KEY))
+ {
+ build = keyValue[1];
+ }
+
+ line = in.readLine();
+ }
+
+ String version = major + "." + minor + "-b" + build;
+ return version;
+ }
+}
\ No newline at end of file
diff --git a/src/pyromaniac/AcaciaMain.java b/src/pyromaniac/AcaciaMain.java
new file mode 100644
index 0000000..9c580db
--- /dev/null
+++ b/src/pyromaniac/AcaciaMain.java
@@ -0,0 +1,1075 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.WindowEvent;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.Properties;
+import java.util.TreeSet;
+import java.util.jar.Attributes;
+import java.util.jar.JarFile;
+import java.util.jar.Manifest;
+
+
+import javax.swing.ImageIcon;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.OptionGroup;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
+
+import pyromaniac.DataStructures.MIDPrimerCombo;
+import pyromaniac.GUI.CustomDialog;
+import pyromaniac.GUI.GridBagUtility;
+import pyromaniac.GUI.TagInputPanel;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * AcaciaMain contains the main method for the Acacia software package. It gets the run parameters from either the command line,
+ * config file or GUI as indicated by the user, and then starts the AcaciaEngine.
+ */
+public class AcaciaMain
+{
+
+ /** The settings flag. */
+ private Object settingsFlag;
+
+ /** The input frame. */
+
+ AcaciaFrame inputFrame;
+
+ /** The program status. */
+ private String programStatus;
+
+ /** The Constant STATUS_USER_INTERACTING. */
+ protected static final String STATUS_USER_INTERACTING = "USER";
+
+ /** The Constant STATUS_USER_SUBMITTED. */
+ protected static final String STATUS_USER_SUBMITTED = "SUBMITTED";
+
+ /** The Constant STATUS_USER_EXITED. */
+ protected static final String STATUS_USER_EXITED = "EXITED";
+
+ /** The Constant FRAME_BACKGROUND_COLOUR. */
+ protected static final Color FRAME_BACKGROUND_COLOUR = Color.decode("#F4E17A");
+
+ /** The Constant WATTLE_LOC. */
+ protected static final String WATTLE_LOC;
+
+ /** The Constant ACACIA_LOGO. */
+ public static final String ACACIA_LOGO;
+
+ /** The Constant DATE_FORMAT_NOW. */
+ protected static final String DATE_FORMAT_NOW = "yyyyMMddHHmmss";
+
+
+ /** The Constant MENU_STRING_EXIT. */
+ protected static final String MENU_STRING_EXIT = "Quit";
+
+ /** The Constant MENU_PROGRAM_INFO. */
+ protected static final String MENU_PROGRAM_INFO = "Program Info";
+
+ //need to be changed to relative to install.
+
+ /** The Constant STANDARD_OUT_NAME. */
+ static final String STANDARD_OUT_NAME;
+
+ /** The Constant STANDARD_ERR_NAME. */
+ static final String STANDARD_ERR_NAME;
+
+ /** The Constant STANDARD_DEBUG_NAME. */
+ static final String STANDARD_DEBUG_NAME;
+
+ static final String STANDARD_OUT_SUFFIX;
+ static final String STANDARD_ERR_SUFFIX;
+
+ static final String STANDARD_DEBUG_SUFFIX;
+
+ static
+ {
+ WATTLE_LOC = "/images/acacia_small_wattle_icon.png";
+ ACACIA_LOGO = "/images/Acacia_logo2.png";
+
+ STANDARD_OUT_NAME = "acacia_standard_output.txt";
+ STANDARD_ERR_NAME = "acacia_standard_error.txt";
+ STANDARD_DEBUG_NAME = "acacia_standard_debug.txt";
+
+ STANDARD_OUT_SUFFIX = "stdout.txt";
+ STANDARD_ERR_SUFFIX = "stderr.txt";
+ STANDARD_DEBUG_SUFFIX = "stddebug.txt";
+ }
+
+ /**
+ * The main method.
+ *
+ * @param args the arguments
+ */
+ @SuppressWarnings("static-access")
+ public static void main(String[] args)
+ {
+ AcaciaMain am = new AcaciaMain();
+ Options options = new Options();
+ OptionGroup runType = new OptionGroup();
+
+ Option genConfigFile = OptionBuilder.withArgName("file").hasArg().withDescription("Write default config to this file").create("g");
+ Option runFromConfig = OptionBuilder.withArgName("file").hasArg().withDescription("Run Acacia with this config").create("c");
+ Option runGUI = OptionBuilder.withDescription("Run Acacia GUI").create("u");
+ Option help = OptionBuilder.withDescription("Show this help message").create("h");
+ Option version = OptionBuilder.withDescription("Version").create("v");
+ Option property = OptionBuilder.withArgName( "property=value" )
+ .hasArgs(2)
+ .withValueSeparator()
+ .withDescription( "use value for given property [when running from command line]" )
+ .create( "D" );
+
+ runType.addOption(genConfigFile);
+ runType.addOption(runFromConfig);
+ runType.addOption(runGUI);
+ runType.addOption(help);
+ runType.addOption(version);
+ runType.addOption(property); //this indicates the user is running from the command line without a config.
+ options.addOptionGroup(runType);
+
+ try
+ {
+ CommandLineParser parser = new PosixParser();
+ CommandLine clObj = parser.parse(options, args);
+
+ if(!(clObj.hasOption('g') ^ clObj.hasOption('c') ^ clObj.hasOption('u') ^ clObj.hasOption('D')^ clObj.hasOption('v')))
+ {
+ usage(options);
+ }
+
+ if(clObj.hasOption('g'))
+ {
+ String config = clObj.getOptionValue('g');
+ am.generateConfig(config);
+ System.exit(0);
+ }
+ else if(clObj.hasOption('c'))
+ {
+ String config = clObj.getOptionValue('c');
+
+ HashMap <String, String> settings = am.loadConfigFromFile(config);
+
+ am.runAcacia(settings);
+ }
+ else if(clObj.hasOption('u'))
+ {
+ am.runAcacia(null);
+ }
+ else if(clObj.hasOption('v'))
+ {
+ System.out.println("Acacia version: " + AcaciaEngine.getVersion());
+ System.exit(0);
+ }
+ else if(clObj.hasOption('D'))
+ {
+ //running from command line...
+ HashMap <String, String> settings = am.populateSettingsFromCommandLine(clObj);
+
+ am.runAcacia(settings);
+ }
+ else
+ {
+ usage(options);
+ }
+ }
+ catch(ParseException pe)
+ {
+ System.out.println(pe.getMessage());
+ pe.printStackTrace();
+ usage(options);
+ }
+ catch(Exception e)
+ {
+
+ e.printStackTrace();
+ am.cleanExit(null, e);
+ }
+ }
+
+
+ /**
+ * Instantiates a new acacia main.
+ */
+ public AcaciaMain()
+ {
+ this.settingsFlag = new Object();
+ this.programStatus = AcaciaMain.STATUS_USER_INTERACTING;
+ }
+
+
+ /**
+ * Load user-configurations from file.
+ *
+ * @param configLocation the config file location
+ * @return the runtime settings, with default values overridden by user-specified values
+ * @throws Exception any exception that occurs while loading the config file
+ */
+ private HashMap <String, String> loadConfigFromFile(String configLocation) throws Exception
+ {
+ HashMap <String, String> settings = AcaciaEngine.getEngine().getDefaultSettings();
+
+ File f = new File(configLocation);
+
+ if (!f.exists())
+ {
+ throw new IOException("Config file does not exist: "
+ + configLocation);
+ }
+
+ BufferedReader in = new BufferedReader(new FileReader(f));
+
+ String line = in.readLine();
+ while (line != null)
+ {
+ String[] keyValue = line.split(AcaciaConstants.CONFIG_DELIMITER);
+ if(settings.containsKey(keyValue[0]))
+ {
+ if(keyValue.length == 2) //user has specified something
+ {
+ System.out.println("Loading from specified config: " + keyValue[0] + AcaciaConstants.CONFIG_DELIMITER + keyValue[1]);
+
+ if(keyValue[1].trim().length() == 0)
+ settings.put(keyValue[0], null);
+ else
+ settings.put(keyValue[0], keyValue[1]);
+ }
+ else if (keyValue.length > 2)
+ {
+ throw new IOException(
+ "Configuration file is incorrectly formatted: expecting key=value, found "
+ + line);
+ }
+ else
+ {
+ //put null for the key.
+ settings.put(keyValue[0], null);
+ }
+ }
+ else
+ {
+ throw new Exception("Invalid parameter in configuration file: " + line);
+ }
+ line = in.readLine();
+ }
+
+ System.out.println("Finished loading config");
+
+
+ return settings;
+ }
+
+ /**
+ * Populate settings from command line.
+ *
+ * @param clObj object containing command line parameters
+ * @return the Acacia run settings, with defaults overriden by user-specified values from the command line
+ * @throws Exception any exception that occurs while populating settings from the command line
+ */
+ private HashMap <String, String> populateSettingsFromCommandLine(CommandLine clObj) throws Exception
+ {
+ HashMap <String, String> settings = AcaciaEngine.getEngine().getDefaultSettings();
+
+ //we are only interested in -D
+
+ Properties p = clObj.getOptionProperties("D");
+
+ for(Object key : p.keySet())
+ {
+ String keyS = (String)key;
+
+ Object val = p.get(key);
+ String valS = (String) val;
+ if(settings.containsKey(keyS))
+ {
+ //only way to set parameter to null using command line.
+ if(valS.equals("null"))
+ {
+ valS = null;
+ }
+
+
+ System.out.println("Loading from commandline: " + keyS + "=" + valS);
+ settings.put(keyS, valS);
+ }
+ else
+ {
+ throw new Exception("No such parameter: " + keyS);
+ }
+ }
+
+ return settings;
+ }
+
+ /**
+ * Generates configuration file with default settings.
+ *
+ * @param string the string
+ */
+ private void generateConfig(String string)
+ {
+ try
+ {
+ File textFile = new File(string);
+ if (!textFile.createNewFile())
+ {
+ throw new IOException("File already exists: " + string
+ + ". Exiting");
+ }
+
+ BufferedWriter out = new BufferedWriter(new FileWriter(textFile));
+ HashMap <String, String> defaultSettings = AcaciaEngine.getEngine().getDefaultSettings();
+ TreeSet<String> keys = new TreeSet<String>(defaultSettings.keySet());
+
+ for(String setting: keys)
+ {
+ String defaultVal = defaultSettings.get(setting);
+
+ out.write(setting + AcaciaConstants.CONFIG_DELIMITER
+ + defaultVal + System.getProperty("line.separator"));
+ }
+
+ out.close();
+ System.out.println("Default config successfully written to "
+ + string);
+ }
+ catch (IOException ie)
+ {
+ System.err.println(ie.getMessage());
+ System.exit(1);
+ }
+ }
+
+ /**
+ * Usage.
+ *
+ * @param options the command line object
+ */
+ private static void usage(Options options)
+ {
+ HelpFormatter formatter = new HelpFormatter();
+ formatter.printHelp( "Acacia", options);
+ System.exit(0);
+ }
+
+
+
+ /**
+ * The Class GUIRunnable.
+ */
+ public class GUIRunnable implements Runnable
+ {
+
+ /** The Acacia Main instance. */
+ private AcaciaMain am;
+
+ /**
+ * Instantiates a new gUI runnable.
+ *
+ * @param am the am
+ */
+ public GUIRunnable(AcaciaMain am)
+ {
+ super();
+ this.am = am;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Runnable#run()
+ */
+ public void run()
+ {
+ try
+ {
+ new AcaciaFrame().setVisible(true); //starts the GUI thread running
+ }
+ catch(Exception e)
+ {
+ //don't have access to the logger here, but most errors should be caught by the Acacia engine
+ System.out.println("An error occurred: " + e.getMessage());
+ System.exit(1);
+ }
+ }
+ }
+
+ //after this method, program status has changed from interacting to either submitted or exiting.
+ /**
+ * Run the Acacia GUI to capture user input.
+ */
+ private void runGUI()
+ {
+ // System.out.println("Running from GUI");
+ GUIRunnable mine = this.new GUIRunnable(this);
+ javax.swing.SwingUtilities.invokeLater(mine);
+ }
+
+ /**
+ * Run from command line.
+ *
+ * @param settings the run time settings
+ * @throws Exception the exception
+ */
+ private void runFromCommandLine(HashMap <String, String> settings) throws Exception
+ {
+ this.checkSettings(settings);
+
+ boolean errorOccurred = false;
+
+ AcaciaLogger logger = new AcaciaLogger();
+ try
+ {
+ AcaciaEngine engine = AcaciaEngine.getEngine();
+
+ //System.out.println("Initialising the log files");
+
+ //TODO: should not be here, but in runAcacia. Why is it here (and is it something to do with the GUI?)
+ //engine.initLogFiles(settings, logger, false, null);
+
+ LinkedList <MIDPrimerCombo> validTags = null;
+
+ if(settings.get(AcaciaConstants.OPT_MID).equals(AcaciaConstants.OPT_LOAD_MIDS))
+ {
+ validTags = engine.loadMIDS(settings.get(AcaciaConstants.OPT_MID_FILE), logger);
+ }
+ else
+ {
+ validTags = new LinkedList <MIDPrimerCombo>();
+ validTags.add(AcaciaConstants.NO_MID_GROUP);
+ }
+
+ engine.runAcacia(settings, validTags, logger, null, AcaciaEngine.getVersion(), false);
+
+ }
+ catch(OutOfMemoryError error)
+ {
+ errorOccurred = true;
+ logger.writeLog(error.getMessage(), AcaciaLogger.LOG_ERROR);
+
+ StackTraceElement [] trace = error.getStackTrace();
+
+ for(int i = 0; i < trace.length; i++)
+ {
+ logger.writeLog(trace[i].toString(), AcaciaLogger.LOG_ERROR);
+ }
+ }
+ catch(Exception e)
+ {
+ errorOccurred = true;
+ System.out.println(e.getMessage());
+ logger.writeLog(e.getMessage(), AcaciaLogger.LOG_ERROR);
+
+ StackTraceElement [] trace = e.getStackTrace();
+
+ for(int i = 0; i < trace.length; i++)
+ {
+ logger.writeLog(trace[i].toString(), AcaciaLogger.LOG_ERROR);
+ }
+ }
+ finally
+ {
+ try
+ {
+ logger.closeLogger();
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ if(errorOccurred)
+ {
+ System.exit(1);
+ }
+ else
+ {
+ System.exit(0);
+ }
+ }
+ }
+
+/* TODO: need to add more parameter checks here.
+
+*
+*
+*/
+ /**
+ * Check settings.
+ *
+ * @param settings the run time settings
+ * @throws Exception the exception
+ */
+ private void checkSettings(HashMap<String, String> settings) throws Exception
+ {
+ if(!(settings.get(AcaciaConstants.OPT_FASTA).equals("TRUE") ^ settings.get(AcaciaConstants.OPT_FASTQ).equals("TRUE")))
+ {
+ throw new Exception("One, and only one of FASTA or FASTQ must be specified");
+ }
+
+ if(settings.get(AcaciaConstants.OPT_FASTA).equals("TRUE") && (settings.get(AcaciaConstants.OPT_FASTA_LOC) == null || ! new File(settings.get(AcaciaConstants.OPT_FASTA_LOC)).exists()))
+ {
+ throw new Exception("FASTA file does not exist: " + settings.get(AcaciaConstants.OPT_FASTA_LOC));
+ }
+
+ if(settings.get(AcaciaConstants.OPT_FASTQ).equals("TRUE") && (settings.get(AcaciaConstants.OPT_FASTQ_LOC) == null || ! new File(settings.get(AcaciaConstants.OPT_FASTQ_LOC)).exists()))
+ {
+ throw new Exception("FASTQ file does not exist: " + settings.get(AcaciaConstants.OPT_FASTQ_LOC));
+ }
+
+ int minQual = Integer.parseInt(settings.get(AcaciaConstants.OPT_MIN_AVG_QUALITY));
+
+ if(minQual < 0 || minQual > 40) //magic numbers to be fixed
+ {
+ throw new Exception("Invalid avg. quality value, needs to be integer in range 0-40: " + minQual);
+ }
+
+ if(! new File(settings.get(AcaciaConstants.OPT_OUTPUT_DIR)).isDirectory())
+ {
+ throw new Exception("Output directory does not exist: " + settings.get(AcaciaConstants.OPT_OUTPUT_DIR));
+ }
+
+ String midOption = settings.get(AcaciaConstants.OPT_MID);
+
+ if(!(midOption.equals(AcaciaConstants.OPT_LOAD_MIDS) ||
+ midOption.equals(AcaciaConstants.OPT_NO_MID) ||
+ midOption.equals(AcaciaConstants.OPT_ROCHE_10MID)||
+ midOption.equals(AcaciaConstants.OPT_ROCHE_5MID)))
+ {
+ throw new Exception("Invalid value for " + AcaciaConstants.OPT_MID +". Value must be in " +
+ AcaciaConstants.OPT_LOAD_MIDS +", " + AcaciaConstants.OPT_NO_MID + ", " + AcaciaConstants.OPT_ROCHE_10MID +
+ ", " + AcaciaConstants.OPT_ROCHE_5MID);
+ }
+
+ if(midOption.equals(AcaciaConstants.OPT_LOAD_MIDS) && ! new File(settings.get(AcaciaConstants.OPT_MID_FILE)).exists())
+ {
+ throw new Exception("Specified MID file does not exist: " + settings.get(AcaciaConstants.OPT_MID_FILE));
+ }
+
+ try
+ {
+ if(settings.get(AcaciaConstants.OPT_TRIM_TO_LENGTH) != null && settings.get(AcaciaConstants.OPT_TRIM_TO_LENGTH).length() > 0)
+ {
+ int trimLength = Integer.parseInt(settings.get(AcaciaConstants.OPT_TRIM_TO_LENGTH));
+
+ }
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new Exception("Specified trim length is not an integer: " + settings.get(AcaciaConstants.OPT_TRIM_TO_LENGTH));
+ }
+
+ if(! isValidFileName(settings.get(AcaciaConstants.OPT_OUTPUT_PREFIX)))
+ {
+ throw new Exception("Specified prefix is not valid for this OS");
+ }
+
+ if(! new File(settings.get(AcaciaConstants.OPT_OUTPUT_DIR)).isDirectory())
+ {
+ throw new Exception("The output directory does not exist, or is not a directory: " + settings.get(AcaciaConstants.OPT_OUTPUT_DIR));
+ }
+
+ int manhattanDist = 0;
+
+ try
+ {
+ manhattanDist = Integer.parseInt(settings.get(AcaciaConstants.OPT_MAXIMUM_MANHATTAN_DIST));
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new Exception("Manhattan distance was not an integer:" + settings.get(AcaciaConstants.OPT_MAXIMUM_MANHATTAN_DIST));
+
+ }
+
+ if(manhattanDist < 0)
+ {
+ throw new Exception("Manhattan distance is less than zero");
+ }
+
+ String significanceLevel = settings.get(AcaciaConstants.OPT_SIGNIFICANCE_LEVEL);
+ if(! significanceLevel.equals(AcaciaConstants.SIGN_THRESHOLD_ZERO))
+ {
+ try
+ {
+ int sigLevel = Integer.parseInt(significanceLevel);
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new Exception("Significance level is not an integer: " + settings.get(AcaciaConstants.OPT_SIGNIFICANCE_LEVEL));
+ }
+ }
+
+ String representative = settings.get(AcaciaConstants.OPT_REPRESENTATIVE_SEQ);
+
+ if(!(representative.equals(AcaciaConstants.OPT_MODE_REPRESENTATIVE) ||
+ representative.equals(AcaciaConstants.OPT_MEDIAN_REPRESENTATIVE) ||
+ representative.equals(AcaciaConstants.OPT_MAX_REPRESENTATIVE) ||
+ representative.equals(AcaciaConstants.OPT_MIN_REPRESENTATIVE)))
+ {
+ throw new Exception("Representative sequence option invalid, must be in " +
+ AcaciaConstants.OPT_MODE_REPRESENTATIVE + ", " + AcaciaConstants.OPT_MEDIAN_REPRESENTATIVE + ", " +
+ AcaciaConstants.OPT_MAX_REPRESENTATIVE + ", " + AcaciaConstants.OPT_MIN_REPRESENTATIVE);
+ }
+
+
+ String split = settings.get(AcaciaConstants.OPT_SPLIT_ON_MID);
+ split = split.trim();
+
+ if(!( split.equals("TRUE") || split.equals("FALSE")))
+ {
+ throw new Exception("Split on MID needs to be TRUE/FALSE, not: " + settings.get(AcaciaConstants.OPT_SPLIT_ON_MID));
+ }
+
+ try
+ {
+ int value = Integer.parseInt(settings.get(AcaciaConstants.OPT_MAX_STD_DEV_LENGTH));
+
+ if(value <= 0)
+ {
+ throw new Exception("Standard deviations needs to be a positive integer, not " + value);
+ }
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new Exception("Standard deviations is not an integer: " + settings.get(AcaciaConstants.OPT_SIGNIFICANCE_LEVEL));
+ }
+
+ String errorModel = settings.get(AcaciaConstants.OPT_ERROR_MODEL);
+
+
+ if(!
+ (errorModel.equals(AcaciaConstants.OPT_ACACIA_TITANIUM_ERROR_MODEL)
+ || errorModel.equals(AcaciaConstants.OPT_FLOWSIM_ERROR_MODEL) ||
+ errorModel.equals(AcaciaConstants.OPT_PYRONOISE_ERROR_MODEL) ||
+ errorModel.equals(AcaciaConstants.OPT_ACACIA_IT_OT_100bp_316_MODEL) ||
+ errorModel.equals(AcaciaConstants.OPT_ACACIA_IT_OT_100bp_314_MODEL) ||
+ errorModel.equals(AcaciaConstants.OPT_ACACIA_IT_MAN_200bp_316_MODEL) ||
+ errorModel.equals(AcaciaConstants.OPT_ACACIA_IT_MAN_200bp_314_MODEL)||
+ errorModel.equals(AcaciaConstants.OPT_ACACIA_IT_OT_200bp_316)||
+ errorModel.equals(AcaciaConstants.OPT_ACACIA_IT_OT_200bp_314)
+
+ ))
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append(AcaciaConstants.OPT_ACACIA_TITANIUM_ERROR_MODEL + "\n");
+ sb.append(AcaciaConstants.OPT_FLOWSIM_ERROR_MODEL + "\n");
+ sb.append(AcaciaConstants.OPT_PYRONOISE_ERROR_MODEL + "\n");
+ sb.append(AcaciaConstants.OPT_ACACIA_IT_OT_100bp_316_MODEL + "\n");
+ sb.append(AcaciaConstants.OPT_ACACIA_IT_OT_100bp_314_MODEL + "\n");
+ sb.append(AcaciaConstants.OPT_ACACIA_IT_MAN_200bp_316_MODEL + "\n");
+ sb.append(AcaciaConstants.OPT_ACACIA_IT_MAN_200bp_314_MODEL + "\n");
+ sb.append(AcaciaConstants.OPT_ACACIA_IT_OT_200bp_316 + "\n");
+ sb.append(AcaciaConstants.OPT_ACACIA_IT_OT_200bp_314 + "\n");
+
+ throw new Exception("Incorrect error model specified, must be one of: \n " + sb.toString());
+ }
+
+ String validNucs = "ATGC";
+ String flowKey = settings.get(AcaciaConstants.OPT_FLOW_KEY);
+ for(int i = 0; i < flowKey.length(); i++)
+ {
+ if(! validNucs.contains((flowKey.charAt(i) + "")))
+ {
+ throw new Exception ("Invalid character in specified flow key: " + flowKey.charAt(i));
+ }
+ }
+
+ try
+ {
+ int recurse = Integer.parseInt(settings.get(AcaciaConstants.OPT_MAX_RECURSE_DEPTH));
+
+ if(recurse < 0)
+ {
+ throw new Exception("Recurse depth needs to be a positive integer");
+ }
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new Exception("Specified recurse depth is not an integer: " + settings.get(AcaciaConstants.OPT_MAX_RECURSE_DEPTH));
+ }
+
+ if(settings.containsKey(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW) && settings.get(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW) != null && settings.get(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW).trim().length() > 0)
+ {
+ try
+ {
+ System.out.println("Truncate consensus to flow contains < " + settings.get(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW) + ">");
+
+ int truncateToFlow = Integer.parseInt(settings.get(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW));
+
+ if(truncateToFlow <= 0)
+ {
+ throw new Exception("Truncate to flow must be a positive integer");
+ }
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new Exception("Specified truncate to flow is not a positive integer: " + settings.get(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW));
+ }
+ }
+
+ if(settings.containsKey(AcaciaConstants.OPT_MIN_READ_REP_BEFORE_TRUNCATION) && settings.get(AcaciaConstants.OPT_MIN_READ_REP_BEFORE_TRUNCATION) != null && settings.get(AcaciaConstants.OPT_MIN_READ_REP_BEFORE_TRUNCATION).trim().length() > 0)
+ {
+ try
+ {
+ double minReadRep = Double.parseDouble(settings.get(AcaciaConstants.OPT_MIN_READ_REP_BEFORE_TRUNCATION));
+
+ if(minReadRep < 0 || minReadRep > 1)
+ {
+ throw new Exception("Specified min read rep before truncation between be a double between 0 and 1.");
+ }
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new Exception("Specified min read rep before truncation is not a double: " + settings.get(AcaciaConstants.OPT_MIN_READ_REP_BEFORE_TRUNCATION));
+ }
+ }
+
+ if(settings.containsKey(AcaciaConstants.OPT_MIN_FLOW_TRUNCATION) && settings.get(AcaciaConstants.OPT_MIN_FLOW_TRUNCATION) != null)
+ {
+ try
+ {
+ int minFlowTruncation = Integer.parseInt(settings.get(AcaciaConstants.OPT_MIN_FLOW_TRUNCATION));
+
+ if(minFlowTruncation < 0)
+ {
+ throw new Exception("Min flow truncation must be a positive integer, if specified");
+ }
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new Exception("Specified min flow truncation is not an integer: " + settings.get(AcaciaConstants.OPT_MIN_FLOW_TRUNCATION));
+ }
+ }
+
+ if(settings.containsKey(AcaciaConstants.OPT_FILTER_READS_WITH_N_BEFORE_POS) && settings.get(AcaciaConstants.OPT_FILTER_READS_WITH_N_BEFORE_POS) != null)
+ {
+ try
+ {
+ int position = Integer.parseInt(settings.get(AcaciaConstants.OPT_FILTER_READS_WITH_N_BEFORE_POS));
+ if(position < 0)
+ {
+ throw new Exception ("Specified read position (FILTER_N_BEFORE_POS) must be a positive integer");
+ }
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new Exception("Specified read position (FILTER_N_BEFORE_POS) is not an integer: "+ settings.get(AcaciaConstants.OPT_FILTER_READS_WITH_N_BEFORE_POS));
+ }
+ }
+
+ if(!( settings.get(AcaciaConstants.OPT_SIGNIFICANT_WHEN_TWO).toUpperCase().equals("TRUE") || settings.get(AcaciaConstants.OPT_SIGNIFICANT_WHEN_TWO).toUpperCase().equals("FALSE")))
+ {
+ throw new Exception("ANY_SIGNIFICANT_DIFF_FOR_TWO_SEQS must be TRUE or FALSE, not: " + settings.get(AcaciaConstants.OPT_SIGNIFICANT_WHEN_TWO));
+ }
+ }
+
+ /**
+ * Checks if is valid file name.
+ *
+ * @param aFileName the a file name
+ * @return true, if is valid file name
+ */
+ public boolean isValidFileName(final String aFileName) //this prevents people from re-writing their runs?
+ {
+ final File aFile = new File(aFileName);
+ boolean isValid = true;
+
+ if(aFile.exists())
+ {
+ return true;
+ }
+
+ try {
+ if (aFile.createNewFile())
+ {
+ aFile.delete();
+ }
+ } catch (IOException e) {
+ isValid = false;
+ }
+ return isValid;
+ }
+
+ /**
+ * Starts the Acacia Engine.
+ *
+ * @param settings the run time settings (GUI or command line)
+ * @throws Exception the exception
+ */
+ private void runAcacia(HashMap <String, String> settings) throws Exception
+ {
+ //run GUI
+ if (settings == null)
+ {
+ runGUI();
+ }
+ else
+ {
+ runFromCommandLine(settings);
+ }
+ }
+
+ /**
+ * Clean exit.
+ *
+ * @param message the error message
+ * @param e the exception
+ */
+ protected void cleanExit(String message, Exception e)
+ {
+ this.inputFrame.setVisible(false);
+ System.exit(0);
+ }
+
+ /**
+ * Gets the platform specific path divider.
+ *
+ * @return the platform specific path divider
+ */
+ public static String getPlatformSpecificPathDivider()
+ {
+ String pathSep = System.getProperty("file.separator");
+ return pathSep;
+ }
+
+ /* Logic for handling 'help' and 'version' info */
+ /**
+ * The listener interface for receiving acaciaMenu events.
+ * The class that is interested in processing a acaciaMenu
+ * event implements this interface, and the object created
+ * with that class is registered with a component using the
+ * component's <code>addAcaciaMenuListener<code> method. When
+ * the acaciaMenu event occurs, that object's appropriate
+ * method is invoked.
+ *
+ * @see AcaciaMenuEvent
+ */
+ protected class AcaciaMenuListener implements ActionListener, ItemListener
+ {
+
+ /** The frame. */
+ AcaciaFrame frame;
+
+ /**
+ * Instantiates a new acacia menu listener.
+ *
+ * @param frame the parent frame
+ */
+ public AcaciaMenuListener(AcaciaFrame frame)
+ {
+ this.frame = frame;
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e)
+ {
+ // ...Get information from the action event...
+ // ...Display it in the text area...
+ System.out.println(e.getActionCommand());
+
+ if(e.getActionCommand().equals(AcaciaMain.MENU_STRING_EXIT))
+ {
+ this.frame.promptForQuit();
+ }
+ else if(e.getActionCommand().equals(AcaciaMain.MENU_PROGRAM_INFO));
+ {
+ String ABOUT_MESSAGE = "Acacia was developed by Lauren Bragg and Glenn Stone (2010). The Acacia logo is a composition by Lauren Bragg which uses the " +
+ "<a href=http://upload.wikimedia.org/wikipedia/commons/6/68/Acacia_genistifolia.jpg> Acacia_Genistifolia.jpg </a> image from Wikimedia.";
+ JDialog dialog = new CustomDialog(this.frame, false, ABOUT_MESSAGE);
+ dialog.setTitle("About");
+ dialog.setVisible(true);
+
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.ItemListener#itemStateChanged(java.awt.event.ItemEvent)
+ */
+ public void itemStateChanged(ItemEvent e)
+ {
+ // ...Get information from the item event...
+ // ...Display it in the text area...
+ }
+ }
+
+ /**
+ * The listener interface for receiving mainFrame events.
+ * The class that is interested in processing a mainFrame
+ * event implements this interface, and the object created
+ * with that class is registered with a component using the
+ * component's <code>addMainFrameListener<code> method. When
+ * the mainFrame event occurs, that object's appropriate
+ * method is invoked.
+ *
+ * @see MainFrameEvent
+ */
+ protected class MainFrameListener extends java.awt.event.WindowAdapter
+ {
+
+ /** The frame. */
+ private AcaciaFrame frame;
+
+ /**
+ * Instantiates a new main frame listener.
+ *
+ * @param frame the frame
+ */
+ public MainFrameListener( AcaciaFrame frame)
+ {
+ this.frame = frame;
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.WindowAdapter#windowClosing(java.awt.event.WindowEvent)
+ */
+ public void windowClosing(WindowEvent e)
+ {
+ this.frame.promptForQuit();
+ }
+ }
+
+ /**
+ * The Class AcaciaFrame.
+ */
+ private class AcaciaFrame extends JFrame
+ {
+
+ /** The TagInputPanel for getting user input. */
+ private TagInputPanel tp;
+
+ /**
+ * Instantiates a new acacia frame.
+ *
+ * @throws Exception the exception
+ */
+ public AcaciaFrame () throws Exception
+ {
+ super("Acacia - pyrosequencing error-correction and de-replication");
+ init();
+ }
+
+ /**
+ * Prompt for quit.
+ */
+ public void promptForQuit()
+ {
+ int response = JOptionPane.showConfirmDialog(null, "Are you sure you want to quit?", "Exit Acacia",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (response == JOptionPane.NO_OPTION)
+ {
+ //do nothing;
+ }
+ else
+ {
+ System.exit(0);
+ //think this needs to be consolidated but no time for it now.
+ }
+ }
+
+ /**
+ * Inits the JFrame for the TagInputPanel.
+ *
+ * @throws Exception the exception
+ */
+ public void init() throws Exception
+ {
+ JFrame.setDefaultLookAndFeelDecorated(true);
+ this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ this.setPreferredSize(new Dimension(1064, 800));
+ this.setMinimumSize(new Dimension(1064, 800));
+
+ URL wattleLoc = getClass().getResource(WATTLE_LOC);
+
+ if(wattleLoc == null)
+ System.out.println("File could not be found: " + WATTLE_LOC);
+
+ this.setIconImage(new ImageIcon(wattleLoc).getImage());
+ this.addWindowListener(new MainFrameListener(this));
+
+ // menu bar for help
+ AcaciaMenuListener listener = new AcaciaMenuListener(this);
+
+ JMenuBar menuBar = new JMenuBar();
+ JMenu menu = new JMenu("Options");
+ menuBar.add(menu);
+
+ JMenuItem quit = new JMenuItem(MENU_STRING_EXIT);
+ JMenuItem info = new JMenuItem(MENU_PROGRAM_INFO);
+ quit.addActionListener(listener);
+ info.addActionListener(listener);
+
+ menu.add(info);
+ menu.add(quit);
+
+ this.setJMenuBar(menuBar);
+
+ GridBagUtility u = new GridBagUtility();
+ // Create and set up the content pane.
+ this.tp = new TagInputPanel(u, this);
+ tp.setOpaque(true);
+
+ this.getContentPane().setLayout(new BorderLayout());
+ this.getContentPane().add(tp, BorderLayout.CENTER);
+ }
+
+ /**
+ * Clear fields.
+ */
+ public void clearFields()
+ {
+ this.tp.clearInterface();
+ }
+ }
+
+}
diff --git a/src/pyromaniac/Algorithm/BalzerOUCallFrequencyTable.java b/src/pyromaniac/Algorithm/BalzerOUCallFrequencyTable.java
new file mode 100644
index 0000000..9dc8ebd
--- /dev/null
+++ b/src/pyromaniac/Algorithm/BalzerOUCallFrequencyTable.java
@@ -0,0 +1,380 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.math.BigDecimal;
+import java.net.URL;
+import java.util.HashMap;
+
+import org.apache.commons.math3.exception.*;
+import org.apache.commons.math3.distribution.NormalDistribution;
+
+import pyromaniac.AcaciaConstants;
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.IO.AcaciaLogger;
+
+
+/**
+ * The Class MaldeOUCallFrequencyTable.
+ */
+public class BalzerOUCallFrequencyTable implements OUFrequencyTable
+{
+
+ /** The Constant SEGMENT_SIZE. */
+ public static final int SEGMENT_SIZE = 40;
+ private static final int SCALE = 9;
+
+ /** The probabilities. */
+ HashMap <Integer, HashMap <Integer, BigDecimal []>> probabilities;
+
+ //hash of SEGMENT: REFLEN
+ HashMap <Integer, Pair <Double, Double>> normalDistParams;
+
+
+ /**
+ * Instantiates a new malde ou call frequency table.
+ *
+ * @param probFile the prob file
+ */
+ public BalzerOUCallFrequencyTable(String probFile)
+ {
+ probabilities = new HashMap<Integer, HashMap <Integer, BigDecimal []>>(20);
+
+ this.normalDistParams = new HashMap <Integer, Pair <Double, Double>>();
+ normalDistParams.put(0, new Pair <Double, Double>(0.1230, 0.737));
+ normalDistParams.put(1, new Pair <Double, Double>(1.0193, 0.1227));
+ normalDistParams.put(2, new Pair <Double, Double> (2.0006, 0.1585));
+ normalDistParams.put(3, new Pair <Double, Double> (2.9934, 0.2188));
+ normalDistParams.put(4, new Pair <Double, Double> (3.9962, 0.3168));
+ normalDistParams.put(5, new Pair <Double, Double> (4.9550, 0.3863));
+
+ if(probFile != null)
+ {
+ loadProbabilities(probFile);
+ }
+ else
+ {
+ bulkCalculateProbabilities();
+ }
+ }
+
+ public int getScale()
+ {
+ return this.SCALE;
+ }
+
+
+ //do I want to, and how.
+ private void bulkCalculateProbabilities()
+ {
+ //note that the hash GOES SEGMENT: REFLEN
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.OUFrequencyTable#loadProbabilities(java.lang.String)
+ */
+ public void loadProbabilities(String probFile)
+ {
+ try
+ {
+ URL url = getClass().getResource(probFile);
+
+ // System.out.println("Path; " + url.getPath());
+
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ String line = in.readLine();
+
+ String header = null;
+ int segment = -1;
+ HashMap <Integer, BigDecimal []> probsForCurrSegment = null;
+
+ while(line != null)
+ {
+ if(header == null || ! line.contains(","))
+ {
+ if(header != null)
+ {
+ this.probabilities.put(segment, probsForCurrSegment);
+ }
+ else
+ {
+ //System.out.println("header was null");
+ }
+ probsForCurrSegment = new HashMap <Integer, BigDecimal [] >();
+ header = line;
+ segment = Integer.parseInt(header);
+ }
+ else
+ {
+ String [] probabilities = line.split(",");
+
+ if(probabilities.length != 4)
+ throw new Exception ("Probability file has incorrect format");
+
+
+ BigDecimal [] probs = new BigDecimal [probabilities.length - 1];
+
+ int mode = Integer.parseInt(probabilities[0]);
+
+ BigDecimal sumProbs = new BigDecimal("0").setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ for(int i = 1; i < probabilities.length; i++)
+ {
+ probs[i-1] = new BigDecimal(probabilities[i]).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ sumProbs = sumProbs.add(probs[i-1]);
+ }
+
+ if(! sumProbs.equals(new BigDecimal("1").setScale(SCALE, BigDecimal.ROUND_HALF_UP)))
+ {
+ probs[OUFrequencyTable.GREATER_THAN] = probs[OUFrequencyTable.GREATER_THAN].divide(sumProbs, SCALE, BigDecimal.ROUND_HALF_UP) ;
+ probs[OUFrequencyTable.EQUAL_TO] = probs[OUFrequencyTable.EQUAL_TO].divide(sumProbs, SCALE, BigDecimal.ROUND_HALF_UP) ;
+ probs[OUFrequencyTable.LESS_THAN] = probs[OUFrequencyTable.LESS_THAN].divide(sumProbs, SCALE, BigDecimal.ROUND_HALF_UP) ;
+ }
+
+
+ probsForCurrSegment.put(mode, probs);
+ }
+
+ line = in.readLine();
+ }
+
+ //add the last cycle
+ this.probabilities.put(segment, probsForCurrSegment);
+ }
+ catch(NumberFormatException nfe)
+ {
+ nfe.printStackTrace();
+ }
+ catch(IOException ie)
+ {
+ ie.printStackTrace();
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.OUFrequencyTable#getProbabilities(int, int)
+ */
+ public BigDecimal [] getProbabilities(AcaciaLogger logger, HashMap <String, Object> factors, FlowCycler cycler) throws Exception
+ {
+ int flowNumber = (Integer) factors.get(OUFrequencyTable.FLOW_POSITION);
+ int obsMode = (Integer) factors.get(OUFrequencyTable.RLE_LENGTH);
+
+ boolean verbose = false;
+
+ if(flowNumber < 1)
+ return null;
+
+ int flowToSegment = _getSegmentForFlow(flowNumber);
+
+ if(verbose)
+ logger.writeLog("Flow to segment returns: " + flowToSegment, AcaciaLogger.LOG_DEBUG);
+
+ if(! this.probabilities.containsKey(flowToSegment))
+ {
+ this.probabilities.put(flowToSegment, new HashMap <Integer, BigDecimal []>());
+ }
+
+ if(! this.probabilities.get(flowToSegment).containsKey(obsMode))
+ {
+ BigDecimal [] probs = _calculateProbabilitiesHelper(flowToSegment, obsMode);
+
+ this.probabilities.get(flowToSegment).put(obsMode, probs);
+ }
+
+ if(verbose)
+ {
+ logger.writeLog("Attempt to get flow to segment for observed mode: " + obsMode + " in segment: " + flowToSegment + " prob: " + this.probabilities.get(flowToSegment).get(obsMode)[1], AcaciaLogger.LOG_DEBUG);
+ }
+
+ return this.probabilities.get(flowToSegment).get(obsMode);
+ }
+
+
+ //flow numbers outside this method are generally starting from zero
+ /**
+ * _get segment for flow.
+ *
+ * @param flowNumber the flow number
+ * @return the int
+ */
+ public int _getSegmentForFlow(int flowNumber)
+ {
+ if(flowNumber < 0)
+ return INVALID_FLOW;
+
+ return (int) Math.floor(flowNumber / SEGMENT_SIZE) + 1;
+ }
+
+ /**
+ * _calculate probability.
+ *
+ * @param mode the mode
+ * @param segmentNumber the segment number
+ * @return the BigDecimal [] of probabilities, all with scale of 10.
+ */
+ private BigDecimal [] _calculateProbabilitiesHelper(int segmentNumber, int mode)
+ {
+ BigDecimal sd, mean, modeBD;
+
+ //this multiplicative factor was taken from elsewhere...
+ BigDecimal flowEffect = new BigDecimal("0.003").multiply(new BigDecimal(segmentNumber)).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ modeBD = new BigDecimal(mode);
+
+ if(mode >= 6)
+ {
+ mean = new BigDecimal(mode).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ //standard deviation is 0.03 + effect of RefLen + effect of flow position
+ sd = new BigDecimal("0.03494").add(mean.multiply(new BigDecimal("0.06856"))).add(flowEffect);
+ }
+ else
+ {
+ mean = new BigDecimal(this.normalDistParams.get(mode).getFirst()).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ sd = new BigDecimal(this.normalDistParams.get(mode).getSecond()).add(flowEffect).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ }
+
+ NormalDistribution norm = new NormalDistribution(mean.doubleValue(), sd.doubleValue());
+
+ try
+ {
+ //due to rounding...
+ //cumulative probability [X <= x]
+ //so prob under is [X <= MODE - 0.51], and prob over is 1 - prob [X <= MODE + 0.49] (i.e. prob X > MODE + 0.49)
+ BigDecimal lowerBound = modeBD.subtract(new BigDecimal(SUBTRACT_FOR_LB)).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ BigDecimal upperBound = modeBD.add(new BigDecimal(ADD_FOR_UB)).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ BigDecimal probLessThan = new BigDecimal(norm.cumulativeProbability(lowerBound.doubleValue())).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ BigDecimal probMoreThan = new BigDecimal("1").subtract(new BigDecimal(norm.cumulativeProbability(upperBound.doubleValue())).setScale(SCALE, BigDecimal.ROUND_HALF_UP));
+ BigDecimal probEqualTo = new BigDecimal("1").subtract(probLessThan).subtract(probMoreThan).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ BigDecimal summed = probLessThan.add(probEqualTo).add(probMoreThan).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ if(!summed.equals(new BigDecimal("1").setScale(SCALE, BigDecimal.ROUND_HALF_UP)))
+ {
+ probLessThan = probLessThan.divide(summed, SCALE, BigDecimal.ROUND_HALF_UP);
+ probMoreThan = probMoreThan.divide(summed, SCALE, BigDecimal.ROUND_HALF_UP);
+ probEqualTo = probEqualTo.divide(summed, SCALE, BigDecimal.ROUND_HALF_UP);
+ }
+
+ BigDecimal [] probs = {probLessThan, probEqualTo, probMoreThan};
+
+
+
+
+ return probs;
+ }
+ catch(MathIllegalStateException me)
+ {
+ me.getStackTrace();
+ }
+ return null;
+ }
+
+
+ @Override
+ public BigDecimal [] estimateProbability(AcaciaLogger logger, HashMap<String, Object> factors, FlowCycler cycler) throws Exception
+ {
+ int obsMode = (Integer) factors.get(OUFrequencyTable.RLE_LENGTH);
+ int flowNumber = (Integer) factors.get(OUFrequencyTable.FLOW_POSITION);
+ int segmentNumber = this._getSegmentForFlow(flowNumber);
+
+ return this._calculateProbabilitiesHelper(obsMode, segmentNumber);
+ }
+
+ @Override
+ public BigDecimal [] getEmpiricalProbability(AcaciaLogger logger, HashMap<String, Object> factors, FlowCycler cycler) throws Exception
+ {
+ int flowNumber = (Integer) factors.get(OUFrequencyTable.FLOW_POSITION);
+ int obsMode = (Integer) factors.get(OUFrequencyTable.RLE_LENGTH);
+ int segmentNumber = this._getSegmentForFlow(flowNumber);
+
+ if(this.probabilities.containsKey(segmentNumber) && this.probabilities.get(segmentNumber).containsKey(obsMode))
+ {
+ return this.probabilities.get(segmentNumber).get(obsMode);
+ }
+
+ return null;
+ }
+
+ // TESTING
+ public static void main(String [] args)
+ {
+ AcaciaLogger logger = new AcaciaLogger();
+ FlowCycler cycler = new FlowCycler(AcaciaConstants.OPT_FLOW_CYCLE_454, logger);
+
+ try
+ {
+ BalzerOUCallFrequencyTable it = new BalzerOUCallFrequencyTable(AcaciaConstants.FLOWSIM_PROBS_LOCATION);
+
+
+ //probs zero works
+ BigDecimal [] res = it._calculateProbabilitiesHelper(0,1);
+
+ for(int i = 0; i < res.length; i++)
+ System.out.println(res[i]);
+
+ BigDecimal [] res2 = it._calculateProbabilitiesHelper(2,5);
+
+ for(int i = 0; i < res2.length; i++)
+ System.out.println(res2[i]);
+
+ //okay all the get probabilities are tested. Interestingly should cache them so not calculating again.
+ HashMap <String, Object> factors = new HashMap <String, Object>();
+ factors.put(OUFrequencyTable.FLOW_POSITION, 33);
+ factors.put(OUFrequencyTable.RLE_LENGTH, 2);
+
+ //what I was actually looking up is PIC 1 in cycle 1 for reflen 2.
+ BigDecimal [] res4 = it.getProbabilities(logger, factors, cycler);
+
+ System.out.println("Res4: ");
+ for(int i = 0; i < res4.length; i++)
+ System.out.println(res4[i]);
+
+
+ //pretend there is a cycle 12..
+ HashMap <String, Object> factors2 = new HashMap <String, Object>();
+ factors2.put(OUFrequencyTable.FLOW_POSITION, 50);
+ factors2.put(OUFrequencyTable.RLE_LENGTH, 5);
+
+ BigDecimal [] res5 = it.getProbabilities(logger, factors2, cycler);
+
+ for(int i = 0; i < res5.length; i++)
+ System.out.println(res5[i]);
+
+
+ }
+ catch(Exception e)
+ {
+ System.out.println("An exception ocurred: " + e.getMessage());
+ e.printStackTrace();
+
+ }
+ }
+}
+
+
diff --git a/src/pyromaniac/Algorithm/BigDecimalUtils.java b/src/pyromaniac/Algorithm/BigDecimalUtils.java
new file mode 100644
index 0000000..7590ed5
--- /dev/null
+++ b/src/pyromaniac/Algorithm/BigDecimalUtils.java
@@ -0,0 +1,380 @@
+package pyromaniac.Algorithm;
+
+//code taken from dr.math package, https://code.google.com/p/beast-mcmc/
+//for BEAST project
+
+import java.math.BigInteger;
+import java.math.BigDecimal;
+
+/**
+ * Several useful BigDecimal mathematical functions.
+ */
+public class BigDecimalUtils {
+ /**
+ * Compute x^exponent to a given scale. Uses the same
+ * algorithm as class numbercruncher.mathutils.IntPower.
+ * @param x the value x
+ * @param exponent the exponent value
+ * @param scale the desired scale of the result
+ * @return the result value
+ */
+ public static BigDecimal intPower(BigDecimal x, long exponent,
+ int scale)
+ {
+ // If the exponent is negative, compute 1/(x^-exponent).
+ if (exponent < 0) {
+ return BigDecimal.valueOf(1)
+ .divide(intPower(x, -exponent, scale), scale,
+ BigDecimal.ROUND_HALF_EVEN);
+ }
+
+ BigDecimal power = BigDecimal.valueOf(1);
+
+ // Loop to compute value^exponent.
+ while (exponent > 0) {
+
+ // Is the rightmost bit a 1?
+ if ((exponent & 1) == 1) {
+ power = power.multiply(x)
+ .setScale(scale, BigDecimal.ROUND_HALF_EVEN);
+ }
+
+ // Square x and shift exponent 1 bit to the right.
+ x = x.multiply(x)
+ .setScale(scale, BigDecimal.ROUND_HALF_EVEN);
+ exponent >>= 1;
+
+ Thread.yield();
+ }
+
+ return power;
+ }
+
+ /**
+ * Compute the integral root of x to a given scale, x >= 0.
+ * Use Newton's algorithm.
+ * @param x the value of x
+ * @param index the integral root value
+ * @param scale the desired scale of the result
+ * @return the result value
+ */
+ public static BigDecimal intRoot(BigDecimal x, long index,
+ int scale)
+ {
+ // Check that x >= 0.
+ if (x.signum() < 0) {
+ throw new IllegalArgumentException("x < 0");
+ }
+
+ int sp1 = scale + 1;
+ BigDecimal n = x;
+ BigDecimal i = BigDecimal.valueOf(index);
+ BigDecimal im1 = BigDecimal.valueOf(index-1);
+ BigDecimal tolerance = BigDecimal.valueOf(5)
+ .movePointLeft(sp1);
+ BigDecimal xPrev;
+
+ // The initial approximation is x/index.
+ x = x.divide(i, scale, BigDecimal.ROUND_HALF_EVEN);
+
+ // Loop until the approximations converge
+ // (two successive approximations are equal after rounding).
+ do {
+ // x^(index-1)
+ BigDecimal xToIm1 = intPower(x, index-1, sp1);
+
+ // x^index
+ BigDecimal xToI =
+ x.multiply(xToIm1)
+ .setScale(sp1, BigDecimal.ROUND_HALF_EVEN);
+
+ // n + (index-1)*(x^index)
+ BigDecimal numerator =
+ n.add(im1.multiply(xToI))
+ .setScale(sp1, BigDecimal.ROUND_HALF_EVEN);
+
+ // (index*(x^(index-1))
+ BigDecimal denominator =
+ i.multiply(xToIm1)
+ .setScale(sp1, BigDecimal.ROUND_HALF_EVEN);
+
+ // x = (n + (index-1)*(x^index)) / (index*(x^(index-1)))
+ xPrev = x;
+ x = numerator
+ .divide(denominator, sp1, BigDecimal.ROUND_DOWN);
+
+ Thread.yield();
+ } while (x.subtract(xPrev).abs().compareTo(tolerance) > 0);
+
+ return x;
+ }
+
+ /**
+ * Compute e^x to a given scale.
+ * Break x into its whole and fraction parts and
+ * compute (e^(1 + fraction/whole))^whole using Taylor's formula.
+ * @param x the value of x
+ * @param scale the desired scale of the result
+ * @return the result value
+ */
+ public static BigDecimal exp(BigDecimal x, int scale)
+ {
+ // e^0 = 1
+ if (x.signum() == 0) {
+ return BigDecimal.valueOf(1);
+ }
+
+ // If x is negative, return 1/(e^-x).
+ else if (x.signum() == -1) {
+ return BigDecimal.valueOf(1)
+ .divide(exp(x.negate(), scale), scale,
+ BigDecimal.ROUND_HALF_EVEN);
+ }
+
+ // Compute the whole part of x.
+ BigDecimal xWhole = x.setScale(0, BigDecimal.ROUND_DOWN);
+
+ // If there isn't a whole part, compute and return e^x.
+ if (xWhole.signum() == 0) return expTaylor(x, scale);
+
+ // Compute the fraction part of x.
+ BigDecimal xFraction = x.subtract(xWhole);
+
+ // z = 1 + fraction/whole
+ BigDecimal z = BigDecimal.valueOf(1)
+ .add(xFraction.divide(
+ xWhole, scale,
+ BigDecimal.ROUND_HALF_EVEN));
+
+ // t = e^z
+ BigDecimal t = expTaylor(z, scale);
+
+ BigDecimal maxLong = BigDecimal.valueOf(Long.MAX_VALUE);
+ BigDecimal result = BigDecimal.valueOf(1);
+
+ // Compute and return t^whole using intPower().
+ // If whole > Long.MAX_VALUE, then first compute products
+ // of e^Long.MAX_VALUE.
+ while (xWhole.compareTo(maxLong) >= 0) {
+ result = result.multiply(
+ intPower(t, Long.MAX_VALUE, scale))
+ .setScale(scale, BigDecimal.ROUND_HALF_EVEN);
+ xWhole = xWhole.subtract(maxLong);
+
+ Thread.yield();
+ }
+ return result.multiply(intPower(t, xWhole.longValue(), scale))
+ .setScale(scale, BigDecimal.ROUND_HALF_EVEN);
+ }
+
+ /**
+ * Compute e^x to a given scale by the Taylor series.
+ * @param x the value of x
+ * @param scale the desired scale of the result
+ * @return the result value
+ */
+ private static BigDecimal expTaylor(BigDecimal x, int scale)
+ {
+ BigDecimal factorial = BigDecimal.valueOf(1);
+ BigDecimal xPower = x;
+ BigDecimal sumPrev;
+
+ // 1 + x
+ BigDecimal sum = x.add(BigDecimal.valueOf(1));
+
+ // Loop until the sums converge
+ // (two successive sums are equal after rounding).
+ int i = 2;
+ do {
+ // x^i
+ xPower = xPower.multiply(x)
+ .setScale(scale, BigDecimal.ROUND_HALF_EVEN);
+
+ // i!
+ factorial = factorial.multiply(BigDecimal.valueOf(i));
+
+ // x^i/i!
+ BigDecimal term = xPower
+ .divide(factorial, scale,
+ BigDecimal.ROUND_HALF_EVEN);
+
+ // sum = sum + x^i/i!
+ sumPrev = sum;
+ sum = sum.add(term);
+
+ ++i;
+ Thread.yield();
+ } while (sum.compareTo(sumPrev) != 0);
+
+ return sum;
+ }
+
+ /**
+ * Compute the natural logarithm of x to a given scale, x > 0.
+ */
+ public static BigDecimal ln(BigDecimal x, int scale)
+ {
+ // Check that x > 0.
+ if (x.signum() <= 0) {
+ throw new IllegalArgumentException("x <= 0");
+ }
+
+ // The number of digits to the left of the decimal point.
+ int magnitude = x.toString().length() - x.scale() - 1;
+
+ if (magnitude < 3) {
+ return lnNewton(x, scale);
+ }
+
+ // Compute magnitude*ln(x^(1/magnitude)).
+ else {
+
+ // x^(1/magnitude)
+ BigDecimal root = intRoot(x, magnitude, scale);
+
+ // ln(x^(1/magnitude))
+ BigDecimal lnRoot = lnNewton(root, scale);
+
+ // magnitude*ln(x^(1/magnitude))
+ return BigDecimal.valueOf(magnitude).multiply(lnRoot)
+ .setScale(scale, BigDecimal.ROUND_HALF_EVEN);
+ }
+ }
+
+ /**
+ * Compute the natural logarithm of x to a given scale, x > 0.
+ * Use Newton's algorithm.
+ */
+ private static BigDecimal lnNewton(BigDecimal x, int scale)
+ {
+ int sp1 = scale + 1;
+ BigDecimal n = x;
+ BigDecimal term;
+
+ // Convergence tolerance = 5*(10^-(scale+1))
+ BigDecimal tolerance = BigDecimal.valueOf(5)
+ .movePointLeft(sp1);
+
+ // Loop until the approximations converge
+ // (two successive approximations are within the tolerance).
+ do {
+
+ // e^x
+ BigDecimal eToX = exp(x, sp1);
+
+ // (e^x - n)/e^x
+ term = eToX.subtract(n)
+ .divide(eToX, sp1, BigDecimal.ROUND_DOWN);
+
+ // x - (e^x - n)/e^x
+ x = x.subtract(term);
+
+ Thread.yield();
+ } while (term.compareTo(tolerance) > 0);
+
+ return x.setScale(scale, BigDecimal.ROUND_HALF_EVEN);
+ }
+
+ /**
+ * Compute the arctangent of x to a given scale, |x| < 1
+ * @param x the value of x
+ * @param scale the desired scale of the result
+ * @return the result value
+ */
+ public static BigDecimal arctan(BigDecimal x, int scale)
+ {
+ // Check that |x| < 1.
+ if (x.abs().compareTo(BigDecimal.valueOf(1)) >= 0) {
+ throw new IllegalArgumentException("|x| >= 1");
+ }
+
+ // If x is negative, return -arctan(-x).
+ if (x.signum() == -1) {
+ return arctan(x.negate(), scale).negate();
+ }
+ else {
+ return arctanTaylor(x, scale);
+ }
+ }
+
+ /**
+ * Compute the arctangent of x to a given scale
+ * by the Taylor series, |x| < 1
+ * @param x the value of x
+ * @param scale the desired scale of the result
+ * @return the result value
+ */
+ private static BigDecimal arctanTaylor(BigDecimal x, int scale)
+ {
+ int sp1 = scale + 1;
+ int i = 3;
+ boolean addFlag = false;
+
+ BigDecimal power = x;
+ BigDecimal sum = x;
+ BigDecimal term;
+
+ // Convergence tolerance = 5*(10^-(scale+1))
+ BigDecimal tolerance = BigDecimal.valueOf(5)
+ .movePointLeft(sp1);
+
+ // Loop until the approximations converge
+ // (two successive approximations are within the tolerance).
+ do {
+ // x^i
+ power = power.multiply(x).multiply(x)
+ .setScale(sp1, BigDecimal.ROUND_HALF_EVEN);
+
+ // (x^i)/i
+ term = power.divide(BigDecimal.valueOf(i), sp1,
+ BigDecimal.ROUND_HALF_EVEN);
+
+ // sum = sum +- (x^i)/i
+ sum = addFlag ? sum.add(term)
+ : sum.subtract(term);
+
+ i += 2;
+ addFlag = !addFlag;
+
+ Thread.yield();
+ } while (term.compareTo(tolerance) > 0);
+
+ return sum;
+ }
+
+ /**
+ * Compute the square root of x to a given scale, x >= 0.
+ * Use Newton's algorithm.
+ * @param x the value of x
+ * @param scale the desired scale of the result
+ * @return the result value
+ */
+ public static BigDecimal sqrt(BigDecimal x, int scale)
+ {
+ // Check that x >= 0.
+ if (x.signum() < 0) {
+ throw new IllegalArgumentException("x < 0");
+ }
+
+ // n = x*(10^(2*scale))
+ BigInteger n = x.movePointRight(scale << 1).toBigInteger();
+
+ // The first approximation is the upper half of n.
+ int bits = (n.bitLength() + 1) >> 1;
+ BigInteger ix = n.shiftRight(bits);
+ BigInteger ixPrev;
+
+ // Loop until the approximations converge
+ // (two successive approximations are equal after rounding).
+ do {
+ ixPrev = ix;
+
+ // x = (x + n/x)/2
+ ix = ix.add(n.divide(ix)).shiftRight(1);
+
+ Thread.yield();
+ } while (ix.compareTo(ixPrev) != 0);
+
+ return new BigDecimal(ix, scale);
+ }
+}
\ No newline at end of file
diff --git a/src/pyromaniac/Algorithm/BinomialTest.java b/src/pyromaniac/Algorithm/BinomialTest.java
new file mode 100644
index 0000000..129e6ad
--- /dev/null
+++ b/src/pyromaniac/Algorithm/BinomialTest.java
@@ -0,0 +1,120 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import pyromaniac.IO.AcaciaLogger;
+import umontreal.iro.lecuyer.probdist.BinomialDist;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class BinomialTest.
+ */
+public class BinomialTest extends HypothesisTest
+{
+
+ /**
+ * Instantiates a new binomial test.
+ *
+ * @param obsAbove the number of observations above the mode
+ * @param obsBelow the number of observations below the mode
+ * @param obsMode the number observed modal homopolymer length
+ * @param modeLength the mode homopolymer length
+ * @param P the p-value
+ * @param alpha the significance threshold
+ * @param avgFlowPos the average flow position
+ * @param logger the logger
+ * @param verbose the verbose
+ */
+ public BinomialTest(int obsAbove, int obsBelow, int obsMode,int modeLength, double [] P, double alpha, double avgFlowPos, AcaciaLogger logger, boolean verbose)
+ {
+ super(obsAbove, obsBelow, obsMode, modeLength, P, alpha, avgFlowPos, logger, verbose);
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.HypothesisTest#runTest()
+ */
+ public void runTest() throws Exception
+ {
+ if (observationsBelowMode == 0 && observationsAboveMode == 0)
+ {
+ this.p = 1;
+ }
+ else if (alpha > 0 && (observationsAboveMode == observationsAtMode
+ || observationsBelowMode == observationsAtMode))
+ {
+ this.significantAbove = true;
+ this.significantBelow = true;
+ this.p = alpha;
+ }
+ else
+ {
+ double obsErrorFreqAbove = (double) observationsAboveMode;
+ double errorProbFreqAbove = P[2];
+
+ //P(X >= x)
+ BinomialDist binomialDistOvercall = new BinomialDist(this.N, errorProbFreqAbove);
+
+ if(errorProbFreqAbove < 0 || errorProbFreqAbove > 1)
+ {
+ throw new Exception("Obs below: " + this.observationsBelowMode + " Obs above: " + this.observationsAboveMode + " obsMode " + this.observationsAtMode);
+ }
+
+ double pAbove = binomialDistOvercall.barF(obsErrorFreqAbove);
+
+
+ this.p = pAbove; //regardless of significance
+
+ if (this.alpha > 0 )
+ {
+ this.significantAbove = (pAbove <= this.alpha);
+ if(verbose)
+ {
+ logger.writeLog("Significant above: p=" + pAbove + "and alpha= " + this.significantAbove, AcaciaLogger.LOG_DEBUG);
+ }
+ }
+ else
+ {
+ this.significantAbove = false;
+ }
+
+ double obsErrorFreqBelow = (double) observationsBelowMode;
+ double errorProbModeBelow = P[1];
+
+ BinomialDist binomialDistUndercall = new BinomialDist(this.N, errorProbModeBelow);
+
+ double pBelow = binomialDistUndercall.barF(obsErrorFreqBelow);
+
+
+ if (this.alpha > 0 )
+ {
+ this.significantBelow = (pBelow <= this.alpha);
+ if(this.significantBelow)//if significant
+ this.p = pBelow;
+ if(verbose)
+ {
+ logger.writeLog("Significant below: p=" + pBelow + "and alpha= " + this.significantBelow, AcaciaLogger.LOG_DEBUG);
+ }
+ }
+ else
+ {
+ this.significantBelow = false;
+ }
+ }
+ }
+}
diff --git a/src/pyromaniac/Algorithm/ClusterAligner.java b/src/pyromaniac/Algorithm/ClusterAligner.java
new file mode 100644
index 0000000..14f58ba
--- /dev/null
+++ b/src/pyromaniac/Algorithm/ClusterAligner.java
@@ -0,0 +1,60 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import java.io.BufferedWriter;
+import java.util.ArrayDeque;
+import java.util.HashMap;
+import java.util.LinkedList;
+
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Interface ClusterAligner.
