[med-svn] [artemis] 01/01: New upstream version 16.0.17+dfsg
Sascha Steinbiss
satta at debian.org
Wed Dec 7 23:45:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch upstream
in repository artemis.
commit 30a81b955840926a2ad45a554692687d1f74b13b
Author: Sascha Steinbiss <satta at debian.org>
Date: Mon Dec 5 09:11:15 2016 +0000
New upstream version 16.0.17+dfsg
---
.classpath | 2 +
.travis.yml | 26 +
AUTHORS | 3 +
ChangeLog | 2 +-
INSTALL | 48 +-
LICENSE | 680 ++++++++++
Makefile | 213 +--
README => README.md | 12 +-
act | 2 +
art | 3 +
docs/act_manual.sgml | 2 +-
docs/act_start_chapter.sgml | 2 +-
docs/feature_edit.gif | Bin 30763 -> 34452 bytes
docs/jvm_options.sgml | 23 +
docs/main_window_chapter.sgml | 1 +
docs/manual.sgml | 3 +-
docs/menus.sgml | 56 +-
docs/qualifier_list.gif | Bin 0 -> 12357 bytes
docs/qualifier_list2.gif | Bin 0 -> 15166 bytes
docs/start_chapter.sgml | 2 +-
docs/tick.png | Bin 0 -> 394 bytes
docs/unix_args.sgml | 8 -
docs/validation_report.png | Bin 0 -> 55887 bytes
docs/validator.sgml | 181 +++
etc/feature_keys_gff | 6 +-
etc/key_mapping | 7 +-
etc/options | 14 +-
etc/project.properties | 6 +-
etc/qualifier_types | 4 +-
etc/results_to_netscape | 15 +-
etc/versions | 6 +-
etc/writedb_entry | 9 +-
gff2embl | 106 ++
install_dependencies.sh | 57 +
test/data/MAL_8h.bam | Bin 0 -> 97476 bytes
test/data/MAL_8h.bam.bai | Bin 0 -> 264 bytes
.../components/alignment/MappedReadsTest.java | 143 ++
.../artemis/io/GFF3AttributeBuilderTest.java | 295 ++++
test/uk/ac/sanger/artemis/io/GFF3EncoderTest.java | 102 ++
uk/ac/sanger/artemis/AlignMatchVector.java | 16 +-
uk/ac/sanger/artemis/FeatureVector.java | 2 +-
uk/ac/sanger/artemis/chado/ArtemisUtils.java | 3 +-
.../artemis/chado/ChadoTransactionManager.java | 14 +-
uk/ac/sanger/artemis/components/EditMenu.java | 17 +
uk/ac/sanger/artemis/components/EntryEdit.java | 2 +-
uk/ac/sanger/artemis/components/FeatureEdit.java | 21 +-
.../sanger/artemis/components/RunBlastAtNCBI.java | 4 +-
.../artemis/components/RunPfamSearchThread.java | 4 +-
uk/ac/sanger/artemis/components/SelectMenu.java | 68 +-
uk/ac/sanger/artemis/components/Splash.java | 2 +-
.../components/alignment/AbstractGraphPanel.java | 11 +-
.../artemis/components/alignment/BamUtils.java | 208 ++-
.../artemis/components/alignment/BamView.java | 68 +-
.../alignment/CRAMReferenceSequenceFile.java | 7 +-
.../components/alignment/CoveragePanel.java | 86 +-
.../artemis/components/alignment/MappedReads.java | 359 ++---
.../artemis/components/alignment/ReadCount.java | 40 +
.../components/alignment/ReadCountDialog.java | 7 +-
.../components/genebuilder/GeneEditorPanel.java | 44 +-
.../artemis/components/genebuilder/GeneUtils.java | 5 +-
.../genebuilder/gff/PropertiesPanel.java | 24 +-
uk/ac/sanger/artemis/io/DocumentEntryFactory.java | 15 +-
.../sanger/artemis/io/GFF3AttributeAggregator.java | 38 +
uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java | 214 +++
uk/ac/sanger/artemis/io/GFF3Encoder.java | 38 +
uk/ac/sanger/artemis/io/GFFStreamFeature.java | 1411 +++++++++-----------
.../sanger/artemis/io/GenbankTblOutputStream.java | 96 +-
uk/ac/sanger/artemis/io/GffToEMBL.java | 2 +-
uk/ac/sanger/artemis/io/KeyVector.java | 26 +-
uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java | 24 +-
.../sanger/artemis/io/SimpleEntryInformation.java | 8 +-
uk/ac/sanger/artemis/io/StreamQualifier.java | 16 +-
uk/ac/sanger/artemis/plot/Algorithm.java | 2 +-
uk/ac/sanger/artemis/plot/UserDataAlgorithm.java | 34 +-
uk/ac/sanger/artemis/util/DatabaseDocument.java | 91 +-
uk/ac/sanger/artemis/util/FastVector.java | 26 +-
uk/ac/sanger/artemis/util/StringVector.java | 34 +-
77 files changed, 3545 insertions(+), 1581 deletions(-)
diff --git a/.classpath b/.classpath
index 3d63d38..200d980 100644
--- a/.classpath
+++ b/.classpath
@@ -1,6 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="corba"/>
+ <classpathentry kind="src" path="lib"/>
<classpathentry including="nsdb/|seqdb/|type/" kind="src" path="ant-build/src/main"/>
<classpathentry excluding="ant-build/src/main/|uk/ac/sanger/artemis/ExternalProgramUtils.java" including="nsdb/|org/|seqdb/|type/|uk/" kind="src" path=""/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
@@ -23,5 +24,6 @@
<classpathentry kind="lib" path="lib/batik/batik-svggen.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-util.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-xml.jar"/>
+ <classpathentry kind="lib" path="lib/commons-lang-2.6.jar"/>
<classpathentry kind="output" path="ant-build/classes/main"/>
</classpath>
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..065180d
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,26 @@
+language: java
+jdk:
+ - openjdk7
+ - openjdk6
+ - oraclejdk7
+sudo: false
+env:
+ global:
+ - BUILD_CMD='make'
+matrix:
+ include:
+ - jdk: openjdk7
+ env: BUILD_CMD='ant -f build.xml'
+cache:
+ directories:
+ - "${HOME}/dependencies"
+before_install:
+ - "export CASHER_TIME_OUT=300"
+ - "export DISPLAY=:99.0"
+ - "sh -e /etc/init.d/xvfb start"
+ - "source install_dependencies.sh"
+install:
+ - "$BUILD_CMD"
+ - "cd test"
+ - "ln -s $(pwd)/../etc/log4j.properties ."
+script: ant -f build-test.xml test -DEMBOSS_ROOT=$EMBOSS_ROOT | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ]
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..f3ff3b3
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,3 @@
+Tim Carver (path-help at sanger.ac.uk)
+Sascha Steinbiss (path-help at sanger.ac.uk)
+Kim Rutherford (path-help at sanger.ac.uk)
diff --git a/ChangeLog b/ChangeLog
index ac4dd04..612a9ba 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,4 @@
-Version XX
+Version 16
Add 'Features Within Selection' option to the 'Select' menu to select
features that are contained by a selected base range.
diff --git a/INSTALL b/INSTALL
index 0240478..a3e2c3c 100644
--- a/INSTALL
+++ b/INSTALL
@@ -1,11 +1,10 @@
Installation instructions for UNIX
+==================================
1. change to /some/directory
-
2. uncompress and untar the artemis_compiled.tar.gz file
- On UNIX the command is: gzip -d < artemis_compiled.tar.gz | tar xf -
-
+ On UNIX the command is: tar xzvf artemis_compiled.tar.gz
This will create a "artemis" directory containing all the java classes. On
Unix the easiest way to run the program is to run the script called art in the
@@ -18,7 +17,8 @@ menus. From the File menu you can open a flat file containing an
entry. If it reads the entry successfully a new window will open,
which shows the sequence and features for the entry.
-====================================================================
+Download and Install from GitHub
+================================
Installation instructions for GitHub download
@@ -30,4 +30,42 @@ Installation instructions for GitHub download
3. Run Artemis:
./art
or ACT:
- ./act
\ No newline at end of file
+ ./act
+
+Makefile targets
+================
+
+make - compile code
+make jar - create Artemis (jar_build/artemis.jar) and ACT
+ (jar_build/act.jar) jar files.
+make dist - create a tar ball of the Artemis/ACT distribution
+
+Creating signed jar files for Artemis/ACT Java Web Start launch
+===============================================================
+
+Use 'make jar' to create jar_build/artemis.jar. See the following pages
+for a description of deploying and signing jar files:
+
+http://java.sun.com/docs/books/tutorial/deployment/webstart/deploying.html
+http://java.sun.com/docs/books/tutorial/deployment/jar/signing.html
+
+Use the Java keytool to generate a keystore (e.g. artemisstore below) file:
+
+keytool -genkey -alias signFiles -dname "CN=$NAME, \
+ OU=$ORGU, O=$ORG, L=$LOC, S=$STATE, C=$CODE" \
+ -keypass $KEYPASS -storepass $STOREPASS -keystore artemisstore -validity $VALID
+
+The following can be used to view the key store and list entry details:
+
+keytool -list -v -keystore artemisstore
+
+Then use the following to create a signed jar to use in the JNLP file:
+
+jarsigner -keystore artemisstore -storepass $STOREPASS -keypass $KEYPASS \
+ -signedjar sartemis.jar artemis.jar signFiles
+
+Running the test suite
+======================
+
+cd test
+ant -f build-test.xml
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..3f03f8b
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,680 @@
+This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
+
+This is free software, licensed under:
+
+ The GNU General Public License, Version 3, June 2007
+
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
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+
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+ d) Limiting the use for publicity purposes of names of licensors or
+ authors of the material; or
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+ e) Declining to grant rights under trademark law for use of some
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+ material by anyone who conveys the material (or modified versions of
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+ any liability that these contractual assumptions directly impose on
+ those licensors and authors.
+
+ All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further
+restriction, you may remove that term. If a license document contains
+a further restriction but permits relicensing or conveying under this
+License, you may add to a covered work material governed by the terms
+of that license document, provided that the further restriction does
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+
+ If you add terms to a covered work in accord with this section, you
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+where to find the applicable terms.
+
+ Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.
+
+ 8. Termination.
+
+ You may not propagate or modify a covered work except as expressly
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+this License (including any patent licenses granted under the third
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+ However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
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+holder fails to notify you of the violation by some reasonable means
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+ Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
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+your receipt of the notice.
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+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
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+ You may not impose any further restrictions on the exercise of the
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+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
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+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
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+ A contributor's "essential patent claims" are all patent claims
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+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
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+covered work in a country, or your recipient's use of the covered work
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+arrangement, you convey, or propagate by procuring conveyance of, a
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+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
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+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
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+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
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+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
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+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ 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/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/Makefile b/Makefile
index 8dc99b0..9b33c29 100644
--- a/Makefile
+++ b/Makefile
@@ -1,210 +1,12 @@
# This is a GNU Makefile for Artemis
-# $Header: //tmp/pathsoft/artemis/Makefile,v 1.47 2009-09-21 15:32:03 tjc Exp $
-
SHELL=/bin/sh
#OPT_FLAGS = -g -deprecation
JAVAC := javac -source 1.5 -target 1.5 $(OPT_FLAGS) $(EXTRA_FLAGS)
-REAL_CLASSPATH := CLASSPATH=lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/picard/sam.jar:lib/commons-net-2.2.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:.
