[med-svn] [acacia] 08/09: Update upstream source from tag 'upstream/1.53'
Andreas Tille
tille at debian.org
Fri Dec 1 14:47:58 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 3773515ebbb04dbd2c0bed0871c4a0095fbe4eb0
Merge: 80d75e8 5f3d33c
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 1 15:42:50 2017 +0100
Update upstream source from tag 'upstream/1.53'
Update to upstream version '1.53'
with Debian dir 8dbad39e6f253ec8f81608b59ffbb14140aae524
.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
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 +
176 files changed, 49883 insertions(+)
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