+ */
+public interface ClusterAligner
+{
+
+ /**
+ * Generate alignments.
+ *
+ * @param logger the logger
+ * @param settings the settings
+ * @param cluster the cluster
+ * @param consensus the consensus
+ * @param outputHandles the output handles
+ * @param representativeSeqs the representative seqs
+ * @param allResults the all results
+ * @param singletons the singletons
+ * @throws Exception the exception
+ */
+ public void generateAlignments(
+ AcaciaLogger logger,
+ HashMap <String, String> settings,
+ LinkedList <Pyrotag> cluster,
+ String consensus, //consensus from hashmapping
+ HashMap <String, BufferedWriter> outputHandles,
+ HashMap <Pyrotag,Integer> representativeSeqs,
+ ArrayDeque<Pair<RLEAlignmentIndelsOnly, HashMap<Pyrotag, Pair<Integer, Character>>>> allResults,
+ LinkedList <Pyrotag> singletons
+ ) throws Exception;
+}
diff --git a/src/pyromaniac/Algorithm/ClusterGenerator.java b/src/pyromaniac/Algorithm/ClusterGenerator.java
new file mode 100644
index 0000000..578ce55
--- /dev/null
+++ b/src/pyromaniac/Algorithm/ClusterGenerator.java
@@ -0,0 +1,84 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import java.io.BufferedWriter;
+import java.util.HashMap;
+import java.util.LinkedList;
+
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class Clustomatic.
+ */
+public abstract class ClusterGenerator
+{
+
+ /** The initial clusters. */
+ protected HashMap <String, LinkedList <Pyrotag>> initialClusters;
+
+ /** The settings. */
+ protected HashMap <String, String> settings;
+
+ /** The logger. */
+ protected AcaciaLogger logger;
+
+ /** The output handles. */
+ protected HashMap <String, BufferedWriter> outputHandles;
+
+
+ //clustomatic MODIFIES the initialClusters
+ /**
+ * Instantiates a new clustomatic.
+ */
+ public ClusterGenerator()
+ {
+ this.initialClusters = null;
+ this.settings = null;
+ this.logger = null;
+ this.outputHandles = null;
+ }
+
+ /**
+ * Run clustering.
+ *
+ * @throws Exception the exception
+ */
+ public abstract void runClustering() throws Exception;
+
+ /**
+ * Inits the fundamental variables.
+ *
+ * @param initialClusters the initial clusters
+ * @param settings the settings
+ * @param logger the logger
+ * @param outputHandles the output handles
+ */
+ public void initialise(HashMap <String, LinkedList <Pyrotag>> initialClusters,
+ HashMap <String, String> settings, AcaciaLogger logger, HashMap <String, BufferedWriter> outputHandles)
+
+ {
+ this.initialClusters = initialClusters;
+ this.settings = settings;
+ this.logger = logger;
+ this.outputHandles = outputHandles;
+ }
+}
diff --git a/src/pyromaniac/Algorithm/CoarseAlignSplitter.java b/src/pyromaniac/Algorithm/CoarseAlignSplitter.java
new file mode 100644
index 0000000..8c2c4b1
--- /dev/null
+++ b/src/pyromaniac/Algorithm/CoarseAlignSplitter.java
@@ -0,0 +1,443 @@
+package pyromaniac.Algorithm;
+
+import java.io.BufferedWriter;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import pyromaniac.AcaciaConstants;
+import pyromaniac.Algorithm.RLEAlignmentIndelsOnly.AlignmentColumn;
+import pyromaniac.DataStructures.DistanceMatrix;
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.IO.AcaciaLogger;
+
+public class CoarseAlignSplitter
+{
+ private static CoarseAlignSplitter instance;
+
+
+ private CoarseAlignSplitter()
+ {
+ }
+
+ public static CoarseAlignSplitter getInstance()
+ {
+ if(instance == null)
+ instance = new CoarseAlignSplitter();
+ return instance;
+ }
+
+ public HashSet <HashSet<Pyrotag>> scanAlignmentForObviousDeviations
+ (
+ AcaciaLogger logger,
+ HashMap<String, String> settings,
+ HashMap<String, BufferedWriter> outputHandles,
+ Pair<RLEAlignmentIndelsOnly, HashMap<Pyrotag, Pair<Integer, Character>>> alignRes,
+ FlowCycler fc
+ )
+ {
+ RLEAlignmentIndelsOnly motherAlign = alignRes.getFirst();
+ HashMap <Pyrotag, Pair <Integer, Character>> motherFlow = alignRes.getSecond();
+
+ HashSet <Pyrotag> toProcess = motherAlign.getAllTags(); //grabs the results of the last run
+
+ //running over ThreadedAlignment... always clone the flow hash, in preparation for error correction later
+ //these are here should we change the way that the clustering value is predicted.
+ //HashMap <Pyrotag, Pair <Integer,Character>> flowMap = AcaciaEngine.getEngine().cloneFlowHash(motherFlow); //this cloning operation is unavoidable unless huge changes made.
+ //OUFrequencyTable table = AcaciaEngine.getErrorModel(settings);
+
+ Iterator <AlignmentColumn> it = motherAlign.iterator();
+
+ int numNodes = 0;
+
+ char [] bases = {'A', 'T', 'G', 'C'};
+
+ while(it.hasNext())
+ {
+ AlignmentColumn curr = it.next();
+
+ numNodes++;
+
+ for(char base : bases)
+ {
+ AlignmentColumn ac = curr.getInsertionCorrespondingTo(base);
+ if(ac != null)
+ {
+ numNodes++;
+ }
+ }
+ }
+
+ double [][] readCounts = new double [toProcess.size()][numNodes];
+
+ for(int i = 0; i < readCounts.length; i++)
+ {
+ for(int j = 0; j < readCounts[i].length; j++)
+ {
+ readCounts[i][j] = -1;
+ }
+ }
+
+ HashMap <Pyrotag, Integer> tagToRow = new HashMap <Pyrotag, Integer> ();
+ HashMap <Integer, Pyrotag> rowToTag = new HashMap <Integer, Pyrotag> ();
+
+ int colIndex = 0;
+ int tagCounter = 0;
+
+
+ it = motherAlign.iterator();
+
+ while(it.hasNext())
+ {
+ AlignmentColumn curr = it.next();
+ HashMap <Integer, HashSet <Pyrotag>> tags = curr.getHPLengthToTags(toProcess);
+
+ for(int length: tags.keySet())
+ {
+ for(Pyrotag p: tags.get(length))
+ {
+ if(! tagToRow.containsKey(p))
+ {
+ tagToRow.put(p, tagCounter);
+ rowToTag.put(tagCounter, p);
+ tagCounter++;
+ }
+
+ int relRow = tagToRow.get(p);
+ readCounts[relRow][colIndex] = length;
+ }
+ }
+ colIndex++;
+
+ for(char base: bases)
+ {
+ AlignmentColumn ac = curr.getInsertionCorrespondingTo(base);
+ if(ac != null)
+ {
+ HashMap <Integer, HashSet <Pyrotag>> innerTags = ac.getHPLengthToTags(toProcess);
+ for(int length: innerTags.keySet())
+ {
+ for(Pyrotag p: innerTags.get(length))
+ {
+ if(! tagToRow.containsKey(p))
+ {
+ tagToRow.put(p, tagCounter);
+ rowToTag.put(tagCounter, p);
+ tagCounter++;
+ }
+
+ int relRow = tagToRow.get(p);
+ readCounts[relRow][colIndex] = length;
+ }
+ }
+ colIndex++;
+ }
+ }
+ }
+ return clusterAndSplit(settings, readCounts, rowToTag);
+ }
+
+ //might have to mask later columns too.
+ private HashSet <HashSet <Pyrotag>> clusterAndSplit(HashMap <String, String> settings, double [][] hpMatrix, HashMap <Integer, Pyrotag> rowToTag)
+ {
+ int [] numNoObs = new int [hpMatrix[0].length];
+ HashSet <Integer> toMask = new HashSet <Integer>();
+
+ for(int col = 0; col < hpMatrix[0].length; col++)
+ {
+ for(int row = 0; row < hpMatrix.length; row++)
+ {
+ double value = hpMatrix[row][col];
+
+ if(value < 0)
+ {
+ numNoObs[col] = numNoObs[col] + 1;
+ value = 0;
+ }
+ hpMatrix[row][col] = Math.sqrt(value);
+ }
+
+ if(((double)numNoObs[col] / hpMatrix.length) > 0)
+ {
+ toMask.add(col);
+ }
+ }
+
+ DistanceMatrix dm = null;
+
+ try {
+ dm = calculateScaledEuclideanDistanceForReads(hpMatrix, toMask, rowToTag);
+ } catch (Exception e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ return completeLinkageClustering(settings, dm, rowToTag);
+ }
+
+
+ //get alot less observations with zero dist than in R.
+ public DistanceMatrix calculateScaledEuclideanDistanceForReads(double[][] hpMatrix, HashSet<Integer> toMask, HashMap<Integer, Pyrotag> rowToTag) throws Exception
+ {
+ //have every reason to believe the standard deviation is correct.
+ for(int col = 0; col < hpMatrix[0].length; col++)
+ {
+ double stdDevForCol = this.calculateStandardDeviationForColumn(hpMatrix, col);
+ for(int row = 0; row < hpMatrix.length; row++)
+ {
+ hpMatrix[row][col] = hpMatrix[row][col] * stdDevForCol;
+ }
+ }
+
+ DistanceMatrix dm = new DistanceMatrix(hpMatrix.length); //DM for reads
+
+ for(int row1 = 0; row1 < hpMatrix.length - 1; row1++)
+ {
+ for(int row2 = row1 + 1; row2 < hpMatrix.length; row2++)
+ {
+ double sum = 0;
+
+ for(int col = 0; col < hpMatrix[row1].length; col++)
+ {
+ if(toMask != null && toMask.contains(col))
+ {
+ sum += 0;
+ }
+ else
+ {
+ sum += (hpMatrix[row1][col] - hpMatrix[row2][col]) * (hpMatrix[row1][col] - hpMatrix[row2][col]);
+ }
+ }
+
+ double dist = Math.sqrt(sum);
+ dm.setValue(row1, row2, dist);
+ }
+ }
+ return dm;
+ }
+
+ private double calculateStandardDeviationForColumn(double [][] matrix, int col)
+ {
+ double sumX = 0;
+ double xMinusXBar = 0;
+
+ for(int i = 0; i < matrix.length; i++)
+ {
+ sumX += matrix[i][col];
+ }
+
+ double mean = sumX / (double)matrix.length;
+
+ for(int i = 0; i < matrix.length; i++)
+ {
+ xMinusXBar += Math.pow(matrix[i][col] - mean,2);
+ }
+
+ double sd = Math.sqrt((1.0 / (((double)matrix.length) - 1.0) * xMinusXBar));
+ return sd;
+ }
+
+ //this does it by column.
+ public DistanceMatrix calculatePearsonsForColumns(double [][] matrix)
+ {
+ DistanceMatrix dm = new DistanceMatrix(matrix[0].length);
+ //first lets see if any of the features are correlated
+
+ //so we have correlations between features...
+ for(int col = 0; col < matrix[0].length; col++)
+ {
+ for(int innerCol = col + 1; innerCol < (matrix[0].length - 1); innerCol++)
+ {
+ double SumXprodY = 0;
+ double sumX = 0;
+ double sumY = 0;
+ double sumXSquared = 0;
+ double sumYSquared = 0;
+ double n = matrix.length;
+
+ for(int row = 0; row < matrix.length; row++)
+ {
+ SumXprodY += (matrix[row][col] * matrix[row][innerCol]);
+ sumX += matrix[row][col];
+ sumY += matrix[row][innerCol];
+ sumXSquared += (matrix[row][col] * matrix[row][col]);
+ sumYSquared += (matrix[row][innerCol] * matrix[row][innerCol]);
+ }
+
+ double numerator = ((n * SumXprodY) - (sumX * sumY));
+ double denominator = (Math.sqrt((n * sumXSquared) - (sumX * sumX)) * Math.sqrt((n * sumYSquared) - (sumY * sumY)));
+ double ri = (denominator == 0.0)? 0 : numerator / denominator;
+
+
+
+ try
+ {
+ dm.setValue(col, innerCol, ri);
+ }
+ catch(Exception e)
+ {
+ System.out.println(e.getMessage());
+ System.exit(1);
+ }
+ }
+ }
+ return dm;
+ }
+
+ public HashSet<HashSet<Pyrotag>> completeLinkageClustering (HashMap <String, String> settings, DistanceMatrix dm, HashMap <Integer, Pyrotag> rowToTag)
+ {
+ int numObs = dm.getNumberOfObservations();
+
+ HashMap <Integer, HashSet <Integer>> newClusters = new HashMap <Integer, HashSet <Integer>>();
+
+ double maxDist = Double.parseDouble(settings.get(AcaciaConstants.OPT_MAX_COMPLETE_LINKAGE_DIST));
+
+ for(int i = 0; i < numObs; i++)
+ {
+ boolean distBelowThresh = false;
+ //problem with complete linkage is order of recruitment.
+
+ for(int j = i + 1; j < numObs; j++)
+ {
+ if(dm.getValue(i, j) <= maxDist)
+ {
+ distBelowThresh = true;
+ if(newClusters.containsKey(i) && newClusters.containsKey(j))
+ {
+ if(newClusters.get(i) != newClusters.get(j) && canBeRecruited(dm, newClusters.get(i), newClusters.get(j), maxDist))
+ {
+ HashSet <Integer> newCluster = new HashSet <Integer>();
+ newCluster.addAll(newClusters.get(i));
+ newCluster.addAll(newClusters.get(j));
+ for(int tag: newCluster)
+ {
+ newClusters.put(tag, newCluster);
+ }
+ }
+ }
+ else if (newClusters.containsKey(i))
+ {
+ HashSet <Integer> singleton = new HashSet <Integer>();
+ singleton.add(j);
+ if(canBeRecruited(dm, newClusters.get(i), singleton, maxDist))
+ {
+ newClusters.get(i).add(j);
+ newClusters.put(j, newClusters.get(i));
+ }
+ else
+ {
+ newClusters.put(j, singleton);
+ }
+ }
+ else if (newClusters.containsKey(j))
+ {
+ HashSet <Integer> singleton = new HashSet <Integer>();
+ singleton.add(i);
+ if(canBeRecruited(dm, newClusters.get(j), singleton, maxDist))
+ {
+ newClusters.get(j).add(i);
+ newClusters.put(i, newClusters.get(j));
+ }
+ else
+ {
+ newClusters.put(i, singleton);
+ }
+ }
+ else
+ {
+ HashSet <Integer> newCluster = new HashSet <Integer>();
+ newCluster.add(i);
+ newCluster.add(j);
+ newClusters.put(i, newCluster);
+ newClusters.put(j, newCluster);
+ }
+ }
+ }
+
+ if(! distBelowThresh &! newClusters.containsKey(i))
+ {
+ HashSet <Integer> singleton = new HashSet <Integer>();
+ singleton.add(i);
+ newClusters.put(i, singleton);
+ }
+ }
+
+ HashSet <HashSet <Pyrotag>> res = new HashSet <HashSet <Pyrotag>>();
+ HashSet <HashSet <Integer>> processed = new HashSet <HashSet <Integer>>();
+
+ for(int read: newClusters.keySet())
+ {
+ if(! processed.contains(newClusters.get(read)))
+ {
+ HashSet <Pyrotag> tagCluster = new HashSet <Pyrotag>();
+
+ for(int member : newClusters.get(read))
+ {
+ tagCluster.add(rowToTag.get(member));
+ }
+ res.add(tagCluster);
+ processed.add(newClusters.get(read));
+ }
+ }
+
+ return res;
+ }
+
+ public boolean canBeRecruited(DistanceMatrix dm, HashSet <Integer> firstCluster, HashSet <Integer> secondCluster, double maxDist)
+ {
+ for(int i: firstCluster)
+ {
+ for(int j: secondCluster)
+ {
+ if(dm.getValue(i, j) > maxDist)
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
+
+ public DistanceMatrix calculatePearsonsForRows(double [][] matrix)
+ {
+ DistanceMatrix dm = new DistanceMatrix(matrix.length);
+ //first lets see if any of the features are correlated
+ //so we have correlations between features...
+ for(int row = 0; row < matrix.length; row++)
+ {
+ for(int innerRow = row + 1; innerRow < (matrix.length - 1); innerRow++)
+ {
+ double SumXprodY = 0;
+ double sumX = 0;
+ double sumY = 0;
+ double sumXSquared = 0;
+ double sumYSquared = 0;
+ double n = matrix.length;
+
+ for(int col = 0; col < matrix[0].length; col++)
+ {
+ SumXprodY += (matrix[row][col] * matrix[innerRow][col]);
+ sumX += matrix[row][col];
+ sumY += matrix[innerRow][col];
+ sumXSquared += (matrix[row][col] * matrix[row][col]);
+ sumYSquared += (matrix[innerRow][col] * matrix[innerRow][col]);
+ }
+
+ double ri = ((n * SumXprodY) - (sumX * sumY)) / (Math.sqrt((n * sumXSquared) - (sumX * sumX)) * Math.sqrt((n * sumYSquared) - (sumY * sumY)));
+ try
+ {
+ dm.setValue(row, innerRow, ri);
+ }
+ catch(Exception e)
+ {
+ System.out.println("An error occurred: " + e.getMessage());
+ // System.exit(1);
+ }
+ }
+ }
+ return dm;
+ }
+}
diff --git a/src/pyromaniac/Algorithm/ConsensusGenerator.java b/src/pyromaniac/Algorithm/ConsensusGenerator.java
new file mode 100644
index 0000000..b221288
--- /dev/null
+++ b/src/pyromaniac/Algorithm/ConsensusGenerator.java
@@ -0,0 +1,61 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+package pyromaniac.Algorithm;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.DataStructures.PatriciaTrie;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Interface ConsensusGenerator.
+ */
+public interface ConsensusGenerator
+{
+
+ /**
+ * Generate consensus.
+ *
+ * @param logger the logger
+ * @param settings the settings
+ * @param ta the ta
+ * @param tagsToProcess the tags to process
+ * @param consensusClusters the consensus clusters
+ * @param tagToCurrPosInFlow the tag to curr pos in flow
+ * @param varyIdentically the vary identically
+ * @return the divergent tag result
+ * @throws Exception the exception
+ */
+ public DivergentTagResult generateConsensus
+ (
+ AcaciaLogger logger,
+ HashMap<String, String> settings,
+ RLEAlignmentIndelsOnly ta,
+ HashSet <Pyrotag> tagsToProcess,
+ LinkedList <HashSet <Pyrotag>> consensusClusters,
+ HashMap<Pyrotag, Pair<Integer, Character>> tagToCurrPosInFlow,
+ FlowCycler cycler,
+ boolean varyIdentically
+ ) throws Exception;
+}
\ No newline at end of file
diff --git a/src/pyromaniac/Algorithm/ConsensusGeneratorLocalTests.java b/src/pyromaniac/Algorithm/ConsensusGeneratorLocalTests.java
new file mode 100644
index 0000000..002fcde
--- /dev/null
+++ b/src/pyromaniac/Algorithm/ConsensusGeneratorLocalTests.java
@@ -0,0 +1,1034 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import java.math.BigDecimal;
+import java.math.RoundingMode;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+
+import pyromaniac.AcaciaConstants;
+import pyromaniac.AcaciaEngine;
+import pyromaniac.Algorithm.RLEAlignmentIndelsOnly.AlignmentColumn;
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.DataStructures.PatriciaTrie;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class ConsensusGeneratorLocalTests.
+ */
+public class ConsensusGeneratorLocalTests implements ConsensusGenerator
+{
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.ConsensusGenerator#generateConsensus(pyromaniac.IO.AcaciaLogger, java.util.HashMap, pyromaniac.Algorithm.ThreadedAlignment, java.util.LinkedList, java.util.HashMap, boolean)
+ */
+
+ //at return returns unprocessed tags,
+ public UnprocessedPyrotagResult generateConsensus
+ (
+ AcaciaLogger logger,
+ HashMap<String, String> settings,
+ RLEAlignmentIndelsOnly ta,
+ HashSet <Pyrotag> tagsToProcess,
+ LinkedList <HashSet <Pyrotag>> consensusClusters,
+ HashMap<Pyrotag, Pair<Integer, Character>> tagToCurrPosInFlow,
+ FlowCycler cycler,
+ boolean varyIdentically) throws Exception
+ {
+ if(tagsToProcess.size() == 1)
+ {
+ consensusClusters.add(tagsToProcess);
+ return null;
+ }
+
+ OUFrequencyTable table = AcaciaEngine.getErrorModel(logger, settings);
+
+ //go through corrected branches here!!!
+ double thresholdPValue = AcaciaEngine.getEngine().parseSignificanceThreshold(settings.get(AcaciaConstants.OPT_SIGNIFICANCE_LEVEL));
+
+
+ int alignmentCounter = 0;
+ Iterator <AlignmentColumn> it = ta.iterator();
+ int numSignificant = 0;
+
+ int columnIndex = 0;
+
+ //option is to record the number of transgressions of a particular pyrotag? And also co-varying things?
+ HashMap <Pyrotag, HashMap <Pyrotag, Integer>> varyingTogether = new HashMap <Pyrotag, HashMap <Pyrotag, Integer>> ();
+ HashMap <Pyrotag, Integer> numDifferences = new HashMap <Pyrotag, Integer>();
+
+ //iterate through all the alignment positions, identify those that differ from the mode at each point, and record that they 'differ'
+ //ignore sequences that appear to have disagreed already ??
+
+ int numTests = 0;
+ int initialSize = -1;
+ AlignmentColumn premBreak = null;
+
+ Integer minFlowTrunc = this.getMinFlowTrunc(settings);
+ Double minReadRepTruncation = AcaciaEngine.getEngine().getMinReadRepTruncation(settings);
+
+
+ while(it.hasNext())
+ {
+ AlignmentColumn ac = it.next();
+ alignmentCounter++;
+
+ char lastChar;
+
+ if(columnIndex != 0)
+ {
+ if(initialSize == -1)
+ {
+ initialSize = ac.getTags().size();
+ }
+
+ double prop = (double)ac.getTags().size() / (double)initialSize;
+
+ HypothesisTest test = processAlignmentColumn(logger, settings, tagToCurrPosInFlow, ac,
+ tagsToProcess, table, thresholdPValue, varyingTogether, numDifferences, varyIdentically, false, ta, cycler);
+
+
+ if(test != null && (minReadRepTruncation != null && minFlowTrunc != null && prop < minReadRepTruncation && minFlowTrunc <= test.getAvgFlowPos()))
+ {
+ premBreak = ac;
+ break;
+ }
+
+ if(test != null)
+ numTests++;
+
+ if(test != null && (test.isSignificantAbove() || test.isSignificantBelow()))
+ {
+ numSignificant++;
+ }
+
+ lastChar = ac.getValue();
+ }
+ else
+ {
+ lastChar = Pyrotag.CYCLE_START; //this is the easy way to do it, assuming the last char for any of the sequences
+ //is unlikely to be consistent.
+ }
+
+ columnIndex++;
+
+ char [] validBases = {'A', 'T', 'G', 'C'};
+
+ for(char base: validBases)
+ {
+ AlignmentColumn insert = ac.getInsertionCorrespondingTo(base);
+
+ if(insert != null)
+ {
+ HypothesisTest testInner = processAlignmentColumn(logger, settings, tagToCurrPosInFlow, insert,
+ tagsToProcess, table, thresholdPValue, varyingTogether, numDifferences, varyIdentically, false, ta, cycler);
+
+ //at the end of the alignment
+ if(testInner == null)
+ continue;
+
+ numTests++;
+
+ if(testInner.isSignificantAbove() || testInner.isSignificantBelow())
+ {
+ numSignificant++;
+ }
+ }
+
+ }
+ }
+
+ //caveat is that if I change the alignment algorithm, such that it tolerates double insertions, this will break.
+ /*
+ //iterate through the insertion columns
+ AlignmentColumn firstInsert = ac.nextInsertionGivenLastFlow(lastChar);
+ AlignmentColumn lastInsert = firstInsert;
+
+ do
+ {
+ if(lastInsert == null)
+ break;
+
+
+ HypothesisTest testInner = processAlignmentColumn(logger, settings, tagToCurrPosInFlow, lastInsert,
+ tagsToProcess, table, thresholdPValue, varyingTogether, numDifferences, varyIdentically, false, ta);
+
+ //at the end of the alignment
+ if(testInner == null)
+ continue;
+
+ numTests++;
+
+ lastInsert = ac.nextInsertionGivenLastFlow(lastInsert.getValue());
+
+ if(testInner.isSignificantAbove() || testInner.isSignificantBelow())
+ {
+ numSignificant++;
+ }
+ }
+ while(lastInsert != firstInsert);
+ }
+ */
+
+ if(numSignificant == 0)
+ {
+ consensusClusters.add(tagsToProcess);
+ return null;
+ }
+
+ HashSet <Pyrotag> tagsToRemove = new HashSet <Pyrotag>();
+
+ if(numSignificant > 0)
+ {
+ for(Pyrotag p: numDifferences.keySet()) //there is no consensus? In this case? Seems really grossly inefficient...
+ {
+ //bugfix: changed numDifferences.contains to tagsToProcess.contains
+ if(tagsToProcess.contains(p) && numDifferences.get(p) >= 1)
+ {
+ tagsToRemove.add(p); //tagsToRemove contains non-consensus tags, puts everything in there for vary identically.
+ }
+ }
+ }
+
+ //consensus for this cluster. But if in vary identically, this should be empty.
+ HashSet <Pyrotag> tagsToKeep = new HashSet <Pyrotag>();
+
+ for(Pyrotag p: tagsToProcess)
+ {
+ if(! tagsToRemove.contains(p))
+ {
+ tagsToKeep.add(p);
+ }
+ }
+
+ //this is the stuff up here... won't be created here using varyIdentically...
+ if(tagsToKeep.size() > 0)
+ {
+ consensusClusters.add(tagsToKeep);
+ }
+
+ UnprocessedPyrotagResult utr = new UnprocessedPyrotagResult(tagsToRemove, varyingTogether, numDifferences);
+ return utr;
+ }
+
+ /**
+ * The Class UnprocessedPyrotagResult.
+ */
+ public class UnprocessedPyrotagResult implements DivergentTagResult
+ {
+
+ /** The tags. */
+ HashSet <Pyrotag> tags;
+
+ /** The varying together. */
+ HashMap <Pyrotag, HashMap <Pyrotag, Integer>> varyingTogether;
+
+ /** The num disagreements. */
+ HashMap <Pyrotag, Integer> numDisagreements;
+
+ /**
+ * Instantiates a new unprocessed pyrotag result.
+ *
+ * @param tags the tags
+ * @param varyingTogether the varying together
+ * @param numDisagreements the num disagreements
+ */
+ public UnprocessedPyrotagResult(HashSet <Pyrotag> tags, HashMap <Pyrotag, HashMap <Pyrotag, Integer>> varyingTogether,
+ HashMap <Pyrotag, Integer> numDisagreements)
+ {
+ this.tags = tags;
+ this.varyingTogether = varyingTogether;
+ this.numDisagreements = numDisagreements;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.DivergentTagResult#getTags()
+ */
+ public HashSet <Pyrotag> getTags()
+ {
+ return this.tags;
+ }
+
+ /**
+ * Gets the varying together.
+ *
+ * @return the varying together
+ */
+ public HashMap <Pyrotag, HashMap <Pyrotag, Integer>> getVaryingTogether()
+ {
+ return this.varyingTogether;
+ }
+
+ /**
+ * Gets the num disagreements.
+ *
+ * @return the num disagreements
+ */
+ public HashMap <Pyrotag, Integer> getNumDisagreements()
+ {
+ return this.numDisagreements;
+ }
+ }
+
+ //this will generate the set of sub clusters that need to be processed
+ /**
+ * Generate clusters from vary together.
+ *
+ * @param logger the logger
+ * @param settings the settings
+ * @param consensusClusters the consensus clusters
+ * @param upr the upr
+ * @param verbose the verbose
+ * @return the linked list
+ * @throws Exception the exception
+ */
+ public LinkedList <HashSet<Pyrotag>> generateClustersFromVaryTogether
+ (
+ AcaciaLogger logger,
+ HashMap<String, String> settings,
+ LinkedList <HashSet <Pyrotag>> consensusClusters,
+ UnprocessedPyrotagResult upr,
+ boolean verbose
+ ) throws Exception
+ {
+ //this function is allowing a read to be both a member of consensus clusters and be processed again
+
+ HashMap <Pyrotag, HashSet <Pyrotag>> otherBranches = new HashMap <Pyrotag, HashSet <Pyrotag>> ();
+ HashSet <Pyrotag> goingSolo = new HashSet <Pyrotag>();
+
+ //identify which ones varied in the same direction,they can go into a new set.
+ //ideally, if one sequence does not vary with another all the time, or the set is too small.. should be broken up.
+ //this should be for the initial split only
+
+ for(Pyrotag p: upr.getTags()) //changing from varyingTogether to tags to Remove
+ {
+ boolean processed = false;
+
+ //how can processed evaluate to false, but the data be inside branches?
+ for(Pyrotag second : upr.getTags())
+ {
+ if(second == p)
+ continue; //ignore me for now!
+
+ if(goingSolo.contains(second))
+ {
+ continue;
+ }
+
+ //this checks whether p or second should be put in the same cluster, if not, moves to the next pyrotag.
+ //if neither varies with the other, that is silly.
+
+ int numDiff = 0;
+
+ if(upr.getVaryingTogether().containsKey(p) && upr.getVaryingTogether().get(p).containsKey(second))
+ {
+ numDiff = upr.getVaryingTogether().get(p).get(second);
+ }
+ else if(upr.getVaryingTogether().containsKey(second) && upr.getVaryingTogether().get(second).containsKey(p))
+ {
+ numDiff = upr.getVaryingTogether().get(second).get(p);
+ }
+ else
+ {
+ continue; //next inner pyrotag.
+ }
+
+
+
+ if(
+ numDiff != upr.getNumDisagreements().get(p) ||
+ numDiff != upr.getNumDisagreements().get(second)
+ )
+ {
+ continue;//both have to have the same number of differences... so complete linkage.
+ }
+
+
+ //they are not already clustered.
+ if(!otherBranches.containsKey(p) && !otherBranches.containsKey(second))
+ {
+ //create a new set of tags containing both p and second...
+ HashSet <Pyrotag> newBranch = new HashSet <Pyrotag>();
+ newBranch.add(p);
+ newBranch.add(second);
+ otherBranches.put(p, newBranch);
+ otherBranches.put(second, newBranch);
+
+ }
+ else if(otherBranches.containsKey(p) && otherBranches.containsKey(second))
+ {
+ //check they are in the same cluster... otherwise, they possibly should be merged.
+ if(otherBranches.get(p) != otherBranches.get(second))
+ {
+ HashSet <Pyrotag> merged = new HashSet <Pyrotag>();
+ merged.addAll(otherBranches.get(p));
+ merged.addAll(otherBranches.get(second));
+
+ for(Pyrotag pMerged: merged)
+ {
+ otherBranches.remove(pMerged);
+ otherBranches.put(pMerged, merged);
+ }
+ }
+ }
+ else if(otherBranches.containsKey(p))
+ {
+ otherBranches.get(p).add(second);
+ otherBranches.put(second,otherBranches.get(p));
+ }
+ else if(otherBranches.containsKey(second))
+ {
+ otherBranches.get(second).add(p);
+ otherBranches.put(p, otherBranches.get(second));
+ }
+
+ //processed = true; still not sure why this didnt work
+ }
+
+ if(goingSolo.contains(p) || otherBranches.containsKey(p))
+ {
+ processed = true;
+ }
+
+ //never varied with anything
+ if(!processed)
+ {
+ HashSet <Pyrotag> soloP = new HashSet<Pyrotag>();
+ soloP.add(p);
+ goingSolo.add(p);
+ consensusClusters.add(soloP);
+ }
+ }
+
+ //detects all the new branches...
+ int numNewBranches = 0;
+
+ HashSet <HashSet <Pyrotag>> seenBefore = new HashSet <HashSet <Pyrotag>>();
+
+ for(Pyrotag p: otherBranches.keySet())
+ {
+ if(! seenBefore.contains(otherBranches.get(p)))
+ {
+ numNewBranches++;
+ seenBefore.add(otherBranches.get(p));
+ }
+ }
+
+ //does this clean anything up
+ otherBranches.clear();
+ otherBranches = null;
+
+ LinkedList <HashSet <Pyrotag>> retVal = new LinkedList <HashSet<Pyrotag>>();
+ retVal.addAll(seenBefore) ;
+
+ return retVal;
+ }
+
+ //assumes singletons have been removed.
+ /**
+ * Generate trie from unprocessed tags.
+ *
+ * @param logger the logger
+ * @param tagsRemaining the tags remaining
+ * @return the patricia trie
+ * @throws Exception the exception
+ */
+ public PatriciaTrie generateTrieFromUnprocessedTags
+ (
+ AcaciaLogger logger,
+ HashSet <Pyrotag> tagsRemaining
+ ) throws Exception
+ {
+ assert(tagsRemaining.size() > 0);
+
+ PatriciaTrie trie = new PatriciaTrie();
+ for(Pyrotag p: tagsRemaining)
+ {
+ trie.insertString(new String(p.getProcessedString()), p);
+ }
+ return trie;
+ }
+
+
+
+
+ //singleton pattern
+ /**
+ * Gets the single instance of ConsensusGeneratorLocalTests.
+ *
+ * @return single instance of ConsensusGeneratorLocalTests
+ */
+ public static ConsensusGeneratorLocalTests getInstance()
+ {
+ return ConsensusGeneratorHolder.getInstance();
+ }
+
+ /**
+ * The Class ConsensusGeneratorHolder.
+ */
+ public static class ConsensusGeneratorHolder
+ {
+
+ /** The Constant INSTANCE. */
+ private static final ConsensusGeneratorLocalTests INSTANCE = new ConsensusGeneratorLocalTests();
+
+ /**
+ * Gets the single instance of ConsensusGeneratorHolder.
+ *
+ * @return single instance of ConsensusGeneratorHolder
+ */
+ public static ConsensusGeneratorLocalTests getInstance()
+ {
+ return ConsensusGeneratorHolder.INSTANCE;
+ }
+ }
+
+
+ /**
+ * Gets the min flow trunc.
+ *
+ * @param settings the settings
+ * @return the min flow trunc
+ */
+ private Integer getMinFlowTrunc(HashMap<String, String> settings)
+ {
+ if(settings.get(AcaciaConstants.OPT_MIN_FLOW_TRUNCATION) != null)
+ {
+ return Integer.parseInt(settings.get(AcaciaConstants.OPT_MIN_FLOW_TRUNCATION));
+ }
+ return null;
+ }
+
+ //prepares the variables for hypothesis testing on an individual column
+ /**
+ * Process alignment column.
+ *
+ * @param logger the logger
+ * @param settings the settings
+ * @param tagToCurrPosInFlow the tag to curr pos in flow
+ * @param ac the ac
+ * @param tagsInCluster the tags in cluster
+ * @param table the table
+ * @param significanceLevel the significance level
+ * @param varyingTogether the varying together
+ * @param numDifferences the num differences
+ * @param varyIdentically the vary identically
+ * @param verbose the verbose
+ * @param ta the ta
+ * @return the hypothesis test
+ * @throws Exception the exception
+ */
+
+ //can guarantee that numDifferences will be populated if varyIdentically, but not varyingTogether.
+
+ //fix this
+ private HypothesisTest processAlignmentColumn(
+ AcaciaLogger logger,
+ HashMap <String, String> settings,
+ HashMap <Pyrotag, Pair<Integer, Character>> tagToCurrPosInFlow,
+ AlignmentColumn ac,
+ HashSet <Pyrotag> tagsInCluster,
+ OUFrequencyTable table,
+ double significanceLevel,
+ HashMap<Pyrotag, HashMap<Pyrotag, Integer>> varyingTogether,
+ HashMap<Pyrotag, Integer> numDifferences,
+ boolean varyIdentically,
+ boolean verbose,
+ RLEAlignmentIndelsOnly ta,
+ FlowCycler cycler
+
+ ) throws Exception
+ {
+
+ HashMap <Integer, HashSet <Pyrotag>> observationsAtPosition = ac.getHPLengthToTags(tagsInCluster);
+
+
+ int mode = -1;
+ int modeFreq = -1;
+
+ HashMap <Integer, Integer> flowToNumReads = new HashMap <Integer, Integer>();
+
+ char currValue = ac.getValue();
+
+ if(verbose)
+ {
+ logger.writeLog("Curr value: " + currValue, AcaciaLogger.LOG_DEBUG);
+ }
+
+ //all columns should be processed... so the flow should be correct...
+ for(Integer obsLength: observationsAtPosition.keySet())
+ {
+
+ //get tags that have the observed length.
+ HashSet <Pyrotag> tagsWithObsLength = observationsAtPosition.get(obsLength);
+
+ //if the size is greater than the curr freq, than this must be the mode...
+ if(tagsWithObsLength.size() > modeFreq)
+ {
+ modeFreq = tagsWithObsLength.size();
+ mode = obsLength;
+ }
+
+ //for each of the pyrotags with this length
+ for(Pyrotag p : tagsWithObsLength)
+ {
+
+ //get previous position in flow
+ Pair <Integer, Character> prevPosInFlow = tagToCurrPosInFlow.get(p);
+
+ int prevPos = prevPosInFlow.getFirst();
+
+ if(verbose)
+ {
+ logger.writeLog("Previous position: " + prevPos + "with char <" + prevPosInFlow.getSecond() + "> for read " + p.getID(), AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("Has observed length : " + obsLength + " for read " + p.getID(), AcaciaLogger.LOG_DEBUG);
+ }
+
+ //calculate the distance between the flows.
+ //how is it possible that the previous base is the same as the curr base?
+
+
+ int currPosInFlow = prevPosInFlow.getFirst();
+
+ if(obsLength > 0)
+ {
+ int dist = p.getFlowCycler().minPossibleFlowsBetweenFlowPosXAndCharY(prevPos, currValue);
+
+
+ if(verbose)
+ {
+ logger.writeLog("Dist is " + dist, AcaciaLogger.LOG_DEBUG);
+ }
+
+ currPosInFlow += dist;
+ tagToCurrPosInFlow.put(p, new Pair <Integer, Character> (currPosInFlow, currValue)); //update
+ }
+
+ //initialise flowToNumReads if not defined
+ if(!flowToNumReads.containsKey(currPosInFlow))
+ {
+ flowToNumReads.put(currPosInFlow, 0);
+ }
+
+ //increment flowToNumReads
+ flowToNumReads.put(currPosInFlow, flowToNumReads.get(currPosInFlow) + 1);
+ }
+ }
+
+ if(mode == -1)
+ {
+ return null;
+ }
+
+
+ int obsBelow = 0;
+ int obsAbove = 0;
+
+ for(Integer obsLength : observationsAtPosition.keySet())
+ {
+ if(obsLength > mode)
+ {
+ obsAbove += observationsAtPosition.get(obsLength).size();
+ }
+ else if(obsLength < mode)
+ {
+ obsBelow += observationsAtPosition.get(obsLength).size();
+ }
+ }
+
+ if(verbose)
+ {
+ logger.writeLog("About to do test: mode is " + mode + ", obs below: " + obsBelow + " obsAbove: " + obsAbove + " obsAt: " + modeFreq, AcaciaLogger.LOG_DEBUG);
+
+ logger.writeLog("Flow position to number of reads: ", AcaciaLogger.LOG_DEBUG);
+
+ for(int position: flowToNumReads.keySet())
+ {
+ logger.writeLog("There are " + flowToNumReads.get(position) + " reads with flow position: " + position, AcaciaLogger.LOG_DEBUG);
+ }
+
+ }
+
+ boolean verbose2 = verbose; //too much information from run test for significance
+
+
+ //perform test for significance, get result
+ HypothesisTest res = this._runTestForSignificance(logger, mode, obsBelow,obsAbove, modeFreq,
+ flowToNumReads, table, significanceLevel, cycler, verbose2);
+
+
+ //to handle introduced deletions for very small clusters.
+ //overrides the result of the hypothesis test
+ if(modeFreq + obsAbove + obsBelow == 2 && modeFreq != 2)
+ {
+ boolean splitIfDifferent = Boolean.parseBoolean(settings.get(AcaciaConstants.OPT_SIGNIFICANT_WHEN_TWO));
+ if(splitIfDifferent)
+ {
+ if(obsAbove > 0)
+ {
+ res.significantAbove = true;
+ }
+ else
+ {
+ res.significantBelow = true;
+ }
+ }
+ }
+
+ if(verbose)
+ {
+ logger.writeLog("Sig above: " + res.isSignificantAbove(), AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("Sig below: " + res.isSignificantBelow(), AcaciaLogger.LOG_DEBUG);
+
+ }
+
+ if(verbose && (res.isSignificantAbove() || res.isSignificantBelow()))
+ {
+ logger.writeLog("Nucleotide: " + ac.getValue(), AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("Mode is " + mode + " with freq: " + modeFreq, AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("Above: " + obsAbove + ", Below: " + obsBelow + " at ", AcaciaLogger.LOG_DEBUG);
+
+ }
+
+ ArrayList <Pyrotag> obsAboveMode = new ArrayList <Pyrotag>();
+ ArrayList <Pyrotag> obsBelowMode = new ArrayList <Pyrotag>();
+
+ if(verbose)
+ logger.writeLog("Iterating through observations to count numDifferences", AcaciaLogger.LOG_DEBUG);
+
+ for(Integer obsLength: observationsAtPosition.keySet())
+ {
+ if(obsLength != mode)
+ {
+ for(Pyrotag p: observationsAtPosition.get(obsLength))
+ {
+ //three things need to be done in this loop
+ if((obsLength > mode && res.isSignificantAbove()) || (obsLength < mode && res.isSignificantBelow()))
+ {
+ if(! numDifferences.containsKey(p))
+ {
+ numDifferences.put(p, 0);
+ }
+ numDifferences.put(p, numDifferences.get(p) + 1);
+ }
+
+ //for the other bit.
+ if(obsLength < mode)
+ {
+ obsBelowMode.add(p);
+ }
+ else if (obsLength > mode)
+ {
+ obsAboveMode.add(p);
+ }
+ }
+ }
+ }
+
+ if(varyIdentically)
+ return res;
+
+ //else we record whether they varied together above or below the mode.
+
+ if(verbose)
+ logger.writeLog("Running the code varying together", AcaciaLogger.LOG_DEBUG);
+
+ _varyingTogether(varyingTogether, obsBelowMode);
+ _varyingTogether(varyingTogether, obsAboveMode);
+
+ if(verbose)
+ logger.writeLog("Returning from hypothesis testing", AcaciaLogger.LOG_DEBUG);
+
+ return res;
+ }
+
+ //populates the varying together hash
+ /**
+ * _varying together.
+ *
+ * @param varyingTogether the varying together
+ * @param tags the tags
+ */
+ private void _varyingTogether(HashMap<Pyrotag, HashMap<Pyrotag, Integer>> varyingTogether, ArrayList <Pyrotag> tags)
+ {
+ for(int i = 0; i < tags.size(); i++)
+ {
+ Pyrotag p = tags.get(i);
+
+ for(int j = i + 1; j < tags.size(); j++)
+ {
+ Pyrotag pInner = tags.get(j);
+
+ if(varyingTogether.containsKey(p))
+ {
+ if(varyingTogether.get(p).containsKey(pInner))
+ {
+ varyingTogether.get(p).put(pInner, varyingTogether.get(p).get(pInner) + 1);
+ }
+ else
+ {
+ varyingTogether.get(p).put(pInner, 1);
+ }
+ }
+ else if (varyingTogether.containsKey(pInner))
+ {
+ if(varyingTogether.get(pInner).containsKey(p))
+ {
+ varyingTogether.get(pInner).put(p, varyingTogether.get(pInner).get(p) + 1);
+ }
+ else
+ {
+ varyingTogether.get(pInner).put(p, 1);
+ }
+ }
+ else //just put it in p.
+ {
+ varyingTogether.put(p, new HashMap <Pyrotag, Integer>());
+ varyingTogether.get(p).put(pInner, 1);
+ }
+
+ /*
+ if(! varyingTogether.containsKey(p))
+ {
+ varyingTogether.put(p, new HashMap <Pyrotag, Integer>());
+ }
+ if(! varyingTogether.containsKey(pInner))
+ {
+ varyingTogether.put(pInner, new HashMap <Pyrotag, Integer>());
+ }
+
+ if(! varyingTogether.get(p).containsKey(pInner))
+ {
+ varyingTogether.get(p).put(pInner, 0);
+ }
+ if(! varyingTogether.get(pInner).containsKey(p))
+ {
+ varyingTogether.get(pInner).put(p, 0);
+ }
+
+ varyingTogether.get(p).put(pInner, varyingTogether.get(p).get(pInner) + 1);
+ varyingTogether.get(pInner).put(p, varyingTogether.get(pInner).get(p) + 1);
+ */
+ }
+
+ /*
+ //new code, check first that p is in there.
+ if(!varyingTogether.containsKey(p))
+ {
+ varyingTogether.put(p, new HashMap <Pyrotag, Integer>());
+ }
+ */
+
+ /*
+ //even though this will never happen
+ if(! varyingTogether.get(p).containsKey(p))
+ {
+ varyingTogether.get(p).put(p, 0);
+ }
+ varyingTogether.get(p).put(p, varyingTogether.get(p).get(p) + 1); //so we now record whether a sequence varies with itself!
+ */
+ }
+ }
+
+ /**
+ * _run test for significance.
+ *
+ * @param logger the logger
+ * @param modeVal the mode val
+ * @param obsBelow the obs below
+ * @param obsAbove the obs above
+ * @param obsAt the obs at
+ * @param flowPosToFreq the flow pos to freq
+ * @param table the table
+ * @param thresholdPValue the threshold p value
+ * @param verbose the verbose
+ * @return the hypothesis test
+ * @throws Exception the exception
+ */
+ private HypothesisTest _runTestForSignificance(
+ AcaciaLogger logger,
+ int modeVal,
+ int obsBelow,
+ int obsAbove,
+ int obsAt,
+ HashMap <Integer, Integer> flowPosToFreq,
+ OUFrequencyTable table,
+ double thresholdPValue,
+ FlowCycler cycler,
+ boolean verbose) throws Exception
+ {
+
+ BigDecimal [] weightedP = {new BigDecimal(0), new BigDecimal(0),new BigDecimal(0)};
+
+ double flowSum = 0.0;
+ double numSeqs = 0.0;
+
+ //okay things might be relevant
+ //flow position, position in cycle, base, rle length, are all things that relate
+
+
+ HashMap <String, Object> probFactors = new HashMap <String, Object>();
+ probFactors.put(OUFrequencyTable.RLE_LENGTH, modeVal);
+
+ double weightedSum = 0;
+
+ StringBuilder sb = new StringBuilder(); //for DEBUG
+
+ for(Integer flowPos: flowPosToFreq.keySet())
+ {
+ //replace this every time, to save on hashmap construction
+ probFactors.put(OUFrequencyTable.FLOW_POSITION, flowPos);
+
+
+
+ BigDecimal freq = new BigDecimal(flowPosToFreq.get(flowPos));
+
+
+ //double check this behaviour, but need to round to a certain number of dec. places
+
+ BigDecimal sumObs = new BigDecimal(obsBelow + obsAt + obsAbove);
+ BigDecimal prop = freq.divide(sumObs,table.getScale(), BigDecimal.ROUND_HALF_UP);
+
+
+ sb.append("Flowpos: " + flowPos + " freq " + freq + " seq proportion: " + prop.doubleValue() + "\n");
+
+ flowSum += (freq.doubleValue() * flowPos);
+ numSeqs += freq.doubleValue();
+
+ BigDecimal [] oldP = table.getProbabilities(logger, probFactors, cycler);
+
+ for(BigDecimal bd: oldP)
+ {
+ sb.append(bd + "\n");
+ }
+
+ //double [] oldP = table.getProbabilities(modeVal, flowPos);
+ BigDecimal [] rearrangedP = new BigDecimal [] {oldP[OUFrequencyTable.EQUAL_TO],
+ oldP[OUFrequencyTable.LESS_THAN], oldP[OUFrequencyTable.GREATER_THAN]};
+
+ // It is weighted because sequences will be at different
+ // positions in the flow. Therefore... the probabilities need to be weighted by the proportion of reads which are
+ // at that flow segment.
+
+ BigDecimal sumOld = new BigDecimal("0").setScale(table.getScale(), BigDecimal.ROUND_HALF_UP);
+
+ for(int i= 0; i < weightedP.length; i++)
+ {
+ sumOld = sumOld.add(rearrangedP[i]);
+ sb.append("Rearrangedp [" + i + "] = " + rearrangedP[i] + "\n");
+ weightedP[i] = weightedP[i].add(prop.multiply(rearrangedP[i]).setScale(table.getScale(), BigDecimal.ROUND_HALF_UP));
+ sb.append("Weighted [" + i + "] = " + weightedP[i].doubleValue() + "\n");
+ }
+
+ sb.append("Sum old: " + sumOld + "\n");
+ }
+
+ BigDecimal sum = new BigDecimal("0");
+ for(int i = 0;i < weightedP.length; i++)
+ {
+ sum = sum.add(weightedP[i]);
+ }
+
+ if(! sum.equals(new BigDecimal("1").setScale(table.getScale(), BigDecimal.ROUND_HALF_UP)))
+ {
+ weightedP[0] = weightedP[0].divide(sum, table.getScale(), BigDecimal.ROUND_HALF_UP);
+ weightedP[1] = weightedP[1].divide(sum, table.getScale(), BigDecimal.ROUND_HALF_UP);
+ weightedP[2] = weightedP[2].divide(sum, table.getScale(), BigDecimal.ROUND_HALF_UP);
+ }
+
+
+ double [] preciseWeighted = new double [3];
+ for(int i = 0; i < preciseWeighted.length; i++)
+ {
+ preciseWeighted[i] = weightedP[i].doubleValue();
+
+ if(preciseWeighted[i] < 0)
+ {
+ System.out.println(sb);
+ throw new Exception("Weighted value was less than zero: " + preciseWeighted[i] + " , big decimal : " + weightedP[i]);
+
+ }
+
+ }
+
+
+ probFactors = null; //clean up
+
+ double avgFlow = flowSum / numSeqs;
+
+ HypothesisTest ht = null;
+ int minSize = 100;
+
+
+ //TODO: fix this
+ for(int i = 0; i < weightedP.length; i++)
+ {
+ int expected = (int) (weightedP[i].doubleValue() * (obsAbove + obsBelow + obsAt));
+
+ if(expected < minSize)
+ {
+ minSize = expected;
+ }
+ }
+
+ //only way we could be doing 'worse' is if the binomial is less sensitive.
+ if(minSize < 5) //minimum size in any category is less than the golden number
+ {
+ if(verbose)
+ System.out.println("Running binomial");
+ ht = new BinomialTest(obsAbove, obsBelow, obsAt, modeVal, preciseWeighted, thresholdPValue, avgFlow, logger, verbose);
+ }
+ else
+ {
+ if(verbose)
+ System.out.println("Running multinomial");
+ // One-sided multinomial test of significance
+ ht = new MultinomialOneSidedTest(obsAbove, obsBelow, obsAt, modeVal, preciseWeighted, thresholdPValue, avgFlow, logger, verbose);
+ }
+
+ try
+ {
+ ht.runTest();
+ }
+ catch(Exception e)
+ {
+ double localsum = 0;
+ for(double prob: preciseWeighted)
+ {
+ System.out.println("Prob: " + prob);
+ localsum+= prob;
+ }
+
+ System.out.println("Sum was " + localsum);
+ System.out.println(e.getMessage());
+ e.printStackTrace();
+
+ }
+
+
+ return ht;
+ }
+
+}
diff --git a/src/pyromaniac/Algorithm/DivergentTagResult.java b/src/pyromaniac/Algorithm/DivergentTagResult.java
new file mode 100644
index 0000000..588b3ac
--- /dev/null
+++ b/src/pyromaniac/Algorithm/DivergentTagResult.java
@@ -0,0 +1,20 @@
+package pyromaniac.Algorithm;
+
+import java.util.HashSet;
+import pyromaniac.DataStructures.Pyrotag;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Interface DivergentTagResult.
+ */
+public interface DivergentTagResult
+{
+
+ /**
+ * Gets the tags.
+ *
+ * @return the tags
+ */
+ public HashSet <Pyrotag> getTags();
+
+}
diff --git a/src/pyromaniac/Algorithm/HypothesisTest.java b/src/pyromaniac/Algorithm/HypothesisTest.java
new file mode 100644
index 0000000..ccfcfe4
--- /dev/null
+++ b/src/pyromaniac/Algorithm/HypothesisTest.java
@@ -0,0 +1,159 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class HypothesisTest.
+ */
+public abstract class HypothesisTest
+{
+
+ /** The observations above mode. */
+ protected int observationsAboveMode;
+
+ /** The observations below mode. */
+ protected int observationsBelowMode;
+
+ /** The observations at mode. */
+ protected int observationsAtMode;
+
+ /** The mode length. */
+ protected int modeLength;
+
+ /** The avg flow pos. */
+ private double avgFlowPos;
+
+ /** The N. */
+ protected int N;
+
+ /** The P. */
+ protected double [] P;
+
+ /** The p. */
+ protected double p;
+
+ /** The logger. */
+ protected AcaciaLogger logger;
+
+ /** The alpha. */
+ protected double alpha;
+
+ /** The verbose. */
+ boolean verbose;
+
+ /** The significant above. */
+ protected boolean significantAbove;
+
+ /** The significant below. */
+ protected boolean significantBelow;
+
+ /**
+ * Instantiates a new hypothesis test.
+ *
+ * @param obsAbove the obs above
+ * @param obsBelow the obs below
+ * @param obsMode the obs mode
+ * @param modeLength the mode length
+ * @param P the p
+ * @param alpha the alpha
+ * @param avgFlowPos the avg flow pos
+ * @param logger the logger
+ * @param verbose the verbose
+ */
+ public HypothesisTest(int obsAbove, int obsBelow, int obsMode,int modeLength, double [] P, double alpha, double avgFlowPos, AcaciaLogger logger, boolean verbose)
+ {
+ this.observationsAboveMode = obsAbove;
+ this.observationsBelowMode = obsBelow;
+ this.observationsAtMode = obsMode;
+ this.modeLength = modeLength;
+ this.P = P;
+ this.p = -1;
+ this.logger = logger;
+ this.alpha = alpha;
+ this.N = this.observationsAboveMode + this.observationsBelowMode + this.observationsAtMode;
+ this.verbose = verbose;
+ this.significantAbove = false;
+ this.significantBelow = false;
+ this.setAvgFlowPos(avgFlowPos);
+ }
+
+ /**
+ * Checks if is significant above.
+ *
+ * @return true, if is significant above
+ */
+ public boolean isSignificantAbove() {
+ return significantAbove;
+ }
+
+ /**
+ * Sets the significant above.
+ *
+ * @param significantAbove the new significant above
+ */
+ public void setSignificantAbove(boolean significantAbove) {
+ this.significantAbove = significantAbove;
+ }
+
+ /**
+ * Checks if is significant below.
+ *
+ * @return true, if is significant below
+ */
+ public boolean isSignificantBelow() {
+ return significantBelow;
+ }
+
+ /**
+ * Sets the significant below.
+ *
+ * @param significantBelow the new significant below
+ */
+ public void setSignificantBelow(boolean significantBelow) {
+ this.significantBelow = significantBelow;
+ }
+
+ /**
+ * Run test.
+ *
+ * @throws Exception the exception
+ */
+ public abstract void runTest() throws Exception;
+
+ /**
+ * Sets the avg flow pos.
+ *
+ * @param avgFlowPos the new avg flow pos
+ */
+ public void setAvgFlowPos(double avgFlowPos) {
+ this.avgFlowPos = avgFlowPos;
+ }
+
+ /**
+ * Gets the avg flow pos.
+ *
+ * @return the avg flow pos
+ */
+ public double getAvgFlowPos() {
+ return avgFlowPos;
+ }
+}
diff --git a/src/pyromaniac/Algorithm/IonTorrentOUCallFrequencyTable.java b/src/pyromaniac/Algorithm/IonTorrentOUCallFrequencyTable.java
new file mode 100644
index 0000000..09e4fc3
--- /dev/null
+++ b/src/pyromaniac/Algorithm/IonTorrentOUCallFrequencyTable.java
@@ -0,0 +1,561 @@
+package pyromaniac.Algorithm;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.math.BigDecimal;
+import java.math.MathContext;
+import java.math.RoundingMode;
+import java.net.URL;
+import java.util.HashMap;
+
+import pyromaniac.AcaciaConstants;
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.IO.AcaciaLogger;
+
+//rename to table
+public class IonTorrentOUCallFrequencyTable implements OUFrequencyTable
+{
+ private NestedHash myProbs;
+ private HashMap <String, BigDecimal> coeffZeroH;
+ private HashMap <String, Pair <BigDecimal, BigDecimal>> coeffOneH;
+ private HashMap <String, Pair <BigDecimal, BigDecimal>> coeffOtherH;
+
+ private static final int maxPreLoadCycles = 8;
+ private static final int maxPreLoadHPLen = 6;
+ private static final int SCALE = 12;
+
+
+ public int getScale()
+ {
+ return this.SCALE;
+ }
+
+
+
+ public IonTorrentOUCallFrequencyTable(HashMap <String, String> settings, AcaciaLogger logger, String probFile, String coeffZero, String coeffOne, String coeffOther) throws Exception
+ {
+ this.myProbs = new NestedHash();
+
+ this.coeffZeroH = new HashMap <String, BigDecimal>();
+ this.coeffOneH = new HashMap <String, Pair <BigDecimal, BigDecimal>>();
+ this.coeffOtherH = new HashMap <String, Pair <BigDecimal, BigDecimal>>();
+
+ loadCoeff(coeffZero, coeffOne, coeffOther);
+
+ if(probFile == null)
+ {
+ bulkCalculateProbabilities(settings, logger);
+ }
+ else
+ {
+ loadProbabilities(probFile);
+ }
+ }
+
+ private void loadCoeff(String coeffZero, String coeffOne, String coeffOther) throws Exception
+ {
+ URL url = getClass().getResource(coeffZero);
+
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ //BufferedReader in = new BufferedReader(new FileReader(coeffZero));
+
+ String line = in.readLine();
+ while(line != null)
+ {
+ // System.out.println("Reading: " + line);
+ line = line.replace("\"", "");
+
+ String [] split = line.split(",");
+
+ if(split[0].equals("(Intercept)"))
+ {
+ coeffZeroH.put("Intercept", new BigDecimal(split[1]));
+ }
+ else
+ {
+ coeffZeroH.put(split[0], new BigDecimal(split[1]));
+ }
+ line = in.readLine();
+ }
+
+ //manually put this in, as there is no 'coefficient' corresponding to baseline PIC0
+ coeffZeroH.put("PIC0", new BigDecimal("0"));
+
+ //this is a multinomial for ones
+ url = getClass().getResource(coeffOne);
+
+ // System.out.println("Path; " + url.getPath());
+
+ in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ //in = new BufferedReader(new FileReader(coeffOne));
+
+ line = in.readLine();
+
+ while(line != null)
+ {
+ line = line.replace("\"", "");
+ // System.out.println("Reading " + line);
+ String [] split = line.split(",");
+
+ //format: variable, under, over
+ if(split[0].equals("(Intercept)"))
+ {
+ coeffOneH.put("Intercept", new Pair<BigDecimal, BigDecimal> (new BigDecimal(split[1]), new BigDecimal(split[2])));
+ }
+ else
+ {
+ coeffOneH.put(split[0], new Pair<BigDecimal, BigDecimal> (new BigDecimal(split[1]), new BigDecimal(split[2])));
+ }
+ line = in.readLine();
+ }
+
+ //manually put this in, as there is no 'coefficient' corresponding to baseline PIC0
+ coeffOneH.put("PIC0", new Pair <BigDecimal, BigDecimal>(new BigDecimal("0"), new BigDecimal("0")));
+
+ //this is the multinomial for others
+
+ url = getClass().getResource(coeffOther);
+
+ // System.out.println("Path; " + url.getPath());
+
+ in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ //in = new BufferedReader(new FileReader(coeffOther));
+
+ line = in.readLine();
+
+ while(line != null)
+ {
+ line = line.replace("\"", "");
+ // System.out.println("Reading " + line);
+ String [] split = line.split(",");
+ if(split[0].equals("(Intercept)"))
+ {
+ coeffOtherH.put("Intercept", new Pair<BigDecimal, BigDecimal> (new BigDecimal(split[1]), new BigDecimal(split[2])));
+ }
+ else
+ {
+ coeffOtherH.put(split[0], new Pair<BigDecimal, BigDecimal> (new BigDecimal(split[1]), new BigDecimal(split[2])));
+ }
+ line = in.readLine();
+ }
+ //manually put these in, as there is no 'coefficients' corresponding to baseline PIC0
+ coeffOtherH.put("PIC0", new Pair <BigDecimal, BigDecimal>(new BigDecimal("0"),new BigDecimal("0")));
+ coeffOtherH.put("Cycle:PIC0", new Pair <BigDecimal, BigDecimal>(new BigDecimal("0"), new BigDecimal("0")));
+ coeffOtherH.put("RefLen:PIC0", new Pair <BigDecimal, BigDecimal>(new BigDecimal("0"), new BigDecimal("0")));
+ }
+
+ @Override
+ public void loadProbabilities(String probFile)
+ {
+ try
+ {
+ URL url = getClass().getResource(probFile);
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ //TESTING
+ //BufferedReader in = new BufferedReader(new FileReader(probFile));
+
+ String header = in.readLine();
+
+ if(header.split(",").length != 6)
+ {
+ throw new Exception("Call probabilities does not have six columns as expected");
+ }
+
+ String line = in.readLine();
+
+ while(line != null)
+ {
+ String [] fields = line.split(",");
+
+ int mode = Integer.parseInt(fields[0]);
+ int cycleNumber = Integer.parseInt(fields[1]);
+ int flowInCycleNumber = Integer.parseInt(fields[2]);
+
+ BigDecimal lessThan = new BigDecimal(fields[3]).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ BigDecimal equalTo = new BigDecimal(fields[4]).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ BigDecimal moreThan = new BigDecimal(fields[5]).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ BigDecimal summed = lessThan.add(equalTo).add(moreThan).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ //attempt to fix rounding errors (large ones) due to R precision.
+ if(! summed.equals(new BigDecimal(1).setScale(SCALE, BigDecimal.ROUND_HALF_UP)))
+ {
+ //R flow arithemetic may result in prob > 1. So, take it out of the equal to class.