-
-# NAMES:= \
-# uk/ac/sanger/artemis/OptionChangeListener \
-# uk/ac/sanger/artemis/OptionChangeEvent \
-# uk/ac/sanger/artemis/Options \
-# uk/ac/sanger/artemis/Selection \
-# uk/ac/sanger/artemis/components/ArtemisMain \
-# uk/ac/sanger/artemis/components/ActMain \
-# uk/ac/sanger/artemis/components/Splash \
-# uk/ac/sanger/artemis/components/ListDialog \
-# uk/ac/sanger/artemis/components/FeatureListFrame \
-# uk/ac/sanger/artemis/components/FeatureList \
-# uk/ac/sanger/artemis/components/FeatureDisplay \
-# uk/ac/sanger/artemis/components/CanvasPanel \
-# uk/ac/sanger/artemis/components/EntryGroupDisplay \
-# uk/ac/sanger/artemis/components/EntryHeaderEdit \
-# uk/ac/sanger/artemis/components/BasePlotGroup \
-# uk/ac/sanger/artemis/components/EntryEditVector \
-# uk/ac/sanger/artemis/components/EntryEdit \
-# uk/ac/sanger/artemis/components/WritableEMBLCorbaEntrySource \
-# uk/ac/sanger/artemis/components/DbfetchEntrySource \
-# uk/ac/sanger/artemis/components/EMBLCorbaEntrySource \
-# uk/ac/sanger/artemis/components/CorbaEntrySource \
-# uk/ac/sanger/artemis/components/BioJavaEntrySource \
-# uk/ac/sanger/artemis/components/FileDialogEntrySource \
-# uk/ac/sanger/artemis/components/EntryActionListener \
-# uk/ac/sanger/artemis/components/DisplayComponent \
-# uk/ac/sanger/artemis/components/EntryFileDialog \
-# uk/ac/sanger/artemis/components/StickyFileChooser \
-# uk/ac/sanger/artemis/components/LogReadListener \
-# uk/ac/sanger/artemis/components/Selector \
-# uk/ac/sanger/artemis/components/Navigator \
-# uk/ac/sanger/artemis/components/EntryGroupPanel \
-# uk/ac/sanger/artemis/components/FeaturePopup \
-# uk/ac/sanger/artemis/components/WriteMenu \
-# uk/ac/sanger/artemis/components/SelectMenu \
-# uk/ac/sanger/artemis/components/GraphMenu \
-# uk/ac/sanger/artemis/components/RunMenu \
-# uk/ac/sanger/artemis/components/AddMenu \
-# uk/ac/sanger/artemis/components/ViewMenu \
-# uk/ac/sanger/artemis/components/GotoMenu \
-# uk/ac/sanger/artemis/components/EditMenu \
-# uk/ac/sanger/artemis/components/SelectionMenu \
-# uk/ac/sanger/artemis/components/SelectionViewer \
-# uk/ac/sanger/artemis/components/FeaturePlotGroup \
-# uk/ac/sanger/artemis/components/FeaturePlot \
-# uk/ac/sanger/artemis/components/FeatureEdit \
-# uk/ac/sanger/artemis/components/FeatureViewer \
-# uk/ac/sanger/artemis/components/SearchResultViewer \
-# uk/ac/sanger/artemis/components/LogViewer \
-# uk/ac/sanger/artemis/components/FileViewer \
-# uk/ac/sanger/artemis/components/MessageFrame \
-# uk/ac/sanger/artemis/components/MessageDialog \
-# uk/ac/sanger/artemis/components/YesNoDialog \
-# uk/ac/sanger/artemis/components/KeyChooser \
-# uk/ac/sanger/artemis/components/KeyChoice \
-# uk/ac/sanger/artemis/components/QualifierEditor \
-# uk/ac/sanger/artemis/components/QualifierTextArea \
-# uk/ac/sanger/artemis/components/QualifierChoice \
-# uk/ac/sanger/artemis/components/ChoiceFrame \
-# uk/ac/sanger/artemis/components/SelectionInfoDisplay \
-# uk/ac/sanger/artemis/components/EntryGroupMenu \
-# uk/ac/sanger/artemis/components/EntryGroupInfoDisplay \
-# uk/ac/sanger/artemis/components/Utilities \
-# uk/ac/sanger/artemis/components/MarkerRangeRequester \
-# uk/ac/sanger/artemis/components/MarkerRangeRequesterListener \
-# uk/ac/sanger/artemis/components/MarkerRangeRequesterEvent \
-# uk/ac/sanger/artemis/components/TextRequester \
-# uk/ac/sanger/artemis/components/TextRequesterListener \
-# uk/ac/sanger/artemis/components/TextRequesterEvent \
-# uk/ac/sanger/artemis/components/TextDialog \
-# uk/ac/sanger/artemis/components/BasePlot \
-# uk/ac/sanger/artemis/components/ProcessWatcher \
-# uk/ac/sanger/artemis/components/ProcessWatcherEvent \
-# uk/ac/sanger/artemis/components/ProcessWatcherListener \
-# uk/ac/sanger/artemis/components/ExternalProgramOptions \
-# uk/ac/sanger/artemis/components/Plot \
-# uk/ac/sanger/artemis/components/PlotMouseListener \
-# uk/ac/sanger/artemis/components/FeatureAminoAcidViewer \
-# uk/ac/sanger/artemis/components/FeatureBaseViewer \
-# uk/ac/sanger/artemis/components/SequenceViewer \
-# uk/ac/sanger/artemis/components/FeatureInfo \
-# uk/ac/sanger/artemis/components/DisplayAdjustmentListener \
-# uk/ac/sanger/artemis/components/DisplayAdjustmentEvent \
-# uk/ac/sanger/artemis/components/ScoreChanger \
-# uk/ac/sanger/artemis/components/ScoreScrollbar \
-# uk/ac/sanger/artemis/components/ScoreChangeListener \
-# uk/ac/sanger/artemis/components/ScoreChangeEvent \
-# uk/ac/sanger/artemis/components/InputStreamProgressDialog \
-# uk/ac/sanger/artemis/plot/KarlinSigAlgorithm \
-# uk/ac/sanger/artemis/plot/UserDataAlgorithm \
-# uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm \
-# uk/ac/sanger/artemis/plot/ATDeviationAlgorithm \
-# uk/ac/sanger/artemis/plot/GCDeviationAlgorithm \
-# uk/ac/sanger/artemis/plot/GCFrameAlgorithm \
-# uk/ac/sanger/artemis/plot/CodonUsageAlgorithm \
-# uk/ac/sanger/artemis/plot/CodonUsageFormatException \
-# uk/ac/sanger/artemis/plot/CodonUsageWeight \
-# uk/ac/sanger/artemis/plot/CodonWeight \
-# uk/ac/sanger/artemis/plot/AGWindowAlgorithm \
-# uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm \
-# uk/ac/sanger/artemis/plot/GCWindowAlgorithm \
-# uk/ac/sanger/artemis/plot/HydrophilicityAlgorithm \
-# uk/ac/sanger/artemis/plot/HydroAlgorithm \
-# uk/ac/sanger/artemis/plot/HydrophobicityAlgorithm \
-# uk/ac/sanger/artemis/plot/CoilFeatureAlgorithm \
-# uk/ac/sanger/artemis/plot/FeatureAlgorithm \
-# uk/ac/sanger/artemis/plot/BaseAlgorithm \
-# uk/ac/sanger/artemis/plot/Algorithm \
-# uk/ac/sanger/artemis/Logger \
-# uk/ac/sanger/artemis/ExternalProgramListener \
-# uk/ac/sanger/artemis/ExternalProgramException \
-# uk/ac/sanger/artemis/ExternalProgramVector \
-# uk/ac/sanger/artemis/SimpleExternalProgramMonitor \
-# uk/ac/sanger/artemis/ProcessMonitor \
-# uk/ac/sanger/artemis/ProcessMonitor \
-# uk/ac/sanger/artemis/ExternalProgramMonitor \
-# uk/ac/sanger/artemis/ExternalProgram \
-# uk/ac/sanger/artemis/EntryGroupChangeListener \
-# uk/ac/sanger/artemis/EntryGroupChangeEvent \
-# uk/ac/sanger/artemis/EntryChangeListener \
-# uk/ac/sanger/artemis/EntryChangeEvent \
-# uk/ac/sanger/artemis/FilteredEntryGroup \
-# uk/ac/sanger/artemis/SimpleEntryGroup \
-# uk/ac/sanger/artemis/EntryGroup \
-# uk/ac/sanger/artemis/EntryVector \
-# uk/ac/sanger/artemis/EntrySourceVector \
-# uk/ac/sanger/artemis/EntrySource \
-# uk/ac/sanger/artemis/Entry \
-# uk/ac/sanger/artemis/LastSegmentException \
-# uk/ac/sanger/artemis/FeatureFromVectorPredicate \
-# uk/ac/sanger/artemis/FeatureKeyQualifierPredicate \
-# uk/ac/sanger/artemis/FeatureKeyPredicate \
-# uk/ac/sanger/artemis/FeaturePatternPredicate \
-# uk/ac/sanger/artemis/FeaturePredicateConjunction \
-# uk/ac/sanger/artemis/FeaturePredicate \
-# uk/ac/sanger/artemis/FeaturePredicateVector \
-# uk/ac/sanger/artemis/FeatureEnumeration \
-# uk/ac/sanger/artemis/FeatureSegmentVector \
-# uk/ac/sanger/artemis/FeatureChangeListener \
-# uk/ac/sanger/artemis/FeatureChangeEvent \
-# uk/ac/sanger/artemis/FeatureVector \
-# uk/ac/sanger/artemis/Feature \
-# uk/ac/sanger/artemis/FeatureSegment \
-# uk/ac/sanger/artemis/ActionController \
-# uk/ac/sanger/artemis/ActionVector \
-# uk/ac/sanger/artemis/Action \
-# uk/ac/sanger/artemis/ChangeListener \
-# uk/ac/sanger/artemis/ChangeEventVector \
-# uk/ac/sanger/artemis/ChangeEvent \
-# uk/ac/sanger/artemis/GotoListener \
-# uk/ac/sanger/artemis/GotoEvent \
-# uk/ac/sanger/artemis/GotoEventSource \
-# uk/ac/sanger/artemis/SimpleGotoEventSource \
-# uk/ac/sanger/artemis/SelectionChangeListener \
-# uk/ac/sanger/artemis/SelectionChangeEvent \
-# uk/ac/sanger/artemis/Selectable \
-# uk/ac/sanger/artemis/sequence/NoSequenceException \
-# uk/ac/sanger/artemis/sequence/MarkerRangeVector \
-# uk/ac/sanger/artemis/sequence/MarkerRange \
-# uk/ac/sanger/artemis/sequence/MarkerChangeListener \
-# uk/ac/sanger/artemis/sequence/MarkerChangeEvent \
-# uk/ac/sanger/artemis/sequence/Marker \
-# uk/ac/sanger/artemis/sequence/Strand \
-# uk/ac/sanger/artemis/sequence/BasePatternFormatException \
-# uk/ac/sanger/artemis/sequence/BasePattern \
-# uk/ac/sanger/artemis/sequence/Bases \
-# uk/ac/sanger/artemis/sequence/AminoAcidSequence \
-# uk/ac/sanger/artemis/sequence/SequenceChangeListener \
-# uk/ac/sanger/artemis/sequence/SequenceChangeEvent \
-# uk/ac/sanger/artemis/io/BioJavaFeature \
-# uk/ac/sanger/artemis/io/BioJavaSequence \
-# uk/ac/sanger/artemis/io/BioJavaEntry \
-# uk/ac/sanger/artemis/io/GenbankStreamSequence \
-# uk/ac/sanger/artemis/io/RWCorbaEntry \
-# uk/ac/sanger/artemis/io/CorbaEntry \
-# uk/ac/sanger/artemis/io/DocumentEntryFactory \
-# uk/ac/sanger/artemis/io/BlastDocumentEntry \
-# uk/ac/sanger/artemis/io/MSPcrunchDocumentEntry \
-# uk/ac/sanger/artemis/io/GFFDocumentEntry \
-# uk/ac/sanger/artemis/io/GenbankDocumentEntry \
-# uk/ac/sanger/artemis/io/EmblDocumentEntry \
-# uk/ac/sanger/artemis/io/PublicDBDocumentEntry \
-# uk/ac/sanger/artemis/io/SimpleDocumentEntry \
-# uk/ac/sanger/artemis/io/DocumentEntry \
-# uk/ac/sanger/artemis/io/Entry \
-# uk/ac/sanger/artemis/io/ReadOnlyEntry \
-# uk/ac/sanger/artemis/io/QualifierInfoException \
-# uk/ac/sanger/artemis/io/QualifierInfo \
-# uk/ac/sanger/artemis/io/QualifierInfoVector \
-# uk/ac/sanger/artemis/io/QualifierInfoHash \
-# uk/ac/sanger/artemis/chado/DbSqlConfig \
-# uk/ac/sanger/artemis/circular/DNADraw \
-# uk/ac/sanger/artemis/circular/digest/Utils \
-# uk/ac/sanger/artemis/circular/digest/CircularGenomeController \
-# uk/ac/sanger/artemis/io/GffToEMBL
+REAL_CLASSPATH := CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/picard/sam.jar:lib/commons-net-2.2.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:.