+ lessThan = lessThan.divide(summed, SCALE, BigDecimal.ROUND_HALF_EVEN);
+ equalTo = equalTo.divide(summed, SCALE, BigDecimal.ROUND_HALF_EVEN);
+ moreThan = moreThan.divide(summed, SCALE, BigDecimal.ROUND_HALF_EVEN);
+ }
+
+ BigDecimal [] probs = {lessThan, equalTo, moreThan};
+ this.myProbs.put(mode,cycleNumber, flowInCycleNumber, probs);
+ line = in.readLine();
+ }
+ }
+ catch(NumberFormatException nfe)
+ {
+ nfe.printStackTrace();
+ }
+ catch(IOException ie)
+ {
+ ie.printStackTrace();
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ public void bulkCalculateProbabilities(HashMap <String, String> settings, AcaciaLogger logger) throws Exception
+ {
+ String flowCycle = settings.get(AcaciaConstants.OPT_FLOW_CYCLE_ION_TORRENT);
+
+ for(int i = 0; i <= maxPreLoadHPLen ;i++)
+ {
+ for(int j = 0; j < maxPreLoadCycles; j++)
+ {
+ for (int k = 0; k < flowCycle.length(); k++)
+ {
+ BigDecimal [] probs = _calculateProbabilitiesHelper(i, j, k);
+ this.myProbs.put(i, j, k, probs);
+ }
+ }
+ }
+ }
+
+
+ public BigDecimal [] calculateProbabilities(AcaciaLogger logger, HashMap <String, Object> factors, FlowCycler cycler) throws Exception
+ {
+ int flowPosition = (Integer)factors.get(OUFrequencyTable.FLOW_POSITION);
+ int cycleNumber = cycler.flowPositionToCycleNumber(flowPosition);
+ int posInCycle = cycler.flowPositionToPosInCycle(flowPosition);
+ int obsMode = (Integer)factors.get(OUFrequencyTable.RLE_LENGTH);
+
+ return _calculateProbabilitiesHelper(obsMode, cycleNumber, posInCycle);
+ }
+
+ public BigDecimal [] _calculateProbabilitiesHelper(int obsMode, int cycleNumber, int posInCycle) throws Exception
+ {
+ //need to calculate probability for zero
+ //need to calculate probability for one
+ //need to calculate probability for more than one
+ BigDecimal [] res;
+ switch(obsMode)
+ {
+ case 0:
+ res = calculateProbsZero(cycleNumber, posInCycle);
+ break;
+ case 1:
+ res = calculateProbsOne(cycleNumber, posInCycle);
+ break;
+ default:
+ res = calculateProbsAll(obsMode, cycleNumber, posInCycle);
+ break;
+ }
+
+ BigDecimal sum = new BigDecimal("0");
+ sum = sum.add(res[0].add(res[1].add(res[2]))).setScale(SCALE);
+
+ if(! sum.equals(new BigDecimal("1").setScale(SCALE)))
+ {
+ res[0] = res[0].divide(sum, SCALE, BigDecimal.ROUND_HALF_EVEN);
+ res[1] = res[1].divide(sum, SCALE, BigDecimal.ROUND_HALF_EVEN);
+ res[2] = res[2].divide(sum, SCALE, BigDecimal.ROUND_HALF_EVEN);
+ }
+
+ return res;
+ }
+
+
+ private BigDecimal [] calculateProbsZero (int cycleNumber, int posInCycle) throws Exception
+ {
+ //to do the binomial model
+ BigDecimal PICCoef = coeffZeroH.get("PIC" + posInCycle);
+ BigDecimal cycleCoef = coeffZeroH.get("Cycle");
+ BigDecimal intercept = coeffZeroH.get("Intercept");
+ BigDecimal cyc = new BigDecimal(cycleNumber);
+
+ BigDecimal probOfOvercall = new BigDecimal("1").divide(
+ new BigDecimal("1").add(new BigDecimal("1").divide(
+ new BigDecimal(Math.exp(intercept.add(PICCoef).add(cycleCoef.multiply(cyc)).doubleValue())), SCALE, BigDecimal.ROUND_HALF_EVEN)),
+ SCALE, BigDecimal.ROUND_HALF_EVEN);
+
+ BigDecimal [] probabilities = {new BigDecimal("0"), new BigDecimal("1").subtract(probOfOvercall), probOfOvercall};
+
+ return probabilities;
+ }
+
+ private BigDecimal [] calculateProbsOne (int cycleNumber, int posInCycle) throws Exception
+ {
+ String picString = "PIC" + posInCycle;
+ Pair <BigDecimal, BigDecimal> intercept = this.coeffOneH.get("Intercept");
+ Pair <BigDecimal, BigDecimal> PICCoef = this.coeffOneH.get(picString);
+ Pair <BigDecimal, BigDecimal> cycleCoef = this.coeffOneH.get("Cycle");
+ BigDecimal cyc = new BigDecimal(cycleNumber);
+
+ BigDecimal predUnder = intercept.getFirst().add(cycleCoef.getFirst().multiply(cyc)).add(PICCoef.getFirst());
+ BigDecimal predOver = intercept.getSecond().add(cycleCoef.getSecond().multiply(cyc)).add(PICCoef.getSecond());
+ BigDecimal predAt = new BigDecimal("1").subtract(predUnder).subtract(predOver);
+
+ BigDecimal probUnder = BigDecimalUtils.exp(predUnder, SCALE).divide((BigDecimalUtils.exp(predUnder, SCALE).add(BigDecimalUtils.exp(predOver, SCALE)).add(BigDecimalUtils.exp(predAt, SCALE))), SCALE, BigDecimal.ROUND_HALF_UP);
+
+ BigDecimal probOver = BigDecimalUtils.exp(predOver, SCALE).divide(BigDecimalUtils.exp(predUnder, SCALE).add(BigDecimalUtils.exp(predOver, SCALE)).add(BigDecimalUtils.exp(predAt, SCALE)), SCALE, BigDecimal.ROUND_HALF_UP);
+ //this is a multinomial
+ return new BigDecimal [] {probUnder, new BigDecimal("1.0").subtract(probUnder).subtract(probOver).setScale(SCALE, BigDecimal.ROUND_HALF_UP), probOver}; //make sure this is returning the correct order.
+ }
+
+ private BigDecimal [] calculateProbsAll(int obsMode, int cycleNumber, int posInCycle)
+ {
+ String picString = "PIC" + posInCycle;
+
+ BigDecimal obsModeBD = new BigDecimal(obsMode);
+ BigDecimal cycleNumberBD = new BigDecimal(cycleNumber);
+
+ //all the coefficient values
+ Pair <BigDecimal, BigDecimal> intercept = this.coeffOtherH.get("Intercept");
+ Pair <BigDecimal, BigDecimal> PICCoef = this.coeffOtherH.get(picString);
+ Pair <BigDecimal, BigDecimal> cycleCoef = this.coeffOtherH.get("Cycle");
+ Pair <BigDecimal, BigDecimal> reflenCoef = this.coeffOtherH.get("RefLen");
+ Pair <BigDecimal, BigDecimal> reflenSquaredCoef = this.coeffOtherH.get("I(RefLen^2)");
+ Pair <BigDecimal, BigDecimal> cyclePICCoef = this.coeffOtherH.get("Cycle:"+picString);
+ Pair <BigDecimal, BigDecimal> reflenCycleCoef = this.coeffOtherH.get("RefLen:Cycle");
+ Pair <BigDecimal,BigDecimal> reflenPICCoef = this.coeffOtherH.get("RefLen:"+ picString);
+
+ BigDecimal predUnder =
+ intercept.getFirst().add(
+ reflenCoef.getFirst().multiply(obsModeBD)).add(
+ BigDecimalUtils.intPower(obsModeBD, 2, SCALE).multiply(reflenSquaredCoef.getFirst())).add(
+ cycleCoef.getFirst().multiply(cycleNumberBD)).add(
+ PICCoef.getFirst()).add(
+ cyclePICCoef.getFirst().multiply(cycleNumberBD)).add(
+ reflenCycleCoef.getFirst().multiply(obsModeBD).multiply(cycleNumberBD)).add(
+ reflenPICCoef.getFirst().multiply(obsModeBD));
+
+ BigDecimal predOver =
+ intercept.getSecond().add(
+ reflenCoef.getSecond().multiply(obsModeBD)).add(
+ BigDecimalUtils.intPower(obsModeBD, 2, SCALE).multiply(reflenSquaredCoef.getSecond())).add(
+ cycleCoef.getSecond().multiply(cycleNumberBD)).add(
+ PICCoef.getSecond()).add(
+ cyclePICCoef.getSecond().multiply(cycleNumberBD)).add(
+ reflenCycleCoef.getSecond().multiply(obsModeBD).multiply(cycleNumberBD)).add(
+ reflenPICCoef.getSecond().multiply(obsModeBD));
+
+ BigDecimal predAt = new BigDecimal("0");
+ BigDecimal probUnder = BigDecimalUtils.exp(predUnder, SCALE).divide(
+ BigDecimalUtils.exp(predUnder, SCALE).add(BigDecimalUtils.exp(predOver, SCALE)).add(
+ BigDecimalUtils.exp(predAt, SCALE)), SCALE, BigDecimal.ROUND_HALF_UP
+
+
+ );
+
+ BigDecimal probOver = BigDecimalUtils.exp(predOver, SCALE).divide(
+ BigDecimalUtils.exp(predUnder, SCALE).add(BigDecimalUtils.exp(predOver, SCALE)).add(
+ BigDecimalUtils.exp(predAt, SCALE)), SCALE, BigDecimal.ROUND_HALF_UP
+ );
+
+ //this is a multinomial
+ return new BigDecimal [] {probUnder, (new BigDecimal("1").subtract(probUnder).subtract(probOver).setScale(SCALE, BigDecimal.ROUND_HALF_UP)), probOver}; //make sure this is returning the correct order.
+ //this is a multinomial.
+ }
+
+ @Override
+ public BigDecimal [] getProbabilities(AcaciaLogger logger, HashMap<String, Object> factors, FlowCycler cycler) throws Exception
+ {
+ //cycler knows all..
+ int flowPosition = (Integer)factors.get(OUFrequencyTable.FLOW_POSITION);
+ int cycleNumber = cycler.flowPositionToCycleNumber(flowPosition);
+ int posInCycle = cycler.flowPositionToPosInCycle(flowPosition);
+ int refLen = (Integer)factors.get(OUFrequencyTable.RLE_LENGTH);
+
+ boolean calculatedProbs = false;
+
+ if(! this.myProbs.contains(refLen, cycleNumber, posInCycle))
+ {
+ BigDecimal [] res = calculateProbabilities(logger, factors, cycler); //stores it in the hash
+ this.myProbs.put(refLen, cycleNumber, posInCycle, res);
+ calculatedProbs = true;
+ }
+
+ BigDecimal sumProbs = new BigDecimal("0");
+
+ for(BigDecimal prob: this.myProbs.get(refLen, cycleNumber, posInCycle))
+ {
+ sumProbs = sumProbs.add(prob);
+ }
+
+ if(! sumProbs.setScale(10, BigDecimal.ROUND_HALF_UP).equals(new BigDecimal("1").setScale(10, BigDecimal.ROUND_HALF_UP)))
+ {
+ throw new Exception("Sum of probabilities less than zero or greater than 1: Calculated? " + calculatedProbs);
+ }
+
+ return this.myProbs.get(refLen, cycleNumber, posInCycle);
+ }
+
+ @Override
+ public BigDecimal [] estimateProbability(AcaciaLogger logger, HashMap<String, Object> factors, FlowCycler cycler)throws Exception
+ {
+ return this.calculateProbabilities(logger, factors, cycler);
+ }
+
+ @Override
+ public BigDecimal [] getEmpiricalProbability(AcaciaLogger logger, HashMap<String, Object> factors, FlowCycler cycler) throws Exception
+ {
+ int flowPosition = (Integer)factors.get(OUFrequencyTable.FLOW_POSITION);
+ int cycleNumber = cycler.flowPositionToCycleNumber(flowPosition);
+ int posInCycle = cycler.flowPositionToPosInCycle(flowPosition);
+ int rleLength = (Integer)factors.get(OUFrequencyTable.RLE_LENGTH);
+
+ if(this.myProbs.contains(rleLength, cycleNumber, posInCycle))
+ {
+ return this.myProbs.get(rleLength, cycleNumber, posInCycle);
+ }
+ return null;
+ }
+
+ private class NestedHash
+ {
+ //RLE LENGTH, CYCLE POS, PIC POS,
+
+ private HashMap <Integer, HashMap <Integer, HashMap <Integer, BigDecimal [] >>> nesty;
+
+ public NestedHash()
+ { //RefLen //Cycle //PIC
+ this.nesty = new HashMap <Integer, HashMap <Integer, HashMap <Integer, BigDecimal [] >>> ();
+ }
+
+ public void put(int rleLength, int cycleNumber, int flowInCycleNumber, BigDecimal [] probs) throws Exception
+ {
+ HashMap <Integer, HashMap <Integer, BigDecimal [] >> rleHash;
+
+ if(! nesty.containsKey(rleLength))
+ {
+ rleHash = new HashMap <Integer, HashMap <Integer, BigDecimal [] >> ();
+ nesty.put(rleLength, rleHash);
+ }
+ else
+ {
+ rleHash = nesty.get(rleLength);
+ }
+
+ HashMap <Integer, BigDecimal []> cycleNumberHash;
+
+ if(! rleHash.containsKey(cycleNumber))
+ {
+ cycleNumberHash = new HashMap <Integer, BigDecimal []>();
+ rleHash.put(cycleNumber, cycleNumberHash);
+ }
+ else
+ {
+ cycleNumberHash = rleHash.get(cycleNumber);
+ }
+
+ cycleNumberHash.put(flowInCycleNumber, probs);
+ }
+
+ public BigDecimal [] get(int rleLength, int cycleNumber, int flowInCycleNumber) throws Exception
+ {
+ if(this.nesty.containsKey(rleLength) && this.nesty.get(rleLength).containsKey(cycleNumber)
+ && this.nesty.get(rleLength).get(cycleNumber).containsKey(flowInCycleNumber))
+ return this.nesty.get(rleLength).get(cycleNumber).get(flowInCycleNumber);
+ return null;
+ }
+
+ public boolean contains(int rleLength, int cycleNumber, int flowInCycleNumber)
+ {
+ if(this.nesty.containsKey(rleLength))
+ {
+ if(this.nesty.get(rleLength).containsKey(cycleNumber))
+ {
+ if(this.nesty.get(rleLength).get(cycleNumber).containsKey(flowInCycleNumber))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ }
+
+// TESTING
+ /*
+ public static void main(String [] args)
+ {
+ AcaciaLogger logger = new AcaciaLogger();
+ FlowCycler cycler = new FlowCycler(AcaciaConstants.OPT_FLOW_CYCLE_ION_TORRENT, logger);
+
+ try
+ {
+ //TODO: to ensure it found the file, had to change alot of code, which will need to change back.
+
+
+ IonTorrentOUCallFrequencyTable it = new IonTorrentOUCallFrequencyTable(null, logger,
+ "E:\\GitRepo\\AcaciaEclipse\\Acacia\\src\\data\\100bpOneTouch_316_counts_complete.csv",
+ "E:\\GitRepo\\AcaciaEclipse\\Acacia\\src\\data\\100bpOneTouch_316_counts_complete_model_zeroes.csv",
+ "E:\\GitRepo\\AcaciaEclipse\\Acacia\\src\\data\\100bpOneTouch_316_counts_complete_model_ones.csv",
+ "E:\\GitRepo\\AcaciaEclipse\\Acacia\\src\\data\\100bpOneTouch_316_counts_complete_model_others.csv");
+
+
+ //probs zero works
+
+ BigDecimal [] res;
+
+ for(int i = 0; i <= 25; i++)
+ {
+ res = it._calculateProbabilitiesHelper(0, i, 0);
+ System.out.println("Probabilities for i: "+ i + " " + res[0] + ", " + res[1] +", " + res[2]);
+
+ }
+
+ BigDecimal [] res2 = it._calculateProbabilitiesHelper(1,0,6);
+
+ for(int i = 0; i < res2.length; i++)
+ System.out.println(res2[i].setScale(SCALE, BigDecimal.ROUND_HALF_UP));
+
+ BigDecimal [] res3 = it._calculateProbabilitiesHelper(2, 3, 12);
+
+ for(int i = 0; i < res3.length; i++)
+ System.out.println(res3[i].setScale(SCALE, BigDecimal.ROUND_HALF_UP));
+
+ //okay all the get probabilities are tested. Interestingly should cache them so not calculating again.
+
+ HashMap <String, Object> factors = new HashMap <String, Object>();
+ factors.put(OUFrequencyTable.FLOW_POSITION, 33);
+ factors.put(OUFrequencyTable.RLE_LENGTH, 2);
+
+ System.out.println("Getting probabilities");
+
+ //what I was actually looking up is PIC 1 in cycle 1 for reflen 2.
+ BigDecimal [] res4 = it.getProbabilities(logger, factors, cycler);
+
+ for(int i = 0; i < res4.length; i++)
+ System.out.println(res4[i].setScale(SCALE, BigDecimal.ROUND_HALF_UP));
+
+
+ //pretend there is a cycle 12..
+ HashMap <String, Object> factors2 = new HashMap <String, Object>();
+ factors2.put(OUFrequencyTable.FLOW_POSITION, 386);
+ factors2.put(OUFrequencyTable.RLE_LENGTH, 1);
+
+ BigDecimal [] res5 = it.getProbabilities(logger, factors2, cycler);
+
+ for(int i = 0; i < res5.length; i++)
+ System.out.println(res5[i].setScale(SCALE, BigDecimal.ROUND_HALF_UP));
+
+
+ }
+ catch(Exception e)
+ {
+ System.out.println("An exception ocurred: " + e.getMessage());
+ e.printStackTrace();
+
+ }
+ }
+ */
+}
diff --git a/src/pyromaniac/Algorithm/MultinomialOneSidedTest.java b/src/pyromaniac/Algorithm/MultinomialOneSidedTest.java
new file mode 100644
index 0000000..e21473e
--- /dev/null
+++ b/src/pyromaniac/Algorithm/MultinomialOneSidedTest.java
@@ -0,0 +1,170 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+package pyromaniac.Algorithm;
+
+import java.util.HashSet;
+
+import org.apache.commons.math3.distribution.NormalDistribution;
+
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class MultinomialOneSidedTest.
+ */
+public class MultinomialOneSidedTest extends HypothesisTest
+{
+
+ /**
+ * Instantiates a new multinomial one sided test.
+ *
+ * @param obsAbove the obs above
+ * @param obsBelow the obs below
+ * @param obsMode the obs mode
+ * @param modeLength the mode length
+ * @param P the p
+ * @param alpha the alpha
+ * @param avgFlowPos the avg flow pos
+ * @param logger the logger
+ * @param verbose the verbose
+ */
+ public MultinomialOneSidedTest(int obsAbove, int obsBelow, int obsMode,int modeLength, double [] P, double alpha, double avgFlowPos, AcaciaLogger logger, boolean verbose)
+ {
+ super(obsAbove, obsBelow, obsMode, modeLength, P, alpha, avgFlowPos, logger,verbose);
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.HypothesisTest#runTest()
+ */
+ public void runTest() throws Exception
+ {
+ //not significant if no observations below and no observations above
+ if (observationsBelowMode == 0 && observationsAboveMode == 0)
+ {
+ this.p = 1;
+ }//significant if the number of observations above mode is equal to that at the mode.
+ /* else if(N <= 5 && observationsAtMode != N)
+ {
+ this.significant = true;
+ this.p = 0;
+ }*/
+ else if ( alpha > 0 && (observationsAboveMode == observationsAtMode
+ || observationsBelowMode == observationsAtMode))
+ {
+ this.significantAbove = true;
+ this.significantBelow = true;
+ //this.significantCombined = true;
+ this.p = 0;
+ }
+ else
+ {
+
+ int indexBelowMode = 1;
+ int indexAboveMode = 2;
+
+ double [] X = new double [] {this.observationsAtMode, this.observationsBelowMode, this.observationsAboveMode};
+ double [] xDivN = new double [] {(double)this.observationsAtMode / (double)this.N,
+ (double)this.observationsBelowMode / (double)this.N, (double)this.observationsAboveMode / (double)this.N};
+ HashSet <Integer> gamma = new HashSet <Integer> ();
+
+ if(verbose)
+ {
+ for(int i = 0; i < X.length; i++)
+ {
+ logger.writeLog("X[" + i + "] = " + X[i], AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("XDivN[" + i + "] = " + xDivN[i], AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("P[" + i + "] = " + P[i], AcaciaLogger.LOG_DEBUG);
+ }
+ }
+
+ for(int i = 1; i < xDivN.length; i++)
+ {
+ if(xDivN[i] >= P[i])
+ {
+ gamma.add(i);
+ }
+ }
+
+ double sumX = 0;
+ double sumP = 0;
+
+ for(int index: gamma)
+ {
+ sumX += X[index];
+ sumP += P[index];
+ }
+
+ while(gamma.size() < 2)
+ {
+ boolean added = false;
+
+ for(int i = 1; i < xDivN.length; i++)
+ {
+ double adjP = X[i] * (1 - sumP) /(this.N - sumX);
+
+ if(adjP > P[i] & ! gamma.contains(i))
+ {
+ gamma.add(i);
+ added = true;
+ }
+ }
+
+ if(! added)
+ {
+ break;
+ }
+
+ sumP = 0;
+ sumX = 0;
+
+ for(int index: gamma)
+ {
+ sumX += X[index];
+ sumP += P[index];
+ }
+ }
+
+ NormalDistribution norm = new NormalDistribution();
+
+ double w2Num = Math.pow(((N - sumX) - N * (1 - sumP)),2) ;
+ double w2Denom =(N * (1 - sumP));
+ double resSum = 0;
+ for(int index: gamma)
+ {
+ resSum += Math.pow(X[index] - N * P[index], 2) / (N * P[index]);
+ }
+
+ double w2 = (w2Num/w2Denom) + resSum;
+ double m = Math.sqrt(P[indexBelowMode] * P[indexAboveMode] / (1 - P[indexBelowMode] - P[indexAboveMode]));
+ double calcP = (0.25 + (Math.atan(m) / (2 * Math.PI))) * Math.exp(-w2 / 2) + (1 - norm.cumulativeProbability(Math.sqrt(w2)));
+
+ this.p = calcP;
+
+ if (this.alpha > 0 )
+ {
+ boolean sig = (this.p <= this.alpha);
+ this.significantAbove = sig;
+ this.significantBelow = sig;
+ // this.significantCombined = sig;
+ }
+ else //alpha == zero
+ {
+ }
+ }
+ }
+}
diff --git a/src/pyromaniac/Algorithm/OUFrequencyTable.java b/src/pyromaniac/Algorithm/OUFrequencyTable.java
new file mode 100644
index 0000000..d4afe60
--- /dev/null
+++ b/src/pyromaniac/Algorithm/OUFrequencyTable.java
@@ -0,0 +1,76 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import java.math.BigDecimal;
+import java.math.MathContext;
+import java.math.RoundingMode;
+import java.util.HashMap;
+
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Interface OUFrequencyTable.
+ */
+public interface OUFrequencyTable
+{
+
+ /** The Constant LESS_THAN. */
+ public static final int LESS_THAN = 0;
+
+ /** The Constant EQUAL_TO. */
+ public static final int EQUAL_TO = 1;
+
+ /** The Constant GREATER_THAN. */
+ public static final int GREATER_THAN = 2;
+
+ public static final int INVALID_FLOW = -1;
+
+
+ public static final String RLE_LENGTH = "RLE_LENGTH";
+ public static final String FLOW_POSITION = "FLOW_POSITION";
+
+ public static final String SUBTRACT_FOR_LB = "0.51";
+ public static final String ADD_FOR_UB = "0.49";
+
+
+ /**
+ * Load probabilities.
+ *
+ * @param probFile the prob file
+ */
+ public void loadProbabilities(String probFile);
+
+ /**
+ * Gets the probabilities.
+ *
+ * @param obsMode the obs mode
+ * @param flowNumber the flow number
+ * @return the probabilities
+ */
+ //all of interest to the observer. However helpers will do most of the code.
+ public BigDecimal [] getProbabilities(AcaciaLogger logger, HashMap <String, Object> factors, FlowCycler cycler) throws Exception;
+ public BigDecimal [] estimateProbability(AcaciaLogger logger, HashMap <String, Object> factors, FlowCycler cycler) throws Exception;
+ public BigDecimal [] getEmpiricalProbability(AcaciaLogger logger, HashMap <String, Object> factors, FlowCycler cycler) throws Exception;
+
+ public int getScale();
+
+}
diff --git a/src/pyromaniac/Algorithm/OligomerClusterGenerator.java b/src/pyromaniac/Algorithm/OligomerClusterGenerator.java
new file mode 100644
index 0000000..fe2582b
--- /dev/null
+++ b/src/pyromaniac/Algorithm/OligomerClusterGenerator.java
@@ -0,0 +1,429 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.Set;
+
+import pyromaniac.AcaciaConstants;
+import pyromaniac.DataStructures.MutableInteger;
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class OligomerClustering.
+ */
+public class OligomerClusterGenerator extends ClusterGenerator
+{
+
+ /** The hc. */
+ private ManhattanClustering hc;
+
+ /**
+ * Instantiates a new oligomer clustering.
+ */
+ public OligomerClusterGenerator ()
+ {
+ super();
+ hc = null;
+ }
+
+
+
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.Clustomatic#runClustering()
+ */
+ @Override
+ public void runClustering() throws Exception
+ {
+ HashMap <String, int [] > hexReps = new HashMap <String, int [] >();
+ HashMap <String, Integer> hexToPos = new HashMap <String, Integer>();
+ MutableInteger index = new MutableInteger(0);
+
+ LinkedList <Pair <String, String>> mergeThisWithThat = new LinkedList <Pair <String, String>>();
+
+ Integer maximumManhattan = Integer.parseInt(settings.get(AcaciaConstants.OPT_MAXIMUM_MANHATTAN_DIST));
+
+ int prefixLength = -1;
+
+ if(initialClusters.size() == 0)
+ {
+ throw new Exception("Perfect clusters is empty!");
+ }
+
+ for(String seq: initialClusters.keySet())
+ {
+ if(prefixLength == -1)
+ prefixLength = seq.length(); //was determined in the perfect clusters original case.
+ hexReps.put(seq, getHex(seq, hexToPos, index));
+ } //initialises the hexamer representations of each 'perfect identity representative'
+
+ LinkedList <String> freqSortedList = sortedBasedOnFreq(initialClusters);
+
+
+ boolean verbose = false;
+
+ if(verbose)
+ {
+ for(String s: freqSortedList)
+ {
+ logger.writeLog("Sorted on size: " + initialClusters.get(s).size() + ", rep: " + s, AcaciaLogger.LOG_DEBUG);
+ }
+ }
+
+
+ //all things for tracking whilst using an iterator.
+
+ String toProcess = null;
+ boolean done = false;
+
+
+ //DONE means I have worked my way up the list based on abundance, and
+ //identified the best match for each sequence further up in the list
+
+ while(!done)
+ {
+ Iterator <String> it = freqSortedList.iterator(); //have to keep going through the list, and don't have a pointer to the last compared :/
+
+ int ctr = 0;
+ //boolean seen = false;
+ boolean processed = true; //assume it is processed
+
+ int bestMatch = -1;
+ int bestDist = 100000; //arbitrarily large distance
+ int bestClusterSize = 0;
+
+ //to process is the first in the list, assuming it is low abundance.
+ if(it.hasNext() && toProcess == null)
+ {
+ toProcess = it.next(); //first element is the first to Process
+ ctr++;
+ processed = false; //have not processed the prefix 'processing'.
+ //seen = true;
+ }
+
+ //this seems to only happen if there is only one rep to begin with, rare!
+ if(!it.hasNext())
+ {
+ done = true;
+ }
+
+ while(it.hasNext())
+ {
+ String curr = it.next(); //get the next element
+
+ if(verbose)
+ {
+ logger.writeLog("toProcess: " + toProcess + " with " + initialClusters.get(toProcess).size(),AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("Current prefix is: " + curr + ", consisting of " + initialClusters.get(curr).size() + "tags!", AcaciaLogger.LOG_DEBUG);
+ }
+
+ if(processed && curr == toProcess)//working back through the iterator, start at the next spot!
+ {
+ if(verbose)
+ {
+ System.out.println("Curr == lastProcessed");
+ }
+
+ if(it.hasNext()) //process them!
+ {
+ if(verbose)
+ {
+ System.out.println("There are more to process");
+ }
+ ctr++;
+ toProcess = it.next();
+ processed = false;
+
+ if(!it.hasNext())
+ {
+ done = true;
+ }
+ }
+ else
+ {
+ if(verbose)
+ {
+ System.out.println("We are done");
+ }
+ done = true;
+ }
+ }
+ else if(!processed)
+ {
+ //we are going to process "curr"
+ int [] hexToProcess = hexReps.get(toProcess);
+ int [] hexCurr = hexReps.get(curr);
+
+
+ int dist = calculateHexDist(hexToProcess, hexCurr);
+
+
+ if(verbose)
+ {
+ logger.writeLog("curr: " + curr + " with " + initialClusters.get(curr).size(),AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("toProcess: " + toProcess + " with " + initialClusters.get(toProcess).size(),AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("dist: " + dist, AcaciaLogger.LOG_DEBUG);
+
+ LinkedList <Pyrotag> currCluster = initialClusters.get(curr);
+ LinkedList <Pyrotag> processCluster = initialClusters.get(toProcess);
+
+ if(currCluster.size() == 1)
+ {
+ logger.writeLog("Curr contains: " + currCluster.getFirst().getID(), AcaciaLogger.LOG_DEBUG);
+ logger.writeLog("Process contains: " + processCluster.getFirst().getID(), AcaciaLogger.LOG_DEBUG);
+ }
+
+ }
+
+ //better to merge with the biggest cluster
+ if(dist <= bestDist && dist <= maximumManhattan && bestClusterSize < initialClusters.get(curr).size())
+ {
+ if(verbose)
+ {
+ logger.writeLog("Dist is < bestDist: " + dist + " < " + bestDist,AcaciaLogger.LOG_DEBUG);
+ }
+
+ bestDist = dist;
+ bestMatch = ctr;
+ bestClusterSize = initialClusters.get(curr).size();
+ }
+ }
+ ctr++;
+ }
+
+ if(bestDist < maximumManhattan)
+ {
+ if(verbose)
+ {
+ logger.writeLog("bestDist less than max manhattan: " + bestDist, AcaciaLogger.LOG_DEBUG);
+ }
+ mergeThisWithThat.add(new Pair <String, String> (toProcess, freqSortedList.get(bestMatch)));
+ }
+ //adding this
+ processed = true;
+ }
+
+ //merge this with that - does not seem to be used.
+ for(Pair <String, String> toMerge: mergeThisWithThat)
+ {
+ String smallClusterRep = toMerge.getFirst();
+ String bigClusterRep = toMerge.getSecond();
+
+ if(bigClusterRep == null)
+ {
+ throw new Exception("Cluster representative is not defined for bigger cluster.");
+ }
+
+ LinkedList <Pyrotag> bigCluster = initialClusters.get(bigClusterRep);
+ LinkedList <Pyrotag> smallCluster = initialClusters.get(smallClusterRep);
+
+ bigCluster.addAll(smallCluster);
+ initialClusters.remove(smallClusterRep);
+
+ }
+
+ //remembers the hexamer position, and the prefix length. Maybe it was for parallelisation?
+ ManhattanClustering hc = new ManhattanClustering (hexToPos, index,prefixLength); //why do I keep this around? If I have to do multiple clusterings or something?
+ this.hc = hc;
+
+ }
+
+ /**
+ * The Class ManhattanClustering.
+ */
+ private class ManhattanClustering
+ {
+
+ /**
+ * Gets the last index.
+ *
+ * @return the last index
+ */
+ public MutableInteger getLastIndex()
+ {
+ return lastIndex;
+ }
+
+ /**
+ * Sets the last index.
+ *
+ * @param lastIndex the new last index
+ */
+ public void setLastIndex(MutableInteger lastIndex)
+ {
+ this.lastIndex = lastIndex;
+ }
+
+ /**
+ * Gets the sub string length.
+ *
+ * @return the sub string length
+ */
+ public int getSubStringLength() {
+ return subStringLength;
+ }
+
+ /**
+ * Sets the sub string length.
+ *
+ * @param subStringLength the new sub string length
+ */
+ public void setSubStringLength(int subStringLength) {
+ this.subStringLength = subStringLength;
+ }
+
+ /**
+ * Gets the hexes.
+ *
+ * @return the hexes
+ */
+ public HashMap<String, Integer> getHexes() {
+ return hexes;
+ }
+
+ /**
+ * Sets the hexes.
+ *
+ * @param hexes the hexes
+ */
+ public void setHexes(HashMap<String, Integer> hexes) {
+ this.hexes = hexes;
+ }
+
+ /** The last index. */
+ private MutableInteger lastIndex;
+
+ /** The sub string length. */
+ private int subStringLength;
+
+ /** The hexes. */
+ HashMap <String, Integer> hexes;
+
+ /**
+ * Instantiates a new manhattan clustering.
+ *
+ * @param hexes the hexes
+ * @param lastIndex the last index
+ * @param subStringLength the sub string length
+ */
+ public ManhattanClustering(HashMap <String, Integer> hexes, MutableInteger lastIndex, int subStringLength)
+ {
+ this.hexes = hexes;
+ this.lastIndex = lastIndex;
+ this.subStringLength = subStringLength;
+ }
+ }
+
+ /**
+ * Calculate hex dist.
+ *
+ * @param hexToProcess the hex to process
+ * @param hexCurr the hex curr
+ * @return the int
+ */
+ private int calculateHexDist(int[] hexToProcess, int[] hexCurr)
+ {
+ int numEdits = 0;
+ for(int i = 0; i < hexToProcess.length; i++)
+ {
+ numEdits += Math.abs(hexToProcess[i] - hexCurr[i]);
+ }
+ return numEdits;
+ }
+
+ /**
+ * Gets the hex.
+ *
+ * @param sequence the sequence
+ * @param hexToPos the hex to pos
+ * @param index the index
+ * @return the hex
+ */
+ private int [] getHex(String sequence, HashMap <String, Integer> hexToPos, MutableInteger index)
+ {
+ double numHex = Math.pow(4,AcaciaConstants.CLUSTERING_OLIGO_LENGTH);
+ int [] hexCounts = new int [(int)numHex];
+
+ for(int i = 0; i <numHex; i++)
+ {
+ hexCounts[i] = 0;
+ }
+
+ for(int i = 0; (sequence.length() - i) >= AcaciaConstants.CLUSTERING_OLIGO_LENGTH ; i++)
+ {
+ String hexamer = sequence.substring(i, i + AcaciaConstants.CLUSTERING_OLIGO_LENGTH);
+
+ if(!hexToPos.containsKey(hexamer))
+ {
+ hexToPos.put(hexamer, index.value());
+ index.increment();
+ }
+
+ hexCounts[hexToPos.get(hexamer)] = hexCounts[hexToPos.get(hexamer)] + 1;
+ }
+
+ return hexCounts;
+ }
+
+ /**
+ * Sorted based on frequency.
+ *
+ * @param perfectClusters the perfect clusters
+ * @return the linked list
+ */
+ private LinkedList <String> sortedBasedOnFreq(HashMap <String, LinkedList <Pyrotag>> perfectClusters)
+ {
+ Set <String> _set = perfectClusters.keySet();
+
+ LinkedList <String> sortedBasedOnFreq = new LinkedList <String>();
+
+ for(String s: _set)
+ {
+ int size = perfectClusters.get(s).size();
+
+ int index = 0;
+
+ Iterator <String> it = sortedBasedOnFreq.iterator();
+
+ //insert at index.
+ while(it.hasNext())
+ {
+ String next = it.next();
+
+ if(perfectClusters.get(next).size() > size)
+ {
+ break;
+ }
+ else
+ {
+ index++;
+ }
+ }
+
+ sortedBasedOnFreq.add(index, s);
+ }
+ return sortedBasedOnFreq;
+ }
+}
diff --git a/src/pyromaniac/Algorithm/QuinceOUFrequencyTable.java b/src/pyromaniac/Algorithm/QuinceOUFrequencyTable.java
new file mode 100644
index 0000000..fd4e448
--- /dev/null
+++ b/src/pyromaniac/Algorithm/QuinceOUFrequencyTable.java
@@ -0,0 +1,281 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
+package pyromaniac.Algorithm;
+
+import org.apache.commons.math3.exception.*;
+
+import org.apache.commons.math3.distribution.NormalDistribution;
+
+import pyromaniac.AcaciaConstants;
+import pyromaniac.Algorithm.OUFrequencyTable;
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.IO.AcaciaLogger;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.math.BigDecimal;
+import java.net.URL;
+import java.util.HashMap;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class QuinceFrequencyTable.
+ */
+public class QuinceOUFrequencyTable implements OUFrequencyTable
+{
+
+ /** The probabilities. */
+ HashMap <Integer, BigDecimal []> probabilities;
+ public static int MAX_PRELOAD = 10;
+ public static final int SCALE = 9;
+
+ /**
+ * Instantiates a new quince frequency table.
+ *
+ * @param probFile the prob file
+ */
+ public QuinceOUFrequencyTable(String probFile)
+ {
+ probabilities = new HashMap<Integer, BigDecimal []>(20);
+
+ if(probFile == null)
+ {
+ bulkComputeProbabilities();
+ }
+ else
+ {
+ loadProbabilities(probFile);
+ }
+ }
+
+ public int getScale()
+ {
+ return this.SCALE;
+ }
+
+ private void bulkComputeProbabilities()
+ {
+ for(int i = 1; i <= MAX_PRELOAD;i++)
+ {
+ _calculateProbabilitiesHelper(i);
+ }
+ }
+
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.OUFrequencyTable#loadProbabilities(java.lang.String)
+ */
+ public void loadProbabilities(String probFile)
+ {
+ try
+ {
+ URL url = getClass().getResource(probFile);
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ String header = in.readLine();
+
+ if(header.split(",").length != 4)
+ {
+ throw new Exception("Call probabilities does not have four columns as expected");
+ }
+
+ String line = in.readLine();
+
+ while(line != null)
+ {
+ String [] fields = line.split(",");
+
+ int mode = Integer.parseInt(fields[0]);
+ BigDecimal lessThan = new BigDecimal(fields[1]).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ BigDecimal equalTo = new BigDecimal(fields[2]).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ BigDecimal moreThan = new BigDecimal(fields[3]).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ BigDecimal sum = lessThan.add(equalTo).add(moreThan).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ if(! sum.equals(new BigDecimal("1").setScale(SCALE, BigDecimal.ROUND_HALF_UP)))
+ {
+ lessThan = lessThan.divide(sum, SCALE,BigDecimal.ROUND_HALF_UP);
+ equalTo = equalTo.divide(sum, SCALE, BigDecimal.ROUND_HALF_UP);
+ moreThan = moreThan.divide(sum, SCALE, BigDecimal.ROUND_HALF_UP);
+ }
+
+ BigDecimal [] probs = {lessThan, equalTo, moreThan};
+ this.probabilities.put(mode, probs);
+ line = in.readLine();
+ }
+ }
+ catch(NumberFormatException nfe)
+ {
+ nfe.printStackTrace();
+ }
+ catch(IOException ie)
+ {
+ ie.printStackTrace();
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ }
+
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.OUFrequencyTable#getProbabilities(int, int)
+ * If probability does not exist in empirical table, it is estimated, saved in the table, and returned
+ */
+ public BigDecimal [] getProbabilities(AcaciaLogger logger, HashMap <String, Object> factors, FlowCycler cycler)
+ {
+ int mode = (Integer)factors.get(OUFrequencyTable.RLE_LENGTH);
+
+ if(this.probabilities.containsKey(mode))
+ {
+ return this.probabilities.get(mode);
+ }
+ else
+ {
+ BigDecimal [] res = _calculateProbabilitiesHelper(mode);
+ this.probabilities.put(mode, res);
+ return res;
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.OUFrequencyTable#calculateProbabilities(int, int)
+ */
+
+ private BigDecimal [] _calculateProbabilitiesHelper(int mode)
+ {
+ BigDecimal sd = new BigDecimal("0.04").add(new BigDecimal(mode).multiply(new BigDecimal("0.03")));
+ BigDecimal modeBD = new BigDecimal(mode);
+
+ BigDecimal lowerBound = modeBD.subtract(new BigDecimal(SUBTRACT_FOR_LB)).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ BigDecimal upperBound = modeBD.add(new BigDecimal(ADD_FOR_UB)).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ NormalDistribution norm = new NormalDistribution(mode, sd.doubleValue());
+
+ try
+ {
+ BigDecimal probLessThan = new BigDecimal(norm.cumulativeProbability(lowerBound.doubleValue())).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ BigDecimal probMoreThan = new BigDecimal("1").subtract(new BigDecimal(norm.cumulativeProbability(upperBound.doubleValue()))).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+ BigDecimal probEqualTo = new BigDecimal("1").subtract(probLessThan).subtract(probMoreThan).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ BigDecimal totalProb = probLessThan.add(probEqualTo).add(probMoreThan).setScale(SCALE, BigDecimal.ROUND_HALF_UP);
+
+ if(!totalProb.equals(new BigDecimal("1").setScale(SCALE, BigDecimal.ROUND_HALF_UP)))
+ {
+ probLessThan = probLessThan.divide(totalProb, SCALE, BigDecimal.ROUND_HALF_UP);
+ probMoreThan = probMoreThan.divide(totalProb, SCALE, BigDecimal.ROUND_HALF_UP);
+ probEqualTo = probEqualTo.divide(totalProb,SCALE, BigDecimal.ROUND_HALF_UP);
+ }
+
+ BigDecimal [] probs = {probLessThan, probEqualTo, probMoreThan};
+ return probs;
+ }
+ catch(MathIllegalStateException me)
+ {
+ me.getStackTrace();
+ }
+ return null;
+ }
+
+
+ @Override
+ public BigDecimal [] estimateProbability(AcaciaLogger logger, HashMap<String, Object> factors, FlowCycler cycler) throws Exception
+ {
+ // TODO Auto-generated method stub
+ int mode = (Integer)factors.get(OUFrequencyTable.RLE_LENGTH);
+ return _calculateProbabilitiesHelper(mode);
+ }
+
+ @Override
+ public BigDecimal [] getEmpiricalProbability(AcaciaLogger logger, HashMap<String, Object> factors, FlowCycler cycler) throws Exception
+ {
+ int mode = (Integer)factors.get(OUFrequencyTable.RLE_LENGTH);
+ if (this.probabilities.containsKey(mode))
+ {
+ return this.probabilities.get(mode);
+ }
+ return null;
+ }
+
+
+
+ // TESTING
+ public static void main(String [] args)
+ {
+ AcaciaLogger logger = new AcaciaLogger();
+ FlowCycler cycler = new FlowCycler(AcaciaConstants.OPT_FLOW_CYCLE_454, logger);
+
+ try
+ {
+ //TODO: to ensure it found the file, had to change alot of code, which will need to change back.
+
+
+ QuinceOUFrequencyTable it = new QuinceOUFrequencyTable(AcaciaConstants.PYRONOISE_PROBS_LOCATION);
+
+
+ //probs zero works
+ BigDecimal [] res = it._calculateProbabilitiesHelper(0);
+
+ for(int i = 0; i < res.length; i++)
+ System.out.println(res[i]);
+
+ BigDecimal [] res2 = it._calculateProbabilitiesHelper(2);
+
+ for(int i = 0; i < res2.length; i++)
+ System.out.println(res2[i]);
+
+ //okay all the get probabilities are tested. Interestingly should cache them so not calculating again.
+ HashMap <String, Object> factors = new HashMap <String, Object>();
+ factors.put(OUFrequencyTable.FLOW_POSITION, 33);
+ factors.put(OUFrequencyTable.RLE_LENGTH, 2);
+
+ System.out.println("Res 4 ");
+ //what I was actually looking up is PIC 1 in cycle 1 for reflen 2.
+ BigDecimal [] res4 = it.getProbabilities(logger, factors, cycler);
+
+ for(int i = 0; i < res4.length; i++)
+ System.out.println(res4[i]);
+
+
+ //pretend there is a cycle 12..
+ HashMap <String, Object> factors2 = new HashMap <String, Object>();
+ factors2.put(OUFrequencyTable.FLOW_POSITION, 50);
+ factors2.put(OUFrequencyTable.RLE_LENGTH, 5);
+
+ BigDecimal [] res5 = it.getProbabilities(logger, factors2, cycler);
+
+ for(int i = 0; i < res5.length; i++)
+ System.out.println(res5[i]);
+
+
+ }
+ catch(Exception e)
+ {
+ System.out.println("An exception ocurred: " + e.getMessage());
+ e.printStackTrace();
+
+ }
+ }
+
+}
diff --git a/src/pyromaniac/Algorithm/RLEAlignmentIndelsOnly.java b/src/pyromaniac/Algorithm/RLEAlignmentIndelsOnly.java
new file mode 100644
index 0000000..7957947
--- /dev/null
+++ b/src/pyromaniac/Algorithm/RLEAlignmentIndelsOnly.java
@@ -0,0 +1,1475 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.Set;
+
+import pyromaniac.AcaciaEngine;
+import pyromaniac.DataStructures.MutableInteger;
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.IO.AcaciaLogger;
+
+public class RLEAlignmentIndelsOnly
+{
+
+ /** The head. */
+ private AlignmentColumn head;
+
+ /** The logger. */
+ private AcaciaLogger logger;
+
+ /** The max recurse depth. */
+ private int maxRecurseDepth;
+
+ /** The STAR t_ col. */
+ private static AlignmentColumn START_COL = null;
+
+ /** The truncate from. */
+ private AlignmentColumn truncateFrom; //this column indicates the last column we want to consider in the alignment, due to low coverage.
+
+ //how to know when to truncate at??
+
+ /**
+ * Gets the truncate from.
+ *
+ * @return the truncate from
+ */
+ public AlignmentColumn getTruncateFrom()
+ {
+ return truncateFrom;
+ }
+
+ /**
+ * Sets the truncate from.
+ *
+ * @param truncateFrom the new truncate from
+ */
+ public void setTruncateFrom(AlignmentColumn truncateFrom)
+ {
+ this.truncateFrom = truncateFrom;
+ }
+
+ /**
+ * Instantiates a new threaded alignment.
+ *
+ * @param consensusSeed the consensus seed
+ * @param logger the logger
+ * @param maxRecurseDepth the max recurse depth
+ */
+ public RLEAlignmentIndelsOnly(String consensusSeed, AcaciaLogger logger, int maxRecurseDepth)
+ {
+ this.head = new AlignmentColumn(' ');
+ this.logger = logger;
+ this.maxRecurseDepth = maxRecurseDepth;
+ this.truncateFrom = null;
+
+ if(START_COL == null)
+ {
+ START_COL = new RLEAlignmentIndelsOnly.AlignmentColumn('$');
+ }
+
+ AlignmentColumn curr = head;
+
+ for(int i = 0; i < consensusSeed.length(); i++)
+ {
+ AlignmentColumn newChild = new AlignmentColumn(consensusSeed.charAt(i));
+ newChild.setParent(curr);
+ curr.setChild(newChild);
+ curr = newChild;
+ }
+ }
+
+ /**
+ * Gets the head column.
+ *
+ * @return the head column
+ */
+ public AlignmentColumn getHeadColumn()
+ {
+ return this.head;
+ }
+
+
+
+
+ /**
+ * Instantiates a new threaded alignment.
+ */
+ private RLEAlignmentIndelsOnly()
+ {
+ this.head = null;
+ }
+
+
+ /**
+ * Clone alignment with tags.
+ *
+ * @param p the p
+ * @return the threaded alignment
+ */
+ public RLEAlignmentIndelsOnly cloneAlignmentWithTags(HashSet <Pyrotag> p)
+ {
+ try
+ {
+ RLEAlignmentIndelsOnly ta = new RLEAlignmentIndelsOnly();
+ ta.head = this.head.cloneRecursivelyWithTags(p,null);
+ ta.logger = this.logger;
+ ta.maxRecurseDepth = this.maxRecurseDepth;
+
+ return ta;
+ }
+ catch(Exception e)
+ {
+ System.out.println("logger had an exception");
+ }
+ return null;
+ }
+
+ /**
+ * Clone alignment with tags_truncate at.
+ *
+ * @param p the p
+ * @param truncateAt the truncate at
+ * @return the threaded alignment
+ */
+ public RLEAlignmentIndelsOnly cloneAlignmentWithTags_truncateAt(HashSet <Pyrotag > p, AlignmentColumn truncateAt)
+ {
+ try
+ {
+ RLEAlignmentIndelsOnly ta = new RLEAlignmentIndelsOnly();
+ ta.head = this.head.cloneRecursivelyWithTagsAndTruncateAt(p,null, truncateAt);
+ ta.logger = this.logger;
+ ta.maxRecurseDepth = this.maxRecurseDepth;
+ return ta;
+ }
+ catch(Exception e)
+ {
+ System.out.println("logger had an exception");
+ }
+ return null;
+ }
+
+
+ /**
+ * Gets the all tags.
+ *
+ * @return the all tags
+ */
+ public HashSet<Pyrotag> getAllTags()
+ {
+ HashSet <Pyrotag> allTags = new HashSet <Pyrotag>();
+ if (this.head.child == null)
+ return allTags;
+
+
+
+ //done!
+ allTags.addAll(this.head.child.getTags());
+ allTags.addAll(this.head.child.getInsertionTags());
+
+ return allTags;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+
+ AlignmentColumn curr = this.head;
+ while(curr != null)
+ {
+ sb.append(curr.toString());
+ curr = curr.child;
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Align.
+ *
+ * @param p the p
+ * @param verbose
+ * @return true, if successful
+ * @throws Exception the exception
+ */
+ public boolean align(Pyrotag p, boolean verbose) throws Exception
+ {
+ try
+ {
+ AlignmentColumn nodeBeforeLastMismatch = null;
+ AlignmentColumn curr = this.head.child;
+ AlignmentColumn lastDefined = this.head;
+
+ LinkedList <PendingChange> pendingChanges = new LinkedList <PendingChange>();
+ SearchObject soStart = new SearchObject(curr, lastDefined, nodeBeforeLastMismatch, pendingChanges, p, 0, this, this.logger, 0, verbose);
+
+ boolean successful = soStart.run();
+
+ if(successful)
+ {
+ for(PendingChange pc : soStart.pendingChanges)
+ {
+ pc.performModification();
+ }
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+ catch(Exception e)
+ {
+ logger.writeLog("An exception occurred", AcaciaLogger.LOG_DEBUG);
+ System.exit(1);
+ }
+ return false;
+ }
+
+ /**
+ * Gets the longest consensus.
+ *
+ * @param tagsInCluster the tags in cluster
+ * @return the longest consensus
+ * @throws Exception the exception
+ */
+ public Pair <String, HashMap <Pyrotag, MutableInteger >> getLongestConsensus(HashSet <Pyrotag> tagsInCluster) throws Exception
+ {
+ HashMap <Pyrotag, MutableInteger> cleanedTagLength = new HashMap <Pyrotag, MutableInteger>();
+ StringBuilder consensus = new StringBuilder();
+ AlignmentColumn curr = this.head;
+
+ boolean verbose = false;
+
+ while(curr != null)
+ {
+ char value = curr.getValue();
+ if(value != ' ')
+ {
+ //curr = curr char, consensus is our string builder, and cleaned tag length is our tags + length
+ _helperGetLongestConsensus(curr, tagsInCluster, consensus, cleanedTagLength, verbose);
+ }
+
+ for(int i = 0; i < curr.insertionsAfter.length; i++)
+ {
+ if(curr.insertionsAfter[i] != null)
+ {
+ _helperGetLongestConsensus(curr.insertionsAfter[i], tagsInCluster, consensus, cleanedTagLength, verbose);
+ }
+ }
+ curr = curr.child;
+ }
+
+ return new Pair <String, HashMap <Pyrotag, MutableInteger>>(consensus.toString(), cleanedTagLength);
+ }
+
+ /**
+ * _helper get longest consensus.
+ *
+ * @param curr the curr
+ * @param tagsInCluster the tags in cluster
+ * @param consensus the consensus
+ * @param cleanedTagLength the cleaned tag length
+ * @param verbose the verbose
+ * @return the int
+ * @throws Exception the exception
+ */
+ public int _helperGetLongestConsensus(AlignmentColumn curr, HashSet <Pyrotag> tagsInCluster, StringBuilder consensus,
+ HashMap<Pyrotag, MutableInteger> cleanedTagLength, boolean verbose) throws Exception
+ {
+ char value = curr.getValue();
+ int totalObs = 0;
+
+ if(value != ' ')
+ {
+ int modeObs = -1 ;
+ int modeLength = -1;
+
+ HashMap <Integer, HashSet <Pyrotag>> hpToTags = curr.getHPLengthToTags(tagsInCluster);
+
+ for(Integer length: hpToTags.keySet())
+ {
+ totalObs += hpToTags.get(length).size();
+ if(hpToTags.get(length).size() > modeObs)
+ {
+ modeLength = length;
+ modeObs = hpToTags.get(length).size();
+ }
+ }
+
+ //make sure we keep a record of where these sequences line up to .
+ for(Integer length: hpToTags.keySet())
+ {
+ for(Pyrotag p: hpToTags.get(length))
+ {
+ if(!cleanedTagLength.containsKey(p))
+ {
+ cleanedTagLength.put(p, new MutableInteger(0)); //initialising
+ }
+ cleanedTagLength.get(p).add(modeLength);
+ }
+ }
+
+ for(int i = 0; i < modeLength; i++)
+ {
+ consensus.append(value);
+ }
+ }
+
+ return totalObs;
+ }
+
+ /**
+ * Split non conforming.
+ *
+ * @param nonConforming the non conforming
+ * @return the linked list
+ */
+ public LinkedList <RLEAlignmentIndelsOnly> splitNonConforming(HashSet<HashSet<Pyrotag>> nonConforming)
+ {
+ LinkedList <RLEAlignmentIndelsOnly> newAligns = new LinkedList <RLEAlignmentIndelsOnly>();
+
+ for(HashSet <Pyrotag> tagSet : nonConforming)
+ {
+ newAligns.add(this.cloneAlignmentWithTags(tagSet));
+ }
+
+ return newAligns;
+ }
+
+ /**
+ * Correct read.
+ *
+ * @param p the p
+ * @param cluster the cluster
+ * @return the pair
+ */
+ public Pair <String, Integer> correctRead(Pyrotag p, HashSet <Pyrotag> cluster)
+ {
+ StringBuilder construction = new StringBuilder();
+ MutableInteger position = new MutableInteger(0);
+ MutableInteger numModifications = new MutableInteger(0);
+ AlignmentColumn curr = head; //no recursion
+
+ while(curr != null)
+ {
+ curr.correctRead(p, cluster, construction, position, numModifications);
+ curr = curr.child;
+ }
+
+ return new Pair <String, Integer> (construction.toString(), numModifications.value());
+ }
+
+ /**
+ * The Class SearchObject.
+ */
+ protected class SearchObject
+ {
+
+ /** The curr. */
+ private AlignmentColumn curr;
+
+ /** The last defined. */
+ private AlignmentColumn lastDefined;
+
+ /** The node before last mismatch. */
+ private AlignmentColumn nodeBeforeLastMismatch;
+
+ /** The pending changes. */
+ private LinkedList <PendingChange> pendingChanges;
+
+ /** The p. */
+ private Pyrotag p;
+
+ /** The curr index. */
+ private int currIndex;
+
+ /** The successful. */
+ private boolean successful;
+
+ /** The ta. */
+ private RLEAlignmentIndelsOnly ta;
+
+ /** The logger. */
+ private AcaciaLogger logger;
+
+ /** The indent. */
+ private String indent;
+
+ /** The depth. */
+ private int depth;
+
+ /** The verbose. */
+ private boolean verbose;
+
+
+ /**
+ * Instantiates a new search object.
+ *
+ * @param curr the curr
+ * @param lastDefined the last defined
+ * @param nodeBeforeLastMismatch the node before last mismatch
+ * @param pendingChanges the pending changes
+ * @param p the p
+ * @param currIndex the curr index
+ * @param ta the ta
+ * @param logger the logger
+ * @param depth the depth
+ * @param verbose the verbose
+ */
+ public SearchObject (AlignmentColumn curr, AlignmentColumn lastDefined, AlignmentColumn nodeBeforeLastMismatch, LinkedList <PendingChange> pendingChanges,
+ Pyrotag p, int currIndex, RLEAlignmentIndelsOnly ta, AcaciaLogger logger, int depth, boolean verbose)
+ {
+ this.curr = curr;
+ this.lastDefined = lastDefined;
+ this.nodeBeforeLastMismatch = nodeBeforeLastMismatch;
+ this.pendingChanges = pendingChanges;
+ this.p = p;
+ this.currIndex = currIndex;
+ this.successful = true; //false when we hit a bad point
+ this.ta = ta;
+ this.logger = logger;
+ this.verbose = verbose;
+ this.depth = depth;
+
+ StringBuilder indentB = new StringBuilder();
+
+ for(int i = 0; i < this.depth; i++)
+ {
+ indentB.append(">");
+ }
+
+ this.indent = indentB.toString();
+
+ }
+
+ /**
+ * Run.
+ *
+ * @return true, if successful
+ * @throws Exception the exception
+ */
+ public boolean run() throws Exception
+ {
+ char [] value = p.getProcessedString();
+
+ boolean endOfReference = false;
+ boolean continueProcessing = false;
+
+
+ for(int i = this.currIndex; i < value.length; i++)
+ {
+ char currToken = value[i];
+
+ int startPos = i; //need to re-use this start pos I think, for the deletion case.
+
+ while(i < value.length && currToken == value[i])
+ {
+ i++;
+ }
+
+ int hpLength = i - startPos;
+ i--; //dont want to go too far forward.
+
+ //double check this continue logic, could be whack
+
+ //think of better choice for this.
+ if(endOfReference) //this could be troublesome, assuming that this char is the most common.
+ {
+ AlignmentColumn newChild = new AlignmentColumn(currToken);
+ newChild.obs.put(p, hpLength);
+ newChild.setParent(lastDefined);
+ lastDefined.setChild(newChild);
+ lastDefined = newChild;
+ continueProcessing = true;
+
+ if(verbose)
+ logger.writeLog(this.indent + "EOR: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ }
+ else
+ {
+
+ //first things first, lets check for identity
+ if(currToken == curr.getValue())
+ {
+ pendingChanges.add(new AddObservation(curr, p, hpLength)); //so I can roll back changes if necessary, if a failure occurs later in align.
+ lastDefined = curr;
+ curr = curr.child; //so this will be null if we are at the end.
+ continueProcessing = true;
+
+ if(verbose)
+ logger.writeLog(this.indent + "IDENTITY: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ }
+ else
+ {
+ //consecutive mismatches will not be tolerated.
+ //well, this keeps throwing an exception, because curr.getParent() is null?
+
+ if(verbose)
+ logger.writeLog(this.indent + "Before test that throws exception", AcaciaLogger.LOG_DEBUG);
+
+ if(nodeBeforeLastMismatch != null && nodeBeforeLastMismatch == curr.getParent())
+ {
+ if(verbose)
+ logger.writeLog(this.indent + "CONSECUTIVE MISMATCH: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ this.successful = false;
+
+ return false; //we will not tolerate TWO consecutive errors, so stick it!
+ }
+
+ if(verbose)
+ logger.writeLog(this.indent + "After test that may throw exception", AcaciaLogger.LOG_DEBUG);
+
+ //this is another good condition, as in, we are at the end of the consensus, and this sequence keeps going.
+ if(curr.getChild() == null)
+ {
+
+ if(verbose)
+ logger.writeLog(this.indent + "TERMINAL: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+
+ AlignmentColumn newTerminal = new AlignmentColumn(currToken);
+ newTerminal.obs.put(p, hpLength);
+ endOfReference = true;
+
+ curr.child = newTerminal;
+ curr = newTerminal;
+ lastDefined = newTerminal;
+ newTerminal.parent = curr;
+ continueProcessing = true;
+ this.successful = true; //it must be true, since we're actually modifying the alignment object!
+
+ }
+ else
+ {
+ if(verbose)
+ logger.writeLog(this.indent + " About to try insertion deletion", AcaciaLogger.LOG_DEBUG);
+
+ //okay, we're not matching up, try looking ahead?
+ SearchObject insertion = null;
+ SearchObject deletion = null;
+
+ if(verbose)
+ logger.writeLog("Depth is? " + this.depth, AcaciaLogger.LOG_DEBUG);
+
+ if(this.depth + 1 > this.ta.maxRecurseDepth)
+ {
+ if(verbose)
+ logger.writeLog(this.indent + "MAX_DEPTH: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ this.successful = false;
+ return false;
+ }
+
+ //insertion
+ if(i + 1 < value.length && value[i + 1] == curr.getValue()) //
+ {
+ if(verbose)
+ logger.writeLog(this.indent + "TRY INS: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ LinkedList <PendingChange> clonedPending = this.clonePendingChanges(); //clones all the pending changes
+
+ nodeBeforeLastMismatch = curr.getParent();
+ int newDepth = this.depth + 1;
+
+ insertion = new SearchObject(curr, lastDefined, nodeBeforeLastMismatch, clonedPending, this.p, i + 1,
+ this.ta, this.logger, newDepth, this.verbose);
+
+ boolean insAheadSuccessful = insertion.run();
+
+ AlignmentColumn grandParent = curr.getParent();
+
+ if(insAheadSuccessful)
+ {
+ if(verbose)
+ {
+ logger.writeLog(this.indent + "INS SUCCESSFUL: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+ logger.writeLog(this.indent + "WHAT IS HAPPENING???", AcaciaLogger.LOG_DEBUG);
+ if(grandParent != null)
+ {
+ logger.writeLog(this.indent + "Grandparent have insertion? " + (grandParent.getInsertionCorrespondingTo(currToken) != null), AcaciaLogger.LOG_DEBUG);
+ }
+ else
+ {
+ logger.writeLog(this.indent + "Grandparent is null.", AcaciaLogger.LOG_DEBUG);
+ }
+ }
+
+ //copy the pending changes of 'insertion'
+ this.pendingChanges = insertion.pendingChanges; //double check no pending changes are lost!
+
+ if(grandParent.getInsertionCorrespondingTo(currToken) != null)
+ {
+ if(verbose)
+ logger.writeLog(this.indent + "INS EXISTED: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ AlignmentColumn insertionNode = grandParent.getInsertionCorrespondingTo(currToken);
+ pendingChanges.add(new AddObservation(insertionNode, p, hpLength));
+
+ nodeBeforeLastMismatch = grandParent;
+ }
+ else
+ {
+
+ if(verbose)
+ {
+ logger.writeLog(this.indent + "INS UNIQUE: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+ }
+
+ //make an insertion node representing that insertion
+ pendingChanges.add(new InsertAChild(this.ta, grandParent, p, currToken, hpLength));
+ nodeBeforeLastMismatch = grandParent;
+ }
+
+ if(verbose)
+ {
+ logger.writeLog(this.indent + "RETURN TRUE, INS SUCCESS: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+ }
+
+ //we be done here.
+ //all the results are sitting in pending changes.
+ return true;//do we care that insertions are preferentially selected over deletions, no!
+ }
+ }
+
+ //insertion was not successful
+
+ if(verbose)
+ logger.writeLog(this.indent + "INS FAILED: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ if(curr.getChild().getValue() == value[i]) //clean deletion in the inserted sequence.
+ {
+ if(verbose)
+ logger.writeLog(this.indent + "TRYING DEL: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ LinkedList <PendingChange> clonedPending = this.clonePendingChanges();
+
+ //start pos was i before I started incrementing it to check out the HP length.
+
+ int newDepth = this.depth + 1;
+
+ deletion = new SearchObject(curr.getChild(), lastDefined, curr, clonedPending, this.p, startPos,
+ this.ta, this.logger,newDepth,this.verbose);
+ boolean successful = deletion.run();
+
+ if(successful)
+ {
+ if(verbose)
+ logger.writeLog(this.indent + "DEL SUCCESS:" + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ pendingChanges = deletion.pendingChanges; //keep these
+ pendingChanges.add(new AddObservation(curr, p, 0));
+ return true;
+ }
+ }
+
+ if(verbose)
+ logger.writeLog(this.indent + "DISCONTINUE PROCESSING: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ continueProcessing = false; //neither insertion or deletion worked.
+ }
+ }
+
+ //at end of all alternatives...
+ if(!continueProcessing) //only reason we keep going is end of reference?
+ {
+ if(verbose)
+ logger.writeLog(this.indent + "FAILURE: " + i + " curr token: " + currToken, AcaciaLogger.LOG_DEBUG);
+
+ this.successful = false;
+ return false;
+ }
+ }
+
+ if(curr == null)
+ {
+ endOfReference = true;
+ }
+ }
+ //at end of
+ if(verbose)
+ logger.writeLog(this.indent + "COMPLETE CONSUMED", AcaciaLogger.LOG_DEBUG);
+
+ return true;
+ }
+
+ /**
+ * Clone pending changes.
+ *
+ * @return the linked list
+ */
+ private LinkedList <PendingChange> clonePendingChanges()
+ {
+ LinkedList <PendingChange> clone = new LinkedList <PendingChange>();
+ clone.addAll(this.pendingChanges);
+ return clone;
+ }
+ }
+
+
+
+
+
+ /**
+ * The Class AlignmentColumn.
+ */
+ public class AlignmentColumn
+ {
+
+ /** The obs. */
+ HashMap <Pyrotag, Integer> obs;
+
+ /** The value. */
+ char value;
+
+ /** The child. */
+ AlignmentColumn child;
+
+ /** The parent. */
+ AlignmentColumn parent;
+
+ /** The flow number. */
+ int flowNumber;
+
+ /** The insertions after. */
+ AlignmentColumn [] insertionsAfter;
+
+ /**
+ * Instantiates a new alignment column.
+ *
+ * @param value the value
+ */
+ public AlignmentColumn(char value)
+ {
+ this.value = value;
+ this.obs = new HashMap <Pyrotag, Integer>();
+ this.parent = null;
+ this.child = null;
+ this.insertionsAfter = new AlignmentColumn []{null,null,null}; //will only accept an insertion of another base
+ this.flowNumber = -1;
+ }
+
+
+ /**
+ * Clone recursively with tags.
+ *
+ * @param pToKeep the to keep
+ * @param newParent the new parent
+ * @return the alignment column
+ */
+ public AlignmentColumn cloneRecursivelyWithTags(HashSet<Pyrotag> pToKeep, AlignmentColumn newParent)
+ {
+ AlignmentColumn ac = new AlignmentColumn(this.value);
+ ac.parent = newParent;
+
+ if(newParent != null)
+ newParent.child = ac;
+
+ for(Pyrotag p : this.obs.keySet())
+ {
+ if(pToKeep.contains(p))
+ {
+ ac.obs.put(p, this.obs.get(p));
+ }
+ }
+
+ ac.flowNumber = this.flowNumber;
+
+ for(int i = 0; i < this.insertionsAfter.length; i++)
+ {
+ if(this.insertionsAfter[i] != null)
+ {
+ //f(ofInterest != null)
+ // System.out.print("I:");
+ ac.insertionsAfter[i] = this.insertionsAfter[i].cloneWithTags(pToKeep);
+ }
+ }
+
+ if(child != null)
+ {
+ this.child.cloneRecursivelyWithTags(pToKeep, ac);
+ }
+
+ return ac;
+ }
+
+ /**
+ * Clone recursively with tags and truncate at.
+ *
+ * @param pToKeep the to keep
+ * @param newParent the new parent
+ * @param truncateAt the truncate at
+ * @return the alignment column
+ */
+ public AlignmentColumn cloneRecursivelyWithTagsAndTruncateAt(HashSet<Pyrotag> pToKeep, AlignmentColumn newParent, AlignmentColumn truncateAt)
+ {
+ //initially, this returns the head node. Should never truncate at the head...
+
+ AlignmentColumn ac = new AlignmentColumn(this.value);
+ ac.parent = newParent;
+
+ if(newParent != null)
+ newParent.child = ac;
+
+ for(Pyrotag p : this.obs.keySet())
+ {
+ if(pToKeep.contains(p))
+ {
+ ac.obs.put(p, this.obs.get(p));
+ }
+ }
+
+ ac.flowNumber = this.flowNumber;
+
+ for(int i = 0; i < this.insertionsAfter.length; i++)
+ {
+ if(this.insertionsAfter[i] != null)
+ {
+ //f(ofInterest != null)
+ // System.out.print("I:");
+ ac.insertionsAfter[i] = this.insertionsAfter[i].cloneWithTags(pToKeep);
+ }
+ }
+
+ //handles the case of truncate at.
+ if(child != null && child != truncateAt)
+ {
+ this.child.cloneRecursivelyWithTags(pToKeep, ac);
+ }
+
+ return ac;
+ }
+
+ /**
+ * Clone with tags.
+ *
+ * @param pToKeep the to keep
+ * @return the alignment column
+ */
+ public AlignmentColumn cloneWithTags(HashSet <Pyrotag> pToKeep)
+ {
+ AlignmentColumn ac = new AlignmentColumn(this.value);
+ for(Pyrotag p : this.obs.keySet())
+ {
+ if(pToKeep.contains(p))
+ {
+ ac.obs.put(p, this.obs.get(p));
+ }
+ }
+ return ac;
+ }
+
+
+ /**
+ * Next insertion given last flow.
+ *
+ * @param lastFlow the last flow
+ * @return the alignment column
+ * @throws Exception the exception
+ */
+ /*
+ public AlignmentColumn nextInsertionGivenLastFlow(char lastFlow) throws Exception
+ {
+ char curr = lastFlow;
+ do
+ {
+ for(int i = 0; i < insertionsAfter.length; i++)
+ {
+ if(insertionsAfter[i] != null && insertionsAfter[i].value == curr)
+ {
+ return insertionsAfter[i];
+ }
+ }
+
+ if(! Pyrotag.get.containsKey(curr))
+ {
+ throw new Exception("Curr has invalid char: " + curr);
+ }
+
+ curr = Pyrotag.flowCycle.get(curr); //moves forward
+ }while(curr != lastFlow);
+
+ return null;
+ }
+ */
+
+
+ /**
+ * Sets the flow number.
+ *
+ * @param flowNumber the new flow number
+ */
+ public void setFlowNumber(int flowNumber)
+ {
+ this.flowNumber = flowNumber;
+ }
+
+ /**
+ * Gets the tags.
+ *
+ * @return the tags
+ */
+ public Set <Pyrotag> getTags()
+ {
+ return this.obs.keySet();
+ }
+
+ /**
+ * Gets the insertion tags.
+ *
+ * @return the insertion tags
+ */
+ public Set <Pyrotag> getInsertionTags()
+ {
+ HashSet <Pyrotag> insertTags = new HashSet <Pyrotag>();
+
+ for(int i = 0; i < this.insertionsAfter.length; i++)
+ {
+ if(this.insertionsAfter[i] != null)
+ {
+ for(Pyrotag p: this.insertionsAfter[i].obs.keySet())
+ {
+ insertTags.add(p);
+ }
+ }
+ }
+ return insertTags;
+ }
+
+ /**
+ * Sets the parent.
+ *
+ * @param newParent the new parent
+ */
+ public void setParent(AlignmentColumn newParent)
+ {
+ this.parent = newParent;
+ }
+
+ /**
+ * Gets the parent.
+ *
+ * @return the parent
+ */
+ public AlignmentColumn getParent()
+ {
+ return this.parent;
+ }
+
+ /**
+ * Sets the child.
+ *
+ * @param newChild the new child
+ */
+ public void setChild(AlignmentColumn newChild)
+ {
+ this.child = newChild;
+ }
+
+ /**
+ * Adds the inserted.
+ *
+ * @param insertionAfterThis the insertion after this
+ * @throws Exception the exception
+ */
+ public void addInserted(AlignmentColumn insertionAfterThis) throws Exception
+ {
+ for(int i = 0; i < this.insertionsAfter.length; i++)
+ {
+ if(this.insertionsAfter[i] == null)
+ {
+ this.insertionsAfter[i] = insertionAfterThis;
+ return;
+ }
+ }
+
+ throw new Exception("Node could not be added");
+ }
+
+ /**
+ * Gets the insertion corresponding to.
+ *
+ * @param c the c
+ * @return the insertion corresponding to
+ */
+ public AlignmentColumn getInsertionCorrespondingTo(char c)
+ {
+ for(int i = 0; i < this.insertionsAfter.length; i++)
+ {
+ if(this.insertionsAfter[i]!= null && this.insertionsAfter[i].value == c)
+ return this.insertionsAfter[i];
+ }
+ return null;
+ }
+
+ /**
+ * Gets the child.
+ *
+ * @return the child
+ */
+ public AlignmentColumn getChild()
+ {
+ return this.child;
+ }
+
+ /**
+ * Gets the value.
+ *
+ * @return the value
+ */
+ public char getValue()
+ {
+ return this.value;
+ }
+
+ /**
+ * Gets the observations.
+ *
+ * @return the observations
+ */
+ public HashMap <Pyrotag, Integer> getObservations()
+ {
+ return this.obs;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString()
+ {
+ StringBuilder bd = new StringBuilder();
+ bd.append("[");
+ bd.append(this.value);
+ bd.append(":");
+
+ HashMap <Integer, HashSet <Pyrotag>> lengthToFreq = this.getHPLengthToTags(null);
+ for(int length: lengthToFreq.keySet())
+ {
+ int freq = lengthToFreq.get(length).size();
+ bd.append(freq);
+ bd.append("@");
+ bd.append(length);
+ bd.append(",");
+ }
+
+ bd.deleteCharAt(bd.length() - 1);
+
+
+ bd.append("<");
+ boolean insertExists =false;
+ for(int i = 0; i < this.insertionsAfter.length; i++)
+ {
+ if(this.insertionsAfter[i] != null)
+ {
+ bd.append(this.insertionsAfter[i].toString());
+ insertExists = true;
+ }
+ }
+
+ if(!insertExists)
+ {
+ bd.deleteCharAt(bd.length() - 1);
+ }
+ else
+ {
+ bd.append(">");
+ }
+ bd.append("]");
+
+ return bd.toString();
+ }
+
+ /**
+ * Gets the hP length to tags.
+ *
+ * @param ofInterest the of interest
+ * @return the hP length to tags
+ */
+ public HashMap <Integer, HashSet <Pyrotag>> getHPLengthToTags(HashSet<Pyrotag> ofInterest)
+ {
+ HashMap <Integer, HashSet <Pyrotag>> lengthToFreq = new HashMap <Integer, HashSet <Pyrotag>>();
+
+ for(Pyrotag p: this.obs.keySet())
+ {
+ if(! (ofInterest == null || ofInterest.contains(p)))
+ {
+ continue;
+ }
+
+ Integer length = this.obs.get(p);
+
+ if(! lengthToFreq.containsKey(length))
+ {
+ lengthToFreq.put(length, new HashSet <Pyrotag>());
+ }
+
+ lengthToFreq.get(length).add(p);
+ }
+ return lengthToFreq;
+ }
+
+ /**
+ * Record zero for insertions before.
+ *
+ * @param toAdd the to add
+ */
+ public void recordZeroForInsertionsBefore(Pyrotag toAdd)
+ {
+ AlignmentColumn parent = this.getParent();
+
+ if(parent != null)
+ {
+ for(int i = 0; i < parent.insertionsAfter.length; i++)
+ {
+ if(parent.insertionsAfter[i] != null)
+ {
+ if(!parent.insertionsAfter[i].obs.containsKey(toAdd)) //dont replace the observation!
+ parent.insertionsAfter[i].obs.put(toAdd, 0);
+ }
+ }
+ }
+ }
+
+ //try to avoid recursion, could be the reason for the lag.
+ //boolean tells you if the job is complete.
+ /**
+ * Correct read.
+ *
+ * @param p the p
+ * @param tagsInCluster the tags in cluster
+ * @param construction the construction
+ * @param position the position
+ * @param numModifications the num modifications
+ * @return true, if successful
+ */
+ public boolean correctRead(Pyrotag p, HashSet <Pyrotag> tagsInCluster,StringBuilder construction, MutableInteger position, MutableInteger numModifications)
+ {
+ char [] pStr = p.getCollapsedRead();
+
+ if(this.value == ' ')
+ {
+ return false;
+ }
+ else if(position.value() >= pStr.length) //dont want to go longer than the read is
+ {
+ return true;
+ }
+ else
+ {
+ char curr = pStr[position.value()];
+
+ int modeObs = -1;
+ int modeLength = -1;
+
+ HashMap <Integer, HashSet <Pyrotag>> freq = this.getHPLengthToTags(tagsInCluster);
+
+ int tagObsLength = -1;
+
+ for(Integer length: freq.keySet())
+ {
+ if(freq.get(length).size() > modeObs)
+ {
+ modeLength = length;
+ modeObs = freq.get(length).size();
+ }
+
+ if(freq.get(length).contains(p))
+ {
+ tagObsLength = length;
+ }
+ }
+
+ if(tagObsLength != modeLength)
+ {
+ numModifications.increment();
+ }
+
+ for(int i = 0; i < modeLength; i++)
+ {
+ construction.append(curr);
+ }
+
+ if(modeLength > 0) //takes care of those one-base insertions
+ position.increment();
+
+ for(int i = 0; i < this.insertionsAfter.length; i++)
+ {
+ if(this.insertionsAfter[i] != null)
+ {
+ this.insertionsAfter[i].correctRead(p, tagsInCluster, construction, position, numModifications); //will return because they have no children.
+ }
+ }
+ return false;
+ }
+ }
+ }
+
+ /**
+ * The Interface PendingChange.
+ */
+ public interface PendingChange
+ {
+
+ /**
+ * Perform modification.
+ *
+ * @return true, if successful
+ */
+ boolean performModification();
+
+ /**
+ * To string.
+ *
+ * @return the string
+ */
+ String toString();
+ }
+
+ /**
+ * The Class InsertAChild.
+ */
+ private class InsertAChild implements PendingChange
+ {
+
+ /** The before insertion. */
+ AlignmentColumn beforeInsertion;
+
+ /** The p. */
+ Pyrotag p;
+
+ /** The inserted char. */
+ char insertedChar;
+
+ /** The obs length. */
+ int obsLength;
+
+ /** The ta. */
+ RLEAlignmentIndelsOnly ta;
+
+ /**
+ * Instantiates a new insert a child.
+ *
+ * @param ta the ta
+ * @param beforeInsertion the before insertion
+ * @param p the p
+ * @param insertedChar the inserted char
+ * @param obsLength the obs length
+ */
+ public InsertAChild(RLEAlignmentIndelsOnly ta, AlignmentColumn beforeInsertion, Pyrotag p, char insertedChar, int obsLength)
+ {
+ this.beforeInsertion = beforeInsertion;
+ this.p = p;
+ this.insertedChar = insertedChar;
+ this.obsLength = obsLength;
+ this.ta = ta;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.ThreadedAlignment.PendingChange#performModification()
+ */
+ public boolean performModification()
+ {
+ try
+ {
+ //perform all the stuff required to do an insertion node.
+
+ AlignmentColumn insertionInQuery = new AlignmentColumn(insertedChar);
+ HashSet <Pyrotag> allTags = ta.getAllTags();
+
+ for(Pyrotag noInsert: allTags)
+ {
+ insertionInQuery.obs.put(noInsert, 0);
+ }
+
+ insertionInQuery.obs.put(p, this.obsLength);
+ beforeInsertion.addInserted(insertionInQuery);
+
+ }
+ catch(Exception e)
+ {
+ System.out.println("An error occurred!!!");
+ }
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("Insert a child after node: " + beforeInsertion);
+ sb.append(", for pyrotag: " + p.getID());
+ sb.append("Inserted char: " + insertedChar + " obs length: " + obsLength);
+ return sb.toString();
+ }
+ }
+
+ /**
+ * The Class AddObservation.
+ */
+ private class AddObservation implements PendingChange
+ {
+
+ /** The to update. */
+ AlignmentColumn toUpdate;
+
+ /** The to add. */
+ Pyrotag toAdd;
+
+ /** The obs length. */
+ int obsLength;
+
+ /**
+ * Instantiates a new adds the observation.
+ *
+ * @param toUpdate the to update
+ * @param toAdd the to add
+ * @param obsLength the obs length
+ */
+ public AddObservation(AlignmentColumn toUpdate, Pyrotag toAdd, int obsLength)
+ {
+ this.toUpdate = toUpdate;
+ this.toAdd = toAdd;
+ this.obsLength = obsLength;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.ThreadedAlignment.PendingChange#performModification()
+ */
+ public boolean performModification()
+ {
+ try
+ {
+ this.toUpdate.obs.put(toAdd, obsLength);
+
+ this.toUpdate.recordZeroForInsertionsBefore(toAdd);
+
+ return true;
+ }
+ catch(Exception e)
+ {
+ System.out.println("An exception occurred!!!");
+ System.out.println(e.getMessage());
+ }
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("AddObservation: " + this.toUpdate + ", value " + this.toUpdate.getValue() + " toAdd: " + toAdd.getID() + ", observation: " + this.obsLength);
+ return sb.toString();
+ }
+ }
+
+ /**
+ * Iterator.
+ *
+ * @return the iterator
+ */
+ public Iterator <AlignmentColumn> iterator()
+ {
+ return new AlignmentIterator(this);
+ }
+
+ /**
+ * The Class AlignmentIterator.
+ */
+ private class AlignmentIterator implements Iterator <AlignmentColumn>
+ {
+
+ /** The curr. */
+ private AlignmentColumn curr;
+
+ /** The it head. */
+ private AlignmentColumn itHead;
+
+
+
+ /**
+ * Instantiates a new alignment iterator.
+ *
+ * @param ta the ta
+ */
+ public AlignmentIterator(RLEAlignmentIndelsOnly ta)
+ {
+ this.itHead = ta.head;
+ curr = START_COL;
+ }
+
+ //I think in threaded alignment, it is assumed that the inner layer of ACs are processed.
+ /* (non-Javadoc)
+ * @see java.util.Iterator#hasNext()
+ */
+ public boolean hasNext()
+ {
+ if(curr == START_COL && itHead != null)
+ {
+ return true;
+ }
+ else if(curr.getChild() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ //completely skip the head node in here.
+ /* (non-Javadoc)
+ * @see java.util.Iterator#next()
+ */
+ public AlignmentColumn next()
+ {
+ if(curr == START_COL)
+ {
+ curr = itHead;
+ }
+ else
+ {
+ this.curr = curr.getChild();
+ }
+ return curr;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Iterator#remove()
+ */
+ public void remove()
+ {
+ //I do nothing.
+ }
+ }
+
+
+}
diff --git a/src/pyromaniac/Algorithm/SimpleClusterAligner.java b/src/pyromaniac/Algorithm/SimpleClusterAligner.java
new file mode 100644
index 0000000..f1da496
--- /dev/null
+++ b/src/pyromaniac/Algorithm/SimpleClusterAligner.java
@@ -0,0 +1,456 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.Algorithm;
+
+import java.io.BufferedWriter;
+import java.util.ArrayDeque;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.TreeSet;
+
+import pyromaniac.AcaciaConstants;
+import pyromaniac.AcaciaEngine;
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.MIDPrimerCombo;
+import pyromaniac.DataStructures.Pair;
+import pyromaniac.DataStructures.PatriciaTrie;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.DataStructures.Triplet;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class SimpleClusterAligner.
+ */
+public class SimpleClusterAligner implements ClusterAligner
+{
+
+ /**
+ * Instantiates a new simple cluster aligner.
+ */
+ private SimpleClusterAligner()
+ {
+ }
+
+ //singleton pattern
+ /**
+ * Gets the single instance of SimpleClusterAligner.
+ *
+ * @return single instance of SimpleClusterAligner
+ */
+ public static SimpleClusterAligner getInstance()
+ {
+ return SimpleClusterAlignerHolder.getInstance();
+ }
+
+ /**
+ * The Class SimpleClusterAlignerHolder.
+ */
+ public static class SimpleClusterAlignerHolder
+ {
+
+ /** The Constant INSTANCE. */
+ private static final SimpleClusterAligner INSTANCE = new SimpleClusterAligner();
+
+ /**
+ * Gets the single instance of SimpleClusterAlignerHolder.
+ *
+ * @return single instance of SimpleClusterAlignerHolder
+ */
+ public static SimpleClusterAligner getInstance()
+ {
+ return SimpleClusterAlignerHolder.INSTANCE;
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.Algorithm.ClusterAligner#generateAlignments(pyromaniac.IO.AcaciaLogger, java.util.HashMap, java.util.LinkedList, java.lang.String, java.util.HashMap, java.util.HashMap, java.util.LinkedList, java.util.LinkedList)
+ */
+ public void generateAlignments(
+ AcaciaLogger logger,
+ HashMap <String, String> settings,
+ LinkedList <Pyrotag> cluster,
+ String consensus, //consensus from hash-map
+ HashMap <String, BufferedWriter> outputHandles,
+ HashMap <Pyrotag,Integer> representativeSeqs,
+ ArrayDeque <Pair<RLEAlignmentIndelsOnly, HashMap<Pyrotag, Pair<Integer, Character>>>> allResults,
+ LinkedList <Pyrotag> singletons
+ ) throws Exception
+ {
+ boolean verbose = false;
+
+ //current result
+ Triplet <RLEAlignmentIndelsOnly, HashMap <Pyrotag, Pair<Integer,Character>>, LinkedList <Pyrotag>> result = null;
+
+ int ctr = 0;
+
+ String currConsensus = consensus;
+ LinkedList <Pyrotag> currCluster = cluster;
+
+ //initially, currCluster is not sorted by common sequence to less common. Possible that seeding aligmment sucks
+
+ //LinkedList <Pyrotag> sorted = sortClusterByLongerPrefix(currCluster); //TODO: test!
+
+ //currCluster = sorted;
+
+ /* keep trying to align the cluster
+ * remove sequences that did align
+ * try aligning the remaining sequences, too few form a consensus
+ * use perfect matching alignment (ie. reads align for the length of the smaller read/s).
+ * if the consensus consists of one sequence, treat everyone as a singleton.
+ */
+
+ do
+ {
+
+ result = _alignSequences(logger, settings, currCluster, currConsensus, verbose);
+
+
+ allResults.add(new Pair <RLEAlignmentIndelsOnly, HashMap <Pyrotag, Pair <Integer, Character>>>(result.first, result.second));
+
+ //all aligned
+ if(result.third.size() == 0)
+ {
+ break;
+ }
+ //only one sequence did not fit the alignment, mark it as a signleton
+ if(result.third.size() == 1)
+ {
+ singletons.add(result.third.getFirst());
+ break;
+ }
+
+
+ //'checking' to see if there is a decent consensus...
+ Pair <String, Integer> consensusRes = this._alignSequencesHelper(logger, result.third);
+
+ //there doesn't seem to be any consensus in the RLE, and not much power with the number of sequences to align.
+ //make every sequence a singleton (ie. if there is only 1 sequence as a consensus...)
+ if(consensusRes.getSecond() == 1 && result.third.size() < 5)
+ {
+ for(Pyrotag p: result.third)
+ {
+ singletons.add(p);
+ }
+ break; //we are done here too...
+ }
+
+ /* if there aren't vast improvements in the number of things are being added, we will rely on perfect identity
+ * the condition to use the trie is that we've tried doing it the normal way once, and the previous cluster is only
+ * two larger than the curr cluster (ie. it's not going anywhere)
+ */
+
+ //may or may not make a difference....
+ if(ctr > 1 && currCluster.size() - result.third.size() <= 2 && currCluster.size() < 10)
+ {
+ PatriciaTrie trie = new PatriciaTrie();
+ for(Pyrotag p: result.third)
+ {
+ //insert all the non-conforming sequences intro the trie.
+ trie.insertString(new String(p.getCollapsedRead()), p);
+ }
+
+
+ //it is possible for one sequence to belong to one or more pSets
+
+ //okay so we have inserted all the RLE reads that are not aligning.
+ LinkedList <Pair <HashSet<Pyrotag>, String>> prefixSets = trie.getPrefixSets();
+
+
+ //formally align only those sequences which share identical prefixes.
+ //dont allow a sequence to be added to multiple locations
+
+ HashSet<Pyrotag> processed = new HashSet <Pyrotag>();
+
+ for(Pair <HashSet <Pyrotag>, String> pSet : prefixSets)
+ {
+ LinkedList <Pyrotag> prefixes = new LinkedList <Pyrotag> ();
+
+ //stops reads belonging to multiple alignments.
+ for(Pyrotag p: pSet.getFirst())
+ {
+ if(!processed.contains(p))
+ {
+ prefixes.add(p);
+ processed.add(p);
+ }
+ }
+
+ result = _alignSequences(logger, settings, prefixes, pSet.getSecond(), verbose);
+ //result contains the tags to their initial flow positions, straight after the MID.
+
+ allResults.add(new Pair <RLEAlignmentIndelsOnly, HashMap <Pyrotag, Pair <Integer, Character>>>(result.first, result.second));
+ if(result.third.size() > 0)
+ {
+
+ throw new Exception("Is assumed that result returned will have zero outliers in alignment");
+ }
+
+ }
+ break; //this will be the end
+ }
+ else
+ {
+ currConsensus = consensusRes.getFirst();
+ currCluster = result.third;
+ }
+
+ ctr++;
+
+ }while(result.third.size() > 0);
+ }
+
+ private LinkedList<Pyrotag> sortClusterByLongerPrefix (LinkedList<Pyrotag> currCluster)
+ {
+ //problem is for perfect clusters, did we used a prefix. We now should consider the smallest sequence?
+ //we are interested in a length where 75% of the reads are this long....
+ if(currCluster.size() == 1)
+ {
+ return currCluster;
+ }
+
+ HashMap <Integer, LinkedList <Pyrotag>> sizeToTags = new HashMap <Integer, LinkedList <Pyrotag>>();
+
+ //non unique elements. Boo!
+ for(Pyrotag p: currCluster)
+ {
+ int length = p.getCollapsedRead().length;
+
+ if(! sizeToTags.containsKey(length))
+ {
+ sizeToTags.put(length, new LinkedList <Pyrotag>());
+ }
+ sizeToTags.get(length).add(p);
+ }
+
+ LinkedList <Integer> lengths = new LinkedList<Integer>(sizeToTags.keySet());
+ Collections.sort(lengths);
+
+ int elements = currCluster.size();
+ int twentyFifthPercentile = (int) (elements / 4);
+ int cumulativeTotal = 0;
+ int minLength = 0;
+
+ for(int length: lengths)
+ {
+ cumulativeTotal += sizeToTags.get(length).size();
+
+ if(cumulativeTotal >= twentyFifthPercentile)
+ {
+ minLength = length;
+ break;
+ }
+ }
+
+ HashMap <String, HashSet<Pyrotag>> prefixOcc = new HashMap<String, HashSet <Pyrotag>>();
+
+ for(Pyrotag p: currCluster)
+ {
+ String prefix = (p.getCollapsedRead().length > minLength)? new String(Arrays.copyOf(p.getCollapsedRead(), minLength)) : new String(p.getCollapsedRead());
+ if(!prefixOcc.containsKey(prefix))
+ {
+ prefixOcc.put(prefix, new HashSet <Pyrotag>());
+ }
+ prefixOcc.get(prefix).add(p);
+ }
+
+ LinkedList <HashSet <Pyrotag>> groupedByCommonPrefix = new LinkedList <HashSet <Pyrotag>>(prefixOcc.values());
+ Collections.sort(groupedByCommonPrefix, new ComparatorHashSetPyrotag());
+ //sorted
+
+ LinkedList <Pyrotag> sortedTags = new LinkedList <Pyrotag>();
+ //they are added in the wrong direction.
+
+ for(HashSet <Pyrotag> hs: groupedByCommonPrefix)
+ {
+ sortedTags.addAll(hs);
+ }
+
+ return sortedTags;
+ }
+
+ public class ComparatorHashSetPyrotag implements Comparator<HashSet<Pyrotag>>
+ {
+ public int compare(HashSet<Pyrotag> o1, HashSet<Pyrotag> o2)
+ {
+ return (o1.size() > o2.size() ? -1 : (o1.size() == o2.size() ? 0 : 1));
+ }
+ }
+
+ /**
+ * _align sequences.
+ *
+ * @param logger the logger
+ * @param settings the settings
+ * @param cluster the cluster
+ * @param consensus the consensus
+ * @return the triplet
+ * @throws Exception the exception
+ */
+ private Triplet <RLEAlignmentIndelsOnly, HashMap <Pyrotag, Pair<Integer,Character>>, LinkedList <Pyrotag>> _alignSequences(
+ AcaciaLogger logger,
+ HashMap <String, String> settings,
+ LinkedList <Pyrotag> cluster,
+ String consensus,
+ boolean verbose
+ ) throws Exception
+ {
+
+ Integer maxRecurseDepth = Integer.parseInt(settings.get(AcaciaConstants.OPT_MAX_RECURSE_DEPTH));
+ RLEAlignmentIndelsOnly ta = new RLEAlignmentIndelsOnly(consensus, logger, maxRecurseDepth);
+
+ int count = 0;
+
+ HashMap <Pyrotag, Pair <Integer, Character>> tagToCurrPosInFlow =
+ new HashMap <Pyrotag, Pair<Integer, Character>>();
+
+
+ String key = settings.get(AcaciaConstants.OPT_FLOW_KEY);
+ char lastInKey = key.charAt(key.length() - 1);
+
+
+ //sequences which could not be aligned... should be outputted already... and also the stats of these should be recorded.
+ //prepare tag to flow position hash
+ LinkedList <Pyrotag> unalignableTags = new LinkedList <Pyrotag>();
+
+ int numAlignments = 0;
+
+
+
+
+ for(Pyrotag p: cluster)
+ {
+
+ boolean alignable = ta.align(p, verbose);
+ numAlignments++;
+
+ if(alignable)
+ {
+ count++;
+
+ if(verbose)
+ {
+ logger.writeLog("Could align p: " + p.getID(), AcaciaLogger.LOG_DEBUG);
+ }
+
+
+ //this returns the flow position of the first called base after the key/MID/primer
+ //but this flow position does NOT correspond to the last base of the primer.
+ //so either need to return the flow of the last base in the reference
+ //or use teh base of the first char in the collapsed read
+ // might make moer sense to return the last called base in the primer for the below.
+ //int [] flowPosAfterKeyMID = p.getFlowForCollapsedReadPos(settings.get(AcaciaConstants.OPT_FLOW_KEY), 0);
+
+
+ int [] flowPosAfterKeyMID = p.getFlowPositionForCallPriorToCollapsedReadStart(settings.get(AcaciaConstants.OPT_FLOW_KEY));
+ //base, flowpos, cycle pos
+
+ //position in flow corresponding to last base of MID or last base of key.
+ int posAfterKeyAndMID = flowPosAfterKeyMID[FlowCycler.FLOW_POSITION];
+
+ //base corresponding to either last of key or last of MID/primer. Just realise that below is probably wrong -- are you offsetting for primer and mid or just mid??
+ //definitely after the primer.
+ MIDPrimerCombo mid = p.getMultiplexTag();
+ String midPrimer = mid.getMIDPrimerSequence();
+
+ char currPos = (mid == AcaciaConstants.NO_MID_GROUP)? lastInKey : midPrimer.charAt(midPrimer.length() - 1);
+
+ //if I change this, such that its the iterator... would it be any use?
+ tagToCurrPosInFlow.put(p, new Pair <Integer, Character>(posAfterKeyAndMID,currPos));
+ }
+ else
+ {
+ if(verbose)
+ {
+ logger.writeLog("Could not align p: " + p.getID(), AcaciaLogger.LOG_DEBUG);
+ }
+
+ unalignableTags.add(p);
+ }
+ }
+
+ if(verbose)
+ {
+ logger.writeLog("Done!", AcaciaLogger.LOG_DEBUG);
+ }
+
+ Triplet <RLEAlignmentIndelsOnly, HashMap <Pyrotag, Pair <Integer, Character>>, LinkedList <Pyrotag>> result = new Triplet
+ <RLEAlignmentIndelsOnly, HashMap <Pyrotag, Pair <Integer, Character>>, LinkedList <Pyrotag>> (ta, tagToCurrPosInFlow, unalignableTags);
+ return result;
+ }
+
+ //this method decides whether we should stop attempting to align these sequences, as they will never agree.
+ //there is no consensus if no-one shares a RLE prefix.
+ /**
+ * _align sequences helper.
+ *
+ * @param logger the logger
+ * @param unalignable the unalignable
+ * @return the pair
+ * @throws Exception the exception
+ */
+ private Pair <String,Integer> _alignSequencesHelper(AcaciaLogger logger, LinkedList<Pyrotag> unalignable) throws Exception
+ {
+ //prepare sequences maybe? dunno really...
+ //sequences that made it into this thingy have a substitution. They should try to be aligned again. They may have an insertion error also.
+ int smallestRLELength = -1;
+
+ for(Pyrotag p: unalignable)
+ {
+ char [] rle = p.getCollapsedRead();
+
+ if(smallestRLELength == -1 || rle.length < smallestRLELength)
+ {
+ smallestRLELength = rle.length;
+ }
+ }
+ HashMap <String, Integer> mostCommonPrefix = new HashMap <String, Integer>();
+
+ int mostCommon = -1;
+ String mostCommonSeq = null;
+
+ for(Pyrotag p: unalignable)
+ {
+ char [] seq = p.getCollapsedRead();
+ char [] subseq = Arrays.copyOfRange(seq, 0, smallestRLELength);
+
+ if(!mostCommonPrefix.containsKey(new String(subseq)))
+ {
+ mostCommonPrefix.put(new String(subseq), 0);
+ }
+
+ int newValue = mostCommonPrefix.get(new String(subseq)) + 1;
+
+ if(mostCommon < newValue)
+ {
+ mostCommon = newValue;
+ mostCommonSeq = new String(subseq);
+ }
+
+ mostCommonPrefix.put(new String(subseq), newValue);
+ }
+
+ return new Pair <String, Integer> (mostCommonSeq, mostCommon);
+ }
+}
diff --git a/src/pyromaniac/DataCleaner.java b/src/pyromaniac/DataCleaner.java
new file mode 100644
index 0000000..7536b72
--- /dev/null
+++ b/src/pyromaniac/DataCleaner.java
@@ -0,0 +1,366 @@
+package pyromaniac;
+
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.LinkedList;
+
+import pyromaniac.RunCharacterisation;
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.MIDPrimerCombo;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.IO.AcaciaLogger;
+import pyromaniac.IO.TagImporter;
+
+public class DataCleaner
+{
+ private DataCleaner()
+ {
+ }
+
+ /**
+ * SingletonHolder is loaded on the first execution of Singleton.getInstance()
+ * or the first access to SingletonHolder.INSTANCE, not before.
+ */
+ private static class DataCleanerHolder
+ {
+
+ /** The Constant INSTANCE. */
+ private static final DataCleaner INSTANCE = new DataCleaner();
+
+ /**
+ * Gets the single instance of AcaciaUtilityHolder.
+ *
+ * @return single instance of AcaciaUtilityHolder
+ */
+ public static DataCleaner getInstance()
+ {
+ return DataCleanerHolder.INSTANCE;
+ }
+ }
+
+ public static DataCleaner getDataCleaner()
+ {
+ return DataCleanerHolder.getInstance();
+ }
+
+ public RunCharacterisation initialiseRunCharacterisation(HashMap <String, String> settings, AcaciaLogger logger,
+ LinkedList <MIDPrimerCombo> midsToUse) throws Exception
+ {
+
+ if(midsToUse.size() == 0)
+ midsToUse.add(AcaciaConstants.NO_MID_GROUP);
+
+ HashMap <MIDPrimerCombo, LinkedList <Pyrotag>> MIDToSequences = new HashMap <MIDPrimerCombo, LinkedList <Pyrotag> >();
+ HashMap <MIDPrimerCombo, Integer> MIDseqLength = new HashMap <MIDPrimerCombo, Integer>();
+ HashMap <MIDPrimerCombo, Integer> MIDcollapsedSeqLength = new HashMap <MIDPrimerCombo, Integer>();
+ HashMap <MIDPrimerCombo, Double> MIDqualities = new HashMap <MIDPrimerCombo, Double>();
+
+ int fileIndex = 0;
+
+ logger.writeLog("Preparing sequence importer", AcaciaLogger.LOG_PROGRESS);
+ TagImporter importer = AcaciaEngine.getEngine().getTagImporter(settings, logger);
+
+ Pyrotag p = importer.getPyrotagAtIndex(fileIndex);
+
+ //loading only sequences which have valid MID.
+
+ int invalidMID = 0;
+ int validMID = 0;
+
+ while (p != null)
+ {
+ MIDPrimerCombo matching = p.whichMID(midsToUse);
+
+ if(matching == null)
+ {
+ fileIndex++;
+ p = importer.getPyrotagAtIndex(fileIndex);
+ invalidMID++;
+
+ continue;
+ }
+
+ validMID++;
+
+ p.setMIDPrimerCombo(matching); //may already be initialised?
+
+ if(! MIDToSequences.containsKey(matching))
+ {
+ MIDToSequences.put(matching, new LinkedList <Pyrotag>());
+ }
+ MIDToSequences.get(matching).add(p);
+
+ if(! MIDseqLength.containsKey(matching))
+ {
+ MIDseqLength.put(matching, 0);
+ }
+
+ MIDseqLength.put(matching, MIDseqLength.get(matching) + p.getLength());
+
+ if(p.getQualities() != null)
+ {
+ if(! MIDqualities.containsKey(matching))
+ {
+ MIDqualities.put(matching, 0.0);
+ }
+
+ MIDqualities.put(matching, MIDqualities.get(matching) + p.getUntrimmedAvgQuality());
+ }
+
+ char [] collapsedReadMinusMid = p.getCollapsedRead();
+
+ if(!MIDcollapsedSeqLength.containsKey(matching))
+ {
+ MIDcollapsedSeqLength.put(matching, 0);
+ }
+
+ MIDcollapsedSeqLength.put(matching, MIDcollapsedSeqLength.get(matching) + collapsedReadMinusMid.length);
+
+ fileIndex++;
+ p = importer.getPyrotagAtIndex(fileIndex);
+ }
+
+ RunCharacterisation rc = new RunCharacterisation(MIDToSequences, MIDseqLength, MIDcollapsedSeqLength, MIDqualities, validMID, invalidMID);
+
+ if(rc.getNumValidMIDS() == 0)
+ {
+ logger.writeLog("There were no valid MIDS in the file!", AcaciaLogger.LOG_ERROR);
+ logger.writeLog("There were no valid MIDS in the file!", AcaciaLogger.LOG_PROGRESS);
+ return null;
+ }
+
+ return rc;
+ }
+
+ //this modifies the pyrotag reads, and also removes reads from the run characterisation that did not satisfy requirements.
+ public void filterAndTrimReads(HashMap <String, String> settings, AcaciaLogger logger, RunCharacterisation rc,
+ LinkedList <MIDPrimerCombo> midsToUse, HashMap <String, BufferedWriter> outputHandles) throws Exception
+ {
+ //perhaps better handling of no valid ids.
+ if(rc.getNumValidMIDS() == 0)
+ {
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("Number of reads with invalid MID: " + rc.getNumInvalidMIDS() + System.getProperty("line.separator"));
+ logger.writeLog("There were no valid MIDS in the file!", AcaciaLogger.LOG_ERROR);
+ logger.writeLog("There were no valid MIDS in the file!", AcaciaLogger.LOG_PROGRESS);
+ throw new Exception("No valid reads");
+ }
+
+ double meanLength = rc.getMeanReadLengthForMID(midsToUse);
+ double stdDevRead = rc.calculateLengthStandardDevForRead(midsToUse);
+ double stdDevCollapsed = rc.calculateCollapsedLengthStandardDevForRead(midsToUse);
+
+
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("Mean length (before filtering): " + meanLength + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("Length SD (before filtering): " + stdDevRead + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("Length SD collapsed (before filtering): " + stdDevCollapsed + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("Number of reads with invalid MID: " + rc.getNumInvalidMIDS() + System.getProperty("line.separator"));
+
+ double numStdDev = Double.parseDouble(settings.get(AcaciaConstants.OPT_MAX_STD_DEV_LENGTH));
+
+ int minReadLength = (int) (meanLength - (numStdDev * stdDevRead));
+ int maxReadLength = (int) (meanLength + (numStdDev * stdDevRead));
+
+ if(minReadLength < 0)
+ minReadLength = 0;
+
+ logger.writeLog("Accepting reads in the range: " + minReadLength + " - " + maxReadLength, AcaciaLogger.LOG_PROGRESS);
+
+ int minCollapsedSize = AcaciaConstants.DEFAULT_OPT_TRIM_COLLAPSED;
+ int minQual = Integer.parseInt(settings.get(AcaciaConstants.OPT_MIN_AVG_QUALITY));
+ int usableSeqs = 0;
+ int unusableSeqs = 0;
+ int lowQuality = 0;
+ int outsideLengthRange = 0;
+ int hasNs = 0;
+ int hasWobble = 0;
+ int collapsedTooShort = 0;
+ int trimLengthGeneral = this.getTrim(settings);
+
+ HashMap <String, Integer> dereplicated = new HashMap<String, Integer>();
+
+ boolean verbose = false;
+
+ //another outfile
+ LinkedList <MIDPrimerCombo> midsToProcess = midsToUse;
+
+ if(midsToProcess.size() == 1 && midsToProcess.getFirst() == AcaciaConstants.NO_MID_GROUP)
+ {
+ midsToProcess = new LinkedList <MIDPrimerCombo>(rc.MIDToSequences.keySet());
+ }
+
+ for(MIDPrimerCombo midPrimer: midsToProcess)
+ {
+ //there were no tags for that MID
+ if(!rc.MIDToSequences.containsKey(midPrimer))
+ {
+ continue;
+ }
+
+ LinkedList <Pyrotag> seqs = rc.MIDToSequences.get(midPrimer);
+ LinkedList <Pyrotag> toRemove = new LinkedList <Pyrotag>();
+
+ for(Pyrotag p: seqs)
+ {
+ int trimLength = trimLengthGeneral; //overall trim length.
+ boolean satisfyOverallLength = (p.getReadString().length >= minReadLength) && (p.getReadString().length <= maxReadLength);
+
+ //trim read to a particular flow position
+ if(!
+ (settings.get(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW) == null || settings.get(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW).equals("null")
+ || settings.get(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW).equals("")))
+ {
+ int flowToTrimTo = Integer.parseInt(settings.get(AcaciaConstants.OPT_TRUNCATE_READ_TO_FLOW));
+ int basePosForFlow = p.flowPosToBasePos(flowToTrimTo, settings.get(AcaciaConstants.OPT_FLOW_KEY));
+
+ if(basePosForFlow != Pyrotag.NO_CORRESPONDING_FLOW)
+ {
+ if(trimLength > 0)
+ {
+ trimLength = (trimLength < basePosForFlow)? trimLength : basePosForFlow;
+ }
+ else
+ {
+ trimLength = basePosForFlow;
+ }
+ }
+ }
+
+ //trim to first N.
+ //note that if the first N occurs straight after the MID primer, the read will have length zero.
+ int firstN = p.firstOccurrenceOfAmbiguous(); //
+
+ if(trimLength > 0)
+ {
+ p.setTrimToLength(trimLength);
+ }
+
+ //so why do I set MID primer now?
+ p.setMIDPrimerCombo(midPrimer);
+
+ char [] collapsed = p.getCollapsedRead();
+
+ int minNFlowPos = Integer.parseInt(settings.get(AcaciaConstants.OPT_FILTER_READS_WITH_N_BEFORE_POS)); //default is 350
+
+ //firstly, this pertains to first N position, of which there may be zero.
+ int [] firstFlowForNs = null;
+
+ if(firstN != Pyrotag.NO_N && collapsed.length > 0)
+ {
+ firstFlowForNs = p.getFlowPositionForCollapsedReadPosition(settings.get(AcaciaConstants.OPT_FLOW_KEY), firstN);
+ }
+
+ //this should take care of the fact that N's can occur at the beginning.
+ if(firstN != Pyrotag.NO_N && (trimLength < 0 || trimLength > firstN))
+ {
+ trimLength = firstN;
+ p.setTrimToLength(trimLength);
+ collapsed = p.getCollapsedRead();
+ }
+
+ /* 1. The collapsed read needs to satisfy the minimum collapsed size
+ * 2. There are no quality thresholds or the untrimmed average quality is greater than the min quality
+ * 3. There are no wobbles in the processed string
+ * 4. Either there are no N's or the first flow for N's is greater than the min N flow position.
+ */
+
+ if(satisfyOverallLength &&
+ collapsed.length >= minCollapsedSize
+ && (p.getQualities() == null || p.getUntrimmedAvgQuality() >= minQual)
+ && ! p.hasWobbleInProcessedString()
+ && (firstN == Pyrotag.NO_N || (firstFlowForNs[FlowCycler.FLOW_POSITION] > minNFlowPos))
+ )
+ {
+ usableSeqs++;
+ }
+ else
+ {
+ toRemove.add(p);
+
+ if(!satisfyOverallLength)
+ {
+ outsideLengthRange++;
+ if(verbose)
+ logger.writeLog("Outside acceptable size range [ " + minReadLength + " - " + maxReadLength + " ]: " + p.getID(), AcaciaLogger.LOG_DEBUG);
+ }
+
+ if(firstN > 0 && firstFlowForNs[FlowCycler.FLOW_POSITION] < minNFlowPos)
+ {
+ if(verbose)
+ logger.writeLog("Has N's: " + p.getID(), AcaciaLogger.LOG_DEBUG);
+
+ hasNs++;
+ }
+
+ if(p.hasWobbleInProcessedString())
+ {
+ if(verbose)
+ logger.writeLog("Has wobbles: " + p.getID(), AcaciaLogger.LOG_DEBUG);
+ hasWobble++;
+ }
+
+ if(p.getQualities() != null && p.getUntrimmedAvgQuality() < minQual)
+ {
+ lowQuality++;
+
+ if(verbose)
+ logger.writeLog("Low quality:" + p.getID(), AcaciaLogger.LOG_DEBUG);
+ }
+
+ if(collapsed.length < minCollapsedSize)
+ {
+ collapsedTooShort++;
+ if(verbose)
+ logger.writeLog("Collapsed too short: " + p.getID(), AcaciaLogger.LOG_DEBUG);
+ }
+ //too small, throw out.
+ unusableSeqs++;
+ }
+ }
+
+ if(usableSeqs == 0)
+ {
+ logger.writeLog("MID: " + midPrimer.getDescriptor() + " had no reads", AcaciaLogger.LOG_PROGRESS);
+ }
+
+ //remove the unusable pyrotags, sounds good.
+ seqs.removeAll(toRemove);
+ }
+
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# Seqs usable: " + usableSeqs + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# Seqs thrown out: " + unusableSeqs + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# Low quality: " + lowQuality + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# Outside length range [ " + minReadLength + " - " + maxReadLength + " ]: " + outsideLengthRange + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# with early N's: " + hasNs + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# with wobble's: " + hasWobble + System.getProperty("line.separator")); //really should never happen.
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# collapsed too short: " + collapsedTooShort + System.getProperty("line.separator"));
+ outputHandles.get(AcaciaConstants.STAT_OUT_FILE).write("# Unique sequences: " + dereplicated.size() + System.getProperty("line.separator"));
+
+ if(usableSeqs == 0)
+ {
+ logger.writeLog("No sequences satisified all filters", AcaciaLogger.LOG_PROGRESS);
+ throw new Exception("No sequences satisfied filters");
+ }
+ }
+
+ /**
+ * Gets the trim length.
+ *
+ * @param settings the Acacia settings
+ * @return the trim length
+ * @throws NumberFormatException Any formatting exception that occurs while parsing the trim length parameter
+ */
+ public int getTrim(HashMap <String, String> settings) throws NumberFormatException
+ {
+ String sTrimLength = settings.get(AcaciaConstants.OPT_TRIM_TO_LENGTH);
+ int trimLength = 0;
+ if (sTrimLength != null && !sTrimLength.equals(""))
+ {
+ trimLength = Integer.parseInt(sTrimLength);
+ return trimLength;
+ }
+ return -1; // fail
+ }
+}
diff --git a/src/pyromaniac/DataStructures/DMCell.java b/src/pyromaniac/DataStructures/DMCell.java
new file mode 100644
index 0000000..a41833c
--- /dev/null
+++ b/src/pyromaniac/DataStructures/DMCell.java
@@ -0,0 +1,28 @@
+package pyromaniac.DataStructures;
+
+public class DMCell
+{
+ private int row;
+ private int col;
+ private double value;
+
+ public DMCell(int row, int col, double value)
+ {
+ this.row = row;
+ this.col = col;
+ this.value = value;
+ }
+
+ public int getRow() {
+ return row;
+ }
+
+ public int getCol() {
+ return col;
+ }
+
+ public double getValue() {
+ return value;
+ }
+}
+
diff --git a/src/pyromaniac/DataStructures/DistanceMatrix.java b/src/pyromaniac/DataStructures/DistanceMatrix.java
new file mode 100644
index 0000000..491e146
--- /dev/null
+++ b/src/pyromaniac/DataStructures/DistanceMatrix.java
@@ -0,0 +1,118 @@
+package pyromaniac.DataStructures;
+
+import java.util.Iterator;
+
+import ch.usi.inf.sape.hac.experiment.DissimilarityMeasure;
+import ch.usi.inf.sape.hac.experiment.Experiment;
+
+public class DistanceMatrix implements Iterable, Experiment, DissimilarityMeasure
+{
+ double [][] distMat;
+
+ public DistanceMatrix(int numCompared)
+ {
+ this.distMat = new double [numCompared - 1][];
+
+ for(int i = 0; i < this.distMat.length; i++)
+ {
+ this.distMat[i] = new double [i + 1];
+ }
+ }
+
+ public int numCompared()
+ {
+ return this.distMat.length + 1;
+ }
+
+ public double getValue (int indexI, int indexJ)
+ {
+ int row = (indexI < indexJ)? indexJ: indexI;
+ int col = (indexI < indexJ)? indexI: indexJ;
+
+ row--;
+
+ return this.distMat[row][col];
+ }
+
+ public void setValue (int indexI, int indexJ, double value) throws Exception
+ {
+
+ int row = (indexI < indexJ)? indexJ: indexI;
+ int col = (indexI < indexJ)? indexI: indexJ;
+
+ //whatever the object is, you need to recall that col 0 actually corresponds to object 2?
+ row--;
+
+ if(row >= this.distMat.length || col >= this.distMat[row].length)
+ {
+ throw new Exception("Trying to set value outside of range: " + row +", " + col +" when matrix has dimensions " + this.distMat.length + ", " + this.distMat[row].length);
+ }
+
+ this.distMat[row][col] = value;
+ }
+
+ @Override
+ public DMIterator iterator()
+ {
+ return new DMIterator(this);
+ }
+
+
+ public class DMIterator implements Iterator <DMCell>
+ {
+ private int currRow = 0;
+ private int currCol = 0;
+ private DistanceMatrix dm;
+
+ public DMIterator(DistanceMatrix dm)
+ {
+ this.dm = dm;
+ }
+
+ public boolean hasNext()
+ {
+ return(currRow < (dm.distMat.length - 1) || (currRow < dm.distMat.length && currCol < dm.distMat[currRow].length));
+ }
+
+ @Override
+ public DMCell next()
+ {
+ //now, curr col related to the matrix index, not the actual obj.
+ DMCell retObj = new DMCell(currRow + 1, currCol, this.dm.distMat[currRow][currCol]);
+
+ if(currCol + 1 < dm.distMat[currRow].length)
+ {
+ currCol++;
+ }
+ else
+ {
+ currRow++;
+ }
+ return retObj;
+ }
+
+ @Override
+ public void remove()
+ {
+ // TODO Auto-generated method stub
+
+ }
+ }
+
+
+ @Override
+ public int getNumberOfObservations()
+ {
+ return this.distMat.length + 1;
+ }
+
+ @Override
+ public double computeDissimilarity(Experiment arg0, int arg1, int arg2)
+ {
+ return this.getValue(arg1,arg2);
+ }
+
+
+
+}
+
diff --git a/src/pyromaniac/DataStructures/FlowCycler.java b/src/pyromaniac/DataStructures/FlowCycler.java
new file mode 100644
index 0000000..4465c2c
--- /dev/null
+++ b/src/pyromaniac/DataStructures/FlowCycler.java
@@ -0,0 +1,166 @@
+package pyromaniac.DataStructures;
+
+import java.util.Iterator;
+
+import pyromaniac.AcaciaConstants;
+import pyromaniac.IO.AcaciaLogger;
+
+public class FlowCycler
+{
+// private String cycle; //do I need to store this then?
+ private final char [] cycle;
+ public static final int FLOWED_BASE = 0;
+ public static final int FLOW_POSITION = 1;
+ public static final int WITHIN_CYCLE_POSITION = 2;
+ private AcaciaLogger logger;
+
+ public FlowCycler(String cycleStr, AcaciaLogger logger)
+ {
+ this.cycle = cycleStr.toCharArray();
+ this.logger = logger;
+ }
+
+ //okay, what the alignment needs to know is what flow would this be, given the last base was X, and the current base is X.
+
+ //assumes NO N's.
+ public int minPossibleFlowsBetweenFlowPosXAndCharY(int flowPosX, char y) throws Exception
+ {
+ //recall that there will be no Ns in the 454 at this point.
+ int posInCycle = (flowPosX % cycle.length);
+
+ //does not make sense for consecutive bases to be passed?
+ if(cycle[posInCycle] == y)
+ {
+ return 0;
+ }
+
+ //could choose to grab the iterator, and find this flow cycle pos.
+ int position = posInCycle + 1;
+
+ if(position == cycle.length)
+ position = 0;
+
+ //make sure this makes sense if x == y???
+ int numFlows = 1;
+
+ while(true)
+ {
+ char curr = cycle[position];
+
+ if(curr == y)
+ break;
+ else
+ {
+ if(position == cycle.length - 1)
+ {
+ position = 0;
+ }
+ else
+ {
+ position++;
+ }
+ numFlows++;
+ }
+ }
+
+ return numFlows;
+ }
+
+ public int flowPositionToPosInCycle (int flowPosition)
+ {
+ return flowPosition % this.cycle.length;
+ }
+
+ public int flowPositionToCycleNumber (int flowPosition)
+ {
+ return (flowPosition / this.cycle.length);
+ }
+
+
+ public CycleIterator iterator()
+ {
+ return new CycleIterator();
+ }
+
+ class CycleIterator implements Iterator <int []>
+ {
+ private int cyclePosition;
+ private int flowPosition;
+
+ public CycleIterator()
+ {
+ cyclePosition = 0;
+ flowPosition = 0;
+ }
+
+ //its cyclic.
+ public boolean hasNext()
+ {
+ return true;
+ }
+
+ @Override
+ public int [] next()
+ {
+ char base = cycle[cyclePosition];
+
+ int [] res = new int []{base, flowPosition, cyclePosition};
+ cyclePosition = (cyclePosition == (cycle.length - 1))? 0: cyclePosition + 1;
+ flowPosition++;
+
+ return res;
+ }
+
+ @Override
+ public void remove()
+ {
+ return;
+ }
+ }
+
+ public char getBaseAtCyclePos(int positionInCycle)
+ {
+ return this.cycle[positionInCycle];
+ }
+
+ /*
+ public static void main (String [] args)
+ {
+ AcaciaLogger logger = new AcaciaLogger();
+ FlowCycler fc = new FlowCycler(AcaciaConstants.OPT_FLOW_CYCLE_ION_TORRENT, logger);
+
+ String madeUp = "TCAGATACGA";
+
+ try
+ {
+ System.out.println("Cycle number for flow position: " + fc.flowPositionToCycleNumber(86));
+
+
+
+ int maxFlowsBetween = fc.minPossibleFlowsBetweenFlowPosXAndCharY(9, 'T');
+
+ System.out.println("Max flows between position 9 and the next T is : " + maxFlowsBetween);
+ }
+ catch(Exception e)
+ {
+ System.out.println(e.getMessage());
+ }
+
+
+ CycleIterator it = fc.iterator();
+
+ int [] currFlow = it.next();
+
+ for(int i = 0; i < madeUp.length(); i++)
+ {
+ char curr = madeUp.charAt(i);
+
+ while(curr != currFlow[FlowCycler.FLOWED_BASE])
+ {
+ currFlow = it.next();
+ }
+ System.out.println("Current base <" + curr + "> at position <" + i + "> maps to flow: " + currFlow[FlowCycler.FLOW_POSITION] + " within cycle position: " + currFlow[FlowCycler.WITHIN_CYCLE_POSITION]);
+ }
+ }
+ */
+}
diff --git a/src/pyromaniac/DataStructures/MIDPrimerCombo.java b/src/pyromaniac/DataStructures/MIDPrimerCombo.java
new file mode 100644
index 0000000..eae69bf
--- /dev/null
+++ b/src/pyromaniac/DataStructures/MIDPrimerCombo.java
@@ -0,0 +1,131 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.DataStructures;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class MID.
+ */
+public class MIDPrimerCombo
+{
+
+ /** The MID. */
+ String MID;
+
+ /** The primer. */
+ String primer;
+
+ /** The descriptor. */
+ String descriptor;
+
+ /**
+ * Instantiates a new mID.
+ *
+ * @param MID the mID
+ * @param primer the primer
+ * @param descriptor the descriptor
+ */
+ public MIDPrimerCombo(String MID, String primer, String descriptor)
+ {
+ this.MID = MID;
+ this.primer = primer;
+ this.descriptor = descriptor;
+ }
+
+ /**
+ * Gets the descriptor.
+ *
+ * @return the descriptor
+ */
+ public String getDescriptor()
+ {
+ return descriptor;
+ }
+
+ /**
+ * Gets the mID primer sequence.
+ *
+ * @return the mID primer sequence
+ */
+ public String getMIDPrimerSequence()
+ {
+ return this.MID + this.primer;
+ }
+
+ /**
+ * Sets the descriptor.
+ *
+ * @param descriptor the new descriptor
+ */
+ public void setDescriptor(String descriptor)
+ {
+ this.descriptor = descriptor;
+ }
+
+ /**
+ * Gets the primer.
+ *
+ * @return the primer
+ */
+ public String getPrimer()
+ {
+ return this.primer;
+ }
+
+ /**
+ * Sets the primer.
+ *
+ * @param primer the new primer
+ */
+ public void setPrimer(String primer)
+ {
+ this.primer = primer;
+ }
+
+ /**
+ * Gets the mID.
+ *
+ * @return the mID
+ */
+ public String getMID() {
+ return MID;
+ }
+
+ /**
+ * Sets the mID.
+ *
+ * @param mID the new mID
+ */
+ public void setMID(String mID) {
+ MID = mID;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString()
+ {
+ StringBuilder midString = new StringBuilder();
+ midString.append('\''+ descriptor + '\'');
+ midString.append(":");
+ midString.append('\'' + MID + '\'');
+ return midString.toString();
+ }
+
+}
diff --git a/src/pyromaniac/DataStructures/MutableInteger.java b/src/pyromaniac/DataStructures/MutableInteger.java
new file mode 100644
index 0000000..2934f27
--- /dev/null
+++ b/src/pyromaniac/DataStructures/MutableInteger.java
@@ -0,0 +1,86 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.DataStructures;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class MutableInteger.
+ */
+public class MutableInteger
+{
+
+ /** The value. */
+ private int value;
+
+ /**
+ * Instantiates a new mutable integer.
+ *
+ * @param val the val
+ */
+ public MutableInteger(int val)
+ {
+ this.value = val;
+ }
+
+ /**
+ * Increment.
+ */
+ public void increment()
+ {
+ value++;
+ }
+
+ /**
+ * Decrement.
+ */
+ public void decrement()
+ {
+ value--;
+ }
+
+ /**
+ * Update.
+ *
+ * @param newValue the new value
+ */
+ public void update(int newValue)
+ {
+ this.value = newValue;
+ }
+
+ /**
+ * Value.
+ *
+ * @return the int
+ */
+ public int value()
+ {
+ return this.value;
+ }
+
+ /**
+ * Adds the.
+ *
+ * @param toAdd the to add
+ */
+ public void add(int toAdd)
+ {
+ this.value += toAdd;
+ }
+}
\ No newline at end of file
diff --git a/src/pyromaniac/DataStructures/Pair.java b/src/pyromaniac/DataStructures/Pair.java
new file mode 100644
index 0000000..19a4788
--- /dev/null
+++ b/src/pyromaniac/DataStructures/Pair.java
@@ -0,0 +1,74 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.DataStructures;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class Pair.
+ *
+ * @param <T> the generic type
+ * @param <S> the generic type
+ */
+public class Pair<T, S>
+{
+ //private variables
+ /** The first. */
+ private T first;
+
+ /** The second. */
+ private S second;
+
+ /**
+ * Instantiates a new pair.
+ *
+ * @param f the f
+ * @param s the s
+ */
+ public Pair(T f, S s){
+ first = f;
+ second = s;
+ }
+
+ /**
+ * Gets the first.
+ *
+ * @return the first
+ */
+ public T getFirst(){
+ return first;
+ }
+
+ /**
+ * Gets the second.
+ *
+ * @return the second
+ */
+ public S getSecond() {
+ return second;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString() {
+ return "(" + first.toString() + ", " + second.toString() + ")";
+ }
+
+}
+
diff --git a/src/pyromaniac/DataStructures/PatriciaTrie.java b/src/pyromaniac/DataStructures/PatriciaTrie.java
new file mode 100644
index 0000000..3293570
--- /dev/null
+++ b/src/pyromaniac/DataStructures/PatriciaTrie.java
@@ -0,0 +1,541 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.DataStructures;
+
+import java.util.ArrayDeque;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class PatriciaTrie.