ARTEMIS_DIRS = uk/ac/sanger/artemis \
uk/ac/sanger/artemis/chado \
@@ -226,7 +28,6 @@ uk/ac/sanger/artemis/plot \
uk/ac/sanger/artemis/sequence \
uk/ac/sanger/artemis/util
-#CLASSES := $(NAMES:%=%.class)
SOURCES := $(foreach DIR,$(ARTEMIS_DIRS),$(wildcard $(DIR)/*.java))
CLASSES := $(SOURCES:%.java=%.class)
@@ -271,7 +72,7 @@ manual :
CLASS_FILES := `find org uk nsdb type seqdb -name '*.class' -print`
-OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README`
+OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README.md`
dist :
rm -rf artemis_compiled.tar.gz tar_build
@@ -311,24 +112,24 @@ artemis.jar : $(CLASSES)
done; \
fi; \
cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \
- ../images/PSUlogo.gif ../images/icon.gif ../README ../artemis_sqlmap .
+ ../images/PSUlogo.gif ../images/icon.gif ../README.md ../artemis_sqlmap .
find jar_build -name '*.java' -print | xargs rm -f
find jar_build -name '.svn' -print | xargs rm -rf
cd jar_build; \
rm -rf META-INF/MANIFEST.MF; \
echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \
- jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
+ jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \
- jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README etc \
+ jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README.md etc \
uk org/gmod org/w3c org/apache org/biojava/bio/ com/ibatis/common/jdbc/ net/sf/samtools/ LICENSE.Apache j2ssh.properties; \
echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \
jar cmf manifest-bamview BamView.jar META-INF/services etc uk org/apache org/biojava org/biojavax org/gmod org/w3c net/sf com/ibatis; \
echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \
- jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
+ jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
rm -f etc/log4j.properties; \
- jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README \
+ jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README.md \
uk org/gmod nsdb type seqdb LICENSE.Apache artemis_sqlmap
clean :
diff --git a/README b/README.md
similarity index 90%
rename from README
rename to README.md
index 5109688..5c4d9bb 100644
--- a/README
+++ b/README.md
@@ -1,4 +1,6 @@
-INTRODUCTION
+# INTRODUCTION
+
+[](https://travis-ci.org/sanger-pathogens/Artemis)
Artemis is a free genome browser and annotation tool that allows visualisation
of sequence features, next generation data and the results of analyses within
@@ -13,7 +15,7 @@ difference between genomes and to explore conservation of synteny, in the contex
of the entire sequences and their annotation.
-DOCUMENTATION
+# DOCUMENTATION
The Artemis user manual is at:
http://www.sanger.ac.uk/resources/software/artemis/
@@ -21,12 +23,12 @@ The Artemis user manual is at:
The ACT user manual is at:
http://www.sanger.ac.uk/resources/software/act/
-INSTALLATION
+# INSTALLATION
The installation instructions are included in the user manual.
-DISTRIBUTION
+# DISTRIBUTION
Artemis may be freely distributed under the terms of the GNU Public License,
and should run on any system with a recent version of Java.
@@ -35,7 +37,7 @@ For information on how to get Artemis see this web page:
http://www.sanger.ac.uk/resources/software/artemis/
-COPYRIGHT
+# COPYRIGHT
Copyright (C) 1998-2013 Genome Research Limited
diff --git a/act b/act
index 4200521..365fe5e 100755
--- a/act
+++ b/act
@@ -43,6 +43,8 @@ CLASSPATH=$CLASSPATH:$ACT_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ACT_HOME/lib/iba
# picard jars
CLASSPATH=$ACT_HOME/lib/picard/sam.jar:$ACT_HOME/lib/picard/picard.jar:$CLASSPATH
+CLASSPATH="$ACT_HOME/lib/commons-lang-2.6.jar:$CLASSPATH"
+
export CLASSPATH
ACT_PROPERTIES="-Dartemis.environment=UNIX"
diff --git a/art b/art
index 180d773..f8fe4fe 100755
--- a/art
+++ b/art
@@ -40,6 +40,9 @@ export CLASSPATH
# picard jars
CLASSPATH=$ARTEMIS_HOME/lib/picard/sam.jar:$ARTEMIS_HOME/lib/picard/picard.jar:$ARTEMIS_HOME/lib/commons-net-2.2.jar:$CLASSPATH
+
+CLASSPATH="$ARTEMIS_HOME/lib/commons-lang-2.6.jar:$CLASSPATH"
+
export CLASSPATH
diff --git a/docs/act_manual.sgml b/docs/act_manual.sgml
index 9dbe2b9..44a75f3 100644
--- a/docs/act_manual.sgml
+++ b/docs/act_manual.sgml
@@ -44,7 +44,7 @@
</PRODUCTNAME>
<PUBDATE>16 May 2000</PUBDATE>
<COPYRIGHT>
- <YEAR>2000-2014</YEAR>
+ <YEAR>2000-2016</YEAR>
<HOLDER>Genome Research Limited</HOLDER>
</COPYRIGHT>
<LEGALNOTICE>
diff --git a/docs/act_start_chapter.sgml b/docs/act_start_chapter.sgml
index 45b24c1..b41b456 100644
--- a/docs/act_start_chapter.sgml
+++ b/docs/act_start_chapter.sgml
@@ -170,7 +170,7 @@ cd ~/act
<PARA>
<COMMAND>
-java -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/chado-14-interface.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-codec.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ActMain
+java -mx500m -ms100m -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/ibatis/cglib-nodep-2.2.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-codec.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:lib/commons-lang-2.6.jar:lib/commons-net-2.2.jar:. uk.ac.sanger.a [...]
</COMMAND>
</PARA>
</SECT1>
diff --git a/docs/feature_edit.gif b/docs/feature_edit.gif
index a31014b..3b46dab 100644
Binary files a/docs/feature_edit.gif and b/docs/feature_edit.gif differ
diff --git a/docs/jvm_options.sgml b/docs/jvm_options.sgml
index 242ae1f..65dde42 100644
--- a/docs/jvm_options.sgml
+++ b/docs/jvm_options.sgml
@@ -99,6 +99,29 @@ first (top) sequence in ACT:
</SECT2>
]]>
+ <SECT2 ID="JVM-SHOW-SNPS">
+ <TITLE><LITERAL>-Dshow_snps</LITERAL></TITLE>
+ <PARA>
+Show SNP marks in BAM panels.
+</PARA>
+ </SECT2>
+
+ <SECT2 ID="JVM-SHOW-SNPS-PLOT">
+ <TITLE><LITERAL>-Dshow_snp_plot</LITERAL></TITLE>
+ <PARA>
+Automatically open SNP plots for BAM files that are opened.
+</PARA>
+ </SECT2>
+
+
+ <SECT2 ID="JVM-SHOW-COV-PLOT">
+ <TITLE><LITERAL>-Dshow_cov_plot</LITERAL></TITLE>
+ <PARA>
+Automatically open coverage plots for BAM files that are opened.
+</PARA>
+ </SECT2>
+
+
<SECT2 ID="JVM-CHADO">
<TITLE><LITERAL>-Dchado="hostname:port/database?username"</LITERAL></TITLE>
<PARA>
diff --git a/docs/main_window_chapter.sgml b/docs/main_window_chapter.sgml
index b670839..7dc2bee 100644
--- a/docs/main_window_chapter.sgml
+++ b/docs/main_window_chapter.sgml
@@ -265,5 +265,6 @@ menu items which allow the maximum window size to be set.
</PARA>
</SECT1>
+&validator;
&mousebuttons;
</CHAPTER>
diff --git a/docs/manual.sgml b/docs/manual.sgml
index 3ce768f..e356eb7 100644
--- a/docs/manual.sgml
+++ b/docs/manual.sgml
@@ -21,6 +21,7 @@
<!ENTITY views-directedit SYSTEM "views_directedit.sgml">
<!ENTITY featurelist SYSTEM "feature_list.sgml">
<!ENTITY mousebuttons SYSTEM "mousebuttons.sgml">
+<!ENTITY validator SYSTEM "validator.sgml">
<!ENTITY gettingjava SYSTEM "getting_java.sgml">
<!ENTITY unixargs SYSTEM "unix_args.sgml">
<!ENTITY jvmopts SYSTEM "jvm_options.sgml">
@@ -49,7 +50,7 @@
</PRODUCTNAME>
<PUBDATE>22 February 1999</PUBDATE>
<COPYRIGHT>
- <YEAR>1999-2014</YEAR>
+ <YEAR>1999-2016</YEAR>
<HOLDER>Genome Research Limited</HOLDER>
</COPYRIGHT>
<LEGALNOTICE>
diff --git a/docs/menus.sgml b/docs/menus.sgml
index 204540f..21782ec 100644
--- a/docs/menus.sgml
+++ b/docs/menus.sgml
@@ -165,11 +165,22 @@ similar effect to double clicking the middle button on a base or residue (see
<TITLE>Features Overlapping Selection</TITLE>
<PARA>
Select those (and only those) features that overlap the currently selected
-range of bases or any of the currently selected features. The current
+range of bases or any of the currently selected features. The current
selection will be discarded.
</PARA>
</SECT2>
+
+ <SECT2 ID="SELECTMENU-WITHIN-SELECTION">
+ <TITLE>Features Within Selection</TITLE>
+ <PARA>
+Select those (and only those) features that are fully contained by the currently
+selected range of bases or any of the currently selected features. The current
+selection will be discarded.
+ </PARA>
+ </SECT2>
+
+
<SECT2 ID="SELECTMENU-BASE-RANGE">
<TITLE>Base Range ...</TITLE>
<PARA>
@@ -535,6 +546,16 @@ LINKEND="GRAPHS">. Configuration options for graphs are described in <XREF
LINKEND="OPTIONS-PLOTS">.
</PARA>
</SECT2>
+
+<![ %act-only; [
+ <SECT2 ID="VIEWMENU-ADJUST-HEIGHTS">
+ <TITLE>Adjust panel heights ...</TITLE>
+ <PARA>
+Option in ACT for adjusting the panel heights (BAM, VCF, plots, comparisons) by giving
+them different weights in order to distribute the space between each component.