+ */
+public class PatriciaTrie implements Collection <HashSet <Pyrotag>>
+{
+
+ /** The head. */
+ private Node head;
+
+ /** The Constant MAX_CHILDREN. */
+ public static final int MAX_CHILDREN = 5;
+
+ /** The Constant STRING_END. */
+ public static final char STRING_END = '$';
+
+ /** The Constant baseToArrayPos. */
+ public static final HashMap <Character, Integer> baseToArrayPos;
+
+ /** The Constant arrayPosToBase. */
+ public static final HashMap <Integer, Character> arrayPosToBase;
+
+ static
+ {
+ //alphabetical order
+ baseToArrayPos = new HashMap <Character, Integer>(17);
+ baseToArrayPos.put('$', 0);
+ baseToArrayPos.put('A', 1);
+ baseToArrayPos.put('C', 2);
+ baseToArrayPos.put('G', 3);
+ baseToArrayPos.put('T', 4);
+
+ arrayPosToBase = new HashMap <Integer, Character>(17);
+ arrayPosToBase.put(0, '$');
+ arrayPosToBase.put(1, 'A');
+ arrayPosToBase.put(2, 'C');
+ arrayPosToBase.put(3, 'G');
+ arrayPosToBase.put(4, 'T');
+ }
+
+ /**
+ * Instantiates a new patricia trie.
+ */
+ public PatriciaTrie()
+ {
+ this.head = new Node('^');
+ }
+
+ /**
+ * Insert string.
+ *
+ * @param value the value
+ * @param p the p
+ */
+ public void insertString(String value, Pyrotag p)
+ {
+ this.head.insertSeq(value, 0, p);
+ }
+
+ /**
+ * Gets the prefix sets.
+ *
+ * @return the prefix sets
+ */
+ public LinkedList <Pair <HashSet <Pyrotag>, String>> getPrefixSets()
+ {
+ ArrayDeque <Pair<Node, HashSet <Pyrotag>>> queue = new ArrayDeque<Pair <Node, HashSet <Pyrotag>>>();
+
+ queue.addFirst(new Pair <Node, HashSet <Pyrotag>> (this.head, new HashSet <Pyrotag>()));
+
+ LinkedList <Pair <HashSet <Pyrotag>, String>> sharedPrefixSets = new LinkedList <Pair <HashSet <Pyrotag>, String>> ();
+
+ while(queue.size() > 0)
+ {
+ Pair <Node, HashSet <Pyrotag>> pairToProcess = queue.pop();
+
+ Node noValue = pairToProcess.getFirst().getChild(STRING_END);
+
+ boolean finishedPath = true;
+ for(int i = 0; i < PatriciaTrie.MAX_CHILDREN; i++)
+ {
+ char currChild = arrayPosToBase.get(i);
+ if(currChild != STRING_END && pairToProcess.getFirst().getChild(currChild) != null)
+ {
+ finishedPath = false;
+
+
+ HashSet <Pyrotag> clone = new HashSet <Pyrotag>();
+ clone.addAll(pairToProcess.getSecond());
+
+ if(noValue != null)
+ {
+ clone.addAll(noValue.getTags());
+ }
+
+ queue.push(new Pair <Node, HashSet <Pyrotag>>(pairToProcess.getFirst().getChild(currChild),clone));
+ }
+ }
+
+ if(finishedPath && pairToProcess.getFirst() != this.head) //the second case is silly.
+ {
+ if(noValue != null)
+ {
+ pairToProcess.getSecond().addAll(noValue.getTags());
+ }
+
+ Pyrotag rep = pairToProcess.getSecond().iterator().next(); //the longest sequences shall be the rep.
+ String repSeq = new String(rep.getCollapsedRead());
+ sharedPrefixSets.push(new Pair <HashSet <Pyrotag>, String>(pairToProcess.getSecond(), repSeq));
+ }
+ }
+
+ return sharedPrefixSets;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#iterator()
+ */
+ public PTIterator iterator()
+ {
+ return new PTIterator(this.head);
+ }
+
+ //iterator
+ /**
+ * The Class PTIterator.
+ */
+ class PTIterator implements Iterator <HashSet <Pyrotag>>
+ {
+
+ /** The head. */
+ Node head;
+
+ /** The queue. */
+ ArrayDeque <Pair <Node, HashSet <Pyrotag>>> queue;
+
+ /**
+ * Instantiates a new pT iterator.
+ *
+ * @param head the head
+ */
+ public PTIterator(Node head)
+ {
+ this.head = head;
+ this.queue = new ArrayDeque<Pair <Node, HashSet <Pyrotag>>>();
+ queue.addFirst(new Pair <Node, HashSet <Pyrotag>> (this.head, new HashSet <Pyrotag>()));
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Iterator#hasNext()
+ */
+ public boolean hasNext()
+ {
+ if(queue.size() > 0 && queue.peek().getFirst().hasChildren())
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Iterator#next()
+ */
+ public HashSet<Pyrotag> next()
+ {
+ assert(queue.size() > 0);
+
+ while(queue.size() > 0)
+ {
+ Pair <Node, HashSet <Pyrotag>> pairToProcess = queue.pop();
+ Node noValue = pairToProcess.getFirst().getChild(STRING_END);
+ boolean finishedPath = true;
+ for(int i = 0; i < PatriciaTrie.MAX_CHILDREN; i++)
+ {
+ char currChild = arrayPosToBase.get(i);
+ if(currChild != STRING_END && pairToProcess.getFirst().getChild(currChild) != null)
+ {
+ finishedPath = false;
+
+
+ HashSet <Pyrotag> clone = new HashSet <Pyrotag>();
+ clone.addAll(pairToProcess.getSecond());
+
+ if(noValue != null)
+ {
+ clone.addAll(noValue.getTags());
+ }
+
+ queue.push(new Pair <Node, HashSet <Pyrotag>>(pairToProcess.getFirst().getChild(currChild),clone));
+ }
+ }
+
+ if(finishedPath && pairToProcess.getFirst() != this.head) //the second case is silly.
+ {
+ if(noValue != null)
+ {
+ pairToProcess.getSecond().addAll(noValue.getTags());
+ }
+
+ return pairToProcess.getSecond();
+ }
+ }
+
+ assert(false);
+ //shouldn't ever get to this code.
+ return null;
+ }
+
+ //DOES NOTHING
+ /* (non-Javadoc)
+ * @see java.util.Iterator#remove()
+ */
+ public void remove()
+ {
+ // TODO Auto-generated method stub
+
+ }
+ }
+
+
+
+
+ /**
+ * The Class Node.
+ */
+ class Node
+ {
+
+ /** The value. */
+ private char value;
+
+ /** The children. */
+ private Node [] children;
+
+ /** The tags. */
+ HashSet <Pyrotag> tags;
+
+ /**
+ * Instantiates a new node.
+ *
+ * @param value the value
+ */
+ public Node(char value)
+ {
+ this.value = value;
+ children = null;
+ tags = null;
+ }
+
+ /**
+ * Checks for children.
+ *
+ * @return true, if successful
+ */
+ public boolean hasChildren()
+ {
+ for(Node n: children)
+ {
+ if(n != null)
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * Adds the tag.
+ *
+ * @param p the p
+ */
+ public void addTag(Pyrotag p)
+ {
+ if(tags == null)
+ tags = new HashSet <Pyrotag>();
+
+ tags.add(p);
+ }
+
+ /**
+ * Delete tags.
+ */
+ public void deleteTags()
+ {
+ this.tags = null;
+ }
+
+ /**
+ * Gets the tags.
+ *
+ * @return the tags
+ */
+ public HashSet <Pyrotag> getTags()
+ {
+ return this.tags;
+ }
+
+ /**
+ * Gets the value.
+ *
+ * @return the value
+ */
+ public char getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value.
+ *
+ * @param value the new value
+ */
+ public void setValue(char value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the children.
+ *
+ * @return the children
+ */
+ public Node[] getChildren()
+ {
+ return children;
+ }
+
+ /**
+ * Sets the children.
+ *
+ * @param children the new children
+ */
+ public void setChildren(Node[] children)
+ {
+ this.children = children;
+ }
+
+ /**
+ * Adds the child.
+ *
+ * @param node the node
+ */
+ public void addChild(Node node)
+ {
+ if(this.children == null)
+ this.children = new Node [PatriciaTrie.MAX_CHILDREN];
+
+ this.children[baseToArrayPos.get(node.getValue())] = node;
+ }
+
+ /**
+ * Gets the child.
+ *
+ * @param value the value
+ * @return the child
+ */
+ public Node getChild(char value)
+ {
+ if(this.children == null)
+ return null;
+
+ return this.children[baseToArrayPos.get(value)];
+ }
+
+ /**
+ * Insert seq.
+ *
+ * @param sequence the sequence
+ * @param offset the offset
+ * @param p the p
+ */
+ public void insertSeq(String sequence, int offset, Pyrotag p)
+ {
+ if(sequence.length() == offset)
+ {
+ if(this.getChild(STRING_END) == null)
+ {
+ Node newChild = new Node(STRING_END);
+
+ newChild.addTag(p);
+ this.addChild(newChild);
+ }
+ else
+ {
+ this.getChild(STRING_END).addTag(p);
+ }
+ }
+ else
+ {
+ char currInSeq = sequence.charAt(offset);
+ if(getChild(currInSeq) == null)
+ {
+ Node newChild = new Node(currInSeq);
+ this.addChild(newChild);
+ newChild.insertSeq(sequence, offset + 1, p);
+ }
+ else
+ {
+ getChild(currInSeq).insertSeq(sequence, offset + 1, p);
+ }
+ }
+ }
+ }
+
+
+
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#add(java.lang.Object)
+ */
+ public boolean add(HashSet<Pyrotag> e)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#addAll(java.util.Collection)
+ */
+ public boolean addAll(Collection<? extends HashSet<Pyrotag>> c)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#clear()
+ */
+ public void clear()
+ {
+ // TODO Auto-generated method stub
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#contains(java.lang.Object)
+ */
+ public boolean contains(Object o)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#containsAll(java.util.Collection)
+ */
+ public boolean containsAll(Collection<?> c)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#isEmpty()
+ */
+ public boolean isEmpty()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#remove(java.lang.Object)
+ */
+ public boolean remove(Object o)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#removeAll(java.util.Collection)
+ */
+ public boolean removeAll(Collection<?> c)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#retainAll(java.util.Collection)
+ */
+ public boolean retainAll(Collection<?> c)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#size()
+ */
+ public int size()
+ {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#toArray()
+ */
+ public Object[] toArray()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Collection#toArray(T[])
+ */
+ public <T> T[] toArray(T[] a)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+}
diff --git a/src/pyromaniac/DataStructures/Pyrotag.java b/src/pyromaniac/DataStructures/Pyrotag.java
new file mode 100644
index 0000000..2035e83
--- /dev/null
+++ b/src/pyromaniac/DataStructures/Pyrotag.java
@@ -0,0 +1,1187 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.DataStructures;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.LinkedList;
+
+import pyromaniac.AcaciaConstants;
+import pyromaniac.AcaciaEngine;
+import pyromaniac.DataStructures.FlowCycler.CycleIterator;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class Pyrotag.
+ */
+public class Pyrotag
+{
+ /** The id. */
+ private String id;
+
+ /** The qualities. */
+ private int [] qualities;
+
+ /** The avg quality. */
+ private double avgQuality;
+
+ /** The nucleotides. */
+ private char [] nucleotides;
+
+ /** The description */
+ private String desc;
+
+ /** The mid. */
+ private MIDPrimerCombo mid;
+
+ /** The num ambiguous bases. */
+ private int numAmbiguousBases;
+
+ /** The multiplex tag length. */
+ private int multiplexTagLength;
+
+ /** The trim to length. */
+ private int trimToLength;
+
+ /** The internal id. */
+ private int internalID;
+
+ /** The Constant VALID_BASES_IN_SEQUENCE. */
+ public static final String VALID_BASES_IN_SEQUENCE = "ATGCN";
+
+ /** The constant FlowCycler*/
+ private FlowCycler cycler;
+
+ /** The Constant CYCLE_START. */
+ public static final Character CYCLE_START = 'T';
+
+ /** The Constant NO_TRIM. */
+ public static final int NO_TRIM = -1;
+
+ /** The Constant NO_TAG. */
+ public static final int NO_TAG = -1;
+
+ /** The Constant NO_QUALS. */
+ public static final int NO_QUALS = -1;
+
+ /** The Constant NO_CORRESPONDING_FLOW. */
+ public static final int NO_CORRESPONDING_FLOW = -1;
+
+ /** The Constant NO_N. */
+ public static final int NO_N = -1;
+
+
+
+ /**
+ * Instantiates a new pyrotag.
+ *
+ * @param id the id
+ * @param desc the desc
+ * @param nucleotideSeq the nucleotide seq
+ * @param qualitySeq the quality seq
+ */
+ public Pyrotag(String id, String desc, Sequence <Character> nucleotideSeq, Sequence <Integer> qualitySeq, FlowCycler cycler)
+ {
+ this.id = id;
+ this.desc = desc;
+ this.numAmbiguousBases = 0;
+
+ assert(nucleotideSeq != null);
+
+ this.nucleotides = new char [nucleotideSeq.length()];
+
+ for(int i = 0; i < nucleotideSeq.length(); i++)
+ {
+ this.nucleotides[i] = nucleotideSeq.getValueAtIndex(i);
+
+ if(this.nucleotides[i] == 'N')
+ {
+ this.numAmbiguousBases++;
+ }
+ }
+
+ this.qualities = null;
+ this.avgQuality = NO_QUALS;
+
+ if(qualitySeq != null)
+ {
+ this.qualities = new int [qualitySeq.length()];
+
+ for(int i = 0; i < qualitySeq.length(); i++)
+ {
+ this.qualities[i] = qualitySeq.getValueAtIndex(i);
+ this.avgQuality += this.qualities[i];
+ }
+ }
+
+ if(qualitySeq != null)
+ this.avgQuality = this.avgQuality / this.qualities.length;
+ this.mid = null;
+ this.trimToLength = NO_TRIM;
+ this.multiplexTagLength = NO_TAG;
+ this.cycler = cycler;
+ }
+
+ public final FlowCycler getFlowCycler()
+ {
+ return this.cycler;
+ }
+
+
+ /**
+ * Gets the untrimmed avg quality.
+ *
+ * @return the untrimmed avg quality
+ */
+ public double getUntrimmedAvgQuality()
+ {
+ return this.avgQuality;
+ }
+
+ /**
+ * Sets the internal id.
+ *
+ * @param id the new internal id
+ */
+ public void setInternalID(int id)
+ {
+ this.internalID = id;
+ }
+
+ /**
+ * Gets the internal id.
+ *
+ * @return the internal id
+ */
+ public int getInternalID()
+ {
+ return this.internalID;
+ }
+
+ /**
+ * Sets the iD.
+ *
+ * @param id the new iD
+ */
+ public void setID(String id)
+ {
+ this.id = id;
+ }
+
+ /**
+ * Sets the description.
+ *
+ * @param desc the new description
+ */
+ public void setDescription(String desc)
+ {
+ this.desc = desc;
+ }
+
+ /**
+ * Sets the multiplex tag.
+ *
+ * @param midPrimer the new mID primer combo
+ */
+ public void setMIDPrimerCombo(MIDPrimerCombo midPrimer)
+ {
+ this.mid = midPrimer;
+
+ this.setMultiplexTagLength(midPrimer.getMIDPrimerSequence().length()); //mid and primer sequence.
+ }
+
+ /**
+ * First occurrence of ambiguous base, should return the flow position.
+ *
+ * @return the int
+ */
+ public int firstOccurrenceOfAmbiguous()
+ {
+ for(int i = 0; i < this.nucleotides.length; i++)
+ {
+ if(this.nucleotides[i] == 'N' || this.nucleotides[i] == 'n')
+ {
+ //base position
+
+ return i;
+ }
+ }
+
+ return NO_N;
+ }
+
+
+ //flows from zero.
+ //assume you want first position after key, and MID, if present.
+ /**
+ * Gets the flow for collapsed read pos.
+ *
+ * @param key the key
+ * @param nucPos the nuc pos
+ * @return the flow for collapsed read pos
+ * @throws NFoundAtReadStartException
+ */
+
+ //there has got to be a cleaner way??
+
+ public int [] getFlowPositionForCallPriorToCollapsedReadStart(String key)
+ {
+ CycleIterator it = this.cycler.iterator();
+ return _getFlowPositionForCallPriorToCollapsedReadStart(key, it);
+ }
+
+ public int [] getFlowPositionForCollapsedReadPosition(String key, int nucPos)throws ReadWithZeroLengthException
+ {
+ CycleIterator it = this.cycler.iterator();
+
+ int [] lastFlow = _getFlowPositionForCallPriorToCollapsedReadStart(key, it);
+ char [] collapsed = this.getCollapsedRead(); //doesn't have the MID or primer in it.
+
+ if(collapsed.length == 0)
+ {
+ throw new ReadWithZeroLengthException(this);
+ }
+
+ int [] lastCalledFlow = lastFlow; //last called flow from MID or the key.
+ for(int i = 0; i <= nucPos && i < collapsed.length; i++)
+ {
+ //the first base in collapsed,
+ while(collapsed[i] != lastFlow[FlowCycler.FLOWED_BASE])
+ {
+ if(collapsed[i] == 'N')
+ {
+ do
+ {
+ lastFlow = it.next();
+ }
+ while(lastFlow[FlowCycler.FLOWED_BASE] != lastCalledFlow[FlowCycler.FLOWED_BASE]); //for 454.
+ break;
+ }
+ else
+ {
+ lastFlow = it.next();
+ }
+ }
+
+ lastCalledFlow = lastFlow;
+ }
+
+ return lastFlow;
+ }
+
+ private int [] _getFlowPositionForCallPriorToCollapsedReadStart(String key, CycleIterator it)
+ {
+ int [] lastFlow = it.next(); //starts it off.
+
+ //previous is at the beginning of the key, move through the key now.
+ for(int i = 0; i < key.length(); i++)
+ {
+ char curr = key.charAt(i);
+ while(lastFlow[FlowCycler.FLOWED_BASE] != curr)
+ {
+ lastFlow = it.next();
+ }
+ }
+
+ //account for the MID we clipped off, but are we clipping off MID only or MID AND PRIMER
+ if(this.mid != null && this.mid.getMIDPrimerSequence().length() > 0)
+ {
+ //lastFlow = flowsBetweenLastFlowAndSeqStart(it, mid.MID);
+ //process the mid
+ String midPrimer = mid.getMIDPrimerSequence(); //we require a perfect match in the MID and primer.
+ for(int i = 0; i < midPrimer.length(); i++)
+ {
+ char curr = this.nucleotides[i];
+
+ while(lastFlow[FlowCycler.FLOWED_BASE] != curr)
+ {
+ lastFlow = it.next();
+ }
+ }
+ }
+ return lastFlow;
+ }
+
+
+ //old
+ /*
+ public int [] getFlowForCollapsedReadPos(String key, int nucPos) throws NFoundAtReadStartException, Exception
+ {
+ CycleIterator it = this.cycler.iterator();
+
+ int [] lastFlow = it.next(); //starts it off.
+
+ //previous is at the beginning of the key, move through the key now.
+ for(int i = 0; i < key.length(); i++)
+ {
+ char curr = key.charAt(i);
+ while(lastFlow[FlowCycler.FLOWED_BASE] != curr)
+ {
+ lastFlow = it.next();
+ }
+ }
+
+ //account for the MID we clipped off, but are we clipping off MID only or MID AND PRIMER
+ if(this.mid != null && this.mid.getMIDPrimerSequence().length() > 0)
+ {
+ //lastFlow = flowsBetweenLastFlowAndSeqStart(it, mid.MID);
+ //process the mid
+ String midPrimer = mid.getMIDPrimerSequence(); //we require a perfect match in the MID and primer.
+ for(int i = 0; i < midPrimer.length(); i++)
+ {
+ char curr = this.nucleotides[i];
+
+ while(lastFlow[FlowCycler.FLOWED_BASE] != curr)
+ {
+ lastFlow = it.next();
+ }
+ }
+ }
+
+ char [] collapsed = this.getCollapsedRead(); //doesn't have the MID or primer in it.
+
+ if(collapsed.length == 0)
+ {
+ //TODO: check outside this function that it is empty? Or throw empty string exception?
+ System.out.println(this.id);
+ System.out.println("trim to Length" + this.trimToLength);
+ System.out.println("multiplex tag length "+ this.multiplexTagLength);
+ }
+
+ int currentPosition = 0; //currentPosition in collapsed
+
+ //1. how do we want to handle initial N's.
+ if(collapsed[currentPosition] == 'N')
+ {
+ throw new NFoundAtReadStartException(this);
+ }
+
+
+ int [] lastCalledFlow = lastFlow; //last called flow from MID or the key.
+
+ for(int i = 0; i <= nucPos && i < collapsed.length; i++)
+ {
+ //the first base in collapsed,
+ while(collapsed[i] != lastFlow[FlowCycler.FLOWED_BASE])
+ {
+ if(collapsed[i] == 'N')
+ {
+ do
+ {
+ lastFlow = it.next();
+ }
+ while(lastFlow[FlowCycler.FLOWED_BASE] != lastCalledFlow[FlowCycler.FLOWED_BASE]); //for 454.
+ }
+ else
+ {
+ lastFlow = it.next();
+ }
+ }
+
+ lastCalledFlow = lastFlow;
+ }
+
+ return lastFlow;
+ }
+
+ */
+
+
+ /**
+ * Flows between last flow and seq start. Inclusive of seq start flow
+ *
+ * @param lastFlow the last flow
+ * @param seq the seq
+ * @return the int
+ */
+
+ /*
+ public int flowsBetweenLastFlowAndSeqStart(FlowCycler.CycleIterator it, String seq)
+ {
+
+
+
+ return flowsBetweenLastFlowAndChar(lastFlow, seq.charAt(0));
+ }
+ */
+
+
+ /**
+ * Flows between last flow and char.
+ *
+ * @param lastFlow the last flow
+ * @param start the start
+ * @return the int
+ */
+/* public int flowsBetweenLastFlowAndChar(Character lastFlow, Character start)
+ {
+ Character curr = lastFlow;
+ Character seqFirst = start;
+
+ int offset = 0;
+
+ try
+ {
+ while(! curr.equals(seqFirst))
+ {
+ if(seqFirst == null || !flowCycle.containsKey(seqFirst.charValue()))
+ {
+ throw new Exception("Illegal character in sequence: " + seqFirst.charValue() + ", " + this.getID());
+ }
+
+ curr = flowCycle.get(curr);
+
+ if(curr == null)
+ {
+ throw new Exception("Curr was null: " + seqFirst.charValue());
+ }
+ offset++;
+ }
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ System.out.println(e.getMessage());
+ System.exit(1);
+ }
+
+ return offset;
+ }
+
+ */
+
+ /**
+ * Flows between seq start and seq end.
+ *
+ * @param seq the seq
+ * @return the int
+ * @throws NFoundAtReadStartException
+ */
+/* private int flowsBetweenSeqStartAndSeqEnd(String seq)
+ {
+ int flowOffset = 0;
+ int seqIndex = 0;
+
+ Character prev = seq.charAt(seqIndex);
+ seqIndex++;
+
+ while(seqIndex < seq.length())
+ {
+ Character curr = seq.charAt(seqIndex);
+ while(!prev.equals(curr))
+ {
+ prev = flowCycle.get(prev);
+ flowOffset++;
+ }
+ seqIndex++;
+ }
+ return flowOffset;
+ }
+ */
+
+ public int flowPosToBasePos (int flowPos, String key) throws NFoundAtReadStartException
+ {
+ CycleIterator it = this.cycler.iterator();
+
+ int [] lastFlow = it.next();
+
+
+ //previous is at the beginning of the key, move through the key now.
+ //all reads go through the key
+ for(int i = 0; i < key.length(); i++)
+ {
+ char curr = key.charAt(i);
+ while(lastFlow[FlowCycler.FLOWED_BASE] != curr) //does this automagically cast to char?
+ {
+ lastFlow = it.next();
+ }
+ }
+
+ //now for the MID
+ if(this.mid != null && this.mid.MID.length() > 0)
+ {
+ //process the mid
+
+ for(int i = 0; i < mid.MID.length(); i++)
+ {
+ char curr = mid.MID.charAt(i);
+ while(lastFlow[FlowCycler.FLOWED_BASE] != curr)
+ {
+ lastFlow = it.next();
+ }
+ }
+ }
+ else
+ {
+ //do nothing.
+ //if you take the MIDS and primer away... there needs to be a default position?
+ }
+
+ //base position only corresponds to what is represented in the collapsed string
+ //collapsed string has the MID and PRIMER removed, and is trimmed.
+
+ char [] collapsed = this.getCollapsedRead();
+
+ if(collapsed[0] == 'N')
+ {
+ throw new NFoundAtReadStartException(this);
+ }
+
+ int [] lastCalledFlow = lastFlow;
+
+ for(int i = 0; i < collapsed.length; i++)
+ {
+ if(lastFlow[FlowCycler.FLOW_POSITION] >= flowPos)
+ {
+ return i - 1; //last called base
+ }
+
+ while(collapsed[i] != lastFlow[FlowCycler.FLOWED_BASE])
+ {
+ if(collapsed[i] == 'N')
+ {
+ do
+ {
+ lastFlow = it.next();
+ }
+ while(lastFlow[FlowCycler.FLOWED_BASE] != lastCalledFlow[FlowCycler.FLOWED_BASE]);
+ }
+ else
+ {
+ lastFlow = it.next();
+ }
+ }
+ lastCalledFlow = lastFlow;
+ }
+
+ return collapsed.length - 1; //last base is this.
+
+ }
+
+
+ /**
+ * Flow to base pos.
+ *
+ * @param flowPos the flow pos
+ * @param key the key
+ * @return the int
+ */
+ /*
+ public int flowToBasePos(int flowPos, String key)
+ {
+ int pos = flowsBetweenLastFlowAndSeqStart(Pyrotag.CYCLE_START, key); //incase the key does not start with the first nucleotide
+
+ if(pos == 0)
+ {
+ pos = 1; //should begin at 1.
+ }
+
+ char prev = key.charAt(0);
+
+ for(int i = 1; i < key.length(); i++)
+ {
+ char curr = key.charAt(i);
+
+ while(prev != curr)
+ {
+ // System.out.println("Prev: " + prev);
+ pos++;
+ prev = flowCycle.get(prev);
+ }
+ }
+
+ for(int i= 0; i < nucleotides.length; i++)
+ {
+ while(prev != nucleotides[i])
+ {
+ pos++;
+// System.out.println("Nucleotide: " + prev + " flow " + pos);
+
+ prev = flowCycle.get(prev);
+ if(pos >= flowPos)
+ {
+ return i; //
+ }
+ }
+// System.out.println("Nucleotide: " + prev + " flow " + pos);
+ }
+ return Pyrotag.NO_CORRESPONDING_FLOW;
+ }
+ */
+
+ /**
+ * Sets the multiplex tag length.
+ *
+ * @param length the new multiplex tag length
+ */
+ private void setMultiplexTagLength(int length)
+ {
+ this.multiplexTagLength = length;
+ }
+
+ /**
+ * Gets the num ambiguous bases.
+ *
+ * @return the num ambiguous bases
+ */
+ public int getNumAmbiguousBases()
+ {
+ return numAmbiguousBases;
+ }
+
+ /**
+ * Gets the description.
+ *
+ * @return the description
+ */
+ public String getDescription()
+ {
+ return this.desc;
+ }
+
+ /**
+ * Gets the qualities.
+ *
+ * @return the qualities
+ */
+ public int [] getQualities()
+ {
+ return this.qualities;
+ }
+
+ /**
+ * Trim using min quality.
+ *
+ * @param minQuality the min quality
+ */
+ public void trimUsingMinQuality(int minQuality)
+ {
+ //will set the trimLength..
+ }
+
+ /**
+ * Gets the tag.
+ *
+ * @return the tag
+ */
+ public char [] getTag()
+ {
+ if(this.multiplexTagLength != NO_TAG)
+ {
+ char [] tag = new char [this.multiplexTagLength];
+
+ for(int i = 0; i < tag.length; i++)
+ {
+ tag[i] = this.nucleotides[i];
+ }
+
+ return tag;
+ }
+ return null;
+ }
+
+
+ /**
+ * Gets the base.
+ *
+ * @param index the index
+ * @return the base
+ */
+ public char getBase(int index)
+ {
+ assert(index < nucleotides.length);
+ return nucleotides[index];
+ }
+
+ /**
+ * Gets the length.
+ *
+ * @return the length
+ */
+ public int getLength()
+ {
+ return this.nucleotides.length;
+ }
+
+ /**
+ * Gets the quality.
+ *
+ * @param index the index
+ * @return the quality
+ */
+ public int getQuality(int index)
+ {
+ assert(index < qualities.length);
+ return qualities[index];
+ }
+
+ /**
+ * Gets the read string.
+ *
+ * @return the read string
+ */
+ public char [] getReadString()
+ {
+ return this.nucleotides;
+ }
+
+
+ //changing this code to trim to a given length, ignoring the presence/absence of a MID.
+
+ /**
+ * Gets the processed string.
+ *
+ * @return the processed string
+ */
+ public char [] getProcessedString()
+ {
+ char [] processed;
+
+ if(this.trimToLength == NO_TRIM && this.multiplexTagLength == NO_TAG)
+ {
+ processed = new char [this.nucleotides.length];
+
+ for(int i = 0; i < processed.length; i++)
+ {
+ processed[i] = Character.toUpperCase(this.nucleotides[i]);
+ }
+ return processed;
+ }
+
+
+ int start = (this.multiplexTagLength == NO_TAG)? 0 : this.multiplexTagLength;
+ int end = this.nucleotides.length; //default for now.
+
+ if(this.trimToLength != NO_TRIM)
+ {
+ if(this.trimToLength < start)
+ {
+ end = start;
+ }
+ else if (this.trimToLength > this.nucleotides.length)
+ {
+ end = this.nucleotides.length;
+ }
+ else
+ {
+ end = this.trimToLength;
+ }
+ }
+
+ char [] processedString = new char [end - start];
+
+ for(int i = start; i < end; i++)
+ {
+ processedString[i - start] = Character.toUpperCase(this.nucleotides[i]);
+ }
+
+ return processedString;
+ }
+
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString()
+ {
+ StringBuffer sb = new StringBuffer();
+ int width = 20;
+
+ sb.append(this.id + " " + this.desc);
+ sb.append(System.getProperty("line.separator"));
+
+ int i = 0;
+
+ while((i + width) <= nucleotides.length)
+ {
+ sb.append(nucleotides, i, width);
+ sb.append(System.getProperty("line.separator"));
+
+
+ if(qualities != null)
+ {
+ for(int j = i; j < (i + width); j++)
+ {
+ sb.append(qualities[j]);
+ if(j + 1 < (i + width))
+ {
+ sb.append(" ");
+ }
+ }
+ sb.append(System.getProperty("line.separator"));
+ }
+
+
+ i+= width;
+ if((i + width - 1) >= nucleotides.length)
+ {
+ width = nucleotides.length - i;
+
+ if(width == 0)
+ {
+ break;
+ }
+ }
+ }
+ return sb.toString();
+ }
+
+
+ /**
+ * To fasta.
+ *
+ * @return the string
+ */
+ public String processedToFASTA()
+ {
+ char [] processedStr = this.getProcessedString();
+ StringBuffer sb = new StringBuffer();
+ int width = 80;
+
+ sb.append(">" + this.id + " " + this.desc);
+ sb.append(System.getProperty("line.separator"));
+
+ for(int i = 0; (i + width) < processedStr.length; i+= width)
+ {
+ sb.append(processedStr, i, width);
+ sb.append(System.getProperty("line.separator"));
+
+ if(i + width > processedStr.length)
+ {
+ width = processedStr.length - i;
+ }
+ }
+
+ return sb.toString();
+ }
+
+
+ /**
+ * Gets the iD.
+ *
+ * @return the iD
+ */
+ public String getID()
+ {
+ return this.id;
+ }
+
+ /**
+ * Checks for ns.
+ *
+ * @return true, if successful
+ */
+ public boolean hasNs()
+ {
+ for(int i = 0; i < this.nucleotides.length; i++)
+ {
+ if(nucleotides[i] == 'N')
+ return true;
+ }
+ return false;
+ }
+
+
+ /**
+ * Gets the trimmed average quality.
+ *
+ * @return the trimmed average quality
+ */
+ public int getTrimmedAverageQuality()
+ {
+ if(this.qualities == null)
+ {
+ return NO_QUALS;
+ }
+
+ int posStart = (this.multiplexTagLength == NO_TAG)? 0 : this.multiplexTagLength;
+ int posEnd = (this.trimToLength == NO_TRIM)? this.nucleotides.length: this.trimToLength;
+
+ int currPos = posStart;
+ int sum = 0;
+ while(currPos < posEnd)
+ {
+ sum += this.qualities[currPos];
+ currPos++;
+ }
+
+ int average = (sum / (posEnd - posStart + 1));
+ return average;
+ }
+
+ /**
+ * To flow gram.
+ *
+ * @param flowCycle the flow cycle
+ * @param flowStart the flow start
+ * @param numFlows the num flows
+ * @param key the key
+ * @return the int[]
+ */
+ public int [] toFlowGram(HashMap <Character, Character> flowCycle, char flowStart, int numFlows, String key)
+ {
+ int [] flowGram = new int [numFlows * 4];
+
+ int actualFlowPos = 0;
+ char currNucleotide = flowStart;
+
+ //assuming the key is not present, dont care about the hp counts or anything.
+ for(int i = 0; i < key.length(); i++)
+ {
+ while(currNucleotide != key.charAt(i))
+ {
+ currNucleotide = flowCycle.get(currNucleotide);
+ actualFlowPos++;
+ }
+ }
+ actualFlowPos++; //bring us up to position four.
+ currNucleotide = flowCycle.get(currNucleotide);
+
+ for(int i = 0; i < flowGram.length; i++)
+ {
+ flowGram[i] = 0;
+ }
+
+ //last base was currNucleotide
+
+ //similarly
+
+ int offset = 0;
+ for(int i = 0; i < this.nucleotides.length; i++)
+ {
+ while(currNucleotide != this.nucleotides[i])
+ {
+ offset++;
+ currNucleotide = flowCycle.get(currNucleotide);
+ }
+
+ int j = i + 1;
+
+ while(j < this.nucleotides.length && this.nucleotides[j] == this.nucleotides[i])
+ {
+ j++;
+ }
+
+ flowGram[offset] = j - i;
+ i = j - 1;
+ }
+
+ int [] flowGramShort = new int [offset];
+
+ for(int i = 0; i < flowGramShort.length; i++)
+ {
+ flowGramShort[i] = flowGram[i];
+ }
+
+ return flowGramShort;
+ }
+
+ //MIDoffset is first base afterMID
+ /**
+ * Gets the collapsed read.
+ *
+ * @return the collapsed read
+ */
+ public char [] getCollapsedRead()
+ {
+ char [] collapsed = new char [this.nucleotides.length - this.multiplexTagLength];
+
+ int indexCollapsed = 0;
+ char prev = 'z';
+
+ int maxPos = (this.trimToLength != Pyrotag.NO_TRIM)? ((this.nucleotides.length < this.trimToLength)? this.nucleotides.length : this.trimToLength): this.nucleotides.length;
+
+
+ for(int i = this.multiplexTagLength; i < maxPos; i++)
+ {
+ if(prev != this.nucleotides[i])
+ {
+ collapsed[indexCollapsed] = this.nucleotides[i];
+ indexCollapsed++;
+ }
+ prev = this.nucleotides[i];
+ }
+
+ return Arrays.copyOf(collapsed, indexCollapsed);
+ }
+
+ /**
+ * Gets the trim to length.
+ *
+ * @return the trim to length
+ */
+ public int getTrimToLength()
+ {
+ return this.trimToLength;
+ }
+
+ /**
+ * Sets the trim to length.
+ *
+ * @param trimToLength the new trim to length
+ */
+ public void setTrimToLength(int trimToLength)
+ {
+ this.trimToLength = trimToLength;
+
+ if(this.nucleotides.length > trimToLength && trimToLength > 0)
+ {
+ _trimRead();
+ }
+ }
+
+ //TODO: add this function, see how it goes
+
+ /**
+ * _trim read.
+ */
+ private void _trimRead()
+ {
+ char [] trimmedRead = Arrays.copyOf(nucleotides, this.trimToLength);
+
+ this.nucleotides = trimmedRead;
+
+ if(this.qualities != null)
+ {
+ int [] trimmedQualities = Arrays.copyOf(qualities, this.trimToLength);
+ this.qualities = trimmedQualities;
+ }
+ }
+
+
+ /**
+ * Which mid.
+ *
+ * @param validTags the valid tags
+ * @return the mID
+ */
+ public MIDPrimerCombo whichMID(LinkedList <MIDPrimerCombo> validTags)
+ {
+ HashMap <MIDPrimerCombo, Boolean> notMatched = new HashMap <MIDPrimerCombo, Boolean>();
+
+ int endPos = -1;
+
+ for(int i = 0; i < this.nucleotides.length; i++)
+ {
+ boolean anyThisLong = false;
+ for(MIDPrimerCombo midObj: validTags)
+ {
+ String midPrimerSeq = midObj.MID + midObj.primer;
+
+ if(midPrimerSeq.length() > i)
+ {
+ char [] acceptableSubs = {midPrimerSeq.charAt(i)}; //assume that there are NO substitutions applicable.
+ if(AcaciaConstants.IUPAC_AMBIGUOUS_MAPPINGS.containsKey(midPrimerSeq.charAt(i))) //have a wobble
+ {
+ acceptableSubs = AcaciaConstants.IUPAC_AMBIGUOUS_MAPPINGS.get(midPrimerSeq.charAt(i));
+ }
+
+ boolean anyMatched = false;
+
+ for(char possBase : acceptableSubs)
+ {
+ // System.out.println("Comparing to possible base: " + possBase);
+ if(possBase == this.nucleotides[i])
+ {
+ anyMatched = true;
+ }
+ }
+
+ if(! anyMatched)
+ {
+ notMatched.put(midObj, false);
+ endPos = i;
+ }
+ else
+ {
+ anyThisLong = true;
+ }
+ }
+ }
+ if(! anyThisLong)
+ break;
+ }
+
+ for(MIDPrimerCombo mid: validTags)
+ {
+ if(! notMatched.containsKey(mid))
+ return mid;
+ }
+ return null;
+ }
+
+ /**
+ * Gets the multiplex tag.
+ *
+ * @return the multiplex tag
+ */
+ public MIDPrimerCombo getMultiplexTag()
+ {
+ return this.mid;
+ }
+
+
+//this is fine, but if I ever allowed non valid MID sequences to use this function, it would not check whether there were wobbles in the MID.
+
+ /**
+ * Checks for wobble in processed string.
+ *
+ * @return true, if successful
+ */
+public boolean hasWobbleInProcessedString()
+ {
+ char [] processedString = this.getProcessedString();
+
+ for(char curr : processedString)
+ {
+ if(VALID_BASES_IN_SEQUENCE.indexOf(Character.toUpperCase(curr)) == -1)
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+
+public class NFoundAtReadStartException extends Exception
+{
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ public NFoundAtReadStartException(Pyrotag p)
+ {
+ super("First base of " + p.getID() + " is an N");
+ }
+}
+class ReadWithZeroLengthException extends Exception
+{
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ public ReadWithZeroLengthException(Pyrotag p)
+ {
+ super("When stripped of key, mid " + p.getID() + " has zero length!");
+ }
+}
+
+}
diff --git a/src/pyromaniac/DataStructures/QualitySequence.java b/src/pyromaniac/DataStructures/QualitySequence.java
new file mode 100644
index 0000000..202fc12
--- /dev/null
+++ b/src/pyromaniac/DataStructures/QualitySequence.java
@@ -0,0 +1,163 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
+package pyromaniac.DataStructures;
+
+import java.util.ArrayList;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class QualitySequence.
+ */
+public class QualitySequence
+{
+
+ /** The sequence. */
+ private Integer [] sequence;
+
+ /** The id. */
+ private String id;
+
+ /** The descriptor. */
+ private String descriptor;
+
+ /**
+ * Instantiates a new quality sequence.
+ */
+ public QualitySequence()
+ {
+ sequence = null;
+ id = null;
+ descriptor = null;
+ }
+
+ /**
+ * Instantiates a new quality sequence.
+ *
+ * @param id the id
+ * @param descriptor the descriptor
+ * @param sequence the sequence
+ */
+ @SuppressWarnings("unchecked")
+ public QualitySequence(String id, String descriptor, ArrayList <Integer> sequence)
+ {
+ try
+ {
+ this.sequence = new Integer [sequence.size()];
+ sequence.toArray(this.sequence);
+ this.id = id;
+ this.descriptor = descriptor;
+ }
+ catch(Exception e)
+ {
+ System.out.println("Quality sequence: " + e.getMessage());
+ }
+ }
+
+
+ //returns a clone of the arraylist
+ /**
+ * Gets the sequence.
+ *
+ * @return the sequence
+ */
+ @SuppressWarnings("unchecked")
+ public Integer [] getSequence()
+ {
+ return this.sequence;
+ }
+
+ /**
+ * Gets the quality at base.
+ *
+ * @param index the index
+ * @return the quality at base
+ */
+ public int getQualityAtBase(int index)
+ {
+ assert(sequence != null && index < this.sequence.length);
+ return sequence[index];
+ }
+
+ /**
+ * Sets the quality at base.
+ *
+ * @param index the index
+ * @param qual the qual
+ */
+ public void setQualityAtBase(int index,int qual)
+ {
+ assert(sequence != null && index < this.sequence.length);
+ this.sequence[index] = qual;
+ }
+
+ /**
+ * Gets the descriptor.
+ *
+ * @return the descriptor
+ */
+ public String getDescriptor()
+ {
+ return this.descriptor;
+ }
+
+ /**
+ * Length.
+ *
+ * @return the int
+ */
+ public int length()
+ {
+ return this.sequence.length;
+ }
+
+ /**
+ * Gets the iD.
+ *
+ * @return the iD
+ */
+ public String getID()
+ {
+ return this.id;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString()
+ {
+ StringBuffer result = new StringBuffer("");
+
+ result.append(this.id + " " + this.descriptor);
+ result.append(System.getProperty("line.separator"));
+ for(int i = 0; i < sequence.length; i++)
+ {
+ result.append(sequence[i]);
+ if(i != 0 && i % 70 == 0)
+ {
+ result.append(System.getProperty("line.separator"));
+ }
+ if(i + 1 != sequence.length)
+ {
+ result.append(" ");
+ }
+ }
+ return result.toString();
+ }
+}
diff --git a/src/pyromaniac/DataStructures/Sequence.java b/src/pyromaniac/DataStructures/Sequence.java
new file mode 100644
index 0000000..daf5dad
--- /dev/null
+++ b/src/pyromaniac/DataStructures/Sequence.java
@@ -0,0 +1,181 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.DataStructures;
+
+import java.util.ArrayList;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class Sequence.
+ *
+ * @param <T> the generic type
+ */
+public class Sequence <T>
+{
+
+ /** The sequence. */
+ private Object [] sequence;
+
+ /** The id. */
+ private String id;
+
+ /** The desc. */
+ private String desc;
+
+ /**
+ * Instantiates a new sequence.
+ *
+ * @param seqInit the seq init
+ * @param id the id
+ * @param descriptor the descriptor
+ */
+ public Sequence(ArrayList <T> seqInit, String id, String descriptor)
+ {
+ this.id = id;
+ this.desc = descriptor;
+
+ int seqInitSize = seqInit.size();
+
+ sequence = new Object [seqInitSize];
+
+ for(int i = 0; i <seqInitSize; i++)
+ {
+ sequence [i] = seqInit.get(i);
+ }
+ }
+
+ /**
+ * Gets the sequence.
+ *
+ * @return the sequence
+ */
+ public Object[] getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the sequence.
+ *
+ * @param sequence the new sequence
+ */
+ public void setSequence(Object[] sequence)
+ {
+ this.sequence = sequence;
+ }
+
+ /**
+ * Gets the id.
+ *
+ * @return the id
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the id.
+ *
+ * @param id the new id
+ */
+ public void setId(String id)
+ {
+ this.id = id;
+ }
+
+ /**
+ * Gets the desc.
+ *
+ * @return the desc
+ */
+ public String getDesc()
+ {
+ return desc;
+ }
+
+ /**
+ * Sets the desc.
+ *
+ * @param desc the new desc
+ */
+ public void setDesc(String desc)
+ {
+ this.desc = desc;
+ }
+
+ /**
+ * Length.
+ *
+ * @return the int
+ */
+ public int length()
+ {
+ return this.sequence.length;
+ }
+
+ /**
+ * Gets the value at index.
+ *
+ * @param index the index
+ * @return the value at index
+ */
+ public T getValueAtIndex(int index)
+ {
+ assert(sequence != null && index < this.sequence.length);
+ return (T) sequence[index];
+ }
+
+ /**
+ * Sets the value at index.
+ *
+ * @param index the index
+ * @param value the value
+ */
+ public void setValueAtIndex(int index, T value)
+ {
+ assert(sequence != null && index < this.sequence.length);
+ this.sequence[index] = value;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString()
+ {
+ StringBuffer result = new StringBuffer("");
+
+ result.append(this.id + " " + this.desc);
+ result.append(System.getProperty("line.separator"));
+ for(int i = 0; i < sequence.length; i++)
+ {
+ result.append(sequence[i]);
+ if(i != 0 && i % 70 == 0)
+ {
+ result.append(System.getProperty("line.separator"));
+ }
+ if(i + 1 != sequence.length)
+ {
+ result.append(" ");
+ }
+ }
+ return result.toString();
+ }
+
+}
diff --git a/src/pyromaniac/DataStructures/Triplet.java b/src/pyromaniac/DataStructures/Triplet.java
new file mode 100644
index 0000000..7eced81
--- /dev/null
+++ b/src/pyromaniac/DataStructures/Triplet.java
@@ -0,0 +1,79 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.DataStructures;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class Triplet.
+ *
+ * @param <T1> the generic type
+ * @param <T2> the generic type
+ * @param <T3> the generic type
+ */
+public class Triplet<T1, T2, T3>
+{
+
+ /**
+ * Creates a new instance of Pair.
+ *
+ * @param first first value
+ * @param second second value
+ * @param third the third
+ */
+ public Triplet(T1 first, T2 second, T3 third)
+ {
+ this.first = first;
+ this.second = second;
+ this.third = third;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#equals(java.lang.Object)
+ */
+ public boolean equals(Object obj)
+ {
+ if (obj instanceof Pair) {
+ Triplet other = (Triplet)obj;
+ return (other.first == null ? this.first == null : other.first.equals(this.first)) &&
+ (other.second == null ? this.second == null : other.second.equals(this.second)
+ && (other.third == null? this.third == null : other.third.equals(this.third))
+ );
+ }
+ else
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ public String toString()
+ {
+ return first.toString() +"::"+second.toString() + "::" + third.toString();
+ }
+
+
+ /** The first. */
+ public T1 first;
+
+ /** The second. */
+ public T2 second;
+
+ /** The third. */
+ public T3 third;
+}
diff --git a/src/pyromaniac/ErrorCorrectionWorker.java b/src/pyromaniac/ErrorCorrectionWorker.java
new file mode 100644
index 0000000..5f6d9a4
--- /dev/null
+++ b/src/pyromaniac/ErrorCorrectionWorker.java
@@ -0,0 +1,235 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedList;
+
+import javax.swing.SwingUtilities;
+import javax.swing.SwingWorker;
+
+import pyromaniac.DataStructures.MIDPrimerCombo;
+import pyromaniac.GUI.TagInputPanel;
+import pyromaniac.IO.AcaciaLogger;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class ErrorCorrectionWorker.
+ */
+ at SuppressWarnings("restriction")
+public class ErrorCorrectionWorker extends SwingWorker<Void, Void>
+{
+
+ /** The run settings. */
+ HashMap <String, String> runSettings;
+
+ /** The logger. */
+ AcaciaLogger logger;
+
+ /** The valid mids. */
+ LinkedList <MIDPrimerCombo> validMIDS;
+
+ /** The parent. */
+ TagInputPanel parent;
+
+ /** The worker finished. */
+ Boolean workerFinished;
+
+ //hidden constructor
+ /**
+ * Instantiates a new error correction worker.
+ */
+ @SuppressWarnings("unused")
+ private ErrorCorrectionWorker()
+ {
+
+ }
+
+ /**
+ * Instantiates a new error correction worker.
+ *
+ * @param settings the run time settings
+ * @param logger the AcaciaLogger
+ * @param validMIDS the valid MIDS for processing
+ * @param parent the parent TagInputPanel which instantiated this worked
+ */
+ public ErrorCorrectionWorker(HashMap <String, String> settings, AcaciaLogger logger, LinkedList <MIDPrimerCombo> validMIDS, TagInputPanel parent)
+ {
+ //set up the worker
+ this.runSettings = settings;
+ this.logger = logger;
+ this.validMIDS = validMIDS;
+ this.parent = parent;
+ this.workerFinished = false;
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.SwingWorker#doInBackground()
+ */
+ @Override
+ protected Void doInBackground() throws Exception
+ {
+ ArrayList <String> filesCreated = new ArrayList <String> ();
+ boolean exceptionOccurred = false;
+ try
+ {
+// AcaciaEngine.getEngine().initLogFiles(this.runSettings, this.logger,true, validMIDS);
+ AcaciaEngine.getEngine().runAcacia(this.runSettings, this.validMIDS, logger, this, AcaciaEngine.getVersion(), true);
+ logger.flushLogs();
+ logger.removeLogFiles(); //TODO: this was changed.
+ }
+ catch(InterruptedException ie)
+ {
+ System.out.println(ie.getMessage());
+ ie.printStackTrace();
+ exceptionOccurred = true;
+ }
+ catch(Exception e)
+ {
+ System.out.println(e.getMessage());
+ e.printStackTrace();
+ exceptionOccurred = true;
+ }
+ finally
+ {
+ if(! exceptionOccurred)
+ {
+ System.out.println("No exceptions occurred");
+ SwingUtilities.invokeLater(new FinishedRunnable(this.parent));
+ return null;
+ }
+ for(String filename: filesCreated)
+ {
+ File f = new File(filename);
+
+ if(f.exists())
+ {
+ //this file was successfully opened apparently
+
+ if(!f.canWrite())
+ {
+ throw new IOException("File from cancelled run could not be removed.");
+ }
+ else
+ {
+ f.delete();
+ }
+ }
+ }
+ SwingUtilities.invokeLater(new CancelRunnable(this.parent));
+ }
+ return null;
+ }
+
+ /**
+ * The Class CancelRunnable.
+ */
+ private class CancelRunnable implements Runnable
+ {
+
+ /** The parent. */
+ private TagInputPanel parent;
+
+ /**
+ * Instantiates a new cancel runnable.
+ *
+ * @param parent the parent
+ */
+ public CancelRunnable(TagInputPanel parent)
+ {
+ this.parent = parent;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Runnable#run()
+ */
+ public void run()
+ {
+ this.parent.workerCancelled();
+ }
+ }
+
+ /**
+ * The Class FinishedRunnable.
+ */
+ private class FinishedRunnable implements Runnable
+ {
+
+ /** The parent. */
+ private TagInputPanel parent;
+
+ /**
+ * Instantiates a new finished runnable.
+ *
+ * @param parent the parent
+ */
+ public FinishedRunnable(TagInputPanel parent)
+ {
+ this.parent = parent;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Runnable#run()
+ */
+ public void run()
+ {
+ this.parent.workerFinished();
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.SwingWorker#done()
+ */
+ public void done()
+ {
+ //this is the clean up method after the thread has finished running
+ }
+
+ /**
+ * Prints the cancellation message.
+ */
+ public void printCancellationMessage()
+ {
+ synchronized(this.workerFinished)
+ {
+ try
+ {
+ this.workerFinished = true;
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+ this.workerFinished.notifyAll();
+ }
+ }
+
+ /**
+ * Gets the worker finished.
+ *
+ * @return the worker finished
+ */
+ public Boolean getWorkerFinished()
+ {
+ return this.workerFinished;
+ }
+}
diff --git a/src/pyromaniac/GUI/AcaciaGradientButton.java b/src/pyromaniac/GUI/AcaciaGradientButton.java
new file mode 100644
index 0000000..adeff97
--- /dev/null
+++ b/src/pyromaniac/GUI/AcaciaGradientButton.java
@@ -0,0 +1,304 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
+package pyromaniac.GUI;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GradientPaint;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Paint;
+import java.awt.RenderingHints;
+import java.awt.Stroke;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.geom.Rectangle2D;
+
+import javax.swing.JButton;
+
+// TODO: Auto-generated Javadoc
+//Note - inspiration/code borrowed from : http://www.tek-tips.com/viewthread.cfm?qid=1408697&page=6
+//Author: GrizzlyCrO
+
+/**
+ * The Class AcaciaGradientButton.
+ */
+public class AcaciaGradientButton extends JButton implements MouseListener
+{
+
+ /** The Constant VERTICAL. */
+ public static final int VERTICAL = 0;
+
+ /** The Constant HORIZONTAL. */
+ public static final int HORIZONTAL = 1;
+
+ /** The Constant CENTERED. */
+ public static final int CENTERED = 2;
+
+ /** The Constant DIAGONAL. */
+ public static final int DIAGONAL = 3;
+
+ /** The Constant DEFAULT_BUTTON_WIDTH. */
+ private static final int DEFAULT_BUTTON_WIDTH = 100;
+
+ /** The Constant INACTIVE_BUTTON_COLOR. */
+ public static final Color INACTIVE_BUTTON_COLOR = Color.decode("#CDCDCD");
+
+ /** The first. */
+ private Color first;
+
+ /** The second. */
+ private Color second;
+
+ /** The direction. */
+ private int direction;
+
+ /** The border. */
+ private GradientPaint border;
+
+ /** The default border. */
+ private Color defaultBorder;
+
+ /**
+ * Instantiates a new acacia gradient button.
+ *
+ * @param text the text
+ * @param first the first
+ * @param second the second
+ * @param defaultBorder the default border
+ * @param direction the direction
+ */
+ public AcaciaGradientButton(String text, Color first, Color second, Color defaultBorder, int direction)
+ {
+ super(text);
+
+ this.first = first;
+ this.second = second;
+ this.direction = direction;
+ this.defaultBorder = defaultBorder;
+
+
+ this.setContentAreaFilled(false);
+ this.setFocusPainted(false);
+ this.setBorderPainted(false);
+ this.addMouseListener(this);
+
+
+ Dimension d = this.getPreferredSize();
+ d.width = DEFAULT_BUTTON_WIDTH;
+ this.setPreferredSize(d);
+ this.setSize(d);
+ this.setMaximumSize(d);
+ this.border = getDefaultBorder();
+ }
+
+ /**
+ * Gets the default border.
+ *
+ * @return the default border
+ */
+ private GradientPaint getDefaultBorder()
+ {
+ return this.makeGradientPaint(Color.decode("#BECC28"), this.defaultBorder, AcaciaGradientButton.DIAGONAL);
+ }
+
+
+ /* (non-Javadoc)
+ * @see javax.swing.JComponent#paintComponent(java.awt.Graphics)
+ */
+ @Override
+ protected void paintComponent(Graphics g)
+ {
+ Graphics2D g2 = (Graphics2D) g;
+
+ Paint oldPaint = g2.getPaint();
+
+ //do I change the background paint to grey?
+
+ GradientPaint p;
+ if(this.isEnabled())
+ {
+ p = makeGradientPaint(this.first, this.second, this.direction);
+ }
+ else
+ {
+ p = makeGradientPaint(INACTIVE_BUTTON_COLOR, Color.white, this.direction);
+ }
+
+
+ g2.setPaint(p);
+ g2.fillRect(0, 0, getWidth(), getHeight());
+ g2.setPaint(oldPaint);
+ g2.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
+ RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
+
+ if(this.border != null)
+ {
+ this.drawBorder(g);
+ }
+
+ super.paintComponent(g);
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.MouseListener#mouseEntered(java.awt.event.MouseEvent)
+ */
+ public void mouseEntered(MouseEvent e)
+ {
+ this.border = this.makeGradientPaint(Color.white, Color.orange, AcaciaGradientButton.DIAGONAL);
+ this.repaint();
+ }
+
+ /**
+ * Make gradient paint.
+ *
+ * @param pFirst the first
+ * @param pSecond the second
+ * @param pDirection the direction
+ * @return the gradient paint
+ */
+ private GradientPaint makeGradientPaint(Color pFirst, Color pSecond, int pDirection)
+ {
+ GradientPaint p;
+
+ int v1;
+ int v2;
+ int h1;
+ int h2;
+
+ boolean cyclic = false;
+
+ int maxD = (this.getHeight() > this.getWidth())? this.getHeight() : this.getWidth();
+
+ switch(pDirection)
+ {
+ case AcaciaGradientButton.VERTICAL:
+ h1 = 0;
+ h2 = 0;
+ v1 = 0;
+ v2 = this.getHeight();
+ break;
+
+ case AcaciaGradientButton.HORIZONTAL:
+ h1 = 0;
+ h2 = this.getWidth();
+ v1 = 0;
+ v2 = 0;
+ break;
+
+ case AcaciaGradientButton.CENTERED:
+
+ h1 = 0;
+ h2 = 0;
+
+ v1 = (int)(0.25 * this.getHeight());
+ v2 = this.getHeight();
+ cyclic = true;
+ break;
+
+ case AcaciaGradientButton.DIAGONAL:
+ h1 = 0;
+ h2 = (int)(this.getWidth() * 0.50);
+ v1 = 0;
+ v2 = (int)(this.getHeight() * 0.5);
+ break;
+
+ default:
+ Exception e = new Exception("Unknown option for border");
+ System.out.println(e.getMessage());
+ e.printStackTrace();
+ System.exit(1);
+ return null;
+
+ }
+ p = new GradientPaint(h1, v1, pFirst, h2, v2, pSecond,cyclic);
+ return p;
+ }
+
+ /**
+ * Draw border.
+ *
+ * @param g the g
+ */
+ public void drawBorder(Graphics g)
+ {
+ Paint oldPaint;
+ Stroke oldStroke;
+
+ Graphics2D g2 = (Graphics2D)g;
+ oldPaint = g2.getPaint();
+ oldStroke = g2.getStroke();
+
+ if(this.isEnabled())
+ {
+ g2.setPaint(this.border);
+ }
+ else
+ {
+ g2.setPaint(this.makeGradientPaint(Color.white, INACTIVE_BUTTON_COLOR, AcaciaGradientButton.DIAGONAL));
+ }
+ g2.setStroke(new BasicStroke(3));
+ Rectangle2D rect = new Rectangle2D.Double(0,0,this.getWidth()-1 , this.getHeight()-1);
+ g2.draw(rect);
+ g2.setPaint(oldPaint);
+ g2.setStroke(oldStroke);
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.MouseListener#mouseClicked(java.awt.event.MouseEvent)
+ */
+ public void mouseClicked(MouseEvent arg0)
+ {
+ //perhaps should make the button lighter???
+ this.border = this.getDefaultBorder();
+ this.repaint();
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.MouseListener#mouseExited(java.awt.event.MouseEvent)
+ */
+ public void mouseExited(MouseEvent arg0)
+ {
+ this.border = this.getDefaultBorder();
+ this.repaint();
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.MouseListener#mousePressed(java.awt.event.MouseEvent)
+ */
+ public void mousePressed(MouseEvent arg0)
+ {
+ this.border = this.makeGradientPaint(Color.orange, Color.orange, AcaciaGradientButton.DIAGONAL);
+ this.repaint();
+
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent)
+ */
+ public void mouseReleased(MouseEvent arg0)
+ {
+ this.border = this.getDefaultBorder();
+ this.repaint();
+ }
+
+}
diff --git a/src/pyromaniac/GUI/AcaciaMainFrame.java b/src/pyromaniac/GUI/AcaciaMainFrame.java
new file mode 100644
index 0000000..000285b
--- /dev/null
+++ b/src/pyromaniac/GUI/AcaciaMainFrame.java
@@ -0,0 +1,102 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.GUI;
+
+import java.awt.event.ComponentEvent;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+
+import javax.swing.JFrame;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class AcaciaMainFrame.
+ */
+public class AcaciaMainFrame extends JFrame implements WindowListener
+{
+
+ /**
+ * Instantiates a new acacia main frame.
+ */
+ public AcaciaMainFrame()
+ {
+
+
+
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.WindowListener#windowActivated(java.awt.event.WindowEvent)
+ */
+ public void windowActivated(WindowEvent arg0)
+ {
+
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.WindowListener#windowClosed(java.awt.event.WindowEvent)
+ */
+ public void windowClosed(WindowEvent arg0)
+ {
+
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.WindowListener#windowClosing(java.awt.event.WindowEvent)
+ */
+ public void windowClosing(WindowEvent arg0)
+ {
+
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.WindowListener#windowDeactivated(java.awt.event.WindowEvent)
+ */
+ public void windowDeactivated(WindowEvent arg0)
+ {
+
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.WindowListener#windowDeiconified(java.awt.event.WindowEvent)
+ */
+ public void windowDeiconified(WindowEvent arg0)
+ {
+
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.WindowListener#windowIconified(java.awt.event.WindowEvent)
+ */
+ public void windowIconified(WindowEvent arg0)
+ {
+
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.WindowListener#windowOpened(java.awt.event.WindowEvent)
+ */
+ public void windowOpened(WindowEvent arg0)
+ {
+
+ }
+
+
+
+}
diff --git a/src/pyromaniac/GUI/CustomDialog.java b/src/pyromaniac/GUI/CustomDialog.java
new file mode 100644
index 0000000..a9e102a
--- /dev/null
+++ b/src/pyromaniac/GUI/CustomDialog.java
@@ -0,0 +1,118 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.GUI;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SpringLayout;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class CustomDialog.
+ */
+public class CustomDialog extends JDialog implements ActionListener
+{
+
+ /** The Constant MAXIMUM_WIDTH. */
+ private static final int MAXIMUM_WIDTH = 300;
+
+ /** The Constant PREFERRED_HEIGHT. */
+ private static final int PREFERRED_HEIGHT = 150;
+
+ /** The my panel. */
+ private JPanel myPanel = null;
+
+ /** The ok button. */
+ private JButton okButton = null;
+
+ /**
+ * Instantiates a new custom dialog.
+ *
+ * @param frame the frame
+ * @param modal the modal
+ * @param myMessage the my message
+ */
+ public CustomDialog(JFrame frame, boolean modal, String myMessage)
+ {
+ super(frame, modal);
+
+ myPanel = new JPanel();
+
+ this.getContentPane().add(myPanel);
+
+ SpringLayout layoutManager = new SpringLayout();
+ myPanel.setLayout(layoutManager);
+
+ JLabel messageLabel = new JLabel( "<HTML>"+ myMessage + "</HTML>");
+ messageLabel.setBorder(TagInputPanel.DEFAULT_BORDER);
+ messageLabel.setOpaque(true);
+ messageLabel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ // messageLabel.setFont(TagInputPanel.DEFAULT);
+ messageLabel.setAlignmentY(TOP_ALIGNMENT);
+ messageLabel.setAlignmentX(CENTER_ALIGNMENT);
+
+ int preferredHeight = PREFERRED_HEIGHT;
+ int maxWidth = (messageLabel.getPreferredSize().width > MAXIMUM_WIDTH)? MAXIMUM_WIDTH : messageLabel.getPreferredSize().width;
+
+ Dimension mlMaximum = new Dimension(maxWidth, PREFERRED_HEIGHT);
+ messageLabel.setMaximumSize(mlMaximum);
+ messageLabel.setPreferredSize(new Dimension(maxWidth,PREFERRED_HEIGHT));
+
+
+ myPanel.add(messageLabel);
+ myPanel.setBackground(TagInputPanel.WINDOW_BACKGROUND_COLOUR);
+
+ okButton = new AcaciaGradientButton("OK", TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2, TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ okButton.addActionListener(this);
+ // okButton.setFont(TagInputPanel.DEFAULT);
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.add(okButton);
+ buttonPanel.setBackground(TagInputPanel.WINDOW_BACKGROUND_COLOUR);
+
+ Dimension bpMaximumSize = buttonPanel.getMaximumSize();
+ bpMaximumSize.height = okButton.getPreferredSize().height;
+
+ myPanel.add(buttonPanel);
+
+ SpringUtilities.makeCompactGrid(myPanel, 2, 1, 5, 5, 5, 5);
+
+ this.pack();
+ setLocationRelativeTo(frame);
+ setVisible(true);
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e)
+ {
+ if(e.getSource() == okButton)
+ {
+ setVisible(false);
+ }
+ }
+}
diff --git a/src/pyromaniac/GUI/FeatureIcon.java b/src/pyromaniac/GUI/FeatureIcon.java
new file mode 100644
index 0000000..b696e1e
--- /dev/null
+++ b/src/pyromaniac/GUI/FeatureIcon.java
@@ -0,0 +1,66 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.GUI;
+
+import java.awt.Graphics;
+import java.awt.Point;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Interface FeatureIcon.
+ */
+public interface FeatureIcon
+{
+
+ /**
+ * Draw icon.
+ *
+ * @param g the g
+ */
+ public void drawIcon(Graphics g);
+
+ /**
+ * Gets the anchor join start.
+ *
+ * @return the anchor join start
+ */
+ public Point getAnchorJoinStart();
+
+ /**
+ * Gets the anchor join end.
+ *
+ * @return the anchor join end
+ */
+ public Point getAnchorJoinEnd();
+
+ /**
+ * Sets the anchor join start.
+ *
+ * @param start the new anchor join start
+ */
+ public void setAnchorJoinStart(Point start);
+
+ /**
+ * Sets the anchor join end.
+ *
+ * @param end the new anchor join end
+ */
+ public void setAnchorJoinEnd(Point end);
+
+}
diff --git a/src/pyromaniac/GUI/GridBagUtility.java b/src/pyromaniac/GUI/GridBagUtility.java
new file mode 100644
index 0000000..a81e606
--- /dev/null
+++ b/src/pyromaniac/GUI/GridBagUtility.java
@@ -0,0 +1,152 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.GUI;
+
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import javax.swing.JLabel;
+
+// TODO: Auto-generated Javadoc
+// This code was taken from Philip Isenhour (http://javatechniques.com/blog/gridbaglayout-example-a-simple-form-layout/)
+
+/**
+ * The Class GridBagUtility.
+ */
+public class GridBagUtility
+{
+
+ /** The last constraints. */
+ private GridBagConstraints lastConstraints = null;
+
+ /** The middle constraints. */
+ private GridBagConstraints middleConstraints = null;
+
+ /** The label constraints. */
+ private GridBagConstraints labelConstraints = null;
+
+ /**
+ * Instantiates a new grid bag utility.
+ */
+ public GridBagUtility()
+ {
+ // Set up the constraints for the "last" field in each
+ // row first, then copy and modify those constraints.
+
+ // weightx is 1.0 for fields, 0.0 for labels
+ // gridwidth is REMAINDER for fields, 1 for labels
+ lastConstraints = new GridBagConstraints();
+
+ // Stretch components horizontally (but not vertically)
+ lastConstraints.fill = GridBagConstraints.HORIZONTAL;
+
+ // Components that are too short or narrow for their space
+ // Should be pinned to the northwest (upper left) corner
+ lastConstraints.anchor = GridBagConstraints.NORTHWEST;
+
+ // Give the "last" component as much space as possible
+ lastConstraints.weightx = 1.0;
+
+ // Give the "last" component the remainder of the row
+ lastConstraints.gridwidth = GridBagConstraints.REMAINDER;
+
+ // Add a little padding
+ lastConstraints.insets = new Insets(2, 2, 3, 3);
+
+ // Now for the "middle" field components
+ middleConstraints =
+ (GridBagConstraints) lastConstraints.clone();
+
+ // These still get as much space as possible, but do
+ // not close out a row
+ middleConstraints.gridwidth = GridBagConstraints.RELATIVE;
+
+ // And finally the "label" constrains, typically to be
+ // used for the first component on each row
+ labelConstraints =
+ (GridBagConstraints) lastConstraints.clone();
+
+ // Give these as little space as necessary
+ labelConstraints.weightx = 0.0;
+ labelConstraints.gridwidth = 1;
+ }
+
+ /**
+ * Adds a field component. Any component may be used. The
+ * component will be stretched to take the remainder of
+ * the current row.
+ *
+ * @param c the c
+ * @param parent the parent
+ */
+ public void addLastField(Component c, Container parent)
+ {
+ GridBagLayout gbl = (GridBagLayout) parent.getLayout();
+ gbl.setConstraints(c, lastConstraints);
+ parent.add(c);
+ }
+
+ /**
+ * Adds an arbitrary label component, starting a new row
+ * if appropriate. The width of the component will be set
+ * to the minimum width of the widest component on the
+ * form.
+ *
+ * @param c the c
+ * @param parent the parent
+ */
+ public void addLabel(Component c, Container parent) {
+ GridBagLayout gbl = (GridBagLayout) parent.getLayout();
+ gbl.setConstraints(c, labelConstraints);
+ parent.add(c);
+ }
+
+ /**
+ * Adds a JLabel with the given string to the label column.
+ *
+ * @param s the s
+ * @param parent the parent
+ * @return the j label
+ */
+ public JLabel addLabel(String s, Container parent) {
+ JLabel c = new JLabel(s);
+ c.setFont(parent.getFont());
+ addLabel(c, parent);
+ return c;
+ }
+
+ /**
+ * Adds a "middle" field component. Any component may be
+ * used. The component will be stretched to take all of
+ * the space between the label and the "last" field. All
+ * "middle" fields in the layout will be the same width.
+ *
+ * @param c the c
+ * @param parent the parent
+ */
+ public void addMiddleField(Component c, Container parent)
+ {
+ GridBagLayout gbl = (GridBagLayout) parent.getLayout();
+ gbl.setConstraints(c, middleConstraints);
+ parent.add(c);
+ }
+}
+
diff --git a/src/pyromaniac/GUI/HelpButton.java b/src/pyromaniac/GUI/HelpButton.java
new file mode 100644
index 0000000..ff86f52
--- /dev/null
+++ b/src/pyromaniac/GUI/HelpButton.java
@@ -0,0 +1,172 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
+package pyromaniac.GUI;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dialog;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GradientPaint;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.Paint;
+import java.awt.RenderingHints;
+import javax.swing.JButton;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.net.URL;
+
+import javax.swing.JPanel;
+import java.awt.Font;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.Popup;
+import javax.swing.PopupFactory;
+import javax.swing.JComponent;
+import javax.swing.BoxLayout;
+import javax.swing.SpringLayout;
+import javax.swing.BorderFactory;
+
+import pyromaniac.AcaciaEngine;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class HelpButton.
+ */
+public class HelpButton extends JButton implements ActionListener
+{
+
+ /** The Constant HELP_ICON. */
+ public static final String HELP_ICON = "/images/questionMarkGreen.png";
+
+ /** The Constant HELP_FONT_DEFAULT. */
+ public static final Font HELP_FONT_DEFAULT = new Font("Helvetica", Font.PLAIN, 14);
+
+ /** The help image. */
+ public static Image helpImage;
+
+ /** The help message. */
+ private String helpMessage;
+
+ /** The parent frame. */
+ private JFrame parentFrame;
+
+ /**
+ * Instantiates a new help button.
+ *
+ * @param helpMessage the help message
+ * @param frame the frame
+ * @throws Exception the exception
+ */
+ public HelpButton(String helpMessage, JFrame frame) throws MissingHelpImageException
+ {
+ super();
+
+ URL imageURL;
+ try
+ {
+ imageURL = AcaciaEngine.getImageUrl(HELP_ICON);
+ }
+ catch(Exception e)
+ {
+ throw new MissingHelpImageException(e);
+ }
+
+ helpImage = Toolkit.getDefaultToolkit().getImage(imageURL);
+ MediaTracker mTracker = new MediaTracker(this);
+ mTracker.addImage(helpImage,1);
+
+ this.parentFrame = frame;
+
+ try
+ {
+ mTracker.waitForID(1);
+ }
+ catch(Exception e)
+ {
+ System.out.println("Was interrupted");
+ }
+
+ double height = helpImage.getHeight(null);
+ double width = helpImage.getWidth(null);
+
+ Dimension d = new Dimension( (int) width, (int) height);
+ this.setPreferredSize(d);
+ this.setMaximumSize(d);
+ this.setMinimumSize(d);
+ this.addActionListener(this);
+
+ this.helpMessage = helpMessage;
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.JComponent#paintComponent(java.awt.Graphics)
+ */
+ protected void paintComponent(Graphics g)
+ {
+ Graphics2D g2 = (Graphics2D) g;
+
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ g2.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_QUALITY);
+
+ g2.setColor(Color.green);
+ g2.fillRect(0, 0, this.getWidth(), this.getHeight());
+ g2.drawImage(helpImage,0 , 0, this.getWidth(), this.getHeight(), null);
+ }
+
+ /* (non-Javadoc)
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @SuppressWarnings("deprecation")
+ public void actionPerformed(ActionEvent arg0)
+ {
+
+ JDialog dialog = new CustomDialog(this.parentFrame, false, this.helpMessage);
+ dialog.setTitle("Help");
+ dialog.setVisible(true);
+ }
+
+ public class MissingHelpImageException extends Exception
+ {
+ public MissingHelpImageException(Exception e)
+ {
+ super(e);
+ }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ }
+}
diff --git a/src/pyromaniac/GUI/JoinIcon.java b/src/pyromaniac/GUI/JoinIcon.java
new file mode 100644
index 0000000..1ccd3a8
--- /dev/null
+++ b/src/pyromaniac/GUI/JoinIcon.java
@@ -0,0 +1,52 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
+package pyromaniac.GUI;
+
+import java.awt.Graphics;
+import java.awt.Point;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Interface JoinIcon.
+ */
+public interface JoinIcon
+{
+
+ /**
+ * Draw icon.
+ *
+ * @param g the g
+ */
+ public void drawIcon(Graphics g);
+
+ /**
+ * Sets the start.
+ *
+ * @param start the new start
+ */
+ public void setStart(Point start);
+
+ /**
+ * Sets the end.
+ *
+ * @param end the new end
+ */
+ public void setEnd(Point end);
+}
diff --git a/src/pyromaniac/GUI/LogTextPane.java b/src/pyromaniac/GUI/LogTextPane.java
new file mode 100644
index 0000000..893ac52
--- /dev/null
+++ b/src/pyromaniac/GUI/LogTextPane.java
@@ -0,0 +1,210 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.GUI;
+
+import java.awt.Color;
+import java.awt.Rectangle;
+import java.util.HashMap;
+
+import javax.swing.JTextPane;
+import javax.swing.text.AttributeSet;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.Style;
+import javax.swing.text.StyledDocument;
+import javax.swing.text.StyleContext;
+import javax.swing.text.StyleConstants;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+import pyromaniac.IO.LoggerOutput;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class LogTextPane.
+ */
+public class LogTextPane implements LoggerOutput
+{
+
+ /** The ta. */
+ private JTextPane ta;
+
+ /** The log type to style. */
+ HashMap <Integer, Style> logTypeToStyle;
+
+ /** The progress. */
+ Style regular, error, debug, progress;
+
+ /** The scroller. */
+ JScrollPane scroller;
+
+ /** The closed. */
+ boolean closed;
+
+ /**
+ * Instantiates a new log text pane.
+ *
+ * @param ta the ta
+ * @param scroller the scroller
+ */
+ public LogTextPane(JTextPane ta, JScrollPane scroller)
+ {
+ this.ta = ta;
+ this.scroller = scroller;
+ StyledDocument doc = ta.getStyledDocument();
+ Style def = StyleContext.getDefaultStyleContext().getStyle(StyleContext.DEFAULT_STYLE );
+ regular = doc.addStyle( "regular", def );
+
+ error = doc.addStyle( "error",regular);
+ StyleConstants.setBold(error, true );
+ StyleConstants.setForeground(error, Color.red);
+
+ debug = doc.addStyle("debug", regular);
+ StyleConstants.setBold(debug, true);
+ StyleConstants.setForeground(debug, Color.green);
+
+ progress = doc.addStyle("progress", regular);
+ StyleConstants.setForeground(progress, Color.black);
+ closed = false;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#write(java.lang.StringBuilder, int)
+ */
+ public void write(StringBuilder buffer, int style) throws Exception
+ {
+ //maybe this should be invoke....after
+
+ try
+ {
+ StyledDocument doc = this.ta.getStyledDocument();
+ doc.insertString(doc.getLength(), buffer.toString(), this.getStyle(style));
+ }
+ catch (BadLocationException e)
+ {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }
+
+ SwingUtilities.invokeLater(new UpdateTextRunnable(this.scroller, this.ta, buffer.toString(), this, style));
+
+ }
+
+ /**
+ * Gets the style.
+ *
+ * @param style the style
+ * @return the style
+ */
+ private Style getStyle(int style)
+ {
+ switch(style)
+ {
+ case LoggerOutput.LOG_STYLE_DEBUG:
+ return this.debug;
+ case LoggerOutput.LOG_STYLE_ERROR:
+ return this.error;
+ case LoggerOutput.LOG_STYLE_PROGRESS:
+ return this.progress;
+ default:
+ return this.regular;
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#doHTMLMarkup()
+ */
+ public boolean doHTMLMarkup()
+ {
+ return true;
+ }
+
+ /**
+ * The Class UpdateTextRunnable.
+ */
+ class UpdateTextRunnable implements Runnable
+ {
+
+ /** The scroller. */
+ private JScrollPane scroller;
+
+ /** The new text. */
+ private String newText;
+
+ /** The ta. */
+ private JTextPane ta;
+
+ /** The style. */
+ private int style;
+
+ /** The pane. */
+ LogTextPane pane;
+
+ /**
+ * Instantiates a new update text runnable.
+ *
+ * @param scroller the scroller
+ * @param ta the ta
+ * @param newText the new text
+ * @param pane the pane
+ * @param style the style
+ */
+ public UpdateTextRunnable(JScrollPane scroller, JTextPane ta, String newText, LogTextPane pane, int style)
+ {
+ super();
+ this.scroller = scroller;
+ this.newText = newText;
+ this.pane = pane;
+ this.style = style;
+ this.ta = ta;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Runnable#run()
+ */
+ public void run()
+ {
+ this.scroller.scrollRectToVisible(new Rectangle(0,ta.getHeight()-2,1,1));
+ this.scroller.getVerticalScrollBar().setValue(scroller.getVerticalScrollBar().getMaximum());
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#closeHandle()
+ */
+ public void closeHandle() throws Exception
+ {
+ //do nothing
+ this.closed = true;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#isClosed()
+ */
+ public boolean isClosed()
+ {
+ // TODO Auto-generated method stub
+ return this.closed;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#flush()
+ */
+ public void flush() throws Exception
+ {
+ }
+}
diff --git a/src/pyromaniac/GUI/NonNumericFilter.java b/src/pyromaniac/GUI/NonNumericFilter.java
new file mode 100644
index 0000000..6e52a05
--- /dev/null
+++ b/src/pyromaniac/GUI/NonNumericFilter.java
@@ -0,0 +1,74 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.GUI;
+
+import javax.swing.*;
+import javax.swing.text.*;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class NonNumericFilter.
+ */
+public class NonNumericFilter extends DocumentFilter
+{
+
+ /* (non-Javadoc)
+ * @see javax.swing.text.DocumentFilter#insertString(javax.swing.text.DocumentFilter.FilterBypass, int, java.lang.String, javax.swing.text.AttributeSet)
+ */
+ public void insertString(DocumentFilter.FilterBypass fb, int offset,
+ String text, AttributeSet attr) throws BadLocationException
+ {
+ System.out.println("in insert string");
+
+ }
+
+ // no need to override remove(): inherited version allows all removals
+
+ /* (non-Javadoc)
+ * @see javax.swing.text.DocumentFilter#replace(javax.swing.text.DocumentFilter.FilterBypass, int, int, java.lang.String, javax.swing.text.AttributeSet)
+ */
+ public void replace(DocumentFilter.FilterBypass fb, int offset, int length,
+ String text, AttributeSet attr) throws BadLocationException
+ {
+ System.out.println("In replace string");
+ fb.replace(offset, length, text.replaceAll("\\d", ""), attr);
+ }
+
+ /**
+ * The main method.
+ *
+ * @param args the arguments
+ */
+ public static void main(String[] args)
+ {
+ DocumentFilter dfilter = new NonNumericFilter();
+
+ JTextArea jta = new JTextArea("foo\nbar");
+ JTextField jtf = new JTextField("foo");
+ ((AbstractDocument)jta.getDocument()).setDocumentFilter(dfilter);
+ ((AbstractDocument)jtf.getDocument()).setDocumentFilter(dfilter);
+
+ JFrame frame = new JFrame("NonNumericFilter");
+ frame.getContentPane().add(jta, java.awt.BorderLayout.CENTER);
+ frame.getContentPane().add(jtf, java.awt.BorderLayout.SOUTH);
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ frame.setSize(240, 120);
+ frame.setVisible(true);
+ }
+}
\ No newline at end of file
diff --git a/src/pyromaniac/GUI/SpringUtilities.java b/src/pyromaniac/GUI/SpringUtilities.java
new file mode 100644
index 0000000..6ac3f78
--- /dev/null
+++ b/src/pyromaniac/GUI/SpringUtilities.java
@@ -0,0 +1,241 @@
+/*
+ * Copyright (c) 1995, 2008, Oracle and/or its affiliates. All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in the
+ * documentation and/or other materials provided with the distribution.
+ *
+ * - Neither the name of Oracle or the names of its
+ * contributors may be used to endorse or promote products derived
+ * from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package pyromaniac.GUI;
+
+import javax.swing.*;
+import javax.swing.SpringLayout;
+import java.awt.*;
+
+// TODO: Auto-generated Javadoc
+/**
+ * A 1.4 file that provides utility methods for
+ * creating form- or grid-style layouts with SpringLayout.
+ * These utilities are used by several programs, such as
+ * SpringBox and SpringCompactGrid.
+ */
+public class SpringUtilities {
+
+ /**
+ * A debugging utility that prints to stdout the component's
+ * minimum, preferred, and maximum sizes.
+ *
+ * @param c the c
+ */
+ public static void printSizes(Component c) {
+ System.out.println("minimumSize = " + c.getMinimumSize());
+ System.out.println("preferredSize = " + c.getPreferredSize());
+ System.out.println("maximumSize = " + c.getMaximumSize());
+ }
+
+ /**
+ * Aligns the first <code>rows</code> * <code>cols</code>
+ * components of <code>parent</code> in
+ * a grid. Each component is as big as the maximum
+ * preferred width and height of the components.
+ * The parent is made just big enough to fit them all.
+ *
+ * @param parent the parent
+ * @param rows number of rows
+ * @param cols number of columns
+ * @param initialX x location to start the grid at
+ * @param initialY y location to start the grid at
+ * @param xPad x padding between cells
+ * @param yPad y padding between cells
+ */
+ public static void makeGrid(Container parent,
+ int rows, int cols,
+ int initialX, int initialY,
+ int xPad, int yPad) {
+ SpringLayout layout;
+ try {
+ layout = (SpringLayout)parent.getLayout();
+ } catch (ClassCastException exc) {
+ System.err.println("The first argument to makeGrid must use SpringLayout.");
+ return;
+ }
+
+ Spring xPadSpring = Spring.constant(xPad);
+ Spring yPadSpring = Spring.constant(yPad);
+ Spring initialXSpring = Spring.constant(initialX);
+ Spring initialYSpring = Spring.constant(initialY);
+ int max = rows * cols;
+
+ //Calculate Springs that are the max of the width/height so that all
+ //cells have the same size.
+ Spring maxWidthSpring = layout.getConstraints(parent.getComponent(0)).
+ getWidth();
+ Spring maxHeightSpring = layout.getConstraints(parent.getComponent(0)).
+ getWidth();
+ for (int i = 1; i < max; i++) {
+ SpringLayout.Constraints cons = layout.getConstraints(
+ parent.getComponent(i));
+
+ maxWidthSpring = Spring.max(maxWidthSpring, cons.getWidth());
+ maxHeightSpring = Spring.max(maxHeightSpring, cons.getHeight());
+ }
+
+ //Apply the new width/height Spring. This forces all the
+ //components to have the same size.
+ for (int i = 0; i < max; i++) {
+ SpringLayout.Constraints cons = layout.getConstraints(
+ parent.getComponent(i));
+
+ cons.setWidth(maxWidthSpring);
+ cons.setHeight(maxHeightSpring);
+ }
+
+ //Then adjust the x/y constraints of all the cells so that they
+ //are aligned in a grid.
+ SpringLayout.Constraints lastCons = null;
+ SpringLayout.Constraints lastRowCons = null;
+ for (int i = 0; i < max; i++) {
+ SpringLayout.Constraints cons = layout.getConstraints(
+ parent.getComponent(i));
+ if (i % cols == 0) { //start of new row
+ lastRowCons = lastCons;
+ cons.setX(initialXSpring);
+ } else { //x position depends on previous component
+ cons.setX(Spring.sum(lastCons.getConstraint(SpringLayout.EAST),
+ xPadSpring));
+ }
+
+ if (i / cols == 0) { //first row
+ cons.setY(initialYSpring);
+ } else { //y position depends on previous row
+ cons.setY(Spring.sum(lastRowCons.getConstraint(SpringLayout.SOUTH),
+ yPadSpring));
+ }
+ lastCons = cons;
+ }
+
+ //Set the parent's size.
+ SpringLayout.Constraints pCons = layout.getConstraints(parent);
+ pCons.setConstraint(SpringLayout.SOUTH,
+ Spring.sum(
+ Spring.constant(yPad),
+ lastCons.getConstraint(SpringLayout.SOUTH)));
+ pCons.setConstraint(SpringLayout.EAST,
+ Spring.sum(
+ Spring.constant(xPad),
+ lastCons.getConstraint(SpringLayout.EAST)));
+ }
+
+ /* Used by makeCompactGrid. */
+ /**
+ * Gets the constraints for cell.
+ *
+ * @param row the row
+ * @param col the col
+ * @param parent the parent
+ * @param cols the cols
+ * @return the constraints for cell
+ */
+ private static SpringLayout.Constraints getConstraintsForCell(
+ int row, int col,
+ Container parent,
+ int cols) {
+ SpringLayout layout = (SpringLayout) parent.getLayout();
+ Component c = parent.getComponent(row * cols + col);
+ return layout.getConstraints(c);
+ }
+
+ /**
+ * Aligns the first <code>rows</code> * <code>cols</code>
+ * components of <code>parent</code> in
+ * a grid. Each component in a column is as wide as the maximum
+ * preferred width of the components in that column;
+ * height is similarly determined for each row.
+ * The parent is made just big enough to fit them all.
+ *
+ * @param parent the parent
+ * @param rows number of rows
+ * @param cols number of columns
+ * @param initialX x location to start the grid at
+ * @param initialY y location to start the grid at
+ * @param xPad x padding between cells
+ * @param yPad y padding between cells
+ */
+ public static void makeCompactGrid(Container parent,
+ int rows, int cols,
+ int initialX, int initialY,
+ int xPad, int yPad) {
+ SpringLayout layout;
+ try {
+ layout = (SpringLayout)parent.getLayout();
+ } catch (ClassCastException exc) {
+ System.err.println("The first argument to makeCompactGrid must use SpringLayout.");
+ return;
+ }
+
+ //Align all cells in each column and make them the same width.
+ Spring x = Spring.constant(initialX);
+ for (int c = 0; c < cols; c++) {
+ Spring width = Spring.constant(0);
+ for (int r = 0; r < rows; r++) {
+ width = Spring.max(width,
+ getConstraintsForCell(r, c, parent, cols).
+ getWidth());
+ }
+ for (int r = 0; r < rows; r++) {
+ SpringLayout.Constraints constraints =
+ getConstraintsForCell(r, c, parent, cols);
+ constraints.setX(x);
+ constraints.setWidth(width);
+ }
+ x = Spring.sum(x, Spring.sum(width, Spring.constant(xPad)));
+ }
+
+ //Align all cells in each row and make them the same height.
+ Spring y = Spring.constant(initialY);
+ for (int r = 0; r < rows; r++) {
+ Spring height = Spring.constant(0);
+ for (int c = 0; c < cols; c++) {
+ height = Spring.max(height,
+ getConstraintsForCell(r, c, parent, cols).
+ getHeight());
+ }
+ for (int c = 0; c < cols; c++) {
+ SpringLayout.Constraints constraints =
+ getConstraintsForCell(r, c, parent, cols);
+ constraints.setY(y);
+ constraints.setHeight(height);
+ }
+ y = Spring.sum(y, Spring.sum(height, Spring.constant(yPad)));
+ }
+
+ //Set the parent's size.
+ SpringLayout.Constraints pCons = layout.getConstraints(parent);
+ pCons.setConstraint(SpringLayout.SOUTH, y);
+ pCons.setConstraint(SpringLayout.EAST, x);
+ }
+}
+
diff --git a/src/pyromaniac/GUI/TagInputPanel.java b/src/pyromaniac/GUI/TagInputPanel.java
new file mode 100644
index 0000000..c3381b4
--- /dev/null
+++ b/src/pyromaniac/GUI/TagInputPanel.java
@@ -0,0 +1,2266 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.GUI;
+
+import java.awt.BorderLayout;
+import java.awt.CardLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+
+import javax.swing.JTextPane;
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.ButtonModel;
+import javax.swing.ImageIcon;
+import javax.swing.InputVerifier;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JScrollPane;
+import javax.swing.JSpinner;
+import javax.swing.JTable;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.SpinnerListModel;
+import javax.swing.SpringLayout;
+import javax.swing.border.Border;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.text.AbstractDocument;
+import javax.swing.text.AttributeSet;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.DocumentFilter;
+import javax.swing.BoxLayout;
+import javax.swing.table.DefaultTableModel;
+import javax.swing.table.TableModel;
+import javax.swing.JCheckBox;
+
+import pyromaniac.AcaciaConstants;
+import pyromaniac.AcaciaMain;
+import pyromaniac.AcaciaEngine;
+import pyromaniac.ErrorCorrectionWorker;
+import pyromaniac.DataStructures.MIDPrimerCombo;
+import pyromaniac.IO.AcaciaLogger;
+import pyromaniac.IO.MIDReader;
+import pyromaniac.IO.MIDReader.MIDFormatException;
+
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class TagInputPanel.
+ */
+public class TagInputPanel extends JPanel implements ActionListener,ListSelectionListener
+{
+
+ /** The Constant serialVersionUID. */
+ private static final long serialVersionUID = 1L;
+
+ /** The Constant NUM_VERTICAL_ELEMENTS. */
+ public static final int NUM_VERTICAL_ELEMENTS = 6;
+
+ /** The Constant WINDOW_BACKGROUND_COLOUR. */
+ public static final Color WINDOW_BACKGROUND_COLOUR = Color.decode("#000000");
+
+ /** The Constant FORM_BACKGROUND_COLOUR. */
+ public static final Color FORM_BACKGROUND_COLOUR = Color.decode("#DFE567");
+
+ /** The Constant BORDER_COLOUR. */
+ public static final Color BORDER_COLOUR = Color.decode("#777F19");
+
+ /** The Constant BUTTON_GRADIENT_COLOR2. */
+ public static final Color BUTTON_GRADIENT_COLOR2 = Color.decode("#C3CC66");
+
+ /** The Constant BUTTON_GRADIENT_COLOR1. */
+ public static final Color BUTTON_GRADIENT_COLOR1 = Color.white;
+
+ /** The Constant BUTTON_BORDER_COLOR. */
+ public static final Color BUTTON_BORDER_COLOR = Color.decode("#616633");
+
+ /** The Constant TABLE_SELECTION_COLOUR. */
+ private static final Color TABLE_SELECTION_COLOUR = Color.decode("#E6E614");
+
+ /** The Constant TABLE_BACKGROUND_COLOUR. */
+ private static final Color TABLE_BACKGROUND_COLOUR = Color.decode("#DBE572");
+
+ /** The Constant DEFAULT_BORDER. */
+ public static final Border DEFAULT_BORDER = BorderFactory.createLineBorder(TagInputPanel.BORDER_COLOUR, 2);
+
+ /** The Constant COLUMN_IDENTIFIERS. */
+ public static final Object [] COLUMN_IDENTIFIERS = {"MID", "Primer", "Description"};
+
+ /** The worker. */
+ private ErrorCorrectionWorker worker;
+
+ /** The logger. */
+ private AcaciaLogger logger;
+
+ /** The Constant sigStringToDouble. */
+ public static final HashMap <String, Double> sigStringToDouble = new HashMap <String, Double> ();
+
+
+
+ /** The enclosing bg. */
+ private JPanel enclosingBG;
+
+ /** The bg panel left. */
+ private JPanel bgPanelLeft;
+
+ /** The bg panel right. */
+ private JPanel bgPanelRight;
+
+ /** The data format. */
+ private JPanel dataFormat;
+
+ /** The fasta panel. */
+ private JPanel fastaPanel;
+
+ /** The fastq panel. */
+ private JPanel fastqPanel;
+
+ /** The mids. */
+ private JPanel mids;
+
+ /** The load mids panel. */
+ private JPanel loadMidsPanel;
+
+ /** The quality assurance. */
+ private JPanel qualityAssurance;
+
+ /** The mismatches. */
+ private JPanel mismatches;
+
+ /** The last dir. */
+ private String lastDir;
+
+
+ /** The cancel. */
+ private AcaciaGradientButton cancel;
+
+ /** The submit. */
+ private AcaciaGradientButton submit;
+
+ //relating to the form creation
+ /** The file format. */
+ private ButtonGroup fileFormat;
+
+ /** The mid selection. */
+ private ButtonGroup midSelection;
+
+ /** The split on mid. */
+ private JCheckBox splitOnMID;
+
+
+ //action strings
+ /** The Constant FASTQ. */
+ private static final String FASTQ = "FASTQ";
+
+ /** The Constant FASTA. */
+ private static final String FASTA = "FASTA";
+
+
+ /** The Constant FIND_FASTQ. */
+ private static final String FIND_FASTQ = "Find FASTQ";
+
+ /** The Constant FIND_FASTA. */
+ private static final String FIND_FASTA = "Find FASTA";
+
+ /** The Constant FIND_QUAL. */
+ private static final String FIND_QUAL = "Find QUAL";
+
+ /** The Constant FIND_MIDS. */
+ private static final String FIND_MIDS = "Find MIDS";
+
+ /** The Constant SELECT_ALL_MIDS. */
+ private static final String SELECT_ALL_MIDS = "Select All";
+
+ /** The Constant CLEAR_ALL_MIDS. */
+ private static final String CLEAR_ALL_MIDS = "Clear All";
+
+ /** The Constant OPTION_FIVEBASE. */
+ private static final String OPTION_FIVEBASE = "Roche supplied 5-base MIDs";
+
+ /** The Constant OPTION_TENBASE. */
+ private static final String OPTION_TENBASE = "Roche supplied 10-base MIDs";
+
+ /** The Constant OPTION_LOAD_MIDS. */
+ private static final String OPTION_LOAD_MIDS = "Load user-supplied MID descriptor file";
+
+ /** The Constant OPTION_NO_MIDS. */
+ private static final String OPTION_NO_MIDS = "Ignore MIDs";
+
+ /** The Constant FIND_PROJECT_DIR. */
+ private static final String FIND_PROJECT_DIR = "Select output directory:";
+
+ /** The Constant SUBMIT_FORM. */
+ private static final String SUBMIT_FORM = "Submit form";
+
+
+ /** The Constant DEFAULT_PREFERRED_FIELD_HEIGHT. */
+ private static final int DEFAULT_PREFERRED_FIELD_HEIGHT = 28; //this is the default height for ALL the textfield and button components.
+
+ /** The Constant DEFAULT_TEXTFIELD_MAX_WIDTH. */
+ private static final int DEFAULT_TEXTFIELD_MAX_WIDTH = 120;
+
+ /** The Constant DEFAULT_MINIMUM_LABEL_WIDTH. */
+ private static final int DEFAULT_MINIMUM_LABEL_WIDTH = 80; //this may be useful? TODO
+
+ /** The fastq file choice. */
+ private JTextField fastqFileChoice;
+
+ /** The fasta file choice. */
+ private JTextField fastaFileChoice;
+
+ /** The qual file choice. */
+ private JTextField qualFileChoice;
+
+ /** The project name. */
+ private JTextField projectName;
+
+ /** The mids choice. */
+ private JTextField midsChoice;
+
+ /** The output dir. */
+ private JTextField outputDir;
+
+ /** The trim to length. */
+ private JTextField trimToLength;
+
+ /** The hamming distance. */
+ private JTextField manhattanDistance;
+
+
+ /** The parent. */
+ private JFrame parent;
+
+
+ /** The spinner significance. */
+ private JSpinner spinnerSignificance;
+
+ /** The name panel. */
+ private JPanel namePanel;
+
+ /** The screen mids. */
+ private JPanel screenMIDS;
+
+ /** The standard output. */
+ private JPanel standardOutput;
+
+ /** The standard output field. */
+ private JTextPane standardOutputField;
+
+ /** The mid table. */
+ private JTable midTable;
+
+ /** The MID select all. */
+ private JButton MIDSelectAll;
+
+ /** The MID clear all. */
+ private JButton MIDClearAll;
+
+ /** The num selected. */
+ private JLabel numSelected;
+
+ /** The file format inner panel. */
+ private JPanel fileFormatInnerPanel;
+
+ /** The format card panel. */
+ private JPanel formatCardPanel;
+
+ private JPanel technologyCardPanel;
+
+ /** The quality threshold. */
+ private JSpinner qualityThreshold;
+
+ /** The mid card panel. */
+ private JPanel midCardPanel;
+
+ /** The spinner representative seq. */
+ private JSpinner spinnerRepresentativeSeq;
+
+ /** The no mi ds. */
+ private JRadioButton noMIDs;
+
+ /** The load mi ds. */
+ private JRadioButton loadMIDs;
+
+ /** The SD threshold. */
+ private JSpinner SDThreshold;
+
+ /** The error model spinner. */
+ private JSpinner errorModelSpinner;
+
+ private ButtonGroup techFormat;
+
+ private JPanel techInnerPanel;
+
+// private static final String [] optionsSignificance = new String [] {"0", "0.001", "0.01", "0.025", "0.05", "0.1"};
+
+ /** The Constant optionsSignificance. */
+private static final String [] optionsSignificance = new String [] {"0", "-1", "-2", "-3", "-4", "-5", "-6", "-7", "-8", "-9", "-10", "-Inf"};
+
+ /** The Constant significanceModel. */
+ private static final javax.swing.SpinnerListModel significanceModel = new SpinnerListModel(optionsSignificance);
+
+
+ /** The Constant DEFAULT_BUTTON_WIDTH. */
+ private static final int DEFAULT_BUTTON_WIDTH = 110;
+
+ /** The Constant MIN_QUALITY_SCORE. */
+ private static final int MIN_QUALITY_SCORE = 1;
+
+ /** The Constant MAX_QUALITY_SCORE. */
+ private static final int MAX_QUALITY_SCORE = 40;
+
+ //messages and defaults.
+
+ /** The Constant DONT_LOAD_USER_SUPPLIED_MIDS. */
+ private static final String DONT_LOAD_USER_SUPPLIED_MIDS = "DONT_LOAD_MIDS_PANEL";
+
+ /** The Constant HELP_QUALITY_THRESHOLD_TEXT. */
+ private static final String HELP_QUALITY_THRESHOLD_TEXT = "All reads with an average quality less than this threshold will be removed from dataset. This parameter is ignored when quality values are not supplied.";
+
+ /** The Constant HELP_TRIM_READS_TO_LENGTH. */
+ private static final String HELP_TRIM_READS_TO_LENGTH = "Reads will be trimmed to this length prior to error correction. Leave blank if no trimming desired.";
+
+ /** The Constant HELP_MAX_HAMMING_TEXT. */
+ private static final String HELP_MAX_HAMMING_TEXT = "Used in pre-clustering, this is the <i> maximum </i> hamming distance between the hexamer frequencies in two reads such that they will be clustered together.";
+
+ /** The Constant HELP_SIGNIFICANCE_THRESHOLD_TEXT. */
+ private static final String HELP_SIGNIFICANCE_THRESHOLD_TEXT = "Loci where there are variable homopolymer lengths observed across reads will be tested to see if the difference is due to under/over-call error, or 'real' differences. " +
+ " A hypothesis test is performed to determine whether differences are due to error alone. A lower value provides more sensitivity, at the cost of specificity. Vice versa for a higher value.";
+
+ /** The Constant FIVEBASE_MID_FILE. */
+// private static final String FIVEBASE_MID_FILE = "/data/MID_fivebase.csv";
+
+ /** The Constant TENBASE_MID_FILE. */
+// private static final String TENBASE_MID_FILE = "/data/MID_tenbase.csv";
+
+ /** The Constant HELP_REPRESENTATIVE_TEXT. */
+ private static final String HELP_REPRESENTATIVE_TEXT = "During the de-replication process, a representative read is selected for read 'cluster'. This representative sequence is selected based on its length relative to others in the cluster; the representative sequence may have the minimum, maximum, mode, or median length in the cluster.";
+
+ /** The Constant CLEAR_FORM. */
+private static final String CLEAR_FORM = "CLEAR_FORM";
+
+ /** The Constant CANCEL_RUN. */
+ private static final String CANCEL_RUN = "CANCEL_RUN";
+
+ /** The Constant HELP_SPLIT_MID_TEXT. */
+ private static final String HELP_SPLIT_MID_TEXT = "When switched on, reads will be split into groups based on their MID" +
+ ", ie. each MID-based group will be analysed separately. When switched off, sequences with any of the user-selected MIDs" +
+ "will be processed altogether.";
+
+ /** The Constant HELP_FILTER_BY_LENGTH_SD. */
+ private static final String HELP_FILTER_BY_LENGTH_SD = "Reads which have a un-trimmed length this many standard deviations from the mean are removed from further analysis.";
+
+ /** The Constant HELP_ERROR_MODEL_TEXT. */
+ private static final String HELP_ERROR_MODEL_TEXT =
+ "Two models are currently available: the Balzer et al. (2010) models include flow position as an effect, however these " +
+ "require that the sequences have had the key removed, but not the MID. If some kind of quality assurance has been applied to the reads, trimming the 5' end, the Quince (2009) models are preferable.";
+ //private static final String HELP_MAX_HAMMING_ALIGN_TEXT = "In the second phase of clustering, sequences with less than this hamming distance will be ";
+
+ private static final String TECH_454 = "TECH_454";
+
+ private static final String TECH_ION_TORRENT = "TECH_ION_TORRENT";
+
+ private static final String HELP_TECH_TEXT = "The sequencing platform used to generate the dataset.";
+
+ private static final String [] modelOptions454 = new String [] {AcaciaConstants.OPT_FLOWSIM_ERROR_MODEL, AcaciaConstants.OPT_PYRONOISE_ERROR_MODEL};
+ private static final String [] modelOptionsIT = new String[] {AcaciaConstants.OPT_ACACIA_IT_OT_100bp_314_MODEL,AcaciaConstants.OPT_ACACIA_IT_OT_100bp_316_MODEL,
+ AcaciaConstants.OPT_ACACIA_IT_MAN_200bp_314_MODEL, AcaciaConstants.OPT_ACACIA_IT_MAN_200bp_316_MODEL,
+ AcaciaConstants.OPT_ACACIA_IT_OT_200bp_314, AcaciaConstants.OPT_ACACIA_IT_OT_200bp_316};
+
+ private static final javax.swing.SpinnerListModel errorModel454 = new SpinnerListModel(modelOptions454);
+ private static final javax.swing.SpinnerListModel errorModelIT = new SpinnerListModel(modelOptionsIT);
+
+
+ /**
+ * Instantiates a new TagInputPanel.
+ *
+ * @param util the grid bag utility which assists the layout manager for this panel
+ * @param parent the parent frame
+ * @throws Exception any exception that occurs during the creation of this TagInputPanel
+ */
+ public TagInputPanel(GridBagUtility util, JFrame parent) throws Exception
+ {
+ this.setVisible(true);
+ this.setBackground(WINDOW_BACKGROUND_COLOUR);
+ this.worker = null;
+ fastqFileChoice = null;
+ fastaFileChoice = null;
+ qualFileChoice = null;
+ this.parent = parent;
+ this.logger = new AcaciaLogger();
+ this.lastDir = null;
+ initPanel();
+ }
+
+ /**
+ * Initialises the tag input panel.
+ *
+ * @throws Exception the exception
+ */
+ public void initPanel() throws Exception
+ {
+ //changing main TagInputPanel to have Spring Layout too.
+
+ SpringLayout tagInputLayout = new SpringLayout();
+ this.setLayout(tagInputLayout);
+
+ int parentWidth = this.parent.getWidth();
+ int parentHeight = this.parent.getHeight();
+
+ //setting up the logo on this tag input panel.
+ JPanel logo = createImagePanel(AcaciaMain.ACACIA_LOGO, TagInputPanel.WINDOW_BACKGROUND_COLOUR, "Acacia logo");
+ tagInputLayout.putConstraint(SpringLayout.NORTH, logo, 2, SpringLayout.NORTH, this);
+
+ int westOffset = 5;
+ int distFromEastEdge = parentWidth - logo.getPreferredSize().width - westOffset;
+
+ tagInputLayout.putConstraint(SpringLayout.EAST, logo, -1 * (distFromEastEdge) + 5 , SpringLayout.EAST, this);
+ tagInputLayout.putConstraint(SpringLayout.WEST, logo, westOffset , SpringLayout.WEST, this);
+
+
+ int logoHeight = logo.getPreferredSize().height;
+ int maxPanelHeight = parentHeight - logoHeight;
+ this.add(logo);
+
+ //reference sizes
+
+ Border basic = BorderFactory.createLineBorder(TagInputPanel.BORDER_COLOUR, 2);
+ Dimension enclosingBGDimensions = new Dimension(parentWidth - 5, maxPanelHeight - 15);
+
+// System.out.println("The enclosing BG dimensions are: " + enclosingBGDimensions.width + " , " + enclosingBGDimensions.height);
+
+ this.enclosingBG = new JPanel();
+ this.enclosingBG.setMinimumSize(enclosingBGDimensions);
+ this.enclosingBG.setPreferredSize(enclosingBGDimensions);
+ this.enclosingBG.setSize(enclosingBGDimensions);
+ this.enclosingBG.setBackground(TagInputPanel.WINDOW_BACKGROUND_COLOUR);
+
+ //potentially use spring layout for the rest of the components
+ SpringLayout enclosingBGLayoutManager = new SpringLayout();
+ this.enclosingBG.setLayout(enclosingBGLayoutManager);
+
+ tagInputLayout.putConstraint(SpringLayout.NORTH, this.enclosingBG, 0, SpringLayout.SOUTH,logo);
+ tagInputLayout.putConstraint(SpringLayout.SOUTH, this.enclosingBG, -5, SpringLayout.SOUTH, this);
+ tagInputLayout.putConstraint(SpringLayout.WEST, this.enclosingBG, 2, SpringLayout.WEST, this);
+ tagInputLayout.putConstraint(SpringLayout.EAST, this.enclosingBG, -2, SpringLayout.EAST, this);
+ this.add(enclosingBG);
+
+ Dimension panelPreferredDimension = new Dimension ((this.parent.getWidth()/2) - 10, (int)((maxPanelHeight - 15) * 70));
+ initBGPanelLeft(panelPreferredDimension);
+ initBGPanelRight(panelPreferredDimension);
+
+ JPanel submitPanel = this.createSubmitOrClearPanel(enclosingBG, basic);
+ Dimension submitPanelDimensions = submitPanel.getPreferredSize();
+ submitPanelDimensions.width = enclosingBG.getPreferredSize().width - 10;
+ submitPanelDimensions.height = this.DEFAULT_PREFERRED_FIELD_HEIGHT;
+ submitPanel.setPreferredSize(submitPanelDimensions);
+ submitPanel.setSize(submitPanelDimensions);
+ initStandardOutputPanel(enclosingBG, basic);
+
+ this.enclosingBG.add(bgPanelLeft);
+ this.enclosingBG.add(bgPanelRight);
+ this.enclosingBG.add(submitPanel);
+ this.enclosingBG.add(this.standardOutput);
+
+ //add the panels...
+ enclosingBGLayoutManager.putConstraint(SpringLayout.WEST, bgPanelLeft, 5, SpringLayout.WEST, enclosingBG);
+ enclosingBGLayoutManager.putConstraint(SpringLayout.EAST, bgPanelRight, -5, SpringLayout.EAST, enclosingBG);
+ enclosingBGLayoutManager.putConstraint(SpringLayout.EAST, bgPanelLeft, -5, SpringLayout.WEST, bgPanelRight);
+ enclosingBGLayoutManager.putConstraint(SpringLayout.NORTH, bgPanelLeft, 1, SpringLayout.NORTH, enclosingBG);
+ enclosingBGLayoutManager.putConstraint(SpringLayout.NORTH, bgPanelRight, 1, SpringLayout.NORTH, enclosingBG);
+
+ //add the submit panel
+ enclosingBGLayoutManager.putConstraint(SpringLayout.WEST, submitPanel, 5, SpringLayout.WEST, enclosingBG);
+ enclosingBGLayoutManager.putConstraint(SpringLayout.EAST, submitPanel, -5, SpringLayout.EAST, enclosingBG);
+ enclosingBGLayoutManager.putConstraint(SpringLayout.NORTH, submitPanel, 5, SpringLayout.SOUTH,bgPanelRight);
+ //enclosingBGLayoutManager.putConstraint(SpringLayout.NORTH, submitPanel, 5, SpringLayout.SOUTH,bgPanelLeft);
+
+
+ //add the standard output panel
+ enclosingBGLayoutManager.putConstraint(SpringLayout.NORTH, this.standardOutput, 5, SpringLayout.SOUTH, submitPanel);
+ enclosingBGLayoutManager.putConstraint(SpringLayout.SOUTH, this.standardOutput, -5, SpringLayout.SOUTH, enclosingBG);
+ enclosingBGLayoutManager.putConstraint(SpringLayout.WEST, this.standardOutput, 5, SpringLayout.WEST, enclosingBG);
+ enclosingBGLayoutManager.putConstraint(SpringLayout.EAST, this.standardOutput, -5, SpringLayout.EAST, enclosingBG);
+
+ //this.am.getLogger().flushBuffers();
+ }
+
+ /**
+ * Inits the bg panel left.
+ *
+ * @param preferred the preferred
+ * @throws Exception the exception
+ */
+ private void initBGPanelLeft(Dimension preferred) throws Exception
+ {
+ this.bgPanelLeft = new JPanel();
+ this.bgPanelLeft.setLayout(new SpringLayout());
+ this.bgPanelLeft.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ this.bgPanelLeft.setMinimumSize(preferred);
+
+ //all initialised
+ //assume that these panels are instance variables
+
+ this.addFileFormatPanel(this.bgPanelLeft, DEFAULT_BORDER);
+ this.addQualityAssurancePanel(bgPanelLeft, DEFAULT_BORDER);
+ this.addTreeConstructionPanel(bgPanelLeft, DEFAULT_BORDER);
+ SpringUtilities.makeCompactGrid(bgPanelLeft, 3, 1, 5, 5, 5, 5);
+ }
+
+
+
+ /**
+ * Inits the bg panel right.
+ *
+ * @param preferred the preferred
+ * @throws Exception the exception
+ */
+ private void initBGPanelRight(Dimension preferred) throws Exception
+ {
+ this.bgPanelRight = new JPanel();
+ this.bgPanelRight.setLayout(new SpringLayout());
+ this.bgPanelRight.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ this.addMIDOptionsPanel(this.bgPanelRight, DEFAULT_BORDER);
+ this.addScreenMIDsPanel(this.bgPanelRight, DEFAULT_BORDER);
+ this.addProjectNamePanel(this.bgPanelRight, DEFAULT_BORDER);
+
+ int preferredHeight = this.screenMIDS.getPreferredSize().height + this.namePanel.getPreferredSize().height + this.midCardPanel.getPreferredSize().height + 120; //why 120, dunno
+
+ Dimension minD = new Dimension(preferred.width, preferredHeight);
+ this.bgPanelRight.setMinimumSize(minD);
+ this.bgPanelRight.setPreferredSize(minD);
+
+ SpringUtilities.makeCompactGrid(bgPanelRight, 3, 1, 5, 5, 5, 5);
+
+ }
+
+ /**
+ * Locks the interface, preventing user input.
+ */
+ public void lockInterface()
+ {
+ this.enableInputMethods(false);
+ }
+
+ /**
+ * Adds the tree construction panel.
+ *
+ * @param panelToAddTo the panel to add to
+ * @param b the b
+ * @throws Exception the exception
+ */
+ private void addTreeConstructionPanel(JPanel panelToAddTo, Border b) throws HelpButton.MissingHelpImageException
+ {
+ this.mismatches = new JPanel();
+ this.mismatches.setLayout(new SpringLayout());
+ this.mismatches.setBorder(BorderFactory.createTitledBorder(b, "Analysis",TitledBorder.LEFT,TitledBorder.TOP, this.getFont()));
+ this.mismatches.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+
+ this.techFormat = new ButtonGroup();
+ JRadioButton fourFiveFourButton = new JRadioButton("Roche 454");
+ fourFiveFourButton.setActionCommand(TECH_454);
+ fourFiveFourButton.addActionListener(this);
+ fourFiveFourButton.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ this.setDimensionsToDefault(fourFiveFourButton);
+
+ JRadioButton ionTorrentButton = new JRadioButton("Ion Torrent");
+ ionTorrentButton.setActionCommand(TECH_ION_TORRENT);
+ ionTorrentButton.addActionListener(this);
+ ionTorrentButton.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ this.setDimensionsToDefault(ionTorrentButton);
+
+ this.techFormat.add(fourFiveFourButton);
+ this.techFormat.add(ionTorrentButton);
+ this.techFormat.setSelected(fourFiveFourButton.getModel(),true);
+
+ this.techInnerPanel = new JPanel();
+ techInnerPanel.setLayout(new SpringLayout());
+ techInnerPanel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ techInnerPanel.add(fourFiveFourButton);
+ techInnerPanel.add(ionTorrentButton);
+ SpringUtilities.makeCompactGrid(techInnerPanel, 1, 2, 0, 0, 50, 5);
+
+ JLabel maxHammingDistLabel = new JLabel("Maximum k-mer dist between reads:");
+ adjustLabel(maxHammingDistLabel);
+ setDimensionsToDefault(maxHammingDistLabel);
+
+ this.manhattanDistance = new JTextField();
+ this.manhattanDistance.setText(AcaciaConstants.DEFAULT_OPT_MAXIMUM_MANHATTAN_DIST);
+ this.setDimensionsToDefault(manhattanDistance);
+ this.setTextFieldSize(manhattanDistance);
+ manhattanDistance.setHorizontalAlignment(JTextField.RIGHT);
+
+
+ javax.swing.SpinnerListModel errorModel = errorModel454;
+ errorModel.setValue(AcaciaConstants.OPT_FLOWSIM_ERROR_MODEL);
+
+ JLabel errorModelLabel = new JLabel("Error model to use:");
+ this.errorModelSpinner = new JSpinner(errorModel);
+ Dimension dError = errorModelSpinner.getPreferredSize();
+ dError.width = TagInputPanel.DEFAULT_TEXTFIELD_MAX_WIDTH / 2;
+ errorModelSpinner.setPreferredSize(dError);
+ errorModelSpinner.setMaximumSize(dError);
+ errorModelSpinner.setSize(dError);
+
+ JLabel significanceThreshold = new JLabel("Statistical significance threshold: ");
+ adjustLabel(significanceThreshold);
+ setDimensionsToDefault(significanceThreshold);
+ significanceModel.setValue(AcaciaConstants.DEFAULT_OPT_SIGNIFICANCE_LEVEL);
+
+ spinnerSignificance = new JSpinner(significanceModel);
+
+ Dimension d = spinnerSignificance.getPreferredSize();
+ d.width = TagInputPanel.DEFAULT_TEXTFIELD_MAX_WIDTH / 2;
+ spinnerSignificance.setPreferredSize(d);
+ spinnerSignificance.setMaximumSize(d);
+ spinnerSignificance.setSize(d);
+ setDimensionsToDefault(spinnerSignificance);
+
+ String [] optionsRepresentative = {AcaciaConstants.OPT_MODE_REPRESENTATIVE, AcaciaConstants.OPT_MEDIAN_REPRESENTATIVE, AcaciaConstants.OPT_MAX_REPRESENTATIVE, AcaciaConstants.OPT_MIN_REPRESENTATIVE};
+
+ javax.swing.SpinnerListModel repModel = new SpinnerListModel(optionsRepresentative);
+ repModel.setValue(AcaciaConstants.DEFAULT_OPT_REPRESENTATIVE_SEQ);
+ this.spinnerRepresentativeSeq = new JSpinner(repModel);
+
+
+ JLabel representativeLabel = new JLabel("Representative sequence:");
+ adjustLabel(representativeLabel);
+ setDimensionsToDefault(representativeLabel);
+
+ d = spinnerRepresentativeSeq.getPreferredSize();
+ d.width = TagInputPanel.DEFAULT_TEXTFIELD_MAX_WIDTH / 2;
+ spinnerRepresentativeSeq.setPreferredSize(d);
+ spinnerRepresentativeSeq.setMaximumSize(d);
+ spinnerRepresentativeSeq.setSize(d);
+ setDimensionsToDefault(spinnerRepresentativeSeq);
+
+ JPanel helpPanelMaxHamming = new JPanel();
+ helpPanelMaxHamming.setBackground(FORM_BACKGROUND_COLOUR);
+ helpPanelMaxHamming.setLayout(new BoxLayout(helpPanelMaxHamming, BoxLayout.LINE_AXIS));
+ helpPanelMaxHamming.add(new HelpButton(HELP_MAX_HAMMING_TEXT, this.parent));
+ this.setJPanelToButtonSize(helpPanelMaxHamming);
+
+ JPanel helpPanelSignificance = new JPanel();
+ helpPanelSignificance.setBackground(FORM_BACKGROUND_COLOUR);
+ helpPanelSignificance.setLayout(new BoxLayout(helpPanelSignificance, BoxLayout.LINE_AXIS));
+ helpPanelSignificance.add(new HelpButton(HELP_SIGNIFICANCE_THRESHOLD_TEXT, this.parent));
+ this.setJPanelToButtonSize(helpPanelSignificance);
+
+ JPanel helpPanelRepresentative = new JPanel();
+ helpPanelRepresentative.setBackground(FORM_BACKGROUND_COLOUR);
+ helpPanelRepresentative.setLayout(new BoxLayout(helpPanelRepresentative, BoxLayout.LINE_AXIS));
+ helpPanelRepresentative.add(new HelpButton(HELP_REPRESENTATIVE_TEXT, this.parent));
+
+ JPanel helpPanelModels = new JPanel();
+ helpPanelModels.setBackground(FORM_BACKGROUND_COLOUR);
+ helpPanelModels.setLayout(new BoxLayout(helpPanelModels, BoxLayout.LINE_AXIS));
+ helpPanelModels.add(new HelpButton(HELP_ERROR_MODEL_TEXT, this.parent));
+
+ JPanel helpPanelTech = new JPanel();
+ helpPanelTech.setBackground(FORM_BACKGROUND_COLOUR);
+ helpPanelTech.setLayout(new BoxLayout(helpPanelTech, BoxLayout.LINE_AXIS));
+ helpPanelTech.add(new HelpButton(HELP_TECH_TEXT, this.parent));
+
+ //TODO: new
+
+ JLabel blank = new JLabel();
+ blank.setBackground(FORM_BACKGROUND_COLOUR);
+
+ mismatches.add(techInnerPanel);
+ mismatches.add(blank);
+ mismatches.add(helpPanelTech);
+
+ mismatches.add(maxHammingDistLabel);
+ mismatches.add(manhattanDistance);
+ mismatches.add(helpPanelMaxHamming);
+
+ mismatches.add(errorModelLabel);
+ mismatches.add(errorModelSpinner);
+ mismatches.add(helpPanelModels);
+
+ mismatches.add(significanceThreshold);
+ mismatches.add(spinnerSignificance);
+ mismatches.add(helpPanelSignificance);
+ mismatches.add(representativeLabel);
+ mismatches.add(spinnerRepresentativeSeq);
+ mismatches.add(helpPanelRepresentative);
+
+ SpringUtilities.makeCompactGrid(mismatches, 5, 3, 5, 5, 5, 5);
+ panelToAddTo.add(mismatches);
+ }
+
+
+
+ /**
+ * Creates the submit or clear panel.
+ *
+ * @param panelToAddTo the panel to add to
+ * @param b the b
+ * @return the j panel
+ */
+ private JPanel createSubmitOrClearPanel(JPanel panelToAddTo, Border b)
+ {
+ JPanel submitOrClearPanel = new JPanel();
+ submitOrClearPanel.setBackground(TagInputPanel.WINDOW_BACKGROUND_COLOUR);
+
+ SpringLayout submitLayout = new SpringLayout();
+ submitOrClearPanel.setLayout(submitLayout);
+
+ this.submit = new AcaciaGradientButton("Submit", TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2, TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ submit.setActionCommand(SUBMIT_FORM);
+ submit.addActionListener(this);
+
+ JButton clear = new AcaciaGradientButton("Clear", TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2, TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ clear.setActionCommand(CLEAR_FORM);
+ clear.addActionListener(this);
+
+
+ this.cancel = new AcaciaGradientButton("Cancel", TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2, TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ cancel.setActionCommand(CANCEL_RUN);
+ cancel.addActionListener(this);
+ cancel.setEnabled(false);
+
+ this.setLargeButtonSize(submit);
+ this.setLargeButtonSize(clear);
+ this.setLargeButtonSize(cancel);
+
+ submitOrClearPanel.add(submit);
+ submitOrClearPanel.add(clear);
+ submitOrClearPanel.add(cancel);
+
+ submitLayout.putConstraint(SpringLayout.WEST, clear, 0 , SpringLayout.WEST, submitOrClearPanel);
+ submitLayout.putConstraint(SpringLayout.EAST, cancel, -5,SpringLayout.WEST, submit);
+
+ submitLayout.putConstraint(SpringLayout.EAST, submit,
+ 0,
+ SpringLayout.EAST, submitOrClearPanel);
+ submitLayout.putConstraint(SpringLayout.SOUTH, submitOrClearPanel,
+ 5,
+ SpringLayout.SOUTH, submit);
+
+ return submitOrClearPanel;
+ }
+
+ /**
+ * Adds the project name panel.
+ *
+ * @param panelToAddTo the panel to add to
+ * @param b the b
+ */
+ private void addProjectNamePanel(JPanel panelToAddTo, Border b)
+ {
+ this.namePanel = new JPanel();
+ SpringLayout sl = new SpringLayout();
+
+ this.namePanel.setLayout(sl);
+ this.namePanel.setBorder(BorderFactory.createTitledBorder(b, "Output requirements",TitledBorder.LEFT,TitledBorder.TOP, this.getFont()));
+ this.namePanel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ this.projectName = new JTextField("");
+
+ this.setTextFieldSize(this.projectName);
+ this.setDimensionsToDefault(projectName);
+
+ //add to namePanel
+ JLabel outputFilePrefix = new JLabel("Output file prefix:");
+ this.adjustLabel(outputFilePrefix);
+ this.setDimensionsToDefault(outputFilePrefix);
+
+ JButton openFile = new AcaciaGradientButton("Browse...", TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2,TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ openFile.setActionCommand(FIND_PROJECT_DIR);
+ openFile.addActionListener(this);
+ this.setLargeButtonSize(openFile);
+
+ this.outputDir = new JTextField("");
+ this.setTextFieldSize(this.outputDir);
+
+ Dimension actualSizeTextField = outputDir.getPreferredSize();
+ actualSizeTextField.width = DEFAULT_TEXTFIELD_MAX_WIDTH;
+
+ outputDir.setPreferredSize(actualSizeTextField);
+
+ JLabel selectProjectDir = new JLabel(TagInputPanel.FIND_PROJECT_DIR);
+ this.setDimensionsToDefault(selectProjectDir);
+ this.adjustLabel(selectProjectDir);
+
+ JLabel [] labels = {outputFilePrefix, new JLabel(""), selectProjectDir};
+ JComponent [] middle = {projectName,new JLabel(""),outputDir};
+ JComponent [] last = {new JLabel(""),new JLabel(""),openFile}; //empty anchor used to be 'openFile'
+ prepareFormPanel(namePanel,labels,middle, last);
+
+ panelToAddTo.add(namePanel);
+ }
+
+ /**
+ * Adjust label.
+ *
+ * @param label the label
+ */
+ private void adjustLabel(JLabel label)
+ {
+ Dimension d = label.getPreferredSize();
+ d.width = DEFAULT_MINIMUM_LABEL_WIDTH;
+ label.setMinimumSize(d);
+ label.setPreferredSize(d);
+ }
+
+ /**
+ * Prepare form panel.
+ *
+ * @param parent the parent
+ * @param first the first
+ * @param middle the middle
+ * @param last the last
+ */
+ private void prepareFormPanel(JPanel parent, JLabel [] first, JComponent [] middle, JComponent[] last)
+ {
+ int numRows = first.length;
+ for (int i = 0; i < numRows; i++)
+ {
+ parent.add(first[i]);
+ parent.add(middle[i]);
+ parent.add(last[i]);
+ }
+ SpringUtilities.makeCompactGrid(parent, numRows, 3, 5, 5, 5, 5);
+ }
+
+ /**
+ * Adds the file format panel.
+ *
+ * @param panelToAddTo the panel to add to
+ * @param b the b
+ */
+ private void addFileFormatPanel(JPanel panelToAddTo, Border b)
+ {
+ //creation of the buttons JPanel
+ this.dataFormat = new JPanel();
+ this.dataFormat.setBorder(BorderFactory.createTitledBorder(b, "Pyrotag data format",TitledBorder.LEFT,TitledBorder.TOP, this.getFont()));
+
+ SpringLayout sp = new SpringLayout();
+ this.dataFormat.setLayout(sp);
+ this.dataFormat.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ //prepare buttons!