+ </PARA>
+ </SECT2>
+]]>
</SECT1>
<SECT1 ID="GOTOMENU">
@@ -775,9 +796,6 @@ The feature edit window
<IMAGEOBJECT>
<IMAGEDATA FORMAT="gif" FILEREF="feature_edit.gif">
</IMAGEOBJECT>
- <IMAGEOBJECT>
- <IMAGEDATA FORMAT="eps" FILEREF="feature_edit.eps">
- </IMAGEOBJECT>
</MEDIAOBJECT>
</SCREENSHOT>
<PARA>
@@ -839,9 +857,35 @@ LINKEND="GOTOMENU-GOTO-SELECTION-START"> for more).
</LISTITEM>
<LISTITEM>
<PARA>
-The <LITERAL>Select Feature</LITERAL> button selects this feature (in the same
-way as clicking on the feature in one of the views).
+The <LITERAL>User Qualifiers</LITERAL> button opens a tool for maintaining
+user defined lists of qualifiers (i.e. qualifiers in the form tag = value pairs
+on separate lines) and the option to read qualifiers from <ULINK
+URL="http://www.geneontology.org/GO.format.shtml" TYPE="external">OBO</ULINK> formatted files or
+URLs. In the intial screen (see below) you are invited to import your qualifier list from the import
+options in the "File" menu. These lists can be optionally saved between sessions in the file
+'.artemis.qualifiers' in the home directory.
</PARA>
+ <MEDIAOBJECT>
+ <IMAGEOBJECT>
+ <IMAGEDATA FORMAT="gif" FILEREF="qualifier_list.gif">
+ </IMAGEOBJECT>
+ </MEDIAOBJECT>
+
+ <PARA>
+When a qualifier list or OBO file has been added then it is possible to search for
+keywords within a list. The qualifer selected in the drop down list (under the SEARCH button)
+can then be added to the current feature annotation or added to selected features in &prog;.
+If the keywords text field is left blank then all qualifiers are available from the drop
+down list of qualifier values.
+ </PARA>
+
+ <MEDIAOBJECT>
+ <IMAGEOBJECT>
+ <IMAGEDATA FORMAT="gif" FILEREF="qualifier_list2.gif">
+ </IMAGEOBJECT>
+ </MEDIAOBJECT>
+
+
</LISTITEM>
</ITEMIZEDLIST>
</LISTITEM>
diff --git a/docs/qualifier_list.gif b/docs/qualifier_list.gif
new file mode 100644
index 0000000..3bcd2f0
Binary files /dev/null and b/docs/qualifier_list.gif differ
diff --git a/docs/qualifier_list2.gif b/docs/qualifier_list2.gif
new file mode 100644
index 0000000..c963b15
Binary files /dev/null and b/docs/qualifier_list2.gif differ
diff --git a/docs/start_chapter.sgml b/docs/start_chapter.sgml
index 42d645d..ffb0367 100644
--- a/docs/start_chapter.sgml
+++ b/docs/start_chapter.sgml
@@ -66,7 +66,7 @@ cd ~/artemis
<PARA>
<COMMAND>
-java -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/chado-14-interface.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-codec.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ArtemisMain
+java -mx500m -ms100m -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/ibatis/cglib-nodep-2.2.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-codec.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:lib/commons-lang-2.6.jar:lib/commons-net-2.2.jar:. -Dartemis.env [...]
</COMMAND>
</PARA>
</SECT1>
diff --git a/docs/tick.png b/docs/tick.png
new file mode 100644
index 0000000..9bf53b9
Binary files /dev/null and b/docs/tick.png differ
diff --git a/docs/unix_args.sgml b/docs/unix_args.sgml
index 4b996df..68c37c2 100644
--- a/docs/unix_args.sgml
+++ b/docs/unix_args.sgml
@@ -5,14 +5,6 @@ As well as the listing file names on the command line, the following switches
are available to UNIX users:
</PARA>
- <SECT2 ID="UNIXARGS-QUIET">
- <TITLE><LITERAL>-quiet</LITERAL></TITLE>
- <PARA>
-This option tells &prog; to suppress normal informational messages while
-running.
- </PARA>
- </SECT2>
-
<SECT2 ID="UNIXARGS-OPTIONS">
<TITLE><LITERAL>-options</LITERAL></TITLE>
<PARA>
diff --git a/docs/validation_report.png b/docs/validation_report.png
new file mode 100644
index 0000000..ab37907
Binary files /dev/null and b/docs/validation_report.png differ
diff --git a/docs/validator.sgml b/docs/validator.sgml
new file mode 100644
index 0000000..f2a8ff1
--- /dev/null
+++ b/docs/validator.sgml
@@ -0,0 +1,181 @@
+ <SECT1 ID="VALIDATOR">
+ <TITLE>Annotation Validation</TITLE>
+
+<SECT2 ID="VALIDATOR-RUN">
+ <TITLE>How to Run Validation Checks</TITLE>
+ <PARA>
+&prog; can carry out validations checks to try and minimise annotation errors.
+These checks can be carried out in the following ways:
+ </PARA>
+<ORDEREDLIST ID="VALID-CHECK">
+ <LISTITEM ID="VALID-CHECK-1">
+ <PARA>
+Click on the tick button
+
+<inlinemediaobject>
+ <imageobject>
+ <imagedata fileref="tick.png">
+ </imageobject>
+</inlinemediaobject>
+
+found in the top right hand side of Artemis to validate all features. When complete it will
+open a report window highlighting any features which have failed the checks.
+
+ </PARA>
+ </LISTITEM>
+ <LISTITEM ID="VALID-CHECK-2">
+ <PARA>
+Select the features to be checked in &prog; and open the popup menu by right clicking on the feature display
+and selecting the 'Validation report ...' option.
+ </PARA>
+ </LISTITEM>
+
+ <LISTITEM ID="VALID-CHECK-3">
+ <PARA>
+From the View menu, select the 'Feature Filters' menu item and the 'Validation checks...' option. This opens
+a feature list window for each of the type of check it carries out and these contain the features that have
+failed the check.
+ </PARA>
+ </LISTITEM>
+ <LISTITEM ID="VALID-CHECK-4">
+ <PARA>
+For organisms in a chado database the vaidator can be run from the 'Database and File Manager' window from the
+'File' menu by selecting the 'Validate Selected Sequence / Organism' option.
+ </PARA>
+ </LISTITEM>
+</ORDEREDLIST>
+</SECT2>
+
+<SECT2 ID="VALIDATOR-CHECKS-ALL">
+ <TITLE>Validation Checks For All File Types</TITLE>
+ <PARA>
+The following checks are made on all file types (e.g. EMBL, GFF3):
+ </PARA>
+
+<ITEMIZEDLIST SPACING="compact">
+ <LISTITEM>
+ <PARA>
+CDS have no internal stop codon
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+CDS have a valid stop codon
+ </PARA>
+ </LISTITEM>
+</ITEMIZEDLIST>
+
+ <PARA>
+Additionally &prog; checks GO annotation for:
+ </PARA>
+
+<ITEMIZEDLIST SPACING="compact">
+ <LISTITEM>
+ <PARA>
+unexpected white space in with/from and dbxref columns
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+the WITH/FROM field must be empty when using IDA, NAS, ND, TAS or EXP evidence code
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+GO:0005515 can only have IPI evidence code
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+IEP is not allowed for molecular_function and cellular_component terms
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+the WITH/FROM field must be filled when using ISS, ISA, ISO and ISM codes
+ </PARA>
+ </LISTITEM>
+</ITEMIZEDLIST>
+</SECT2>
+
+<SECT2 ID="VALIDATOR-CHECKS-GFF">
+ <TITLE>Validation Checks For GFF3</TITLE>
+
+ <PARA>
+The following are checks for GFF3 and Chado entries only:
+ </PARA>
+
+<ITEMIZEDLIST SPACING="compact">
+ <LISTITEM>
+ <PARA>
+check that the gene model comprises of at least a gene and a transcript feature
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that the boundaries of the features making up a gene model are consistent
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that all the features in a gene model are on the same strand
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that CDS features have a phase
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check the attribute column to ensure that qualifiers have a value (not empty) and
+that only reserved tags start with an uppercase character
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that partial qualifiers are consistent within a gene model
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that the gene name prefix is consistent within a gene model
+ </PARA>
+ </LISTITEM>
+</ITEMIZEDLIST>
+
+</SECT2>
+
+<SECT2 ID="VALIDATOR-REPORT">
+ <TITLE>Validation Report</TITLE>
+
+ <PARA>
+The validation report window displays a summary for the features that have failed one or
+more of the annotation checks above. The title bar of the window displays the number of
+features that have passed and the number that have failed the validation checks. The
+problems identified are highlighted in red.
+ </PARA>
+
+ <PARA>
+<MEDIAOBJECT>
+ <IMAGEOBJECT>
+ <IMAGEDATA FORMAT="png" FILEREF="validation_report.png"></IMAGEOBJECT>
+ </MEDIAOBJECT>
+ </PARA>
+
+ <PARA>
+Some of the errors can be fixed automatically. The 'Auto-Fix' button opens a window
+with the fixes enabled that are available for the entry type that is loaded in &prog;. For example, it will
+attempt to fix CDS features that have been found not to end in stop codons. If the last codon is not a
+stop codon, but the very next codon is a stop codon, then the end of the feature is
+extended by three bases.
+ </PARA>
+ <PARA>
+For GFF3 and chado entries &prog; will also attempt to fix problems it finds with gene
+boundaries and if a phase is absent then a default phase of 0 is given. Once these are
+fixed the results window will automatically update and remove the problems it has
+managed to resolved.
+ </PARA>
+</SECT2>
+
+ </SECT1>
diff --git a/etc/feature_keys_gff b/etc/feature_keys_gff
index 9f0b36a..afb9f56 100644
--- a/etc/feature_keys_gff
+++ b/etc/feature_keys_gff
@@ -10,12 +10,12 @@ region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ont
contig ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score comment
#supercontig ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score
#chromosome ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified note comment description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score
-gene ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private
+gene ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private comment
#CDS ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified codon_start description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score results note comment job
polypeptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref product molecule_type size organism_name strain topology localization gff_source gff_seqname score mass isoelectric charge source private signal_peptide membrane_structure cytoplasmic_polypeptide_region non_cytoplasmic_polypeptide_region transmembrane_polypeptide_regio [...]
pseudogene ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private
-pseudogenic_exon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private
-pseudogenic_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score product
+pseudogenic_exon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private
+pseudogenic_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score product
intron ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score
exon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified codon_start description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score
three_prime_UTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified systematic_id note comment private curation
diff --git a/etc/key_mapping b/etc/key_mapping
index 31afa98..3a7f179 100644
--- a/etc/key_mapping
+++ b/etc/key_mapping
@@ -21,6 +21,9 @@ direct_repeat repeat_region rpt_type=direct
polypeptide_domain misc_feature
centromere misc_feature note=centromere
modified_amino_acid_feature misc_feature note=modified_amino_acid_feature
-snRNA ncRNA ncRNA_class="snRNA"
-snoRNA ncRNA ncRNA_class="snoRNA"
+snRNA ncRNA ncRNA_class=snRNA
+snoRNA ncRNA ncRNA_class=snoRNA
nucleotide_match misc_feature note=nucleotide_match
+uORF misc_feature note=uORF
+sORF misc_feature note=sORF
+tnaORF misc_feature note=tnaORF
diff --git a/etc/options b/etc/options
index 1987d3f..b1d8988 100644
--- a/etc/options
+++ b/etc/options
@@ -148,7 +148,7 @@ start_codons_4 = atg
translation_table_5 = \
agas aggs atam tgaw
-start_codons_5 = atg ata att
+start_codons_5 = ttg att atc ata atg gtg
#start_codons_5_apis = atg ata atc att
#start_codons_5_polyplacophora = atg ata gtg
@@ -423,7 +423,7 @@ extra_keys = \
TMM signalP
# this list is added to the keys from the feature_keys_gff file
-extra_keys_gff = CDS spliced_leader_RNA sequence_variant fasta_record
+extra_keys_gff = CDS uORF sORF tnaORF spliced_leader_RNA sequence_variant fasta_record
# Names of qualifiers to search when attempting to find the primary or display
# name of a gene. These qualifiers names are searched in order when looking
@@ -439,6 +439,7 @@ systematic_name_qualifiers = systematic_id temporary_systematic_id \
# this list is added to the qualifiers from the qualifier_types file
extra_qualifiers = \
+ alias "text" \
CHROMO_LINK text \
C_processing "text" \
C_processing_BigPi "text" \
@@ -569,6 +570,7 @@ extra_qualifiers = \
# this list is added to the qualifiers from the qualifier_types_gff file
extra_qualifiers_gff = \
+ alias "text" \
blast_score text \
blast_file "text" \
blastn_file "text" \
@@ -830,7 +832,8 @@ common_keys = \
BLASTN_HIT BLASTCDS 3'UTR 5'UTR
# SRS
-srs_url = http://srs.ebi.ac.uk/srsbin/cgi-bin/
+#srs_url = http://srs.ebi.ac.uk/srsbin/cgi-bin/
+srs_url = http://www.bioinformatics.nl/srsbin/cgi-bin/
# hyperlinked databases in feature editor
hyperlinks = \
@@ -854,13 +857,14 @@ hyperlinks = \
AID http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid= \
GeneID http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids= \
Rfam http://rfam.sanger.ac.uk/family/ \
- GI http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi?val=
+ GI http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi?val= \
+ TCDB http://www.tcdb.org/search/result.php?tc=
# BamView
# No. threads used to read from multiple BAM files
bam_read_thread = 2
# Max read coverage to display
-bam_max_coverage = 10000
+bam_max_coverage = 1000000
#
# CHADO DATABASE OPTIONS
diff --git a/etc/project.properties b/etc/project.properties
index df33aa8..164f202 100644
--- a/etc/project.properties
+++ b/etc/project.properties
@@ -1,10 +1,10 @@
-project.Styphi.sequence=ftp://ftp.sanger.ac.uk/pub/pathogens/Salmonella/typhi/St.dna
-project.Styphi.annotation=ftp://ftp.sanger.ac.uk/pub/pathogens/Salmonella/typhi/St.art
+project.Styphi.sequence=ftp://ftp.sanger.ac.uk/pub/project/pathogens/Salmonella/typhi/St.dna
+project.Styphi.annotation=ftp://ftp.sanger.ac.uk/pub/project/pathogens/Salmonella/typhi/St.art
project.Styphi.title=Styphi
#
-project.PF3D7.sequence = ftp://ftp.sanger.ac.uk/pub4/pathogens/Plasmodium/falciparum/3D7/3D7.latest_version/September_2011/Pf3D7_01.embl.gz
+project.PF3D7.sequence = ftp://ftp.sanger.ac.uk/pub/project/pathogens/Plasmodium/falciparum/3D7/3D7.latest_version/September_2011/Pf3D7_01.embl.gz
project.PF3D7.bam = \
http://www.genedb.org/artemis/NAR/Malaria_RNASeq/version2.1.4/MAL_0h.bam \
http://www.genedb.org/artemis/NAR/Malaria_RNASeq/version2.1.4/MAL_8h.bam \
diff --git a/etc/qualifier_types b/etc/qualifier_types
index 7dfd32a..763de70 100644
--- a/etc/qualifier_types
+++ b/etc/qualifier_types
@@ -73,8 +73,8 @@ map no "text"
mating_type yes "text"
mobile_element_type no "text"
mod_base yes list OTHER ac4c chm5u cm cmnm5s2u cmnm5u d fm gal q gm i i6a m1a m1f m1g m1i m22g m2a m2g m3c m5c m6a m7g mam5s2u mam5u man q mcm5s2u mcm5u mo5u ms2i6a ms2t6a mt6a mv o5u osyw p q s2c s2t s2u s4u t t6a tm um x yw
-mol_type yes "list" "unassigned DNA" "unassigned RNA" "genomic DNA" "genomic RNA" "mRNA" "tRNA" "rRNA" "transcribed RNA" "other RNA" "other DNA" "protein" "viral cRNA"
-ncRNA_class yes list "antisense_RNA" "autocatalytically_spliced_intron" "hammerhead_ribozyme" "RNase_P_RNA" "RNase_MRP_RNA" "telomerase_RNA" "guide_RNA" "rasiRNA" "scRNA" "siRNA" "miRNA" "piRNA" "snoRNA" "snRNA" "SRP_RNA" "vault_RNA" "Y_RNA" "other" "ribozyme"
+mol_type yes "list" "unassigned DNA" "unassigned RNA" "genomic DNA" "genomic RNA" "mRNA" "tRNA" "rRNA" "transcribed RNA" "other RNA" "other DNA" "protein" "viral cRNA"
+ncRNA_class yes "list" "antisense_RNA" "autocatalytically_spliced_intron" "hammerhead_ribozyme" "RNase_P_RNA" "RNase_MRP_RNA" "telomerase_RNA" "guide_RNA" "rasiRNA" "scRNA" "siRNA" "miRNA" "piRNA" "snoRNA" "snRNA" "SRP_RNA" "vault_RNA" "Y_RNA" "other" "ribozyme"
note no "text"
number yes number 1 99999999
old_locus_tag no "text"
diff --git a/etc/results_to_netscape b/etc/results_to_netscape
index f313d38..1b97f7e 100755
--- a/etc/results_to_netscape
+++ b/etc/results_to_netscape
@@ -26,6 +26,9 @@ else
done
fi
+if [ ! -f "$NETSCAPE" ]; then
+ NETSCAPE=`which firefox`
+fi
if [ -f "$DIANA_ENVIRONMENT_FILE" ]
then
@@ -93,9 +96,10 @@ BEGIN {
$DNA_DATABASES = "embl";
# change this to point to the wgetz script of your SRS server
- $SRS_SERVER = "www.sanger.ac.uk/srs6bin/cgi-bin/wgetz?-e+";
- $SRS_SERVER = "srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+";
-
+ #$SRS_SERVER = "www.sanger.ac.uk/srs6bin/cgi-bin/wgetz?-e+";
+ #$SRS_SERVER = "srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+";
+ $SRS_SERVER = "www.bioinformatics.nl/srsbin/cgi-bin/wgetz?-e+";
+
$PROTEIN_DATABASES =~ s/ /%20/g;
$DNA_DATABASES =~ s/ /%20/g;
@@ -140,8 +144,9 @@ sub hyperlink_id
}
# Text Entry
- $r = qq#<a href="http://$SRS_SERVER-id+1+\[\{$PROTEIN_DATABASES\}-ID:$id*]|[\{$PROTEIN_DATABASES\}-AccNumber:$id*]+-vn+2">$id</a>#;
-
+ $r = qq#<a href="http://www.uniprot.org/uniprot/$id">$id</a>#;
+
+ #$r = qq#<a href="http://$SRS_SERVER-id+1+\[\{$PROTEIN_DATABASES\}-ID:$id*]|[\{$PROTEIN_DATABASES\}-AccNumber:$id*]+-vn+2">$id</a>#;
#$r = qq#<a href="http://$SRS_SERVER-id+1+\[\{$PROTEIN_DATABASES\}-ID:$id*]|[\{$PROTEIN_DATABASES\}-AccNumber:$id*]">$id</a>#;
}
return $r
diff --git a/etc/versions b/etc/versions
index 8ed02d7..10e531f 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 16.0.0
-ACT Release 13.0.0
+Artemis Release 16.0.17
+ACT Release 13.0.16
DNAPlotter Release 1.11
-BamView 1.2.10
\ No newline at end of file
+BamView 1.2.13
diff --git a/etc/writedb_entry b/etc/writedb_entry
index d747fc4..6fbfcb6 100755
--- a/etc/writedb_entry
+++ b/etc/writedb_entry
@@ -1,6 +1,6 @@
#!/bin/sh -
-#
-# This script reads and writes entries from a database.
+#
+# This script reads and writes entries from a database.
# Examples:
# writedb_entry -help
# writedb_entry -s Pf3D7_01 Pf3D7_05 Pf3D7_07
@@ -28,6 +28,7 @@ done
ARTEMIS_HOME=`dirname "$PRG"`/..
CLASSPATH="$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/macos.jar:$ARTEMIS_HOME/lib/postgresql-8.4-701.jdbc3.jar:$ARTEMIS_HOME/lib/chado-14-interface.jar:$CLASSPATH"
+CLASSPATH="$ARTEMIS_HOME/lib/commons-lang-2.6.jar:$CLASSPATH"
# iBatis jars
CLASSPATH="$CLASSPATH:$ARTEMIS_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ARTEMIS_HOME/lib/ibatis/:$ARTEMIS_HOME/lib/ibatis/log4j-1.2.14.jar:$ARTEMIS_HOME/lib/ibatis/cglib-nodep-2.2.jar:$ARTEMIS_HOME/lib/retrotranslator-runtime-1.1.0.jar"
@@ -42,7 +43,7 @@ while test $# != 0
case $1 in
-Dchado*)
DEFAULT_CONNECTION="$1" ;;
- -D*)
+ -D*)
FLAGS="$FLAGS $1" ;;
*) break ;;
esac
@@ -55,7 +56,7 @@ for arg in "$@"
do
if [ '-c' == "${arg}" ]; then
let "nextID = $idx + 1";
- DEFAULT_CONNECTION="-Dchado=${!nextID}"
+ DEFAULT_CONNECTION="-Dchado=${!nextID}"
fi
if [ '-l' == "${arg}" ]; then
let "nextID = $idx + 2";
diff --git a/gff2embl b/gff2embl
new file mode 100755
index 0000000..6052ebd
--- /dev/null
+++ b/gff2embl
@@ -0,0 +1,106 @@
+#!/bin/sh -
+
+# Command line utility for coverting GFF to EMBL
+PRG=$0
+progname=`basename $0`
+
+ARTEMIS_HOME=`dirname "$PRG"`/.