+ this.fileFormat = new ButtonGroup();
+ JRadioButton fastqButton = new JRadioButton("FASTQ");
+ fastqButton.setActionCommand(FASTQ);
+ fastqButton.addActionListener(this);
+ fastqButton.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ this.setDimensionsToDefault(fastqButton);
+
+ JRadioButton separateButton = new JRadioButton("FASTA (with separate quality file)");
+ separateButton.setActionCommand(FASTA);
+ separateButton.addActionListener(this);
+ separateButton.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ this.setDimensionsToDefault(separateButton);
+
+ this.fileFormat.add(fastqButton);
+ this.fileFormat.add(separateButton);
+ this.fileFormat.setSelected(separateButton.getModel(),true);
+
+ this.fileFormatInnerPanel = new JPanel();
+ fileFormatInnerPanel.setLayout(new SpringLayout());
+ fileFormatInnerPanel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ fileFormatInnerPanel.add(fastqButton);
+ fileFormatInnerPanel.add(separateButton);
+
+ SpringUtilities.makeCompactGrid(fileFormatInnerPanel, 1, 2, 0, 0, 50, 5);
+
+ dataFormat.add(fileFormatInnerPanel);
+
+ this.formatCardPanel = new JPanel();
+ this.formatCardPanel.setLayout(new CardLayout());
+
+ this.initFormatCards();
+
+ Dimension ffd = fileFormatInnerPanel.getPreferredSize();
+ dataFormat.add(this.formatCardPanel);
+ SpringUtilities.makeCompactGrid(dataFormat, 2, 1, 0, 0, 5, 5);
+// SpringUtilities.printSizes(dataFormat);
+
+ Dimension minSize = dataFormat.getMinimumSize();
+ dataFormat.setPreferredSize(minSize);
+ panelToAddTo.add(dataFormat);
+ }
+
+ /**
+ * Inits the format cards.
+ */
+ private void initFormatCards()
+ {
+ createFASTAPanel();
+ createFASTQPanel();
+
+ this.formatCardPanel.add(this.fastaPanel, TagInputPanel.FASTA); //assuming that is fasta selected??
+ this.formatCardPanel.add(this.fastqPanel, TagInputPanel.FASTQ);
+
+ Dimension preferredSizeFASTQ = this.fastqPanel.getPreferredSize();
+ Dimension cardPanelMax = new Dimension(Integer.MAX_VALUE,preferredSizeFASTQ.height);
+ this.formatCardPanel.setMaximumSize(cardPanelMax);
+ CardLayout cl = (CardLayout) this.formatCardPanel.getLayout();
+
+ //default FASTA is selected
+ cl.show(this.formatCardPanel, TagInputPanel.FASTA); //make sure the radiobutton for fasta is selected.
+ }
+
+ /**
+ * Inits the standard output panel.
+ *
+ * @param parent the parent
+ * @param b the b
+ */
+ private void initStandardOutputPanel(JPanel parent, Border b)
+ {
+ this.standardOutput = new JPanel();
+ this.standardOutput.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ standardOutput.setBorder(BorderFactory.createTitledBorder(b, "Acacia Standard Output",TitledBorder.LEFT,TitledBorder.TOP, this.getFont()));
+
+ Dimension stdOutDimensions = new Dimension(parent.getPreferredSize().width - 5, 50);
+ this.standardOutput.setPreferredSize(stdOutDimensions);
+ this.standardOutput.setMaximumSize(stdOutDimensions);
+ this.standardOutput.setSize(stdOutDimensions);
+ SpringLayout soLayoutManager = new SpringLayout();
+
+ this.standardOutput.setLayout(soLayoutManager);
+ this.standardOutputField = new JTextPane();
+ this.standardOutputField.setEditable(false);
+ this.standardOutputField.setBackground(Color.white);
+ this.standardOutputField.setContentType("text/html");
+
+
+ Dimension textFieldSize = new Dimension(parent.getPreferredSize().width - 100, 10);
+ standardOutputField.setPreferredSize(textFieldSize);
+ standardOutputField.setMaximumSize(textFieldSize);
+ standardOutputField.setSize(textFieldSize);
+
+ JScrollPane textFieldViewer = new JScrollPane(this.standardOutputField);
+
+ LogTextPane lta = new LogTextPane(this.standardOutputField, textFieldViewer);
+
+ //this.standardOutputField.
+ this.logger.addOutput(lta, AcaciaLogger.LOG_PROGRESS);
+ this.logger.addOutput(lta, AcaciaLogger.LOG_ERROR);
+
+ soLayoutManager.putConstraint(SpringLayout.EAST, textFieldViewer, -5, SpringLayout.EAST, this.standardOutput);
+ soLayoutManager.putConstraint(SpringLayout.WEST, textFieldViewer, 5, SpringLayout.WEST, this.standardOutput);
+ soLayoutManager.putConstraint(SpringLayout.NORTH, textFieldViewer, 5, SpringLayout.NORTH, this.standardOutput);
+ soLayoutManager.putConstraint(SpringLayout.SOUTH, textFieldViewer, -5, SpringLayout.SOUTH, this.standardOutput);
+ this.standardOutput.add(textFieldViewer);
+ }
+
+ /**
+ * Clear standard output panel.
+ */
+ private void clearStandardOutputPanel()
+ {
+ this.standardOutputField.setText("");
+ }
+
+ /**
+ * Adds the quality assurance panel.
+ *
+ * @param panelToAddTo the panel to add to
+ * @param b the b
+ * @throws Exception the exception
+ */
+ private void addQualityAssurancePanel(JPanel panelToAddTo, Border b) throws Exception
+ {
+ this.qualityAssurance = new JPanel();
+ this.qualityAssurance.setBorder(BorderFactory.createTitledBorder(b, "Tag Quality Assurance",TitledBorder.LEFT,TitledBorder.TOP, this.getFont()));
+ this.qualityAssurance.setLayout(new SpringLayout());
+ this.qualityAssurance.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ this.qualityThreshold = new JSpinner();
+
+ String [] optionsQualities = new String [MAX_QUALITY_SCORE - MIN_QUALITY_SCORE + 2];
+
+ for(int i = MIN_QUALITY_SCORE; i <= MAX_QUALITY_SCORE; i++)
+ {
+ optionsQualities[i] = i + "";
+ }
+
+
+ javax.swing.SpinnerListModel qualityThreshModel = new SpinnerListModel(optionsQualities);
+ qualityThreshModel.setValue(AcaciaConstants.DEFAULT_OPT_MIN_AVG_QUALITY);
+
+ this.qualityThreshold.setModel(qualityThreshModel);
+ this.setDimensionsToDefault(qualityThreshold);
+
+ Dimension d = this.qualityThreshold.getPreferredSize();
+ d.width = TagInputPanel.DEFAULT_TEXTFIELD_MAX_WIDTH;
+
+ this.qualityThreshold.setPreferredSize(d);
+ this.qualityThreshold.setMaximumSize(d);
+ this.qualityThreshold.setMinimumSize(d);
+
+ JLabel qualityLabel = new JLabel("Minimum avg. quality threshold:");
+ qualityLabel.setBackground(FORM_BACKGROUND_COLOUR);
+ this.setDimensionsToDefault(qualityLabel);
+ this.adjustLabel(qualityLabel);
+
+ JPanel helpPanelQualityThreshold = new JPanel();
+ helpPanelQualityThreshold.setBackground(FORM_BACKGROUND_COLOUR);
+ helpPanelQualityThreshold.setLayout(new BoxLayout(helpPanelQualityThreshold, BoxLayout.LINE_AXIS));
+ helpPanelQualityThreshold.add(new HelpButton(HELP_QUALITY_THRESHOLD_TEXT, this.parent));
+ this.setJPanelToButtonSize(helpPanelQualityThreshold);
+ //create a action listener?
+
+ JPanel helpPanelTrimLength = new JPanel();
+ helpPanelTrimLength.setBackground(FORM_BACKGROUND_COLOUR);
+ helpPanelTrimLength.setLayout(new BoxLayout(helpPanelTrimLength, BoxLayout.LINE_AXIS));
+ helpPanelTrimLength.add(new HelpButton(HELP_TRIM_READS_TO_LENGTH, this.parent));
+ this.setJPanelToButtonSize(helpPanelTrimLength);
+
+ this.trimToLength = new JTextField();
+ this.setDimensionsToDefault(trimToLength);
+ this.setTextFieldSize(trimToLength);
+ this.trimToLength.setHorizontalAlignment(JTextField.RIGHT);
+
+ JLabel trimLabel = new JLabel("Trim all reads to length:");
+ this.adjustLabel(trimLabel);
+ this.setDimensionsToDefault(trimLabel);
+
+ JLabel removeReadsSDLabel = new JLabel("Max. no. of SD's from mean length:");
+ this.adjustLabel(removeReadsSDLabel);
+ this.setDimensionsToDefault(removeReadsSDLabel);
+
+
+
+
+ JPanel helpPanelSD = new JPanel();
+ helpPanelSD.setBackground(FORM_BACKGROUND_COLOUR);
+ helpPanelSD.setLayout(new BoxLayout(helpPanelSD, BoxLayout.LINE_AXIS));
+ helpPanelSD.add(new HelpButton(HELP_FILTER_BY_LENGTH_SD, this.parent));
+ this.setJPanelToButtonSize(helpPanelSD);
+
+
+ String [] sdOptions = {"0.5", "1", "1.5", "2", "2.5", "3","4","5"};
+
+
+ this.SDThreshold = new JSpinner();
+
+ javax.swing.SpinnerListModel SDModel = new SpinnerListModel(sdOptions);
+ SDModel.setValue(AcaciaConstants.DEFAULT_OPT_MAX_STD_DEV_LENGTH);
+ this.SDThreshold.setModel(SDModel);
+
+ this.setDimensionsToDefault(this.SDThreshold);
+ Dimension d2 = this.SDThreshold.getPreferredSize();
+ d2.width = TagInputPanel.DEFAULT_TEXTFIELD_MAX_WIDTH;
+
+ this.SDThreshold.setPreferredSize(d2);
+ this.SDThreshold.setMaximumSize(d2);
+ this.SDThreshold.setMinimumSize(d2);
+
+
+ //add all the components
+ qualityAssurance.add(qualityLabel);
+ qualityAssurance.add(qualityThreshold);
+ qualityAssurance.add(helpPanelQualityThreshold);
+ qualityAssurance.add(trimLabel);
+ qualityAssurance.add(trimToLength);
+ qualityAssurance.add(helpPanelTrimLength);
+ qualityAssurance.add(removeReadsSDLabel);
+ qualityAssurance.add(SDThreshold);
+ qualityAssurance.add(helpPanelSD);
+
+
+
+ SpringUtilities.makeCompactGrid(qualityAssurance, 3,3,5,5,5,5);
+ qualityAssurance.setVisible(true);
+
+ //add to this panel
+ panelToAddTo.add(qualityAssurance);
+ }
+
+ /**
+ * Creates the blank button sized label.
+ *
+ * @return the j label
+ */
+ private JLabel createBlankButtonSizedLabel()
+ {
+ JLabel blankLabel = new JLabel("");
+ this.setDimensionsToDefault(blankLabel);
+ Dimension d = blankLabel.getPreferredSize();
+ d.width = DEFAULT_BUTTON_WIDTH;
+ blankLabel.setPreferredSize(d);
+ blankLabel.setSize(d);
+ blankLabel.setMaximumSize(d);
+ return blankLabel;
+ }
+
+ /**
+ * Sets the j panel to button size.
+ *
+ * @param panel the new j panel to button size
+ */
+ private void setJPanelToButtonSize(JPanel panel)
+ {
+ this.setDimensionsToDefault(panel);
+ Dimension d = panel.getPreferredSize();
+ d.width = DEFAULT_BUTTON_WIDTH;
+ panel.setPreferredSize(d);
+ panel.setSize(d);
+ panel.setMaximumSize(d);
+ }
+
+ /**
+ * Adds the screen mi ds panel.
+ *
+ * @param panelToAddTo the panel to add to
+ * @param b the b
+ * @throws Exception the exception
+ */
+ private void addScreenMIDsPanel(JPanel panelToAddTo, Border b) throws Exception
+ {
+ this.screenMIDS = new JPanel();
+ this.screenMIDS.setBackground(FORM_BACKGROUND_COLOUR);
+ this.screenMIDS.setLayout(new SpringLayout());
+
+ DefaultTableModel tableModel = new DefaultTableModel(0, TagInputPanel.COLUMN_IDENTIFIERS.length);
+ tableModel.setColumnIdentifiers(TagInputPanel.COLUMN_IDENTIFIERS);
+
+ this.midTable = new JTable(tableModel);
+ this.midTable.setBackground(TABLE_BACKGROUND_COLOUR);
+
+ midTable.setSelectionBackground(TABLE_SELECTION_COLOUR);
+ midTable.setRowSelectionAllowed(true);
+ midTable.getSelectionModel().addListSelectionListener(this);
+ midTable.getColumnModel().getSelectionModel().addListSelectionListener(this);
+
+ JScrollPane scrollPane = new JScrollPane(midTable);
+ Dimension spPreferred = new Dimension(midTable.getPreferredSize().width, 120);
+ scrollPane.setPreferredSize(spPreferred);
+ scrollPane.setMaximumSize(scrollPane.getPreferredSize());
+ scrollPane.setMinimumSize(scrollPane.getPreferredSize());
+
+ midTable.setPreferredScrollableViewportSize(new Dimension(midTable.getPreferredSize().width, 150));
+
+ this.screenMIDS.setBorder(BorderFactory.createTitledBorder(b, "MID Selection",TitledBorder.LEFT,TitledBorder.TOP, this.getFont()));
+
+ JPanel selectMIDSButtonsPanel = new JPanel();
+ selectMIDSButtonsPanel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ selectMIDSButtonsPanel.setLayout(new SpringLayout());
+
+ this.MIDSelectAll = new AcaciaGradientButton(SELECT_ALL_MIDS,TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2, TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ this.MIDSelectAll.setBackground(BUTTON_GRADIENT_COLOR2);
+ this.MIDSelectAll.addActionListener(this);
+ this.MIDSelectAll.setEnabled(false);
+
+ this.MIDClearAll = new AcaciaGradientButton(CLEAR_ALL_MIDS,TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2, TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ this.MIDClearAll.setBackground(BUTTON_GRADIENT_COLOR2);
+ this.MIDClearAll.addActionListener(this);
+ this.MIDClearAll.setEnabled(false);
+
+ this.setDimensionsToDefault(MIDSelectAll);
+ this.setDimensionsToDefault(MIDClearAll);
+
+ this.numSelected = new JLabel("Number selected: 0");
+ this.setDimensionsToDefault(numSelected);
+ this.adjustLabel(numSelected);
+ this.numSelected.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ selectMIDSButtonsPanel.add(this.numSelected);
+ selectMIDSButtonsPanel.add(this.MIDSelectAll);
+ selectMIDSButtonsPanel.add(this.MIDClearAll);
+
+
+ SpringUtilities.makeCompactGrid(selectMIDSButtonsPanel, 1, 3, 0, 0, 5, 5);
+ this.screenMIDS.add(scrollPane);
+ this.screenMIDS.add(selectMIDSButtonsPanel);
+
+ JPanel aggregateMIDSPanel = new JPanel();
+ aggregateMIDSPanel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ this.splitOnMID = new JCheckBox("Process MIDs separately?");
+ this.splitOnMID.setBackground(FORM_BACKGROUND_COLOUR);
+ this.splitOnMID.setEnabled(false);
+
+ JPanel helpPanelSplitMID = new JPanel();
+ helpPanelSplitMID.setBackground(FORM_BACKGROUND_COLOUR);
+ helpPanelSplitMID.setLayout(new BoxLayout(helpPanelSplitMID, BoxLayout.LINE_AXIS));
+ helpPanelSplitMID.add(new HelpButton(HELP_SPLIT_MID_TEXT, this.parent));
+ this.setJPanelToButtonSize(helpPanelSplitMID);
+ //create a action listener?
+
+
+
+ SpringLayout sl = new SpringLayout();
+ aggregateMIDSPanel.setLayout(sl);
+ //this panel should have a label and radio button?
+ aggregateMIDSPanel.add(splitOnMID);
+ aggregateMIDSPanel.add(helpPanelSplitMID);
+
+ SpringUtilities.makeCompactGrid(aggregateMIDSPanel, 1, 2, 0, 0, 5, 5);
+
+ this.screenMIDS.add(aggregateMIDSPanel);
+
+ SpringUtilities.makeCompactGrid(this.screenMIDS, 3, 1, 5, 5, 5, 5);
+
+ panelToAddTo.add(screenMIDS);
+ }
+
+ /**
+ * Clears the MIDs panel.
+ */
+ private void clearMIDSPanel()
+ {
+ DefaultTableModel tm = (DefaultTableModel) this.midTable.getModel();
+ tm.setDataVector(null, TagInputPanel.COLUMN_IDENTIFIERS);
+ this.splitOnMID.setEnabled(false);
+ this.MIDClearAll.setEnabled(false);
+ this.MIDSelectAll.setEnabled(false);
+ }
+
+ /**
+ * Populate the MIDS panel.
+ *
+ * @param filename the file containing the MID descriptions and sequences
+ */
+ private void populateMIDSPanel(String filename)
+ {
+ DefaultTableModel tm = (DefaultTableModel) this.midTable.getModel();
+
+ if(filename == null || filename.length() == 0)
+ {
+ return;
+ }
+
+// System.out.println("The file path is <" + filename + ">");
+
+ MIDReader mReader = new MIDReader(filename);
+
+
+ LinkedList <MIDPrimerCombo> mids = null;
+
+ try
+ {
+ mids = mReader.loadMIDS();
+ }
+ catch(MIDFormatException mfe)
+ {
+ try
+ {
+ this.logger.writeLog(mfe.getMessage(), AcaciaLogger.LOG_ERROR);
+ }
+ catch(Exception e)
+ {
+ this.cleanExit("", e); //error writing to logger, not the MIDformat exception
+ }
+ return;
+ }
+
+ Object [][] data = new Object [mids.size()][3];
+
+ int i = 0;
+
+ HashSet <String> seenBefore = new HashSet <String>();
+
+ for(MIDPrimerCombo mid : mids)
+ {
+ data[i][0] = mid.getMID();
+ data[i][1] = mid.getPrimer();
+ data[i][2] = mid.getDescriptor();
+ i++;
+ }
+ tm.setDataVector(data, TagInputPanel.COLUMN_IDENTIFIERS);
+
+ this.splitOnMID.setEnabled(true);
+ this.splitOnMID.setSelected(false);
+ this.MIDClearAll.setEnabled(true);
+ this.MIDSelectAll.setEnabled(true);
+ }
+
+ /**
+ * Clean exit. Probably should implement this.
+ *
+ * @param string the string
+ * @param e the e
+ */
+ private void cleanExit(String string, Exception e)
+ {
+ System.out.println("An exception occurred: " + e.getMessage());
+ e.printStackTrace();
+ System.exit(1); //an error occurred
+
+ }
+
+ /**
+ * Removes the screen mids panel.
+ *
+ * @param panelToRemoveFrom the panel to remove from
+ */
+ private void removeScreenMIDsPanel(JPanel panelToRemoveFrom)
+ {
+ panelToRemoveFrom.remove(screenMIDS);
+ }
+
+ /**
+ * Sets the dimensions to default.
+ *
+ * @param component the new dimensions to default
+ */
+ private void setDimensionsToDefault (Component component)
+ {
+ Dimension preferred = component.getPreferredSize();
+ preferred.height = DEFAULT_PREFERRED_FIELD_HEIGHT;
+ component.setPreferredSize(preferred);
+ component.setMinimumSize(preferred);
+ component.setSize(preferred);
+ }
+
+ /**
+ * Adds the mid options panel.
+ *
+ * @param panelToAddTo the panel to add to
+ * @param b the border to use
+ */
+ private void addMIDOptionsPanel(JPanel panelToAddTo, Border b)
+ {
+ /*
+ * Create MID Panel
+ */
+
+ this.mids = new JPanel();
+ this.mids.setLayout(new SpringLayout());
+ this.mids.setBorder(BorderFactory.createTitledBorder(b, "Multiplex ID (MID) Status",TitledBorder.LEFT,TitledBorder.TOP, this.getFont()));
+ this.mids.setBackground(FORM_BACKGROUND_COLOUR);
+
+ //what options do we want the user to have...
+ //MID file, no MIDS,
+ midSelection = new ButtonGroup();
+
+
+ this.loadMIDs = new JRadioButton(OPTION_LOAD_MIDS);
+ loadMIDs.setActionCommand(OPTION_LOAD_MIDS);
+ loadMIDs.addActionListener(this);
+ loadMIDs.setBackground(FORM_BACKGROUND_COLOUR);
+
+ this.noMIDs = new JRadioButton(OPTION_NO_MIDS);
+ noMIDs.setActionCommand(OPTION_NO_MIDS);
+ noMIDs.addActionListener(this);
+ noMIDs.setBackground(FORM_BACKGROUND_COLOUR);
+
+ //midSelection.add(fiveBase);
+ // midSelection.add(tenBase);
+ midSelection.add(loadMIDs);
+ midSelection.add(noMIDs);
+
+ JPanel midsButtonPanel = new JPanel();
+ midsButtonPanel.setLayout(new SpringLayout());
+ midsButtonPanel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ //midsButtonPanel.add(fiveBase);
+ // midsButtonPanel.add(tenBase);
+ midsButtonPanel.add(loadMIDs);
+ midsButtonPanel.add(noMIDs);
+
+ //changed rows to 1 from 2
+ SpringUtilities.makeCompactGrid(midsButtonPanel, 1, 2, 0, 0, 5, 5);
+
+ this.midCardPanel = new JPanel();
+ this.midCardPanel.setLayout(new CardLayout());
+
+ this.initMIDCards();
+
+ this.mids.add(midsButtonPanel);
+ this.mids.add(this.midCardPanel);
+
+ SpringUtilities.makeCompactGrid(this.mids, 2, 1, 5, 5, 5, 5);
+ panelToAddTo.add(mids);
+ }
+
+ /**
+ * Initialises the MID card containers.
+ */
+ private void initMIDCards()
+ {
+ this.initLoadMIDSPanel();
+ JPanel blank = new JPanel();
+ blank.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ this.midCardPanel.add(this.loadMidsPanel, TagInputPanel.OPTION_LOAD_MIDS); //assuming that is fasta selected??
+ this.midCardPanel.add(blank, TagInputPanel.DONT_LOAD_USER_SUPPLIED_MIDS);
+
+ Dimension preferredSizeFASTQ = this.loadMidsPanel.getPreferredSize();
+ Dimension cardPanelMax = new Dimension(Integer.MAX_VALUE,preferredSizeFASTQ.height);
+
+ this.midCardPanel.setMaximumSize(cardPanelMax);
+ CardLayout cl = (CardLayout) this.midCardPanel.getLayout();
+
+ //default FASTA is selected
+ cl.show(this.midCardPanel, TagInputPanel.DONT_LOAD_USER_SUPPLIED_MIDS);
+
+ //make sure the radiobutton for fasta is selected.
+ }
+
+
+ /* (non-Javadoc)
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e)
+ {
+ //these actions are to do with the choice of radio button
+ if(e.getActionCommand().equals(FASTQ))
+ {
+ CardLayout cl = (CardLayout) this.formatCardPanel.getLayout();
+ cl.show(this.formatCardPanel, e.getActionCommand());
+ }
+ else if(e.getActionCommand().equals(FASTA))
+ {
+ CardLayout cl = (CardLayout) this.formatCardPanel.getLayout();
+ cl.show(this.formatCardPanel, e.getActionCommand());
+ }
+ else if(e.getActionCommand().equals(FIND_FASTQ))
+ {
+ //spawn a dialogue box, get the file string, and set it for the respective text field...
+ this.fastqFileChoice.setText(this.getFileChoice(fastqPanel, fastqFileChoice, JFileChooser.FILES_ONLY));
+ }
+ else if(e.getActionCommand().equals(FIND_FASTA))
+ {
+ this.fastaFileChoice.setText(this.getFileChoice(fastaPanel, fastaFileChoice, JFileChooser.FILES_ONLY));
+ }
+ else if(e.getActionCommand().equals(FIND_QUAL))
+ {
+ this.qualFileChoice.setText(this.getFileChoice(fastaPanel, qualFileChoice, JFileChooser.FILES_ONLY));
+ }
+ else if(e.getActionCommand().equals(OPTION_LOAD_MIDS))
+ {
+ //create load mids panel
+ this.midsChoice.setText("");
+ this.clearMIDSPanel();
+
+ CardLayout cl = (CardLayout)this.midCardPanel.getLayout();
+ cl.show(this.midCardPanel, TagInputPanel.OPTION_LOAD_MIDS);
+ }
+ else if(e.getActionCommand().equals(OPTION_NO_MIDS))
+ {
+
+ CardLayout cl = (CardLayout)this.midCardPanel.getLayout();
+ cl.show(this.midCardPanel, TagInputPanel.DONT_LOAD_USER_SUPPLIED_MIDS);
+
+ this.clearMIDSPanel();
+
+ if(e.getActionCommand().equals(OPTION_NO_MIDS))
+ {
+ this.populateMIDSPanel(null);
+ this.midsChoice.setText("");
+ }
+ }
+ else if(e.getActionCommand().equals(FIND_MIDS))
+ {
+ this.midsChoice.setText(this.getFileChoice(this.mids, midsChoice, JFileChooser.FILES_ONLY));
+ this.populateMIDSPanel(this.midsChoice.getText());
+
+ }
+ else if(e.getActionCommand().equals(TECH_454))
+ {
+ this.errorModelSpinner.setModel(errorModel454);
+ errorModel454.setValue(AcaciaConstants.OPT_FLOWSIM_ERROR_MODEL);//needs to be a default it model.
+ }
+ else if(e.getActionCommand().equals(TECH_ION_TORRENT))
+ {
+ //restrict the options for the models...
+ this.errorModelSpinner.setModel(errorModelIT);
+ errorModelIT.setValue(AcaciaConstants.OPT_ACACIA_IT_OT_200bp_316);
+ }
+ else if(e.getActionCommand().equals(FIND_PROJECT_DIR))
+ {
+ if(this.outputDir == null)
+ {
+ System.out.println("Project dir is null");
+ }
+ this.outputDir.setText(this.getFileChoice(this.namePanel, outputDir, JFileChooser.DIRECTORIES_ONLY));
+ }
+ else if(e.getActionCommand().equals(SELECT_ALL_MIDS))
+ {
+ this.midTable.selectAll();
+ }
+ else if(e.getActionCommand().equals(CLEAR_ALL_MIDS))
+ {
+ this.midTable.clearSelection();
+ }
+ else if(e.getActionCommand().equals(SUBMIT_FORM))
+ {
+ processFormContents();
+ }
+ else if(e.getActionCommand().equals(CLEAR_FORM))
+ {
+ this.clearInterface();
+ }
+ else if(e.getActionCommand().equals(CANCEL_RUN))
+ {
+ this.cancelRun();
+ }
+ }
+
+ /**
+ * Cancel run.
+ */
+ private void cancelRun()
+ {
+ if(this.worker != null)
+ {
+ this.worker.cancel(true);
+ }
+ }
+
+ /**
+ * Worker cancelled.
+ */
+ public void workerCancelled()
+ {
+ try
+ {
+ this.logger.writeLog("Job cancelled!", AcaciaLogger.LOG_PROGRESS);
+ //truly finished.
+ this.worker = null;
+ this.submit.setEnabled(true);
+ this.cancel.setEnabled(false);
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ System.exit(1);
+ }
+ }
+
+ /**
+ * Process form contents.
+ */
+ private void processFormContents()
+ {
+ StringBuilder errors = new StringBuilder();
+ String projectName = this.projectName.getText();
+
+ if(projectName.trim().length() == 0)
+ {
+ errors.append("Error: Output prefix not specified" + System.getProperty("line.separator"));
+ }
+
+ String outputDir = this.outputDir.getText();
+ File output = new File(outputDir);
+
+ if(!output.exists())
+ {
+ errors.append("Error: No output directory has been selected" + System.getProperty("line.separator"));
+ }
+
+ if(this.midTable.getRowCount() > 0 && this.midTable.getSelectedRowCount() == 0)
+ {
+ errors.append("Error: No MIDS have been selected " + System.getProperty("line.separator"));
+ }
+
+ if(fileFormat.getSelection().getActionCommand().equals(FASTA))
+ {
+ if(this.fastaFileChoice.getText().length() == 0)
+ {
+ errors.append("Error: Input FASTA file not specified. " + System.getProperty("line.separator"));
+ }
+ else
+ {
+ File fasta = new File (this.fastaFileChoice.getText());
+
+ if(!fasta.exists())
+ {
+ errors.append("Error: file " + this.fastaFileChoice.getText() + " does not exist" + System.getProperty("line.separator"));
+ }
+ }
+ }
+
+ if(fileFormat.getSelection().getActionCommand().equals(FASTA) && (this.qualFileChoice.getText()).length() > 0)
+ {
+ File quality = new File(this.qualFileChoice.getText());
+
+ if(!quality.exists())
+ {
+ errors.append("Error: file " + this.qualFileChoice.getText() + " does not exist" + System.getProperty("line.separator"));
+ }
+ }
+
+ int trimToLength = 0;
+
+ if(this.trimToLength.getText().length() > 0)
+ {
+ try
+ {
+ trimToLength = Integer.parseInt(this.trimToLength.getText());
+ }
+ catch(NumberFormatException nfe)
+ {
+ errors.append("Error: trim length is not a number. " + System.getProperty("line.separator"));
+ }
+ }
+
+ int manDist = 0;
+ if(this.manhattanDistance.getText().length() > 0)
+ {
+ boolean error = false;
+ try
+ {
+ manDist = Integer.parseInt(this.manhattanDistance.getText());
+ }
+ catch(NumberFormatException ife)
+ {
+ errors.append("Error: manhattan distance is not a number " + System.getProperty("line.separator"));
+ error =true;
+ }
+
+ if(!error && manDist < 0)
+ {
+ errors.append("Error: manhattan distance was less than zero " + System.getProperty("line.separator"));
+ }
+ }
+
+
+ if(errors.length() > 0)
+ {
+ errors.insert(0,"The following error/s occurred when processing your input:" + System.getProperty("line.separator"));
+ JOptionPane.showMessageDialog(this,
+ errors.toString(),
+ "Input Error",
+ JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ //if all required settings are valid, then proceed to storing these options...
+ HashMap <String, String> settings = new HashMap <String, String>();
+ settings.put(AcaciaConstants.OPT_OUTPUT_PREFIX, projectName);
+
+
+ if(fileFormat.getSelection().getActionCommand().equals(FASTA))
+ {
+ settings.put(AcaciaConstants.OPT_FASTA, "TRUE");
+ settings.put(AcaciaConstants.OPT_FASTA_LOC, this.fastaFileChoice.getText());
+
+
+ String qualFile = (this.qualFileChoice.getText().trim().length() > 0)? qualFileChoice.getText(): null;
+
+ settings.put(AcaciaConstants.OPT_QUAL_LOC, qualFile);
+ }
+ else
+ {
+ settings.put(AcaciaConstants.OPT_FASTQ, "TRUE");
+ settings.put(AcaciaConstants.OPT_FASTA, "FALSE");
+ settings.put(AcaciaConstants.OPT_FASTQ_LOC, this.fastqFileChoice.getText());
+ }
+
+ if(trimToLength != 0)
+ {
+ settings.put(AcaciaConstants.OPT_TRIM_TO_LENGTH, this.trimToLength.getText());
+ }
+
+
+
+ settings.put(AcaciaConstants.OPT_MAX_STD_DEV_LENGTH, (String) this.SDThreshold.getValue());
+ settings.put(AcaciaConstants.OPT_MIN_AVG_QUALITY, (String) this.qualityThreshold.getValue());
+ settings.put(AcaciaConstants.OPT_MAXIMUM_MANHATTAN_DIST, (String) this.manhattanDistance.getText());
+ settings.put(AcaciaConstants.OPT_ERROR_MODEL, (String) this.errorModelSpinner.getValue());
+
+
+
+ if(this.techFormat.getSelection().getActionCommand().equals(TECH_ION_TORRENT))
+ {
+ settings.put(AcaciaConstants.OPT_FLOW_CYCLE_STRING, AcaciaConstants.OPT_FLOW_CYCLE_ION_TORRENT);
+ }
+
+
+ //settings.put(Acacia, arg1) for align hamming distance.
+ settings.put(AcaciaConstants.OPT_SIGNIFICANCE_LEVEL, (String)this.spinnerSignificance.getValue());
+ settings.put(AcaciaConstants.OPT_OUTPUT_DIR, this.outputDir.getText());
+ settings.put(AcaciaConstants.OPT_REPRESENTATIVE_SEQ, (String)this.spinnerRepresentativeSeq.getValue());
+ settings.put(AcaciaConstants.OPT_SPLIT_ON_MID, (this.splitOnMID.isSelected())? "TRUE" : "FALSE");
+
+ if(this.loadMIDs.isSelected())
+ {
+ settings.put(AcaciaConstants.OPT_MID, AcaciaConstants.OPT_LOAD_MIDS);
+ }
+ else if(this.noMIDs.isSelected())
+ {
+ settings.put(AcaciaConstants.OPT_MID, AcaciaConstants.OPT_NO_MID);
+ }
+
+ LinkedList <MIDPrimerCombo> validTags = this.getSelectedTags();
+
+ //set up objects required by worker thread.
+ // in case a value is not specified, we use the default
+
+ HashMap <String, String> defaults = AcaciaEngine.getEngine().getDefaultSettings();
+
+ for (String key : settings.keySet())
+ {
+ defaults.put(key, settings.get(key));
+
+ System.out.println("User-specified settings: " + key + ": "+ settings.get(key));
+ }
+
+ this.worker = new ErrorCorrectionWorker(defaults, logger,validTags, this);
+ this.cancel.setEnabled(true);
+ this.submit.setEnabled(false);
+ this.worker.execute(); //now running, but GUI should still be relatively responsive?
+ }
+
+ /**
+ * Gets the selected tags.
+ *
+ * @return the selected tags
+ */
+ private LinkedList <MIDPrimerCombo> getSelectedTags()
+ {
+ LinkedList <MIDPrimerCombo> selectedTags = new LinkedList <MIDPrimerCombo>();
+
+ int [] selectedRows = this.midTable.getSelectedRows();
+ DefaultTableModel dft = (DefaultTableModel) this.midTable.getModel();
+
+ for(int i = 0; i < selectedRows.length; i++)
+ {
+ String midValue = (String) dft.getValueAt(selectedRows[i], 0);
+ String primerValue = (String) dft.getValueAt(selectedRows[i], 1);
+ String descriptor = (String) dft.getValueAt(selectedRows[i], 2);
+
+ midValue = midValue.toUpperCase();
+ primerValue = primerValue.toUpperCase();
+
+ MIDPrimerCombo m = new MIDPrimerCombo(midValue, primerValue, descriptor);
+ selectedTags.add(m); //assumption
+ }
+
+ return selectedTags;
+ }
+
+
+ /**
+ * Inits the load mids panel.
+ */
+ private void initLoadMIDSPanel()
+ {
+ if(this.loadMidsPanel == null)
+ {
+ this.loadMidsPanel = new JPanel();
+ this.loadMidsPanel.setLayout(new SpringLayout());
+ this.loadMidsPanel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ JButton openFile = new AcaciaGradientButton("Browse...",TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2,TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ openFile.setActionCommand(FIND_MIDS);
+ openFile.addActionListener(this);
+ this.midsChoice = new JTextField("");
+
+ this.setTextFieldSize(midsChoice);
+
+ JLabel selectMIDS = new JLabel("Select MID descriptor file:");
+ selectMIDS.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ this.adjustLabel(selectMIDS);
+ this.setDimensionsToDefault(selectMIDS);
+
+ loadMidsPanel.add(selectMIDS);
+ loadMidsPanel.add(midsChoice);
+ loadMidsPanel.add(openFile);
+ SpringUtilities.makeCompactGrid(loadMidsPanel, 1, 3, 0, 0, 5, 5);
+ loadMidsPanel.setVisible(true);
+ }
+ }
+
+ /**
+ * Creates the fastq panel.
+ */
+ private void createFASTQPanel()
+ {
+ fastqPanel = new JPanel();
+ fastqPanel.setLayout(new SpringLayout());
+ fastqPanel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ JButton openFile = new AcaciaGradientButton("Browse...",TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2, TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ openFile.setActionCommand(FIND_FASTQ);
+ openFile.addActionListener(this);
+ this.setLargeButtonSize(openFile);
+
+ this.fastqFileChoice = new JTextField("");
+ setTextFieldSize(this.fastqFileChoice);
+
+ JLabel selectFASTQ = new JLabel("Select FASTQ file:");
+ selectFASTQ.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ this.adjustLabel(selectFASTQ);
+ this.setDimensionsToDefault(selectFASTQ);
+
+ fastqPanel.add(selectFASTQ);
+ fastqPanel.add(fastqFileChoice);
+ fastqPanel.add(openFile);
+
+ SpringUtilities.makeCompactGrid(fastqPanel, 1,3, 0, 0, 5, 5);
+ }
+
+ /**
+ * Creates the fasta panel.
+ */
+ private void createFASTAPanel()
+ {
+ this.fastaPanel = new JPanel();
+ this.fastaPanel.setLayout(new SpringLayout());
+ this.fastaPanel.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+
+ //FASTA FILE
+ JButton openFileFasta = new AcaciaGradientButton("Browse...",TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2,TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ openFileFasta.setActionCommand(FIND_FASTA);
+ openFileFasta.addActionListener(this);
+ this.setLargeButtonSize(openFileFasta);
+
+ this.fastaFileChoice = new JTextField("");
+ setTextFieldSize(this.fastaFileChoice);
+
+ JLabel selectFASTA = new JLabel("Select FASTA file:");
+ selectFASTA.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ this.adjustLabel(selectFASTA);
+ this.setDimensionsToDefault(selectFASTA);
+
+ JButton openFileQual = new AcaciaGradientButton("Browse...", TagInputPanel.BUTTON_GRADIENT_COLOR1, TagInputPanel.BUTTON_GRADIENT_COLOR2, TagInputPanel.BUTTON_BORDER_COLOR, AcaciaGradientButton.CENTERED);
+ openFileQual.setActionCommand(FIND_QUAL);
+ openFileQual.addActionListener(this);
+ this.setLargeButtonSize(openFileFasta);
+
+ this.qualFileChoice = new JTextField("");
+ this.setTextFieldSize(this.qualFileChoice);
+
+ JLabel selectQUAL = new JLabel("Select Quality file:");
+ selectQUAL.setBackground(TagInputPanel.FORM_BACKGROUND_COLOUR);
+ this.adjustLabel(selectQUAL);
+ this.setDimensionsToDefault(selectQUAL);
+
+ fastaPanel.add(selectFASTA);
+ fastaPanel.add(fastaFileChoice);
+ fastaPanel.add(openFileFasta);
+ fastaPanel.add(selectQUAL);
+ fastaPanel.add(qualFileChoice);
+ fastaPanel.add(openFileQual);
+ SpringUtilities.makeCompactGrid(fastaPanel, 2, 3, 5, 5, 5, 5);
+ }
+
+ /**
+ * Sets the text field size.
+ *
+ * @param component the new text field size
+ */
+ public void setTextFieldSize(JTextField component)
+ {
+ Dimension preferredSize = component.getPreferredSize();
+ preferredSize.width = TagInputPanel.DEFAULT_TEXTFIELD_MAX_WIDTH;;
+ preferredSize.height = TagInputPanel.DEFAULT_PREFERRED_FIELD_HEIGHT;
+
+ component.setSize(preferredSize);
+ component.setPreferredSize(preferredSize);
+ component.setMaximumSize(preferredSize);
+ }
+
+ public void setLargeButtonSize(JButton component)
+ {
+ Dimension d = component.getPreferredSize();
+ d.width = DEFAULT_BUTTON_WIDTH;
+ d.height = DEFAULT_PREFERRED_FIELD_HEIGHT;
+ component.setPreferredSize(d);
+ component.setSize(d);
+ component.setMinimumSize(d);
+ component.setMaximumSize(d);
+ }
+
+ /**
+ * Gets the file choice.
+ *
+ * @param parent the parent
+ * @param linkedField the linked field
+ * @param selectionMode the selection mode
+ * @return the file choice
+ */
+ private String getFileChoice(JPanel parent, JTextField linkedField, int selectionMode)
+ {
+ try
+ {
+ File f = null;
+
+ if(this.lastDir != null)
+ f = new File(new File(this.lastDir).getCanonicalPath());
+
+ final JFileChooser fc = new JFileChooser(f);
+ fc.setFileSelectionMode(selectionMode);
+
+ int returnVal = fc.showOpenDialog(parent);
+
+ String retVal = null;
+
+ if (returnVal == JFileChooser.APPROVE_OPTION)
+ {
+ File file = fc.getSelectedFile();
+ retVal = file.getAbsolutePath();
+
+
+ if(retVal.equals(""))
+ {
+ return linkedField.getText();
+ }
+
+ this.lastDir = retVal; //store it for next time, to pre-empt stuff;
+ return retVal;
+ }
+ }
+ catch(IOException ie)
+ {
+
+ }
+ return linkedField.getText(); //an error occurs, return the previous text.
+ }
+
+
+ /**
+ * The Class BlankSpaceFilter.
+ */
+ public class BlankSpaceFilter extends DocumentFilter
+ {
+
+ /** The error label. */
+ JLabel errorLabel;
+
+ /** The parent. */
+ TagInputPanel parent;
+
+ /**
+ * Instantiates a new blank space filter.
+ *
+ * @param errorLabel the error label
+ * @param parent the parent
+ */
+ public BlankSpaceFilter (JLabel errorLabel, TagInputPanel parent)
+ {
+ super();
+ this.errorLabel = errorLabel;
+ this.parent = parent;
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.text.DocumentFilter#insertString(javax.swing.text.DocumentFilter.FilterBypass, int, java.lang.String, javax.swing.text.AttributeSet)
+ */
+ public void insertString(DocumentFilter.FilterBypass fb, int offset, String string, AttributeSet attr) throws BadLocationException
+ {
+ boolean containsWhiteSpace = false;
+
+ for(int i = 0; i < string.length(); i++)
+ {
+ if(Character.isWhitespace(string.charAt(i)))
+ {
+ containsWhiteSpace = true;
+ break;
+ }
+ }
+
+ if(containsWhiteSpace)
+ errorLabel.setText("No white-space characters are allowed");
+ else
+ errorLabel.setText("");
+
+ parent.revalidate();
+ fb.insertString(offset, string.trim(), attr);
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.text.DocumentFilter#replace(javax.swing.text.DocumentFilter.FilterBypass, int, int, java.lang.String, javax.swing.text.AttributeSet)
+ */
+ public void replace(DocumentFilter.FilterBypass fb, int offset, int length,
+ String string, AttributeSet attr) throws BadLocationException
+ {
+ boolean containsWhiteSpace = false;
+ for(int i = 0; i < string.length(); i++)
+ {
+ if(Character.isWhitespace(string.charAt(i)))
+ {
+ containsWhiteSpace = true;
+ break;
+ }
+ }
+
+ if(containsWhiteSpace)
+ errorLabel.setText("No white-space characters are allowed");
+ else
+ errorLabel.setText("");
+
+ this.parent.revalidate();
+
+ fb.remove(offset, length);
+ fb.insertString(offset, string.trim(), attr);
+ }
+ }
+
+ /**
+ * The Class NonNumericFilter.
+ */
+ public class NonNumericFilter extends DocumentFilter
+ {
+
+ /** The error label. */
+ JLabel errorLabel;
+
+ /** The parent. */
+ TagInputPanel parent;
+
+ /**
+ * Instantiates a new non numeric filter.
+ *
+ * @param errorLabel the error label
+ * @param parent the parent
+ */
+ public NonNumericFilter (JLabel errorLabel, TagInputPanel parent)
+ {
+ super();
+ this.errorLabel = errorLabel;
+ this.parent = parent;
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.text.DocumentFilter#insertString(javax.swing.text.DocumentFilter.FilterBypass, int, java.lang.String, javax.swing.text.AttributeSet)
+ */
+ public void insertString(DocumentFilter.FilterBypass fb, int offset, String string, AttributeSet attr) throws BadLocationException
+ {
+ boolean containsNonNumeric = false;
+
+ int pos = 0;
+
+ for(;pos < string.length(); pos++)
+ {
+ if(! Character.isDigit(string.charAt(pos)))
+ {
+ containsNonNumeric = true;
+ break;
+ }
+ }
+ String modifiedValue = null;
+
+ if(containsNonNumeric)
+ {
+ errorLabel.setText("Trim length should be a number.");
+ modifiedValue = string.substring(0, pos); //does not include pos
+ this.parent.revalidate();
+ }
+ else
+ {
+ errorLabel.setText("");
+ modifiedValue = string;
+ }
+
+ fb.insertString(offset, modifiedValue, attr);
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.text.DocumentFilter#replace(javax.swing.text.DocumentFilter.FilterBypass, int, int, java.lang.String, javax.swing.text.AttributeSet)
+ */
+ public void replace(DocumentFilter.FilterBypass fb, int offset, int length,
+ String string, AttributeSet attr) throws BadLocationException
+ {
+ boolean containsNonNumeric = false;
+ int pos = 0;
+
+ for(;pos < string.length(); pos++)
+ {
+ if(! Character.isDigit(string.charAt(pos)))
+ {
+ containsNonNumeric = true;
+ break;
+ }
+ }
+ String modifiedValue = null;
+
+ if(containsNonNumeric)
+ {
+ errorLabel.setText("Trim length should be a number.");
+ modifiedValue = string.substring(0, pos); //does not include pos
+ this.parent.revalidate();
+ }
+ else
+ {
+ errorLabel.setText("");
+
+ //this is different, someone has selected stuff, and then started typing...
+
+ modifiedValue = string;
+ }
+
+ fb.remove(offset, length);
+ fb.insertString(offset, modifiedValue, attr);
+ }
+ }
+
+ /**
+ * Creates the image panel.
+ *
+ * @param path the path
+ * @param background the background
+ * @param description the description
+ * @return the j panel
+ */
+ private JPanel createImagePanel(String path, Color background, String description)
+ {
+ URL imgURL = getClass().getResource(path);
+
+// System.out.println(imgURL.getPath());
+
+ if (imgURL != null)
+ {
+ ImageIcon image = new ImageIcon(imgURL, description);
+ JLabel label = new JLabel("", image, JLabel.CENTER);
+ Dimension sizeOfIcon = new Dimension(image.getIconWidth(), image.getIconHeight());
+
+// System.out.println("Size of icon " + sizeOfIcon.width + ", " + sizeOfIcon.height);
+
+ label.setMinimumSize(sizeOfIcon);
+ label.setPreferredSize(sizeOfIcon);
+ label.setMaximumSize(sizeOfIcon);
+ label.setSize(sizeOfIcon);
+
+ JPanel panel = new JPanel(new BorderLayout());
+ panel.add(label, BorderLayout.WEST);
+ panel.setBackground(background);
+
+ panel.setPreferredSize(label.getPreferredSize());
+ // panel.setMinimumSize(label.getPreferredSize());
+ // panel.setMinimumSize(label.getPreferredSize());
+ panel.setSize(label.getPreferredSize());
+
+// System.out.println("Size of panel is " + panel.getPreferredSize().width + ", " + panel.getPreferredSize().height);
+
+ return panel;
+ }
+ else
+ {
+ System.err.println("Couldn't find file: " + path);
+ return null;
+ }
+ }
+
+ /**
+ * Creates the image button.
+ *
+ * @param path the path
+ * @param background the background
+ * @param description the description
+ * @return the j panel
+ */
+ private JPanel createImageButton(String path, Color background, String description)
+ {
+
+
+ File f = new File(System.getProperty("user.dir"));
+
+ URL imgURL = getClass().getResource(path);
+
+
+ if (imgURL != null)
+ {
+ ImageIcon image = new ImageIcon(imgURL, description);
+ JButton imageButton = new JButton("", image);
+ Dimension sizeOfIcon = new Dimension(image.getIconWidth(), image.getIconHeight());
+
+// System.out.println("Size of icon " + sizeOfIcon.width + ", " + sizeOfIcon.height);
+
+ imageButton.setMinimumSize(sizeOfIcon);
+ imageButton.setPreferredSize(sizeOfIcon);
+ imageButton.setMaximumSize(sizeOfIcon);
+ imageButton.setSize(sizeOfIcon);
+
+ JPanel panel = new JPanel();
+ panel.setLayout(new BoxLayout(panel, BoxLayout.PAGE_AXIS));
+ panel.add(imageButton, BorderLayout.CENTER);
+ panel.setBackground(background);
+ panel.setMaximumSize(imageButton.getPreferredSize());
+ panel.setPreferredSize(imageButton.getPreferredSize());
+ panel.setMinimumSize(imageButton.getPreferredSize());
+ panel.setSize(imageButton.getPreferredSize());
+ return panel;
+ }
+ else
+ {
+ try
+ {
+ this.logger.writeLog("Couldn't find file: " + path, AcaciaLogger.LOG_ERROR);
+ }
+ catch(Exception e)
+ {
+ this.cleanExit("Error writing to log", e);
+ }
+ return null;
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.event.ListSelectionListener#valueChanged(javax.swing.event.ListSelectionEvent)
+ */
+ public void valueChanged(ListSelectionEvent arg0)
+ {
+ this.numSelected.setText("Number selected: " + this.midTable.getSelectedRowCount());
+ this.numSelected.repaint();
+ }
+
+ /**
+ * Clear interface.
+ */
+ public void clearInterface()
+ {
+ this.enableInputMethods(true);
+
+ this.projectName.setText("");
+ this.outputDir.setText("");
+ this.fastaFileChoice.setText("");
+ this.fastqFileChoice.setText("");
+ this.qualFileChoice.setText("");
+ this.midsChoice.setText("");
+ this.trimToLength.setText("");
+ this.qualityThreshold.getModel().setValue(AcaciaConstants.DEFAULT_OPT_MIN_AVG_QUALITY);
+ this.spinnerSignificance.getModel().setValue(AcaciaConstants.DEFAULT_OPT_SIGNIFICANCE_LEVEL);
+ this.manhattanDistance.setText(AcaciaConstants.DEFAULT_OPT_MAXIMUM_MANHATTAN_DIST);
+ this.spinnerRepresentativeSeq.getModel().setValue(AcaciaConstants.DEFAULT_OPT_REPRESENTATIVE_SEQ);
+ this.midSelection.setSelected(this.noMIDs.getModel(), true);
+
+ CardLayout cl = (CardLayout)this.midCardPanel.getLayout();
+ cl.show(this.midCardPanel, TagInputPanel.DONT_LOAD_USER_SUPPLIED_MIDS);
+ this.clearMIDSPanel();
+
+ }
+
+ /**
+ * Worker finished.
+ */
+ public void workerFinished()
+ {
+ this.submit.setEnabled(true);
+ this.cancel.setEnabled(false);
+ }
+}
diff --git a/src/pyromaniac/IO/AcaciaLogger.java b/src/pyromaniac/IO/AcaciaLogger.java
new file mode 100644
index 0000000..e3e918b
--- /dev/null
+++ b/src/pyromaniac/IO/AcaciaLogger.java
@@ -0,0 +1,354 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.IO;
+
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.LinkedList;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class AcaciaLogger.
+ */
+public class AcaciaLogger
+{
+
+ /** The closed. */
+ private boolean closed;
+
+ /** The time since last output. */
+ private Date [] timeSinceLastOutput;
+
+ /** The mode to listeners. */
+ private HashMap <String, LinkedList <LoggerOutput>> modeToListeners;
+
+ /** The Constant LOG_DEBUG. */
+ public static final String LOG_DEBUG = "DEBUG";
+
+ /** The Constant LOG_PROGRESS. */
+ public static final String LOG_PROGRESS = "PROGRESS";
+
+ /** The Constant LOG_ERROR. */
+ public static final String LOG_ERROR = "ERROR";
+
+ /** The Constant LOG_ALL. */
+ public static final String LOG_ALL = "ALL";
+
+ /** The Constant LOG_NONE. */
+ public static final String LOG_NONE = "NONE";
+
+ /** The Constant MAX_BUFFER_SIZE. */
+ public static final int MAX_BUFFER_SIZE = 200;
+
+ /** static hashmap log to index. */
+ private static HashMap<String, Integer> LOG_TO_INDEX = new HashMap <String, Integer>();
+
+ /** static hashmap index to log. */
+ private static HashMap <Integer, String> INDEX_TO_LOG = new HashMap <Integer, String>();
+
+ /** static hashmap containg the style of text used for the log type. */
+ private static HashMap <String, Integer> LOG_TYPE_TO_STYLE = new HashMap <String, Integer>();
+
+ static
+ {
+ LOG_TO_INDEX.put(LOG_DEBUG, 0);
+ LOG_TO_INDEX.put(LOG_PROGRESS,1);
+ LOG_TO_INDEX.put(LOG_ERROR,2);
+
+ INDEX_TO_LOG.put(0, LOG_DEBUG);
+ INDEX_TO_LOG.put(1, LOG_PROGRESS);
+ INDEX_TO_LOG.put(2,LOG_ERROR);
+
+ LOG_TYPE_TO_STYLE.put(LOG_DEBUG, LoggerOutput.LOG_STYLE_DEBUG);
+ LOG_TYPE_TO_STYLE.put(LOG_PROGRESS, LoggerOutput.LOG_STYLE_PROGRESS );
+ LOG_TYPE_TO_STYLE.put(LOG_ERROR, LoggerOutput.LOG_STYLE_ERROR);
+ }
+
+ /**
+ * Instantiates a new acacia logger.
+ */
+ public AcaciaLogger()
+ {
+ this.modeToListeners = new HashMap <String, LinkedList<LoggerOutput>>();
+ this.timeSinceLastOutput = new Date [LOG_TO_INDEX.size()];
+
+ closed = false;
+ }
+
+
+ /**
+ * Adds the output.
+ *
+ * @param newOutput the new output
+ * @param mode the mode
+ */
+ public void addOutput(LoggerOutput newOutput, String mode)
+ {
+ synchronized(this.modeToListeners)
+ {
+ if(mode == LOG_ALL)
+ {
+ for(String logType : AcaciaLogger.LOG_TO_INDEX.keySet())
+ {
+ if(! this.modeToListeners.containsKey(logType))
+ {
+ System.out.println("Adding " + logType + " for " + newOutput);
+ this.modeToListeners.put(logType, new LinkedList <LoggerOutput>());
+ }
+ this.modeToListeners.get(logType).add(newOutput);
+ }
+ }
+ else if (mode != LOG_NONE)
+ {
+ if(! this.modeToListeners.containsKey(mode))
+ {
+ this.modeToListeners.put(mode, new LinkedList <LoggerOutput>());
+ }
+ this.modeToListeners.get(mode).add(newOutput);
+ }
+ }
+ }
+
+ /**
+ * Removes the output.
+ *
+ * @param removeMe is the LoggerOutput to remove from the logger
+ * @param mode is the mode of output for which removeMe is a subscriber
+ */
+ public void removeOutput(LoggerOutput removeMe, String mode)
+ {
+ synchronized(this.modeToListeners)
+ {
+ if(this.modeToListeners.containsKey(mode))
+ {
+ this.modeToListeners.get(mode).remove(removeMe);
+ }
+ }
+ }
+
+ //for now, no thread safety.
+
+ /**
+ * Adds the time stamp.
+ *
+ * @param message the message
+ * @return the string
+ */
+ public String addTimeStamp(String message)
+ {
+ DateFormat dateFormat = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss ");
+ Calendar cal = Calendar.getInstance();
+ String modified = (dateFormat.format(cal.getTime()) + message);
+ return modified;
+ }
+
+ /**
+ * Append time stamp.
+ *
+ * @param message the message
+ */
+ public void appendTimeStamp(StringBuilder message)
+ {
+ DateFormat dateFormat = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss ");
+ Calendar cal = Calendar.getInstance();
+ String timeStamp = dateFormat.format(cal.getTime());
+ message.append(timeStamp);
+ }
+
+ /**
+ * Write log.
+ *
+ * @param message the message
+ * @param logType the log type
+ * @throws Exception the exception
+ */
+ public void writeLog(String message, String logType) throws Exception
+ {
+ synchronized(this.modeToListeners)
+ {
+ if(logType == LOG_ALL)
+ {
+ if(this.modeToListeners.containsKey(logType))
+ {
+ _write(message, logType);
+ }
+ }
+ else
+ {
+ if(logType == LOG_NONE)
+ {
+ return;
+ }
+
+ if(logType == LOG_DEBUG)
+ {
+ _write(message, LOG_DEBUG);
+ }
+ else if(logType == LOG_PROGRESS)
+ {
+ _write(message, LOG_PROGRESS);
+ }
+ else if(logType == LOG_ERROR)
+ {
+ _write(message, LOG_ERROR);
+ }
+ else
+ {
+ return; //TODO: an unknown option!
+ }
+ }
+ }
+ }
+
+ /**
+ * Adds the markup.
+ *
+ * @param toModify the to modify
+ * @param logType the log type
+ * @return the string builder
+ */
+ private StringBuilder addMarkup(String toModify, String logType)
+ {
+ StringBuilder improved = new StringBuilder();
+ this.appendTimeStamp(improved);
+ improved.append(" " + logType);
+ improved.append(": ");
+ improved.append(toModify);
+ improved.append(System.getProperty("line.separator"));
+ return improved;
+ }
+
+ /**
+ * _write.
+ *
+ * @param originalMessage the original message
+ * @param logType the log type
+ * @throws Exception the exception
+ */
+ private void _write(String originalMessage, String logType) throws Exception
+ {
+ synchronized(this.modeToListeners)
+ {
+ StringBuilder modified = this.addMarkup(originalMessage, logType);
+
+ if(this.modeToListeners.get(logType) == null)
+ return;
+
+ LinkedList <LoggerOutput> los = this.modeToListeners.get(logType);
+ for(LoggerOutput lo: los)
+ {
+ lo.write(modified, AcaciaLogger.LOG_TYPE_TO_STYLE.get(logType));
+ }
+ this.modeToListeners.notifyAll();
+ }
+ this.timeSinceLastOutput[AcaciaLogger.LOG_TO_INDEX.get(logType)] = Calendar.getInstance().getTime();
+ }
+
+
+ /**
+ * Removes the log files.
+ *
+ * @throws Exception the exception
+ */
+ public void removeLogFiles() throws Exception
+ {
+ synchronized (this.modeToListeners)
+ {
+ System.out.println("Removing log files: " + Thread.currentThread().getName());
+ for(String mode: this.modeToListeners.keySet())
+ {
+ LinkedList <LoggerOutput> forMode = this.modeToListeners.get(mode);
+
+ LinkedList <LoggerOutput> toRemove = new LinkedList <LoggerOutput>();
+ for(LoggerOutput lo : forMode)
+ {
+ if(lo instanceof LogFileHandle || lo instanceof StandardOutputHandle)
+ {
+ toRemove.add(lo);
+
+ }
+ lo.flush();
+ }
+
+ for(LoggerOutput lo: toRemove)
+ {
+ lo.closeHandle();
+ forMode.remove(lo);
+ }
+ }
+ System.out.println("Finished removing log files: " + Thread.currentThread().getName());
+ this.modeToListeners.notifyAll();
+ }
+ }
+
+
+ /**
+ * Close logger.
+ *
+ * @throws Exception the exception
+ */
+ public void closeLogger() throws Exception
+ {
+ synchronized(this.modeToListeners)
+ {
+ System.out.println("Closing logger: " + Thread.currentThread().getName());
+ //this.flushBuffers();
+ for(String mode: this.modeToListeners.keySet())
+ {
+ LinkedList <LoggerOutput> los = this.modeToListeners.get(mode);
+ for(LoggerOutput lo: los)
+ {
+ if(!lo.isClosed())
+ lo.closeHandle();
+ }
+ }
+ System.out.println("Finished closing logger: " + Thread.currentThread().getName());
+ }
+ this.closed = true;
+ }
+
+ /**
+ * Flush logs.
+ *
+ * @throws Exception the exception
+ */
+ public void flushLogs() throws Exception
+ {
+
+ synchronized(this.modeToListeners)
+ {
+ System.out.println("Closing logger: " + Thread.currentThread().getName());
+ //this.flushBuffers();
+ for(String mode: this.modeToListeners.keySet())
+ {
+ LinkedList <LoggerOutput> los = this.modeToListeners.get(mode);
+ for(LoggerOutput lo: los)
+ {
+ if(!lo.isClosed())
+ {
+ lo.flush();
+ }
+ }
+ }
+ }
+ }
+}
diff --git a/src/pyromaniac/IO/LogFileHandle.java b/src/pyromaniac/IO/LogFileHandle.java
new file mode 100644
index 0000000..87fc069
--- /dev/null
+++ b/src/pyromaniac/IO/LogFileHandle.java
@@ -0,0 +1,94 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+package pyromaniac.IO;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class LogFileHandle.
+ */
+public class LogFileHandle implements LoggerOutput
+{
+
+ /** The out. */
+ private BufferedWriter out;
+
+ /** The closed. */
+ boolean closed;
+
+ /**
+ * Instantiates a new log file handle.
+ *
+ * @param out the out
+ * @throws IOException Signals that an I/O exception has occurred.
+ */
+ public LogFileHandle(BufferedWriter out) throws IOException
+ {
+ this.out = out;
+ this.closed = false;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#write(java.lang.StringBuilder, int)
+ */
+ public void write(StringBuilder buffer, int LOG_STYLE) throws IOException
+ {
+ // System.out.println("Writing to buffer!");
+ this.out.write(buffer.toString());
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#doHTMLMarkup()
+ */
+ public boolean doHTMLMarkup()
+ {
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#closeHandle()
+ */
+ public void closeHandle() throws IOException
+ {
+ //System.out.println("CLosing buffer");
+ this.out.flush();
+ this.out.close();
+ this.closed = true;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#isClosed()
+ */
+ public boolean isClosed() {
+ return closed;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#flush()
+ */
+ public void flush() throws Exception
+ {
+ this.out.flush();
+ }
+
+}
diff --git a/src/pyromaniac/IO/LoggerOutput.java b/src/pyromaniac/IO/LoggerOutput.java
new file mode 100644
index 0000000..3752192
--- /dev/null
+++ b/src/pyromaniac/IO/LoggerOutput.java
@@ -0,0 +1,74 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
+package pyromaniac.IO;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Interface LoggerOutput.
+ */
+public interface LoggerOutput
+{
+
+ /** The LO g_ styl e_ error. */
+ public static int LOG_STYLE_ERROR = 0;
+
+ /** The LO g_ styl e_ progress. */
+ public static int LOG_STYLE_PROGRESS = 1;
+
+ /** The LO g_ styl e_ debug. */
+ public static int LOG_STYLE_DEBUG = 2;
+
+ /**
+ * Write.
+ *
+ * @param buffer the buffer
+ * @param LOG_STYLE the lO g_ style
+ * @throws Exception the exception
+ */
+ public void write(StringBuilder buffer, int LOG_STYLE) throws Exception;
+
+ /**
+ * Do html markup.
+ *
+ * @return true, if successful
+ */
+ public boolean doHTMLMarkup();
+
+ /**
+ * Close handle.
+ *
+ * @throws Exception the exception
+ */
+ public void closeHandle() throws Exception;
+
+ /**
+ * Checks if is closed.
+ *
+ * @return true, if is closed
+ */
+ public boolean isClosed();
+
+ /**
+ * Flush.
+ *
+ * @throws Exception the exception
+ */
+ public void flush() throws Exception;
+}
diff --git a/src/pyromaniac/IO/MIDReader.java b/src/pyromaniac/IO/MIDReader.java
new file mode 100644
index 0000000..434d77b
--- /dev/null
+++ b/src/pyromaniac/IO/MIDReader.java
@@ -0,0 +1,166 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.IO;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedList;
+
+import pyromaniac.AcaciaEngine;
+import pyromaniac.DataStructures.MIDPrimerCombo;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class MIDReader.
+ */
+public class MIDReader
+{
+
+ /** The input. */
+ BufferedReader input;
+
+ /** The input location. */
+ String inputLocation;
+
+ /**
+ * Instantiates a new mID reader.
+ *
+ * @param inputFile the input file
+ */
+ public MIDReader(String inputFile)
+ {
+ try
+ {
+ if(inputFile == null || inputFile.length() == 0)
+ {
+ throw new Exception("Input file for MIDS is not valid");
+ }
+
+ this.inputLocation = inputFile;
+
+ URL pathToFile = getClass().getResource(this.inputLocation);
+ File f = new File(inputFile);
+
+
+ if (pathToFile != null)
+ this.input = new BufferedReader(new InputStreamReader(pathToFile.openStream()));
+ else if(f.exists())
+ {
+ this.input = new BufferedReader(new FileReader(inputFile));
+ }
+ else
+ {
+ throw new Exception("MID file not found: " + inputFile);
+ }
+ }
+ catch(Exception e)
+ {
+ System.out.println(e.getMessage());
+ e.printStackTrace();
+ System.exit(1);
+ }
+ }
+
+ /**
+ * Load mids.
+ *
+ * @return the linked list
+ * @throws MIDFormatException the mID format exception
+ */
+ public LinkedList<MIDPrimerCombo> loadMIDS() throws MIDFormatException
+ {
+ LinkedList <MIDPrimerCombo> MIDTags = new LinkedList <MIDPrimerCombo>();
+ int midCount = 0;
+ try
+ {
+ String line = input.readLine();
+ while (line != null)
+ {
+ if(line.trim().length() == 0)
+ {
+ line = input.readLine();
+ continue;
+ }
+
+ String[] columns = line.split(",");
+ if(columns.length != 3)
+ {
+ columns = line.split("\t");
+
+ if(columns.length != 3)
+ throw new MIDFormatException("Incorrect number of columns in " + inputLocation);
+ }
+
+ // assuming that columns[0] is the MIDtag, and columns[1] is the
+ // descriptor.
+
+ //for now, make the descriptor in the first column.
+
+ String descriptor = columns[0].trim();
+ String midTag = columns[1].trim();
+ String primerSeq = columns[2].trim();
+
+ for(int i = 0; i < midTag.length();i++)
+ {
+ char curr = midTag.charAt(i);
+ if(! AcaciaEngine.getEngine().isIUPAC(curr))
+ {
+ throw new MIDFormatException("Invalid MID sequence: " + midTag);
+ }
+ }
+
+ midTag = midTag.replace("\"", "");
+ descriptor = descriptor.replace("\"", "");
+
+ //bugfix, to uppercase.
+ MIDTags.add(new MIDPrimerCombo(midTag.toUpperCase(), primerSeq.toUpperCase(), descriptor));
+ line = input.readLine();
+ midCount++;
+ }
+ }
+ catch (IOException ie)
+ {
+ System.out.println("An input exception occurred from " + inputLocation);
+ }
+ return MIDTags;
+ }
+
+ /**
+ * The Class MIDFormatException.
+ */
+ public class MIDFormatException extends Exception
+ {
+
+ /**
+ * Instantiates a new mID format exception.
+ *
+ * @param message the message
+ */
+ public MIDFormatException(String message)
+ {
+ super("MID formatting error: " + message);
+ }
+ }
+}
diff --git a/src/pyromaniac/IO/MMFastaImporter.java b/src/pyromaniac/IO/MMFastaImporter.java
new file mode 100644
index 0000000..5da6b49
--- /dev/null
+++ b/src/pyromaniac/IO/MMFastaImporter.java
@@ -0,0 +1,501 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.IO;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.nio.CharBuffer;
+import java.nio.MappedByteBuffer;
+import java.nio.channels.FileChannel;
+import java.nio.charset.CharacterCodingException;
+import java.util.ArrayList;
+import org.apache.commons.math3.util.Pair;
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.MutableInteger;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.DataStructures.Sequence;
+
+
+
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class MMFastaImporter.
+ */
+public class MMFastaImporter extends TagImporter
+{
+
+ /** The logger. */
+ private AcaciaLogger logger;
+
+ /** The seq file. */
+ private String seqFile;
+
+ /** The qual file. */
+ private String qualFile;
+
+ /** The length of the files as longs */
+ private long qualSizeLong;
+ private long seqSizeLong;
+
+ private ArrayList <Pair<Integer, Long>> qualStartsLL;
+ private ArrayList <Pair<Integer, Long>> seqStartsLL;
+
+
+
+ /** The Constant BEGINNING_FASTA_HEADER. */
+ public static final char BEGINNING_FASTA_HEADER = '>';
+
+ /** The Constant ACCEPTIBLE_IUPAC_CHARS. */
+ public static final String ACCEPTIBLE_IUPAC_CHARS = "ATGCNURYWSMKBHDV";
+
+ /** The seq buffer. */
+ private ArrayList <MappedByteBuffer> seqBuffers;
+
+ /** The qual buffer. */
+ private ArrayList <MappedByteBuffer> qualBuffers;
+
+ private FlowCycler cycler;
+
+ /**
+ * Instantiates a new mM fasta importer.
+ *
+ * @param seqFile the seq file
+ * @param qualFile the qual file
+ * @param flowCycle
+ * @param logger the logger
+ */
+ public MMFastaImporter(String seqFile, String qualFile, String flowCycle, AcaciaLogger logger)
+ {
+ this.seqFile = seqFile;
+ this.qualFile = qualFile;
+ this.logger = logger;
+ this.seqBuffers = new ArrayList <MappedByteBuffer>();
+ this.qualBuffers = new ArrayList <MappedByteBuffer>();
+ this.cycler = new FlowCycler(flowCycle, logger);
+ this.init();
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.TagImporter#getNumberOfSequences()
+ */
+ public int getNumberOfSequences()
+ {
+ return this.seqStartsLL.size();
+ }
+
+ /**
+ * Initialises the qual and seq starts.
+ */
+ public void init()
+ {
+ //essentially all I want to do is look for delimiters in the file.
+ try
+ {
+ _initSeq();
+
+ if(!(this.qualFile == null || this.qualFile.trim().length() == 0 || this.qualFile.equals("null")))
+ {
+ _initQual();
+ }
+ else
+ {
+ this.qualFile = null;
+ }
+ }
+ catch (CharacterCodingException cce)
+ {
+ throw new RuntimeException(cce);
+
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+
+ /**
+ * _init qual.
+ *
+ * @throws Exception the exception
+ */
+ private void _initQual() throws Exception
+ {
+ FileInputStream tempStream = new FileInputStream(new File(this.qualFile));
+ FileChannel fcQual = tempStream.getChannel();
+ this.qualSizeLong = fcQual.size();
+
+ //qual starts LL contains pairs, marking file #no (in qualBuffers) and position #no (in the buffer).
+ this.qualStartsLL = new ArrayList <Pair<Integer,Long>>();
+
+ for (long startPosition = 0L; startPosition < this.qualSizeLong; startPosition += HALF_GIGA)
+ {
+ MappedByteBuffer qualBuffer = fcQual.map(FileChannel.MapMode.READ_ONLY, startPosition, Math.min(this.qualSizeLong - startPosition, HALF_GIGA)); //map half a gig to this channel.
+ this.qualBuffers.add(qualBuffer);
+ int qbf_pos = qualBuffers.size() - 1;
+ int maxBuffer = 2048;
+ int bufferSize = (qualBuffer.capacity() > maxBuffer)? maxBuffer: qualBuffer.capacity();
+
+ qualBuffer.limit(bufferSize);
+ qualBuffer.position(0);
+
+ while(qualBuffer.position() != qualBuffer.capacity())
+ {
+ int prevPos = qualBuffer.position();
+ CharBuffer result = decoder.decode(qualBuffer);
+ qualBuffer.position(prevPos);
+
+ for(int i = 0; i < result.capacity(); i++)
+ {
+ char curr = result.charAt(i);
+ int posInFile = prevPos + i ;
+
+ if(curr == BEGINNING_FASTA_HEADER)
+ {
+ qualStartsLL.add(new Pair<Integer, Long>(qbf_pos, new Long(posInFile)));
+ }
+ }
+
+ int newPos = qualBuffer.limit();
+
+ if(qualBuffer.limit() + bufferSize > qualBuffer.capacity())
+ qualBuffer.limit(qualBuffer.capacity());
+ else
+ qualBuffer.limit(qualBuffer.limit() + bufferSize);
+ qualBuffer.position(newPos);
+ }
+ qualBuffer.rewind();
+ }
+ }
+
+ /**
+ * _init seq.
+ *
+ * @throws Exception the exception
+ */
+ private void _initSeq() throws Exception
+ {
+ FileInputStream tempStream = new FileInputStream(new File(this.seqFile));
+ FileChannel fcSeq = tempStream.getChannel();
+ this.seqSizeLong = fcSeq.size();
+ this.seqStartsLL = new ArrayList <Pair<Integer,Long>>();
+
+ for (long startPosition = 0L; startPosition < this.seqSizeLong; startPosition += HALF_GIGA)
+ {
+ MappedByteBuffer seqBuffer = fcSeq.map(FileChannel.MapMode.READ_ONLY, startPosition,
+ Math.min(this.seqSizeLong - startPosition, HALF_GIGA));
+
+ this.seqBuffers.add(seqBuffer);
+ int sbf_pos = seqBuffers.size() - 1;
+ int maxBuffer = 2048;
+ int bufferSize = (seqBuffer.capacity() > maxBuffer)? maxBuffer: seqBuffer.capacity();
+
+ seqBuffer.limit(bufferSize);
+ seqBuffer.position(0);
+
+ while(seqBuffer.position() != seqBuffer.capacity())
+ {
+ int prevPos = seqBuffer.position();
+ CharBuffer result = decoder.decode(seqBuffer);
+ seqBuffer.position(prevPos);
+
+ for(int i = 0; i < result.capacity(); i++)
+ {
+ char curr = result.charAt(i);
+ int posInFile = prevPos + i ;
+
+ if(curr == BEGINNING_FASTA_HEADER)
+ {
+ seqStartsLL.add(new Pair <Integer, Long>(sbf_pos, new Long(posInFile)));
+ }
+ }
+
+ int newPos = seqBuffer.limit();
+
+ if(seqBuffer.limit() + bufferSize > seqBuffer.capacity())
+ seqBuffer.limit(seqBuffer.capacity());
+ else
+ seqBuffer.limit(seqBuffer.limit() + bufferSize);
+ seqBuffer.position(newPos);
+ }
+ seqBuffer.rewind();
+ }
+
+
+ }
+
+ //pyrotag at index.
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.TagImporter#getPyrotagAtIndex(int)
+ */
+ public Pyrotag getPyrotagAtIndex(int index) throws Exception
+ {
+ if(index >= this.seqStartsLL.size())
+ return null;
+
+ char [] relSeqBlock = getBlock(this.seqStartsLL, index, this.seqBuffers);
+
+ //construct the pyrotag in this block.
+ Sequence <Character> pyrotagSeq = processSeqBlock(relSeqBlock);
+ Sequence <Integer> qualitySeq = null;
+
+ if(this.qualFile != null)
+ {
+ char [] relQualBlock = getBlock(this.qualStartsLL, index, this.qualBuffers);
+ qualitySeq = processQualBlock(relQualBlock);
+ }
+
+ Pyrotag p = new Pyrotag(pyrotagSeq.getId(), pyrotagSeq.getDesc(), pyrotagSeq, qualitySeq, this.cycler);
+
+ p.setInternalID(index);
+ return p;
+ }
+
+
+ /**
+ * Process seq block.
+ *
+ * @param pyrotagBlock the pyrotag block
+ * @return the sequence
+ */
+ public Sequence <Character> processSeqBlock(char [] pyrotagBlock)
+ {
+ try
+ {
+ MutableInteger index = new MutableInteger(0);
+ String identifier = _readIdentifier(pyrotagBlock,index); //read identifier and read sequence need to be fixed.
+ String [] idComp = parseIdentifierLine(identifier);
+ ArrayList <Character> nucleotides = this._readSequence(pyrotagBlock, index);
+
+ Sequence <Character> pyrotagSeq = new Sequence<Character> (nucleotides, idComp[0], idComp[1]);
+ return pyrotagSeq;
+ }
+ catch(SeqFormattingException sfe)
+ {
+ System.out.println(sfe.getMessage());
+ System.exit(1);
+ }
+ return null;
+ }
+
+ /**
+ * Process qual block.
+ *
+ * @param qualBlock the qual block
+ * @return the sequence
+ */
+ public Sequence <Integer> processQualBlock(char [] qualBlock)
+ {
+ try
+ {
+ MutableInteger index = new MutableInteger(0);
+ String identifier = _readIdentifier(qualBlock,index);
+ String [] idComp = parseIdentifierLine(identifier);
+ ArrayList <Integer> qualities = this._readQualities(qualBlock, index);
+
+ Sequence <Integer> pyrotagQual = new Sequence<Integer> (qualities, idComp[0], idComp[1]);
+ return pyrotagQual;
+ }
+ catch(SeqFormattingException sfe)
+ {
+ System.out.println(sfe.getMessage());
+ System.exit(1);
+ }
+ return null;
+ }
+
+ /**
+ * Parses the identifier line.
+ *
+ * @param identifierLine the identifier line
+ * @return the string[]
+ */
+ public String [] parseIdentifierLine(String identifierLine)
+ {
+ int posAngle = identifierLine.indexOf(BEGINNING_FASTA_HEADER);
+ int posWhite = identifierLine.indexOf(" ");
+
+ String [] IDAndDescription = new String [2];
+ if(posWhite > 0)
+ {
+ IDAndDescription[0] = identifierLine.substring(posAngle + 1, posWhite);
+ IDAndDescription[1] = identifierLine.substring(posWhite + 1, identifierLine.length());
+ }
+ else
+ {
+ IDAndDescription[0] = identifierLine.substring(posAngle + 1, identifierLine.length());
+ IDAndDescription[1] = "";
+ }
+ return IDAndDescription;
+ }
+
+ /**
+ * _read sequence.
+ *
+ * @param pyrotagBlock the pyrotag block
+ * @param pos the pos
+ * @return the array list
+ * @throws SeqFormattingException the seq formatting exception
+ */
+ public ArrayList <Character> _readSequence(char [] pyrotagBlock, MutableInteger pos) throws SeqFormattingException
+ {
+ ArrayList <Character> characters = new ArrayList <Character>();
+
+ char curr;
+ int index = pos.value();
+
+ while(index < pyrotagBlock.length)
+ {
+ curr = pyrotagBlock[index];
+ curr = Character.toUpperCase(curr); //reads are read in upper case
+ if(Character.isLetter((char)curr))
+ {
+ if(ACCEPTIBLE_IUPAC_CHARS.indexOf(curr) == -1)
+ {
+ throw new SeqFormattingException("Non-IUPAC character (" + curr + ") in sequence", this.seqFile);
+ }
+ else
+ {
+ characters.add(curr);
+ }
+ }
+ index++;
+ }
+ pos.update(index);
+ return characters;
+ }
+
+ /**
+ * _read qualities.
+ *
+ * @param pyrotagBlock the pyrotag block
+ * @param pos the pos
+ * @return the array list
+ * @throws SeqFormattingException the seq formatting exception
+ */
+ public ArrayList <Integer> _readQualities(char [] pyrotagBlock, MutableInteger pos) throws SeqFormattingException
+ {
+ ArrayList <Integer> qualities = new ArrayList <Integer>();
+
+ String currInt = "";
+ char curr;
+
+ int index = pos.value();
+ try
+ {
+ while(index < pyrotagBlock.length)
+ {
+
+ curr = pyrotagBlock[index];
+
+ if(Character.isLetterOrDigit(curr) || Character.isWhitespace(curr))
+ {
+ if(Character.isLetter(curr))
+ {
+ throw new SeqFormattingException("Non-numeric quality score encountered: " + curr, this.qualFile);
+ }
+ else if(Character.isWhitespace(curr) && currInt.length() > 0)
+ {
+ qualities.add(Integer.parseInt(currInt));
+ currInt = "";
+ }
+ else if(Character.isDigit(curr))
+ {
+ currInt = currInt + curr;
+ }
+ }
+ else if (currInt.length() > 0)
+ {
+ qualities.add(Integer.parseInt(currInt));
+ currInt = "";
+ }
+ index++;
+ }
+ if(currInt.length() > 0)
+ {
+ qualities.add(Integer.parseInt(currInt));
+ }
+ return qualities;
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new SeqFormattingException("Quality score: " + currInt + " is not an integer ", this.qualFile);
+ }
+ }
+
+
+ /**
+ * _read identifier.
+ *
+ * @param pyrotagBlock the pyrotag block
+ * @param pos the pos
+ * @return the string
+ */
+ public String _readIdentifier(char [] pyrotagBlock, MutableInteger pos)
+ {
+ StringBuffer buff = new StringBuffer();
+
+ int currPos = pos.value();
+
+ char curr = pyrotagBlock[currPos];
+
+ while(!(curr == '\n' || curr == '\r'))
+ {
+ buff.append(curr);
+ currPos++;
+ curr = pyrotagBlock[currPos];
+ }
+
+ pos.update(currPos);
+ return buff.toString();
+ }
+
+ /**
+ * The Class SeqFormattingException.
+ */
+ public class SeqFormattingException extends Exception
+ {
+
+ /** The Constant serialVersionUID. */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Instantiates a new seq formatting exception.
+ *
+ * @param message the message
+ * @param filename the filename
+ */
+ public SeqFormattingException(String message, String filename)
+ {
+ super("File: " + filename + " FormattingException: " + message);
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.TagImporter#closeFiles()
+ */
+ public void closeFiles()
+ {
+ //TODO: check for side-effects
+ this.qualBuffers.clear();
+ this.seqBuffers.clear();
+
+ }
+}
diff --git a/src/pyromaniac/IO/MMFastqImporter.java b/src/pyromaniac/IO/MMFastqImporter.java
new file mode 100644
index 0000000..b22a715
--- /dev/null
+++ b/src/pyromaniac/IO/MMFastqImporter.java
@@ -0,0 +1,437 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+package pyromaniac.IO;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.nio.CharBuffer;
+import java.nio.MappedByteBuffer;
+import java.nio.channels.FileChannel;
+import java.nio.charset.CharacterCodingException;
+import java.nio.charset.Charset;
+import java.nio.charset.CharsetDecoder;
+import java.util.ArrayList;
+
+import org.apache.commons.math3.util.Pair;
+
+import pyromaniac.DataStructures.FlowCycler;
+import pyromaniac.DataStructures.MutableInteger;
+import pyromaniac.DataStructures.Pyrotag;
+import pyromaniac.DataStructures.Sequence;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class MMFastqImporter.
+ */
+public class MMFastqImporter extends TagImporter
+{
+
+ /** The logger. */
+ private AcaciaLogger logger;
+
+ /** The fastq file. */
+ private String fastqFile;
+
+ /** The record starts. */
+ private ArrayList <Pair <Integer, Long>> recordStarts; //populate these first
+
+ private long seqSizeLong;
+
+ /** The decoder. */
+ private CharsetDecoder decoder = Charset.forName(System.getProperty("file.encoding")).newDecoder();
+
+ /** The Constant BEGINNING_FASTQ_SEQ. */
+ public static final char BEGINNING_FASTQ_SEQ = '@';
+
+ /** The Constant BEGINNING_FASTQ_QUAL. */
+ public static final char BEGINNING_FASTQ_QUAL = '+';
+
+ /** The Constant ACCEPTIBLE_IUPAC_CHARS. */
+ public static final String ACCEPTIBLE_IUPAC_CHARS = "ATGCNURYWSMKBHDV";
+
+ /** The record buffer. */
+ private ArrayList<MappedByteBuffer> recordBuffers;
+
+ private FlowCycler cycler;
+
+ /**
+ * Instantiates a new mM fastq importer.
+ *
+ * @param fastqFile the fastq file
+ * @param logger the logger
+ */
+ public MMFastqImporter(String fastqFile, String flowCycle, AcaciaLogger logger)
+ {
+ this.fastqFile = fastqFile;
+ this.logger = logger;
+ this.recordBuffers = new ArrayList<MappedByteBuffer>();
+ this.cycler = new FlowCycler(flowCycle, logger);
+ this.init();
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.TagImporter#getNumberOfSequences()
+ */
+ public int getNumberOfSequences()
+ {
+ return this.recordStarts.size();
+ }
+
+ /**
+ * Inits the file.
+ */
+ public void init()
+ {
+ try
+ {
+ _initFile();
+ }
+ catch (CharacterCodingException cce)
+ {
+ throw new RuntimeException(cce);
+
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Helper function for init(). Scans this.fastq file for sequence starts and records their position.
+ * Multiple MappedByteBuffers are used to handle large files.
+ * @throws Exceptions relating to file reading and decoding.
+ */
+ private void _initFile() throws Exception
+ {
+ FileInputStream tempStream = new FileInputStream(new File(this.fastqFile));
+ FileChannel fcSeq = tempStream.getChannel();
+ this.seqSizeLong = fcSeq.size();
+ this.recordStarts = new ArrayList <Pair<Integer,Long>>();
+
+ int state = -1;
+
+ for (long startPosition = 0L; startPosition < this.seqSizeLong; startPosition += HALF_GIGA)
+ {
+ MappedByteBuffer recordBuffer = fcSeq.map(FileChannel.MapMode.READ_ONLY, startPosition,
+ Math.min(this.seqSizeLong - startPosition, HALF_GIGA));
+ this.recordBuffers.add(recordBuffer);
+
+ int sbf_pos = this.recordBuffers.size() - 1;
+
+ int maxBuffer = 2048;
+ int bufferSize = (recordBuffer.capacity() > maxBuffer)? maxBuffer: recordBuffer.capacity();
+
+ recordBuffer.limit(bufferSize);
+ recordBuffer.position(0);
+
+ while(recordBuffer.position() != recordBuffer.capacity())
+ {
+ int prevPos = recordBuffer.position();
+ CharBuffer result = decoder.decode(recordBuffer);
+ recordBuffer.position(prevPos);
+
+ for(int i = 0; i < result.capacity(); i++)
+ {
+ char curr = result.charAt(i);
+ int posInFile = prevPos + i ;
+
+ //I see a fastq header, I am either at beginning of file, or last saw the quality line...
+ if(curr == BEGINNING_FASTQ_SEQ && (state == -1 || state == 4))
+ {
+ this.recordStarts.add(new Pair<Integer, Long>(sbf_pos, new Long(posInFile)));
+ state = 1;
+
+ }
+ else if (curr == BEGINNING_FASTQ_QUAL && (state == 1))
+ {
+ state = 2;
+ }
+ else if((curr == '\n' || curr == '\r') & state == 2)
+ {
+ state = 3;
+ }
+ else if ((curr == '\n' || curr == '\r') & state == 3)
+ {
+ state = 4;
+ }
+ }
+
+ int newPos = recordBuffer.limit();
+
+ if(recordBuffer.limit() + bufferSize > recordBuffer.capacity())
+ recordBuffer.limit(recordBuffer.capacity());
+ else
+ recordBuffer.limit(recordBuffer.limit() + bufferSize);
+ recordBuffer.position(newPos);
+ }
+ recordBuffer.rewind();
+ }
+ }
+
+ /**
+ * Checks if the char is printable
+ *
+ * @param c the c
+ * @return true, if is printable char
+ */
+ public boolean isPrintableChar( char c )
+ {
+ Character.UnicodeBlock block = Character.UnicodeBlock.of( c );
+ return (!Character.isISOControl(c)) &&
+ block != null &&
+ block != Character.UnicodeBlock.SPECIALS;
+ }
+
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.TagImporter#getPyrotagAtIndex(int)
+ */
+ public Pyrotag getPyrotagAtIndex(int index) throws Exception
+ {
+ if(index >= this.recordStarts.size())
+ return null;
+
+ char [] relRecordBlock = getBlock(this.recordStarts, index, this.recordBuffers);
+ //construct the pyrotag in this block.
+ Pyrotag p = processRecordBlock(relRecordBlock);
+ p.setInternalID(index);
+ return p;
+ }
+
+ /**
+ * Process record block.
+ *
+ * @param pyrotagBlock the pyrotag block
+ * @return the pyrotag
+ */
+ public Pyrotag processRecordBlock(char [] pyrotagBlock)
+ {
+ try
+ {
+ MutableInteger index = new MutableInteger(0);
+
+ String identifier = _readIdentifierLine(pyrotagBlock,index); //read identifier and read sequence need to be fixed.
+ String [] idComp = _parseIdentifierLine(identifier);
+
+ ArrayList <Character> nucleotides = this._readSequence(pyrotagBlock, index);
+
+ _readIdentifierLine(pyrotagBlock,index); //throw this result away for now, if I wanted to, could do a check to compare
+ //headers
+
+ ArrayList <Integer> qualities = this._readQualities(pyrotagBlock, index);
+
+ Sequence <Character> pyrotagSeq = new Sequence<Character> (nucleotides, idComp[0], idComp[1]);
+ Sequence <Integer> pyrotagQual = new Sequence <Integer>(qualities, idComp[0], idComp[1]);
+ Pyrotag p = new Pyrotag(idComp[0],idComp[1], pyrotagSeq, pyrotagQual, this.cycler);
+
+ return p;
+ }
+ catch(SeqFormattingException sfe)
+ {
+ System.out.println(sfe.getMessage());
+ System.exit(1);
+ }
+ return null;
+ }
+
+
+
+ /**
+ * _parse identifier line.
+ *
+ * @param identifierLine the identifier line
+ * @return the string[]
+ */
+ public String [] _parseIdentifierLine(String identifierLine)
+ {
+ int posAngle = identifierLine.indexOf(BEGINNING_FASTQ_SEQ);
+ int posWhite = identifierLine.indexOf(" ");
+
+ String [] IDAndDescription = new String [2];
+ if(posWhite > 0)
+ {
+ IDAndDescription[0] = identifierLine.substring(posAngle + 1, posWhite);
+ IDAndDescription[1] = identifierLine.substring(posWhite + 1, identifierLine.length());
+ }
+ else
+ {
+ IDAndDescription[0] = identifierLine.substring(posAngle + 1, identifierLine.length());
+ IDAndDescription[1] = "";
+ }
+ return IDAndDescription;
+ }
+
+ /**
+ * _read sequence.
+ *
+ * @param pyrotagBlock the pyrotag block
+ * @param pos the pos
+ * @return the array list
+ * @throws SeqFormattingException the seq formatting exception
+ */
+ public ArrayList <Character> _readSequence(char [] pyrotagBlock, MutableInteger pos) throws SeqFormattingException
+ {
+ ArrayList <Character> characters = new ArrayList <Character>();
+ char curr;
+ int index = pos.value();
+
+ //push through newlines
+ while(index < pyrotagBlock.length)
+ {
+ curr = pyrotagBlock[index];
+
+ if(! (curr == '\n' || curr == '\r'))
+ break;
+
+ index++;
+ }
+
+ //should be in nucleotides
+ while(index < pyrotagBlock.length)
+ {
+ curr = pyrotagBlock[index];
+ curr = Character.toUpperCase(curr);
+
+ if(curr == '\n' || curr == '\r')
+ break;
+
+ if(Character.isLetter((char)curr))
+ {
+ if(ACCEPTIBLE_IUPAC_CHARS.indexOf(curr) == -1)
+ {
+ String seq = new String(pyrotagBlock);
+
+ throw new SeqFormattingException("Non-IUPAC character (" + curr + ") in sequence : " + seq, this.fastqFile);
+ }
+ else
+ {
+ characters.add(curr);
+ }
+ }
+ index++;
+ }
+ pos.update(index);
+ return characters;
+ }
+
+ //FASTQ qualities need to be mapped back to integers.
+ /**
+ * _read qualities.
+ *
+ * @param pyrotagBlock the pyrotag block
+ * @param pos the pos
+ * @return the array list
+ * @throws SeqFormattingException the seq formatting exception
+ */
+ public ArrayList <Integer> _readQualities(char [] pyrotagBlock, MutableInteger pos) throws SeqFormattingException
+ {
+ ArrayList <Integer> qualities = new ArrayList <Integer>();
+ char curr;
+
+ int index = pos.value();
+
+ //push through newlines
+ while(index < pyrotagBlock.length)
+ {
+ curr = pyrotagBlock[index];
+
+ if(! (curr == '\n' || curr == '\r'))
+ break;
+
+ index++;
+ }
+
+ //qualities should be here.
+ while(index < pyrotagBlock.length)
+ {
+ curr = pyrotagBlock[index];
+
+ if(curr == '\n' || curr == '\r')
+ break;
+
+ int conv = curr - 33;
+ qualities.add(conv);
+ index++;
+ }
+
+ return qualities;
+ }
+
+
+ /**
+ * _read identifier line.
+ *
+ * @param pyrotagBlock the pyrotag block
+ * @param pos the pos
+ * @return the string
+ */
+ public String _readIdentifierLine(char [] pyrotagBlock, MutableInteger pos)
+ {
+ StringBuffer buff = new StringBuffer();
+ int currPos = pos.value();
+
+ char curr = pyrotagBlock[currPos];
+ while(curr == '\n' || curr == '\r')
+ {
+ currPos++;
+ curr = pyrotagBlock[currPos];
+ }
+
+
+ while(!(curr == '\n' || curr == '\r'))
+ {
+ buff.append(curr);
+ currPos++;
+ curr = pyrotagBlock[currPos];
+ }
+
+ pos.update(currPos);
+ return buff.toString();
+ }
+
+ /**
+ * The Class SeqFormattingException.
+ */
+ public class SeqFormattingException extends Exception
+ {
+
+ /** The Constant serialVersionUID. */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Instantiates a new seq formatting exception.
+ *
+ * @param message the message
+ * @param filename the filename
+ */
+ public SeqFormattingException(String message, String filename)
+ {
+ super("File: " + filename + " FormattingException: " + message);
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.TagImporter#closeFiles()
+ */
+ public void closeFiles()
+ {
+ this.recordBuffers.clear();
+
+ }
+}
diff --git a/src/pyromaniac/IO/QualityFile.java b/src/pyromaniac/IO/QualityFile.java
new file mode 100644
index 0000000..85b3b95
--- /dev/null
+++ b/src/pyromaniac/IO/QualityFile.java
@@ -0,0 +1,67 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.IO;
+
+import java.util.Iterator;
+
+import pyromaniac.DataStructures.QualitySequence;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Interface QualityFile.
+ */
+public interface QualityFile
+{
+
+ /**
+ * Iterator.
+ *
+ * @return the iterator
+ */
+ public Iterator <QualitySequence> iterator();
+
+ /**
+ * Gets the file name.
+ *
+ * @return the file name
+ */
+ public String getFileName();
+
+ /**
+ * The Class FormattingException.
+ */
+ public class FormattingException extends Exception
+ {
+
+ /** The Constant serialVersionUID. */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Instantiates a new formatting exception.
+ *
+ * @param message the message
+ * @param filename the filename
+ * @param lineNumber the line number
+ */
+ public FormattingException(String message, String filename, int lineNumber)
+ {
+ super("File: " + filename + "Line: " + lineNumber + " FormattingException: " + message);
+ }
+ }
+}
diff --git a/src/pyromaniac/IO/QualityFile454.java b/src/pyromaniac/IO/QualityFile454.java
new file mode 100644
index 0000000..89eb88e
--- /dev/null
+++ b/src/pyromaniac/IO/QualityFile454.java
@@ -0,0 +1,245 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.IO;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+
+import pyromaniac.DataStructures.QualitySequence;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class QualityFile454.
+ */
+public class QualityFile454 implements QualityFile
+{
+
+ /** The filename. */
+ private String filename;
+
+ /** The Constant BEGINNING_FASTA_HEADER. */
+ public static final char BEGINNING_FASTA_HEADER = '>';
+
+ /**
+ * Instantiates a new quality file454.
+ *
+ * @param filename the filename
+ */
+ public QualityFile454(String filename)
+ {
+ this.filename = filename;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.QualityFile#getFileName()
+ */
+ public String getFileName()
+ {
+ return this.filename;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.QualityFile#iterator()
+ */
+ public pyromaniac.IO.QualityFile454.QualityIterator iterator()
+ {
+ QualityIterator qi = new QualityIterator(this);
+
+ return qi;
+ }
+
+ /**
+ * The Class QualityIterator.
+ */
+ public class QualityIterator implements Iterator <QualitySequence>
+ {
+
+ /** The qf. */
+ private QualityFile qf;
+
+ /** The curr file pos. */
+ private int currFilePos;
+
+ /** The br. */
+ private BufferedReader br;
+
+ /** The curr line. */
+ String currLine;
+
+ /**
+ * Instantiates a new quality iterator.
+ *
+ * @param qf the qf
+ */
+ protected QualityIterator(QualityFile454 qf)
+ {
+ try
+ {
+ this.qf = qf;
+ this.br = new BufferedReader(new FileReader(this.qf.getFileName()));
+ this.currLine = null;
+ this.currFilePos = -1;
+ }
+ catch(IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Iterator#hasNext()
+ */
+ public boolean hasNext()
+ {
+ try
+ {
+ if(this.currFilePos == -1)
+ {
+ currLine = br.readLine();
+ currFilePos = 1;
+ }
+
+ if(currLine == null)
+ {
+ return false;
+ }
+
+ return true;
+ }
+ catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Iterator#next()
+ */
+ public QualitySequence next()
+ {
+ try
+ {
+ //skip over whitespace.
+ while(this.currLine != null && currLine.equals(""))
+ {
+ currLine = br.readLine();
+ this.currFilePos++;
+ }
+ }
+ catch(IOException e)
+ {
+ e.printStackTrace();
+ }
+
+ String id = null;
+ String desc = null;
+ ArrayList <Integer> sequence = new ArrayList <Integer>();
+
+ if(this.currLine != null)
+ {
+ try
+ {
+ if(this.currLine.charAt(0) != BEGINNING_FASTA_HEADER)
+ {
+ throw new FormattingException("Expected '>', found " + this.currLine,
+ qf.getFileName(), currFilePos);
+ }
+ id = this.currLine.substring(1);
+ id.trim();
+
+ if(id.length() == 0)
+ {
+ throw new FormattingException("Sequence identifier has zero length",
+ qf.getFileName(),currFilePos);
+ }
+ else
+ {
+ this.currLine = br.readLine();
+ this.currFilePos++;
+
+ if(this.currLine == null || this.currLine.equals(""))
+ {
+ throw new FormattingException("Expected quality sequence", qf.getFileName(), currFilePos);
+ }
+
+ while(this.currLine != null && this.currLine.charAt(0) != BEGINNING_FASTA_HEADER)
+ {
+ String [] results = this.currLine.split("[\\s\\t]");
+ for(int i = 0; i < results.length; i++)
+ {
+ String temp = results[i];
+ try
+ {
+ Integer parsed = Integer.parseInt(temp);
+ sequence.add(parsed);
+ }
+ catch(NumberFormatException nfe)
+ {
+ throw new FormattingException("Expected integer, found " + temp, qf.getFileName(), currFilePos);
+ }
+ }
+ this.currLine = br.readLine();
+ this.currFilePos++;
+ }
+ }
+ }
+ catch(FormattingException fe)
+ {
+ System.out.println(fe.getMessage());
+ return null;
+ }
+ catch(IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ if(id.length() > 0)
+ {
+ int positionOfWhiteSpace = id.indexOf(" ");
+ if(positionOfWhiteSpace != -1) //whitespace was found
+ {
+ desc = id.substring(positionOfWhiteSpace + 1, id.length());
+ id = id.substring(0, positionOfWhiteSpace);
+ }
+ }
+
+ if(sequence.size() > 0)
+ {
+ return new QualitySequence(id, desc, sequence);
+ }
+
+ return null;
+ }
+
+ //this does nothing
+ /* (non-Javadoc)
+ * @see java.util.Iterator#remove()
+ */
+ public void remove()
+ {
+
+ }
+ }
+
+}
diff --git a/src/pyromaniac/IO/SeqReadingUtility.java b/src/pyromaniac/IO/SeqReadingUtility.java
new file mode 100644
index 0000000..468f19a
--- /dev/null
+++ b/src/pyromaniac/IO/SeqReadingUtility.java
@@ -0,0 +1,480 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.IO;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.RandomAccessFile;
+import java.util.ArrayList;
+
+import pyromaniac.IO.QualityFile.FormattingException;
+import pyromaniac.DataStructures.Sequence;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class SeqReadingUtility.
+ */
+public class SeqReadingUtility
+{
+
+ /** The Constant BEGINNING_FASTA_HEADER. */
+ public static final char BEGINNING_FASTA_HEADER = '>';
+
+ /** The Constant ACCEPTIBLE_IUPAC_CHARS. */
+ public static final String ACCEPTIBLE_IUPAC_CHARS = "ATGCNURYWSMKBHDV";
+
+
+ /**
+ * Instantiates a new seq reading utility.
+ */
+ public SeqReadingUtility()
+ {
+
+ }
+
+ /**
+ * _read identifier line.
+ *
+ * @param tempIn the temp in
+ * @param ram the ram
+ * @param filename the filename
+ * @return the string
+ */
+ public String _readIdentifierLine(BufferedReader tempIn, RandomAccessFile ram, String filename)
+ {
+ try
+ {
+ long initialPos = ram.getFilePointer();
+ int charactersRead = 0;
+
+ char start = (char)tempIn.read();
+ charactersRead++;
+
+ if(start != '>')
+ {
+ throw new SeqFormattingException("Expected '>', found (" + start + ") ", filename);
+ }
+ else
+ {
+ StringBuffer buff = new StringBuffer();
+
+ int currInt = tempIn.read();
+ charactersRead++;
+
+ char curr = (char)currInt;
+ while(!(curr == '\n' || curr == '\r') && currInt != -1)
+ {
+ buff.append(curr);
+ currInt = tempIn.read();
+ charactersRead++;
+ curr = (char)currInt;
+ }
+
+ ram.seek(initialPos + charactersRead); //this SHOULD work...
+ return buff.toString();
+ }
+ }
+ catch(IOException ie)
+ {
+ ie.printStackTrace();
+ }
+ catch(SeqFormattingException sfe)
+ {
+ sfe.printStackTrace();
+ }
+ return null;
+ }
+
+ /**
+ * Parses the identifier line.
+ *
+ * @param identifierLine the identifier line
+ * @return the string[]
+ */
+ public String [] parseIdentifierLine(String identifierLine)
+ {
+
+ int posWhite = identifierLine.indexOf(" ");
+
+ String [] IDAndDescription = new String [2];
+ if(posWhite > 0)
+ {
+ IDAndDescription[0] = identifierLine.substring(0, posWhite);
+ IDAndDescription[1] = identifierLine.substring(posWhite + 1, identifierLine.length());
+ }
+ else
+ {
+ IDAndDescription[0] = identifierLine;
+ IDAndDescription[1] = "";
+ }
+ return IDAndDescription;
+ }
+
+ /**
+ * _read sequence.
+ *
+ * @param seq the seq
+ * @param ram the ram
+ * @param filename the filename
+ * @return the array list
+ */
+ public ArrayList <Character> _readSequence(BufferedReader seq, RandomAccessFile ram, String filename)
+ {
+ try
+ {
+ ArrayList <Character> characters = new ArrayList <Character>();
+
+ int charactersRead = 0;
+
+ long initialPos = ram.getFilePointer();
+
+ System.out.println("Initial position was : " + initialPos);
+
+ int currInt = seq.read();
+ charactersRead++;
+
+ char curr = (char)currInt;
+
+ while(currInt != -1 && curr != '>')
+ {
+ if(Character.isLetter((char)curr))
+ {
+ if(ACCEPTIBLE_IUPAC_CHARS.indexOf(curr) == -1)
+ {
+ throw new SeqFormattingException("Non-IUPAC character (" + curr + ") in sequence", filename);
+ }
+ else
+ {
+ characters.add(curr);
+ }
+ }
+
+ if(seq.ready())
+ {
+ currInt = seq.read(); //reading in one character at a time...
+ charactersRead++;
+ curr = (char)currInt;
+ }
+ else
+ {
+ currInt = -1;
+ }
+ }
+
+ System.out.println("Read " + charactersRead);
+
+ if(curr == '>')
+ {
+ charactersRead--;
+ }
+
+ System.out.println("Before seeking, the curr position of ram was " + ram.getFilePointer());
+
+ ram.seek(initialPos + charactersRead);
+
+ return characters;
+ }
+ catch(SeqFormattingException sfe)
+ {
+ System.out.println("Error: " + sfe.getMessage());
+ sfe.printStackTrace();
+ //System.exit(1);
+ }
+ catch(IOException ie)
+ {
+ System.out.println("Error: " + ie.getMessage());
+ ie.printStackTrace();
+ //System.exit(1);
+ }
+
+ return null;
+ }
+
+ /**
+ * _read quality sequence.
+ *
+ * @param qual the qual
+ * @param ram the ram
+ * @param filename the filename
+ * @return the array list
+ */
+ public ArrayList <Integer> _readQualitySequence(BufferedReader qual, RandomAccessFile ram, String filename)
+ {
+ try
+ {
+ ArrayList <Integer> scores = new ArrayList <Integer>();
+
+ long initialPos = ram.getFilePointer();
+
+ int charactersRead = 0;
+
+ String currScore = "";
+
+ char curr = (char)qual.read();
+ charactersRead++;
+
+ while(curr != -1 && curr != '>')
+ {
+ if(Character.isDigit(curr))
+ {
+ currScore = currScore + curr;
+ }
+ else if(!Character.isWhitespace(curr))
+ {
+ Integer value = Integer.parseInt(currScore);
+ scores.add(value);
+ currScore = "";
+ }
+ curr = (char)qual.read();
+ charactersRead++;
+ }
+
+ if(curr == '>')
+ {
+ charactersRead--;
+ }
+
+ ram.seek(initialPos + charactersRead);
+
+
+ return scores;
+ }
+ catch(IOException ie)
+ {
+ ie.printStackTrace();
+ }
+
+ return null;
+ }
+
+ /**
+ * Gets the next seq.
+ *
+ * @param seq the seq
+ * @param filename the filename
+ * @return the next seq
+ */
+ public Sequence <Character> getNextSeq(RandomAccessFile seq, String filename)
+ {
+ String id = null;
+ String desc = null;
+ ArrayList <Character> sequence;
+
+ try
+ {
+ BufferedReader in = new BufferedReader(new FileReader(seq.getFD()));
+
+ String identifierLine = this._readIdentifierLine(in,seq, filename);
+
+ System.out.println("Identifier: " + identifierLine);
+
+ String [] IDAndDescription = this.parseIdentifierLine(identifierLine);
+
+
+
+ sequence = this._readSequence(in, seq, filename);
+
+ System.out.println("Sequence: " + sequence);
+
+ in = null;
+
+ if(sequence != null && sequence.size() > 0)
+ {
+ return new Sequence <Character> (sequence, IDAndDescription[0], IDAndDescription[1]);
+ }
+ }
+ catch(IOException ie)
+ {
+ System.out.println("Error: " + ie.getMessage());
+ ie.printStackTrace();
+ System.exit(1);
+ }
+ return null;
+ }
+
+ /**
+ * Checks for next seq.
+ *
+ * @param seq the seq
+ * @param filename the filename
+ * @return true, if successful
+ */
+ public boolean hasNextSeq(RandomAccessFile seq, String filename)
+ {
+ try
+ {
+ if(seq.length() == seq.getFilePointer())
+ {
+ System.out.println("Returning false?");
+ return false;
+ }
+
+ BufferedReader in = new BufferedReader(new FileReader(seq.getFD()));
+
+ System.out.println("Position before has next seq " + seq.getFilePointer());
+
+ long initialPos = seq.getFilePointer();
+ char charactersRead = 0;
+
+ int charInt = in.read();
+ charactersRead++;
+
+ //while there is white space, keep moving forward.
+ while(charInt != -1 && Character.isWhitespace((char)charInt))
+ {
+ charInt = in.read();
+ charactersRead++;
+ }
+
+ in = null;
+
+ if(charInt == -1 || (char)charInt != this.BEGINNING_FASTA_HEADER)
+ {
+ System.out.println("Returning false, saw character " + (char)charInt);
+ return false;
+ }
+ else
+ {
+ System.out.println("Returning true");
+ charactersRead--; //go back before >
+ seq.seek(initialPos + charactersRead); //have to reset it.
+ return true;
+ }
+ }
+ catch(IOException ie)
+ {
+ ie.printStackTrace();
+
+ }
+ return false;
+ }
+
+ /**
+ * Gets the next quality seq.
+ *
+ * @param qual the qual
+ * @param filename the filename
+ * @return the next quality seq
+ */
+ public Sequence <Integer> getNextQualitySeq(RandomAccessFile qual, String filename)
+ {
+ String id = null;
+ String desc = null;
+ ArrayList <Integer> sequence;
+
+ try
+ {
+ BufferedReader tempIn = new BufferedReader(new FileReader(qual.getFD()));
+
+
+ String identifierLine = this._readIdentifierLine(tempIn, qual, filename);
+ if(identifierLine == null)
+ {
+ tempIn = null;
+ //tempIn.close();
+ return null;
+ }
+
+ String [] IDAndDescription = this.parseIdentifierLine(identifierLine);
+
+ sequence = this._readQualitySequence(tempIn, qual, filename);
+
+ tempIn = null;
+
+ if(sequence != null && sequence.size() > 0)
+ {
+ return new Sequence <Integer> (sequence, IDAndDescription[0], IDAndDescription[1]);
+ }
+ }
+ catch(IOException ie)
+ {
+ System.out.println("Error: " + ie.getMessage());
+ ie.printStackTrace();
+ System.exit(1);
+ }
+
+ return null;
+ }
+
+ /**
+ * Checks for next quality seq.
+ *
+ * @param qual the qual
+ * @param filename the filename
+ * @return true, if successful
+ */
+ public boolean hasNextQualitySeq(RandomAccessFile qual, String filename)
+ {
+ try
+ {
+ BufferedReader in = new BufferedReader(new FileReader(qual.getFD()));
+
+ int charactersRead = 0;
+ long initialPos = qual.getFilePointer();
+ int charInt = in.read();
+
+
+ while(charInt != -1 && Character.isWhitespace((char)charInt))
+ {
+ charInt = in.read();
+ charactersRead++;
+ }
+
+
+ if(charInt == -1 || (char)charInt != this.BEGINNING_FASTA_HEADER)
+ {
+ return false;
+ }
+ else
+ {
+ charactersRead--;
+ qual.seek(initialPos + charactersRead);
+ return true;
+ }
+ }
+ catch(IOException ie)
+ {
+ ie.printStackTrace();
+
+ }
+ return false;
+ }
+
+ /**
+ * The Class SeqFormattingException.
+ */
+ public class SeqFormattingException extends Exception
+ {
+
+ /** The Constant serialVersionUID. */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Instantiates a new seq formatting exception.
+ *
+ * @param message the message
+ * @param filename the filename
+ */
+ public SeqFormattingException(String message, String filename)
+ {
+ super("File: " + filename + " FormattingException: " + message);
+ }
+ }
+}
diff --git a/src/pyromaniac/IO/StandardOutputHandle.java b/src/pyromaniac/IO/StandardOutputHandle.java
new file mode 100644
index 0000000..bf3db8c
--- /dev/null
+++ b/src/pyromaniac/IO/StandardOutputHandle.java
@@ -0,0 +1,83 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.IO;
+
+import java.io.IOException;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class StandardOutputHandle.
+ */
+public class StandardOutputHandle implements LoggerOutput
+{
+
+ /** The closed. */
+ boolean closed;
+
+ /**
+ * Instantiates a new standard output handle.
+ *
+ * @throws IOException Signals that an I/O exception has occurred.
+ */
+ public StandardOutputHandle() throws IOException
+ {
+ this.closed = false;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#write(java.lang.StringBuilder, int)
+ */
+ public void write(StringBuilder buffer, int LOG_STYLE) throws IOException
+ {
+ System.out.println(buffer.toString());
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#doHTMLMarkup()
+ */
+ public boolean doHTMLMarkup()
+ {
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#closeHandle()
+ */
+ public void closeHandle() throws IOException
+ {
+ this.closed = true;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#isClosed()
+ */
+ public boolean isClosed()
+ {
+ return closed;
+ }
+
+ /* (non-Javadoc)
+ * @see pyromaniac.IO.LoggerOutput#flush()
+ */
+ public void flush() throws Exception
+ {
+ System.out.flush();
+ }
+
+}
diff --git a/src/pyromaniac/IO/TagImporter.java b/src/pyromaniac/IO/TagImporter.java
new file mode 100644
index 0000000..8a2f41b
--- /dev/null
+++ b/src/pyromaniac/IO/TagImporter.java
@@ -0,0 +1,143 @@
+/*
+ * Acacia - GS-FLX & Titanium read error-correction and de-replication software.
+ * Copyright (C) <2011> <Lauren Bragg and Glenn Stone - CSIRO CMIS & University of Queensland>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package pyromaniac.IO;
+
+import java.nio.CharBuffer;
+import java.nio.MappedByteBuffer;
+import java.nio.charset.Charset;
+import java.nio.charset.CharsetDecoder;
+import java.util.ArrayList;
+
+import org.apache.commons.math3.util.Pair;
+
+import pyromaniac.DataStructures.Pyrotag;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Interface TagImporter.
+ */
+public abstract class TagImporter
+{
+ public static final long HALF_GIGA = 536870912;
+ /** The decoder. */
+ static CharsetDecoder decoder = Charset.forName(System.getProperty("file.encoding")).newDecoder();
+ /**
+ * Close files.
+ */
+ public abstract void closeFiles();
+
+ /**
+ * Gets the number of sequences.
+ *
+ * @return the number of sequences
+ */
+ public abstract int getNumberOfSequences();
+
+ /**
+ * Gets the pyrotag at index.
+ *
+ * @param index the index
+ * @return the pyrotag at index
+ * @throws Exception
+ */
+ public abstract Pyrotag getPyrotagAtIndex(int index) throws Exception;
+
+ public char [] getBlock( ArrayList<Pair<Integer, Long>> starts, int index, ArrayList <MappedByteBuffer> buffers) throws Exception
+ {
+ StringBuilder sb = new StringBuilder("");
+
+ if(index >= starts.size())
+ {
+ return null;
+
+ }
+
+ //most cases will be contained within the same memory-mapped chunk.
+ Pair <Integer, Long> startingBlock = starts.get(index);
+
+ //next block can be undefined.
+ Pair <Integer, Long> nextBlock = (starts.size() > index + 1)? starts.get(index + 1): null;
+
+ //very unlikely that a sequence would stretch over half a mega block, but future-proofing...
+ for(int mm_block = startingBlock.getFirst(); mm_block < buffers.size() &&
+ (nextBlock == null || mm_block <= nextBlock.getFirst()); mm_block++)
+ {
+ long blockStart;
+ long blockEnd;
+
+ if(mm_block == startingBlock.getFirst()) //at the start
+ {
+ blockStart = startingBlock.getSecond();
+ blockEnd = blockStart;
+ if(nextBlock != null && nextBlock.getFirst() == startingBlock.getFirst())
+ {
+ blockEnd = nextBlock.getSecond(); //just up to the start of the next sequence in this block
+ }
+ else
+ {
+ blockEnd = buffers.get(mm_block).capacity(); //all the way to the end of this block
+ }
+ }
+ else
+ {
+ blockStart = 0L; // the start of the next memory mapped file
+ if(nextBlock.getFirst() == mm_block)//we are in the last block
+ {
+ blockEnd = nextBlock.getSecond();
+ }
+ else
+ {
+ blockEnd = buffers.get(mm_block).capacity(); //all the way to the end of this block.
+ }
+ }
+ try
+ {
+ buffers.get(mm_block).limit((int)blockEnd);
+ buffers.get(mm_block).position((int)blockStart);
+ CharBuffer resBuffer = decoder.decode(buffers.get(mm_block));
+ sb.append(resBuffer);
+ buffers.get(mm_block).rewind();
+ }
+ catch(Exception e)
+ {
+ String errMes = "Attempted to decode block " + blockStart + " for " + (blockEnd - blockStart + 1) + " chars. Error occurred: " + e.getMessage();
+ throw new ImportException(errMes);
+ }
+ }
+ return sb.toString().toCharArray();
+ }
+
+
+ /**
+ * The Class ImportException.
+ */
+ public class ImportException extends Exception
+ {
+
+ /**
+ * Instantiates a new import exception.
+ *
+ * @param errMessage the err message
+ */
+ public ImportException(String errMessage)
+ {
+ super(errMessage);
+ }
+ }
+}
diff --git a/src/pyromaniac/RunCharacterisation.java b/src/pyromaniac/RunCharacterisation.java
new file mode 100644
index 0000000..a5cfe0c
--- /dev/null
+++ b/src/pyromaniac/RunCharacterisation.java
@@ -0,0 +1,282 @@
+package pyromaniac;
+
+import java.util.HashMap;
+import java.util.LinkedList;
+
+import pyromaniac.DataStructures.MIDPrimerCombo;
+import pyromaniac.DataStructures.Pyrotag;
+
+
+/**
+ * The Class RunCharacterisation. Retains information about the mean and standard deviation in both read length, and run-length encoded read length.
+ */
+public class RunCharacterisation
+{
+
+ /** Hashmap mapping sequences to their corresponding MID. */
+ HashMap <MIDPrimerCombo, LinkedList <Pyrotag>> MIDToSequences;
+
+ /** The MID seq length. */
+ HashMap <MIDPrimerCombo, Integer> MIDseqLength;
+
+ /** The MI dcollapsed seq length. */
+ HashMap <MIDPrimerCombo, Integer> MIDcollapsedSeqLength;
+
+ /** The MId qualities. */
+ HashMap <MIDPrimerCombo, Double> MIDqualities;
+
+ /** The invalid mids. */
+ int invalidMIDS;
+
+ /** The valid mids */
+ int validMIDs;
+
+
+ /**
+ * Instantiates a new run characterisation.
+ *
+ * @param MIDToSequences the mID to sequences
+ * @param MIDSeqLength the mID seq length
+ * @param MIDcollapsedSeqLength the mI dcollapsed seq length
+ * @param MIDqualities the mI dqualities
+ * @param invalidMIDS the invalid mids
+ * @param invalidMID
+ */
+ public RunCharacterisation(HashMap <MIDPrimerCombo, LinkedList <Pyrotag>> MIDToSequences,
+ HashMap <MIDPrimerCombo, Integer> MIDSeqLength,
+ HashMap <MIDPrimerCombo, Integer> MIDcollapsedSeqLength,
+ HashMap <MIDPrimerCombo, Double> MIDqualities, int validMIDs, int invalidMIDS)
+ {
+ this.MIDToSequences = MIDToSequences;
+ this.MIDseqLength = MIDSeqLength;
+ this.MIDcollapsedSeqLength = MIDcollapsedSeqLength;
+ this.MIDqualities = MIDqualities;
+ this.invalidMIDS = invalidMIDS;
+ this.validMIDs = validMIDs;
+ }
+
+ /**
+ * Gets the number of reads which did not match the MIDS.
+ *
+ * @return the number of invalid mids
+ */
+ public int getNumInvalidMIDS()
+ {
+ return this.invalidMIDS;
+ }
+
+ public int getNumValidMIDS()
+ {
+ return this.validMIDs;
+ }
+
+ /**
+ * Calculate length standard dev for read.
+ *
+ * @param midsForCalc only reads with these MIDs will be included in the calculation
+ * @return standard deviation of read lengths for the midsForCalc
+ */
+ public double calculateLengthStandardDevForRead(LinkedList <MIDPrimerCombo> midsForCalc)
+ {
+ return calculateStandardDeviation(midsForCalc, this.MIDseqLength);
+ }
+
+ /**
+ * Calculate collapsed length standard dev for read.
+ *
+ * @param midsForCalc only reads with these MIDSs will be included in the calculation
+ * @return the standard deviation in run length encoded (homopolymer collapsed) reads sequences
+ */
+ public double calculateCollapsedLengthStandardDevForRead(LinkedList <MIDPrimerCombo> midsForCalc)
+ {
+ return calculateStandardDeviation(midsForCalc, this.MIDcollapsedSeqLength);
+ }
+
+ /**
+ * Gets the mean read length for mid.
+ *
+ * @param midsForCalc the mids for calc
+ * @return the mean read length for mid
+ */
+ public double getMeanReadLengthForMID(LinkedList <MIDPrimerCombo> midsForCalc)
+ {
+ return getMeanLengthForMID(midsForCalc, this.MIDseqLength);
+ }
+
+ /**
+ * Gets the mean collapsed read length for mid.
+ *
+ * @param midsForCalc the mids for calc
+ * @return the mean collapsed read length for mid
+ */
+ public double getMeanCollapsedReadLengthForMID(LinkedList <MIDPrimerCombo> midsForCalc)
+ {
+ return getMeanLengthForMID(midsForCalc, this.MIDcollapsedSeqLength);
+ }
+
+
+ /**
+ * Gets the mean length for mid.
+ *
+ * @param midsForCalc the mids for calc
+ * @param sumOfLengths the sum of lengths
+ * @return the mean length for mid
+ */
+ private double getMeanLengthForMID(LinkedList <MIDPrimerCombo> midsForCalc, HashMap <MIDPrimerCombo, Integer> sumOfLengths)
+ {
+
+ LinkedList <MIDPrimerCombo> midsToProcess = midsForCalc;
+
+ if(midsToProcess.size() == 1 && midsToProcess.getFirst() == AcaciaConstants.NO_MID_GROUP)
+ midsToProcess = new LinkedList <MIDPrimerCombo>(this.MIDToSequences.keySet());
+
+ int lengthSum = sumLengthsForMIDs(midsToProcess, sumOfLengths);
+ int tagCount = getTagCountForMIDs(midsToProcess);
+
+ if(tagCount == 0)
+ return -1;
+
+ double mean = lengthSum / tagCount;
+ return mean;
+ }
+
+ /**
+ * Average quality for mids.
+ *
+ * @param midsForCalc the mids for calc
+ * @return the double
+ */
+ public double averageQualityForMIDs(LinkedList <MIDPrimerCombo> midsForCalc)
+ {
+ double qualitySum = 0;
+ int numTags = 0;
+
+ LinkedList <MIDPrimerCombo> midsToProcess = midsForCalc;
+
+ if(MIDqualities.size() == 0)
+ return 0;
+
+ if(midsToProcess.size() == 1 && midsToProcess.getFirst() == AcaciaConstants.NO_MID_GROUP)
+ {
+ midsToProcess = new LinkedList <MIDPrimerCombo>(this.MIDToSequences.keySet());
+ }
+
+ for(MIDPrimerCombo mid: midsToProcess)
+ {
+ if(MIDqualities.containsKey(mid))
+ {
+ qualitySum += MIDqualities.get(mid);
+ numTags += MIDToSequences.get(mid).size();
+ }
+ }
+
+ if(numTags == 0)
+ {
+ return -1;
+ }
+
+ return (qualitySum / numTags);
+ }
+
+ /**
+ * Calculate standard deviation.
+ *
+ * @param midsForCalc the mids for calc
+ * @param sumOfLengths the sum of lengths
+ * @return the double
+ */
+ private double calculateStandardDeviation(LinkedList <MIDPrimerCombo> midsForCalc, HashMap <MIDPrimerCombo, Integer> sumOfLengths)
+ {
+
+ int tagCount = 0;
+ int lengthSum = 0;
+ double mean = 0;
+ double sumXMinusXBarSqr = 0;
+
+ LinkedList <MIDPrimerCombo> midsToProcess = midsForCalc;
+
+ if(midsToProcess.size() == 1 && midsToProcess.getFirst() == AcaciaConstants.NO_MID_GROUP)
+ midsToProcess = new LinkedList <MIDPrimerCombo> (this.MIDToSequences.keySet());
+
+
+ lengthSum = sumLengthsForMIDs(midsToProcess, sumOfLengths);
+ tagCount = getTagCountForMIDs(midsToProcess);
+
+ if(tagCount == 0)
+ return -1;
+
+ mean = (lengthSum / tagCount);
+
+ for(MIDPrimerCombo mid: midsToProcess)
+ {
+ if(!this.MIDToSequences.containsKey(mid))
+ {
+ continue;
+ }
+
+ LinkedList <Pyrotag> relevantPyrotags = this.MIDToSequences.get(mid);
+
+
+ for(Pyrotag p : relevantPyrotags)
+ {
+ double length = p.getLength();
+ double sqrdist = (length - mean) * (length - mean);
+ sumXMinusXBarSqr += sqrdist;
+ }
+ }
+ double sampleStdDev = Math.sqrt(sumXMinusXBarSqr / tagCount);
+ return sampleStdDev;
+
+ }
+
+ /**
+ * Gets the tag count for mi ds.
+ *
+ * @param midsForCalc the mids for calc
+ * @return the tag count for mi ds
+ */
+ public int getTagCountForMIDs(LinkedList <MIDPrimerCombo> midsForCalc)
+ {
+ int tagCount = 0;
+
+ LinkedList <MIDPrimerCombo> midsToProcess = midsForCalc;
+
+ if(midsToProcess.size() == 1 && midsToProcess.getFirst() == AcaciaConstants.NO_MID_GROUP)
+ midsToProcess = new LinkedList <MIDPrimerCombo> (this.MIDToSequences.keySet());
+
+ for(MIDPrimerCombo mid: midsToProcess)
+ {
+ if(MIDToSequences.containsKey(mid))
+ {
+ tagCount += MIDToSequences.get(mid).size();
+ }
+ }
+ return tagCount;
+ }
+
+ /**
+ * Sum lengths for mids.
+ *
+ * @param midsForCalc the mids for calc
+ * @param sumOfLengths the sum of lengths
+ * @return the int
+ */
+ private int sumLengthsForMIDs(LinkedList <MIDPrimerCombo> midsForCalc, HashMap <MIDPrimerCombo, Integer> sumOfLengths)
+ {
+ int lengthSum = 0;
+
+ LinkedList <MIDPrimerCombo> midsToProcess = midsForCalc;
+
+ if(midsToProcess.size() == 1 && midsToProcess.getFirst() == AcaciaConstants.NO_MID_GROUP)
+ midsToProcess = new LinkedList <MIDPrimerCombo>(this.MIDToSequences.keySet());
+
+ for(MIDPrimerCombo mid: midsForCalc)
+ {
+ if(sumOfLengths.containsKey(mid))
+ {
+ lengthSum += sumOfLengths.get(mid);
+ }
+ }
+ return lengthSum;
+ }
+}
\ No newline at end of file
diff --git a/src/pyromaniac/package.html b/src/pyromaniac/package.html
new file mode 100644
index 0000000..7d7d546
--- /dev/null
+++ b/src/pyromaniac/package.html
@@ -0,0 +1,7 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head></head>
+<body>
+ Provides...
+</body>
+</html>
\ No newline at end of file
--
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