+
+CLASSPATH=$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/macos.jar:$ARTEMIS_HOME/lib/postgresql-8.4-701.jdbc3.jar:$ARTEMIS_HOME/lib/chado-14-interface.jar:$CLASSPATH
+
+# j2ssh jars
+CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/j2ssh/commons-logging.jar:$ARTEMIS_HOME/lib/j2ssh/j2ssh-core.jar:$ARTEMIS_HOME/lib/j2ssh/
+
+# iBatis jars
+CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ARTEMIS_HOME/lib/ibatis/:$ARTEMIS_HOME/lib/ibatis/log4j-1.2.14.jar:$ARTEMIS_HOME/lib/ibatis/cglib-nodep-2.2.jar:$ARTEMIS_HOME/lib/retrotranslator-runtime-1.1.0.jar
+export CLASSPATH
+
+# batik jars
+CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/batik/batik-awt-util.jar:$ARTEMIS_HOME/lib/batik/batik-dom.jar:$ARTEMIS_HOME/lib/batik/batik-ext.jar:$ARTEMIS_HOME/lib/batik/batik-svggen.jar:$ARTEMIS_HOME/lib/batik/batik-util.jar:$ARTEMIS_HOME/lib/batik/batik-xml.jar
+
+# picard jars
+CLASSPATH=$ARTEMIS_HOME/lib/picard/sam.jar:$ARTEMIS_HOME/lib/picard/picard.jar:$ARTEMIS_HOME/lib/commons-net-2.2.jar:$CLASSPATH
+CLASSPATH="$ARTEMIS_HOME/lib/commons-lang-2.6.jar:$CLASSPATH"
+export CLASSPATH
+
+if [ $# = 0 ]
+then
+ :
+else
+ if [ "$1" = "-h" -o "$1" = "--help" -o "$1" = "-help" ]
+ then
+ cat <<EOF
+
+SYNOPSIS
+ gff2embl
+USAGE
+ $0 [options] <SEQUENCE_FILE>
+OPTIONS
+ SEQUENCE_FILE A GFF3 file
+
+ -s FILE space separated list of GFF files to read and write out
+ -o OUTPUT_DIR output directory
+ -f [y/n] flatten the gene model, default is y
+ -z gzip output, default is y
+ -a [y|n] for EMBL submission format change to n, default is y
+EXAMPLES
+ % -s /Users/tjc/test.gff -o /Users/tjc
+HOMEPAGE
+ http://www.sanger.ac.uk/resources/software/artemis/
+EOF
+ exit 0
+ fi
+fi
+
+ARTEMIS_PROPERTIES="-Dartemis.environment=UNIX"
+
+# Allow URLs to work from behind firewalls
+if [ "$http_proxy" = "" ]
+then
+ http_proxy=$HTTP_PROXY
+fi
+
+if [ "$http_proxy" = "" ]
+then
+ http_proxy=$HTTP_proxy
+fi
+
+if [ "$http_proxy" != "" ]
+then
+ ARTEMIS_PROPERTIES="$ARTEMIS_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
+fi
+
+
+# "-mx500m" sets the maximum amount of memory that Artemis can use. This may
+# need to be increased when dealing with large files
+MEM="-mx500m -ms20m"
+
+if [ "$JVM_FLAGS" = "" ]
+then
+ FLAGS="$MEM -noverify"
+else
+ FLAGS="$MEM -noverify $JVM_FLAGS"
+fi
+
+
+FLAGS=$FAST_FLAG$FLAGS
+
+if [ "$JAVA_VM" = "" ]
+then
+ if [ "$DEBUG" = yes ]
+ then
+ JAVA=java_g
+ else
+ JAVA=java
+ fi
+else
+ JAVA=$JAVA_VM
+fi
+
+PLATTMP=`uname`
+if [ "$PLATTMP" = "Darwin" ]
+then
+ FLAGS="$FLAGS -Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=Circular Plot"
+fi
+
+$JAVA $MEM uk.ac.sanger.artemis.io.GffToEMBL $*
diff --git a/install_dependencies.sh b/install_dependencies.sh
new file mode 100644
index 0000000..44a15c4
--- /dev/null
+++ b/install_dependencies.sh
@@ -0,0 +1,57 @@
+#!/bin/bash
+
+set -x
+set -e
+
+start_dir=$(pwd)
+
+EMBOSS_VERSION="6.5.7"
+
+EMBOSS_DOWNLOAD_URL="ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-${EMBOSS_VERSION}.tar.gz"
+
+# Make an install location
+if [ ! -d "${HOME}/dependencies" ]; then
+ mkdir ${HOME}/dependencies
+fi
+cd ${HOME}/dependencies
+build_dir=$(pwd)
+
+# DOWNLOAD ALL THE THINGS
+download () {
+ url=$1
+ download_location=$2
+
+ if [ -e $download_location ]; then
+ echo "Skipping download of $url, $download_location already exists"
+ else
+ echo "Downloading $url to $download_location"
+ wget $url -O $download_location
+ fi
+}
+
+download $EMBOSS_DOWNLOAD_URL "${build_dir}/emboss-${EMBOSS_VERSION}.tgz"
+
+# Build all the things
+cd $build_dir
+
+## Emboss
+emboss_dir=$(pwd)/EMBOSS-${EMBOSS_VERSION}
+if [ ! -d $emboss_dir ]; then
+ tar xzf emboss-${EMBOSS_VERSION}.tgz
+fi
+cd $emboss_dir
+if [ -e "${emboss_dir}/build/bin/restrict" ]; then
+ echo "Already built Emboss; skipping build"
+else
+ mkdir build
+ ./configure --prefix ${emboss_dir}/build
+ make
+ make install
+fi
+
+export EMBOSS_ROOT=${emboss_dir}/build
+
+cd $start_dir
+
+set +x
+set +e
diff --git a/test/data/MAL_8h.bam b/test/data/MAL_8h.bam
new file mode 100644
index 0000000..71e8e51
Binary files /dev/null and b/test/data/MAL_8h.bam differ
diff --git a/test/data/MAL_8h.bam.bai b/test/data/MAL_8h.bam.bai
new file mode 100644
index 0000000..146643c
Binary files /dev/null and b/test/data/MAL_8h.bam.bai differ
diff --git a/test/uk/ac/sanger/artemis/components/alignment/MappedReadsTest.java b/test/uk/ac/sanger/artemis/components/alignment/MappedReadsTest.java
new file mode 100644
index 0000000..0c12be4
--- /dev/null
+++ b/test/uk/ac/sanger/artemis/components/alignment/MappedReadsTest.java
@@ -0,0 +1,143 @@
+/*
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2014 Genome Research Limited
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.components.alignment;
+
+import static org.junit.Assert.assertTrue;
+
+import java.awt.GraphicsEnvironment;
+import java.net.URL;
+import java.util.Hashtable;
+import java.util.List;
+
+import javax.swing.JFrame;
+
+import junit.framework.Assert;
+import uk.ac.sanger.artemis.io.Utils;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.components.EntryEdit;
+import uk.ac.sanger.artemis.components.alignment.BamUtils;
+import uk.ac.sanger.artemis.components.alignment.BamView;
+import uk.ac.sanger.artemis.components.alignment.MappedReads;
+import uk.ac.sanger.artemis.components.alignment.ReadCount;
+
+public class MappedReadsTest
+{
+ private static BamView bv;
+ private static FeatureVector fv;
+
+ @BeforeClass
+ public static void setUp()
+ {
+ // ignore if in headless mode with no x11
+ if(GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadless())
+ return;
+ URL entryFile = MappedReadsTest.class.getResource("/data/MAL_8h.bam");
+ System.setProperty("bam", entryFile.getFile());
+ final EntryGroup egrp = Utils.getEntryGroup("/data/MAL1.embl.gz");
+ final EntryEdit ee = new EntryEdit(egrp);
+ ee.setVisible(true);
+
+ while( (bv = ee.getJamView()) == null)
+ {
+ // wait for BamView to be constructed
+ try {
+ Thread.sleep(100);
+ } catch(Exception e){};
+ }
+
+ // get a gene feature
+ fv = new FeatureVector();
+ final FeatureVector features = egrp.getAllFeatures();
+ for(int i=0; i<features.size(); i++)
+ {
+ Feature f = features.elementAt(i);
+ if(f.getSystematicName().equals("PFA0110w"))
+ fv.add(f);
+ }
+ }
+
+ @Test
+ /**
+ * Test the read count for a gene
+ */
+ public void readCounts()
+ {
+ // ignore if in headless mode with no x11
+ if(GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadless())
+ return;
+
+ final Hashtable<String, List<ReadCount>> featureReadCount =
+ BamUtils.calculateMappedReads(bv, fv, false, true, false, null, null);
+ final List<ReadCount> cnts = featureReadCount.get("PFA0110w");
+
+ ReadCount c = cnts.get(0);
+ assertTrue(1495.f == c.senseCnt);
+ assertTrue(998.f == c.antiCnt);
+ }
+
+ @Test
+ /**
+ * Read count for a gene excluding the intron
+ */
+ public void readCountsExcludeIntron()
+ {
+ // ignore if in headless mode with no x11
+ if(GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadless())
+ return;
+
+ final Hashtable<String, List<ReadCount>> featureReadCount =
+ BamUtils.calculateMappedReads(bv, fv, false, false, false, null, null);
+ final List<ReadCount> cnts = featureReadCount.get("PFA0110w");
+
+ ReadCount c = cnts.get(0);
+ assertTrue(1494.f == c.senseCnt);
+ assertTrue(997.f == c.antiCnt);
+ }
+
+ @Test
+ /**
+ * Tes the read count for a gene not including those in the intron
+ */
+ public void rpkm()
+ {
+ // ignore if in headless mode with no x11
+ if(GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadless())
+ return;
+
+ String refName = (String) bv.getCombo().getSelectedItem();
+ int thisLength = bv.getSeqLengths().get(refName);
+ int mappedReads[] = BamUtils.calc(bv, refName, thisLength,
+ false, null);
+
+ Hashtable<String, List<ReadCount>> featureReadCount =
+ BamUtils.calculateMappedReads(bv, fv, false, true, false, mappedReads, null);
+ final List<ReadCount> cnts = featureReadCount.get("PFA0110w");
+
+ ReadCount c = cnts.get(0);
+ assertTrue(183768.719f == c.senseCnt);
+ assertTrue(122676.375f == c.antiCnt);
+ }
+}
diff --git a/test/uk/ac/sanger/artemis/io/GFF3AttributeBuilderTest.java b/test/uk/ac/sanger/artemis/io/GFF3AttributeBuilderTest.java
new file mode 100644
index 0000000..e65c526
--- /dev/null
+++ b/test/uk/ac/sanger/artemis/io/GFF3AttributeBuilderTest.java
@@ -0,0 +1,295 @@
+/*
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2014 Genome Research Limited
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.io;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertEquals;
+import junit.framework.Assert;
+
+import org.junit.Test;
+import org.junit.Before;
+
+import uk.ac.sanger.artemis.io.GFF3AttributeAggregator;
+import uk.ac.sanger.artemis.io.GFF3AttributeBuilder;
+import uk.ac.sanger.artemis.io.GFF3Encoder;
+import uk.ac.sanger.artemis.util.StringVector;
+
+public class GFF3AttributeBuilderTest {
+ private GFF3Encoder enc;
+ private String[] invals = { "foo", "bar" };
+ private String[] invalsC = { "foo,bar", "baz,quux" };
+ private static GFF3AttributeAggregator testProc;
+
+ @Before
+ public void setUp() {
+ enc = new GFF3Encoder();
+ testProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ buffer.append(">>"
+ + GFF3Encoder.encode(values.elementAt(value_index)) + "<<");
+ if (value_index < (values.size()) - 1)
+ buffer.append("|");
+ }
+ }
+ return buffer.toString();
+ }
+ };
+ }
+
+ @Test
+ /**
+ * Tests adding one attribute.
+ */
+ public void testAdd1() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "attr1=foo,bar");
+ }
+
+ @Test
+ /**
+ * Tests adding two different attributes.
+ */
+ public void testAdd2() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.add("attr1", in);
+ ab.add("attr2", in);
+ assertEquals(ab.toString(), "attr1=foo,bar;attr2=foo,bar");
+ }
+
+ @Test
+ /**
+ * Tests adding attributes with custom aggregators.
+ */
+ public void testAddWithAggs() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+ ab.setAggregator("attr1", testProc);
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "attr1=>>foo<<|>>bar<<");
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "attr1=>>foo<<|>>bar<< >>foo<<|>>bar<<");
+ }
+
+ @Test
+ /**
+ * Tests adding attributes (encoded values) with custom aggregators.
+ */
+ public void testAddWithAggsCommas() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invalsC);
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "attr1=foo%2Cbar,baz%2Cquux");
+ ab.add("attr1", in);
+ assertEquals(ab.toString(),
+ "attr1=foo%2Cbar,baz%2Cquux foo%2Cbar,baz%2Cquux");
+ ab = new GFF3AttributeBuilder();
+ ab.setAggregator("attr1", testProc);
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "attr1=>>foo%2Cbar<<|>>baz%2Cquux<<");
+ ab.add("attr1", in);
+ assertEquals(ab.toString(),
+ "attr1=>>foo%2Cbar<<|>>baz%2Cquux<< >>foo%2Cbar<<|>>baz%2Cquux<<");
+ }
+
+ @Test
+ /**
+ * Tests the ignoring of attribute fields in the output.
+ */
+ public void testIgnore() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.ignore("attr1");
+ ab.add("attr1", in);
+ ab.add("attr2", in);
+ assertEquals(ab.toString(), "attr2=foo,bar");
+ ab.unignore("attr1");
+ assertEquals(ab.toString(), "attr1=foo,bar;attr2=foo,bar");
+ }
+
+ @Test
+ /**
+ * Tests the handling of duplicate attributes.
+ */
+ public void testAddMultiAttr() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.add("attr1", in);
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "attr1=foo,bar foo,bar");
+ }
+
+ @Test
+ /**
+ * Tests the handling of duplicate attributes, with delimiter.
+ */
+ public void testAddMultiAttrWithGlue() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.setGlue("attr1", "X");
+ ab.add("attr1", in);
+ ab.add("attr1", in);
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "attr1=foo,barXfoo,barXfoo,bar");
+ }
+
+ @Test
+ /**
+ * Tests cloning of attributes to separate keys with default aggregator.
+ */
+ public void testClone() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.setClone("attr1", "brand_new");
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "attr1=foo,bar;brand_new=foo,bar");
+ ab.add("brand_new", in);
+ assertEquals(ab.toString(), "attr1=foo,bar;brand_new=foo,bar foo,bar");
+ }
+
+ @Test
+ /**
+ * Tests cloning of attributes to separate keys with different aggregators.
+ */
+ public void testCloneWithAggs() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+ ab.setClone("attr1", "brand_new");
+ ab.setAggregator("brand_new", testProc);
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "attr1=foo,bar;brand_new=>>foo<<|>>bar<<");
+ ab.add("attr1", in);
+ assertEquals(ab.toString(),
+ "attr1=foo,bar foo,bar;brand_new=>>foo<<|>>bar<< >>foo<<|>>bar<<");
+ }
+
+ @Test
+ /**
+ * Tests mapping/cloning of attributes to separate keys with different aggregators.
+ */
+ public void testMappingAndCloneWithAggs1() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.setMapping("attr1", "aaaa");
+ ab.setClone("aaaa", "brand_new");
+ ab.setAggregator("brand_new", testProc);
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "aaaa=foo,bar;brand_new=>>foo<<|>>bar<<");
+ ab.add("attr1", in);
+ assertEquals(ab.toString(),
+ "aaaa=foo,bar foo,bar;brand_new=>>foo<<|>>bar<< >>foo<<|>>bar<<");
+ }
+
+ @Test
+ /**
+ * Tests mapping/cloning of attributes to separate keys with different aggregators.
+ */
+ public void testMappingAndCloneWithAggs2() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.setMapping("attr1", "aaaa");
+ ab.setClone("attr1", "brand_new");
+ ab.setAggregator("brand_new", testProc);
+ ab.add("attr1", in);
+ assertEquals(ab.toString(), "aaaa=foo,bar;brand_new=>>foo<<|>>bar<<");
+ ab.add("attr1", in);
+ assertEquals(ab.toString(),
+ "aaaa=foo,bar foo,bar;brand_new=>>foo<<|>>bar<< >>foo<<|>>bar<<");
+ }
+
+ @Test
+ /**
+ * Tests mapping one attribute to a new name.
+ */
+ public void testMapping() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.setMapping("attr1", "brand_new");
+ ab.add("attr1", in);
+ ab.add("attr2", in);
+ assertEquals(ab.toString(), "attr2=foo,bar;brand_new=foo,bar");
+ }
+
+ @Test
+ /**
+ * Tests mapping one attribute to a new name with custom target aggregator.
+ */
+ public void testMappingWithAggs() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+ ab.setMapping("attr1", "brand_new");
+ ab.setAggregator("brand_new", testProc);
+ ab.add("attr1", in);
+ ab.add("attr2", in);
+ assertEquals(ab.toString(), "attr2=foo,bar;brand_new=>>foo<<|>>bar<<");
+ }
+
+ @Test
+ /**
+ * Tests mapping one attribute to a new name with custom target aggregator.
+ */
+ public void testMappingCollision() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.setMapping("attr1", "attr2");
+ ab.add("attr1", in);
+ ab.add("attr2", in);
+ assertEquals(ab.toString(), "attr2=foo,bar foo,bar");
+ }
+
+ @Test
+ /**
+ * Tests mapping one attribute to a new name with custom target aggregator.
+ */
+ public void testMappingCollisionWithAggs() {
+ GFF3AttributeBuilder ab = new GFF3AttributeBuilder();
+ StringVector in = new StringVector(invals);
+
+ ab.setMapping("attr1", "attr2");
+ ab.setAggregator("attr2", testProc);
+ ab.add("attr1", in);
+ ab.add("attr2", in);
+ assertEquals(ab.toString(), "attr2=>>foo<<|>>bar<< >>foo<<|>>bar<<");
+ ab = new GFF3AttributeBuilder();
+ ab.setMapping("attr1", "attr2");
+ ab.setAggregator("attr1", testProc);
+ ab.add("attr1", in);
+ ab.add("attr2", in);
+ assertEquals(ab.toString(), "attr2=>>foo<<|>>bar<< foo,bar");
+ }
+}
diff --git a/test/uk/ac/sanger/artemis/io/GFF3EncoderTest.java b/test/uk/ac/sanger/artemis/io/GFF3EncoderTest.java
new file mode 100644
index 0000000..56f8a5a
--- /dev/null
+++ b/test/uk/ac/sanger/artemis/io/GFF3EncoderTest.java
@@ -0,0 +1,102 @@
+/*
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2014 Genome Research Limited
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.io;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertEquals;
+import junit.framework.Assert;
+
+import org.junit.Test;
+import org.junit.Before;
+
+import uk.ac.sanger.artemis.io.GFF3Encoder;
+
+public class GFF3EncoderTest {
+ private GFF3Encoder enc;
+
+ @Before
+ public void setUp() {
+ enc = new GFF3Encoder();
+ }
+
+ @Test
+ /**
+ * Tests whether there are missing map characters.
+ */
+ public void testMapEqualLength() {
+ assertEquals(GFF3Encoder.mapChars.length, GFF3Encoder.mappedEscapes.length);
+ }
+
+ @Test
+ /**
+ * Tests whether the mapping is correct according to GFF3 spec.
+ */
+ public void testMapChars() {
+ assertEquals(enc.encode("%"), "%25");
+ assertEquals(enc.decode("%25"), "%");
+ assertEquals(enc.encode("&"), "%26");
+ assertEquals(enc.decode("%26"), "&");
+ assertEquals(enc.encode(","), "%2C");
+ assertEquals(enc.decode("%2C"), ",");
+ assertEquals(enc.encode(";"), "%3B");
+ assertEquals(enc.decode("%3B"), ";");
+ assertEquals(enc.encode("="), "%3D");
+ assertEquals(enc.decode("%3D"), "=");
+ assertEquals(enc.encode("\t"), "%09");
+ assertEquals(enc.decode("%09"), "\t");
+ assertEquals(enc.encode("\n"), "%0A");
+ assertEquals(enc.decode("%0A"), "\n");
+ assertEquals(enc.encode("\r"), "%0D");
+ assertEquals(enc.decode("%0D"), "\r");
+ }
+
+ @Test
+ /**
+ * Tests the decoding of escaped characters in GFF files.
+ */
+ public void testDecode() {
+ for (int i=0; i < GFF3Encoder.mappedEscapes.length; i++) {
+ assertEquals(enc.decode("test"+GFF3Encoder.mappedEscapes[i]+"foo"),
+ "test"+GFF3Encoder.mapChars[i]+"foo");
+ assertEquals(enc.decode("test%"+GFF3Encoder.mappedEscapes[i]+"foo"),
+ "test%"+GFF3Encoder.mapChars[i]+"foo");
+ assertEquals(enc.decode("test1"+GFF3Encoder.mappedEscapes[i]+"foo," +
+ "test2"+GFF3Encoder.mappedEscapes[i]),
+ "test1"+GFF3Encoder.mapChars[i]+"foo," +
+ "test2"+GFF3Encoder.mapChars[i]);
+ }
+ }
+
+ @Test
+ /**
+ * Tests the encoding of escaped characters in GFF files.
+ */
+ public void testEncode() {
+ for (int i=0; i < GFF3Encoder.mappedEscapes.length; i++) {
+ assertEquals(enc.encode("test"+GFF3Encoder.mapChars[i]+"foo"),
+ "test"+GFF3Encoder.mappedEscapes[i]+"foo");
+ assertEquals(enc.encode("test%"+GFF3Encoder.mapChars[i]+"foo"),
+ "test%25"+GFF3Encoder.mappedEscapes[i]+"foo");
+ }
+ }
+
+}
diff --git a/uk/ac/sanger/artemis/AlignMatchVector.java b/uk/ac/sanger/artemis/AlignMatchVector.java
index 86dc474..646e82e 100644
--- a/uk/ac/sanger/artemis/AlignMatchVector.java
+++ b/uk/ac/sanger/artemis/AlignMatchVector.java
@@ -3,19 +3,19 @@
* created: Sat Jun 17 2000
*
* This file is part of Artemis
- *
+ *
* Copyright (C) 2000,2001 Genome Research Limited
- *
+ *
* 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 2
* 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, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -51,7 +51,7 @@ public class AlignMatchVector {
public void addElement (AlignMatch item) {
vector.add (item);
}
-
+
/**
* Appends the given AlignMatch object to the vector if and only if it
* isn't already in the vector. (same as addElement ()).
@@ -59,7 +59,7 @@ public class AlignMatchVector {
public void add (AlignMatch item) {
addElement (item);
}
-
+
/**
* Performs the same function as Vector.elementAt ()
**/
@@ -101,13 +101,13 @@ public class AlignMatchVector {
public int size () {
return vector.size ();
}
-
+
/**
* Sort this vector.
* @param cmp The returned vector will be sorted with this Comparator.
**/
public void sort (final Comparator cmp) {
- vector = vector.sort (cmp);
+ vector = vector.mysort (cmp);
}
/**
diff --git a/uk/ac/sanger/artemis/FeatureVector.java b/uk/ac/sanger/artemis/FeatureVector.java
index 4f1c4c6..a0623aa 100644
--- a/uk/ac/sanger/artemis/FeatureVector.java
+++ b/uk/ac/sanger/artemis/FeatureVector.java
@@ -154,7 +154,7 @@ public class FeatureVector {
public FeatureVector sort (final Comparator cmp) {
final FeatureVector return_vector = (FeatureVector) clone ();
- return_vector.vector = return_vector.vector.sort (cmp);
+ return_vector.vector = return_vector.vector.mysort (cmp);
return return_vector;
}
diff --git a/uk/ac/sanger/artemis/chado/ArtemisUtils.java b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
index f0eea5f..277a787 100644
--- a/uk/ac/sanger/artemis/chado/ArtemisUtils.java
+++ b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
@@ -47,6 +47,7 @@ import org.gmod.schema.sequence.FeatureProp;
import org.gmod.schema.sequence.FeatureRelationship;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
+import uk.ac.sanger.artemis.io.GFF3Encoder;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.util.StringVector;
@@ -262,7 +263,7 @@ public class ArtemisUtils
if(this_fcp.getValue().equals(fcp.getValue()))
return true;
- if(this_fcp.getValue().equals(GFFStreamFeature.decode(fcp.getValue())))
+ if(this_fcp.getValue().equals(GFF3Encoder.decode(fcp.getValue())))
return true;
}
return false;
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 8e00d32..3150777 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -1228,8 +1228,10 @@ public class ChadoTransactionManager
{
if(synonym_tags == null)
{
- synonym_tags = DatabaseDocument.getSynonymTypeNames(
+ if(GeneUtils.isDatabaseEntry(feature))
+ synonym_tags = DatabaseDocument.getSynonymTypeNames(
SYNONYM_TAG_CVNAME, feature);
+
if(synonym_tags == null || synonym_tags.length < 1)
{
logger4j.debug("Using default synonym names");
@@ -1250,6 +1252,12 @@ public class ChadoTransactionManager
return false;
}
+ public static String[] getSynonymTags()
+ {
+ return synonym_tags;
+ }
+
+
/**
* Compare the old and new keys and qualifiers and find the qualifiers
* that have changed or been added and UPDATE, INSERT or DELETE accordingly.
@@ -2674,7 +2682,9 @@ public class ChadoTransactionManager
private void loadDbXRefsAndPubs(final String searchStr,
final FeatureCvTerm feature_cvterm)
{
- List<FeatureCvTermDbXRef> featureCvTermDbXRefs = null;
+ Collection<FeatureCvTermDbXRef> featureCvTermDbXRefs = feature_cvterm.getFeatureCvTermDbXRefs();
+ if(featureCvTermDbXRefs.size() == 0)
+ featureCvTermDbXRefs = null;
//StringVector strings = StringVector.getStrings(searchStr, "|");
StringTokenizer tok = new StringTokenizer(searchStr, "|,");
diff --git a/uk/ac/sanger/artemis/components/EditMenu.java b/uk/ac/sanger/artemis/components/EditMenu.java
index 50d124a..db10911 100644
--- a/uk/ac/sanger/artemis/components/EditMenu.java
+++ b/uk/ac/sanger/artemis/components/EditMenu.java
@@ -1768,6 +1768,23 @@ public class EditMenu extends SelectionMenu
{
((Feature)gene1.getGene().getUserData()).addQualifierValues(synQualifier);
((Feature)gene2.getGene().getUserData()).addQualifierValues(synQualifier);
+
+ final Qualifier comment =
+ new Qualifier("comment", "this gene model has previous ID "+prevId+
+ " and was reassigned a new ID as changes in the gene model occurred");
+
+ try
+ {
+ ((Feature)gene1.getProteinOfTranscript( GeneUtils.getUniqueName(
+ gene1.getTranscripts().get(0)) ).getUserData()).addQualifierValues(comment);
+ ((Feature)gene2.getProteinOfTranscript( GeneUtils.getUniqueName(
+ gene2.getTranscripts().get(0)) ).getUserData()).addQualifierValues(comment);
+ }
+ catch (Exception e)
+ {
+ ((Feature)gene1.getGene().getUserData()).addQualifierValues(comment);
+ ((Feature)gene2.getGene().getUserData()).addQualifierValues(comment);
+ }
}
}
diff --git a/uk/ac/sanger/artemis/components/EntryEdit.java b/uk/ac/sanger/artemis/components/EntryEdit.java
index bb7388d..21a3cb7 100644
--- a/uk/ac/sanger/artemis/components/EntryEdit.java
+++ b/uk/ac/sanger/artemis/components/EntryEdit.java
@@ -642,7 +642,7 @@ public class EntryEdit extends JFrame
return bamPanel;
}
- protected BamView getJamView()
+ public BamView getJamView()
{
return bamView;
}
diff --git a/uk/ac/sanger/artemis/components/FeatureEdit.java b/uk/ac/sanger/artemis/components/FeatureEdit.java
index 6b459dd..1626ba3 100644
--- a/uk/ac/sanger/artemis/components/FeatureEdit.java
+++ b/uk/ac/sanger/artemis/components/FeatureEdit.java
@@ -76,7 +76,6 @@ import java.util.Comparator;
import javax.swing.*;
-
/**
* FeatureEdit class
*
@@ -860,7 +859,6 @@ public class FeatureEdit extends JPanel
}
});
-
final JCheckBox oneView = new JCheckBox("Overview", false);
oneView.addItemListener(new ItemListener()
{
@@ -887,6 +885,12 @@ public class FeatureEdit extends JPanel
fillerBox.add(Box.createHorizontalStrut(
tabbedView.getPreferredSize().width ));
}
+ else if(getFeature().getEmblFeature() instanceof GFFStreamFeature)
+ {
+ propertiesPanel = new PropertiesPanel(getFeature());
+ addGffAnnotationView(lower_panel);
+
+ }
else
lower_panel.add(new JScrollPane(qualifier_text_area), "Center");
@@ -1438,8 +1442,8 @@ public class FeatureEdit extends JPanel
qualifier_text_area.setText(getQualifierString());
- if(GeneUtils.isDatabaseEntry(getFeature().getEmblFeature()))
- {
+ if(getFeature().getEmblFeature() instanceof GFFStreamFeature)
+ {
// load synonym
if(cvForm != null)
cvForm.updateFromFeature(getFeature());
@@ -1541,9 +1545,7 @@ public class FeatureEdit extends JPanel
{
qualifiers =
qualifier_text_area.getParsedQualifiers(getEntryInformation ());
-
- updateGffIds(qualifiers);
-
+
// if using controlled vocab form
if(cvForm != null)
{
@@ -1569,6 +1571,7 @@ public class FeatureEdit extends JPanel
if(mapQualifiers != null && mapQualifiers.size() > 0)
qualifiers.addAll(mapQualifiers);
}
+ updateGffIds(qualifiers);
if(matchForm != null)
{
@@ -1679,7 +1682,7 @@ public class FeatureEdit extends JPanel
{
final String newName = ((String) (qualifiers.getQualifierByName("ID").getValues().get(0))).trim();
final String oldName = ((String) (gffFeature.getQualifierByName("ID").getValues().get(0))).trim();
-
+
if(!newName.equals(oldName))
{
int val = JOptionPane.showConfirmDialog(null,
@@ -1704,7 +1707,7 @@ public class FeatureEdit extends JPanel
}
}
}
- catch(Exception e){ }
+ catch(Exception e){ e.printStackTrace(); }
}
}
}
diff --git a/uk/ac/sanger/artemis/components/RunBlastAtNCBI.java b/uk/ac/sanger/artemis/components/RunBlastAtNCBI.java
index 2ae2b6a..76d77f5 100644
--- a/uk/ac/sanger/artemis/components/RunBlastAtNCBI.java
+++ b/uk/ac/sanger/artemis/components/RunBlastAtNCBI.java
@@ -58,7 +58,7 @@ class RunBlastAtNCBI extends Thread
try
{
// Send data
- URL url = new URL("http://www.ncbi.nlm.nih.gov/blast/Blast.cgi");
+ URL url = new URL("https://blast.ncbi.nlm.nih.gov/Blast.cgi");
URLConnection conn = url.openConnection();
conn.setDoOutput(true);
OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream());
@@ -258,4 +258,4 @@ class RunBlastAtNCBI extends Thread
RunBlastAtNCBI blast= new RunBlastAtNCBI(data);
blast.start();
}
-}
\ No newline at end of file
+}
diff --git a/uk/ac/sanger/artemis/components/RunPfamSearchThread.java b/uk/ac/sanger/artemis/components/RunPfamSearchThread.java
index 9dd070d..364fc19 100644
--- a/uk/ac/sanger/artemis/components/RunPfamSearchThread.java
+++ b/uk/ac/sanger/artemis/components/RunPfamSearchThread.java
@@ -41,8 +41,8 @@ import uk.ac.sanger.artemis.editor.BrowserControl;
*/
public class RunPfamSearchThread extends Thread
{
- protected static String pfamUrl = "http://pfam.sanger.ac.uk/search/sequence";
- protected static String rfamUrl = "http://rfam.sanger.ac.uk/search/sequence";
+ protected static String pfamUrl = "http://pfam.xfam.org/search/sequence";
+ protected static String rfamUrl = "http://rfam.xfam.org/search/sequence";
private String searchURL = pfamUrl;
private String residues;
diff --git a/uk/ac/sanger/artemis/components/SelectMenu.java b/uk/ac/sanger/artemis/components/SelectMenu.java
index 4d801fa..c2ac0e9 100644
--- a/uk/ac/sanger/artemis/components/SelectMenu.java
+++ b/uk/ac/sanger/artemis/components/SelectMenu.java
@@ -1000,37 +1000,65 @@ public class SelectMenu extends SelectionMenu
}
}
}
-
/**
- * If there are some selected bases select the features that are
+ * If there are some selected bases or features select the features that are
* fully contained within that selection.
**/
private void selectContainedFeatures () {
final MarkerRange selected_marker_range =
getSelection ().getMarkerRange ();
- if (selected_marker_range == null) {
- new MessageDialog (getParentFrame (), "sequence range is not selected");
- return;
- } else {
- try {
- final FeatureVector featuresInRange =
- getEntryGroup ().getFeaturesInRange (selected_marker_range.getRawRange ());
- final FeatureVector featuresContainedByRange = new FeatureVector();
- for(int i=0; i<featuresInRange.size(); i++)
- {
- Feature f = featuresInRange.elementAt(i);
- Range maxR = f.getMaxRawRange();
- if(selected_marker_range.getRawStart().getRawPosition() <= maxR.getStart() &&
- selected_marker_range.getRawEnd().getRawPosition() >= maxR.getEnd())
- featuresContainedByRange.add(f);
+ final FeatureVector featuresContainedByRange;
+ try
+ {
+ if (selected_marker_range == null) {
+ final FeatureVector selected_features = getSelection ().getAllFeatures ();
+ if (selected_features.size () == 0) {
+ new MessageDialog (getParentFrame (), "nothing selected");
+ return;
}
- getSelection ().set (featuresContainedByRange);
- } catch (OutOfRangeException e) {
- throw new Error ("internal error - unexpected exception: " + e);
+
+ featuresContainedByRange = new FeatureVector();
+ for(int i=0; i<selected_features.size(); i++) {
+ Range r = selected_features.elementAt(i).getMaxRawRange();
+ final FeatureVector featuresContained = getFeaturesContainedByRange(r);
+ for(int j=0; j<featuresContained.size(); j++) {
+ final Feature f = featuresContained.elementAt(j);
+ if(!featuresContainedByRange.contains(f) && !selected_features.contains(f))
+ featuresContainedByRange.add(f);
+ }
+ }
+ } else {
+ featuresContainedByRange = getFeaturesContainedByRange(
+ selected_marker_range.getRawRange());
}
+ } catch (OutOfRangeException e) {
+ throw new Error ("internal error - unexpected exception: " + e);
+ }
+ getSelection ().set (featuresContainedByRange);
+ }
+
+ /**
+ * Return the features that are contained by a given range
+ * @param r
+ * @return
+ * @throws OutOfRangeException
+ */
+ private FeatureVector getFeaturesContainedByRange(Range r) throws OutOfRangeException
+ {
+ final FeatureVector featuresInRange =
+ getEntryGroup ().getFeaturesInRange (r);
+ final FeatureVector featuresContainedByRange = new FeatureVector();
+ for(int i=0; i<featuresInRange.size(); i++)
+ {
+ Feature f = featuresInRange.elementAt(i);
+ Range maxR = f.getMaxRawRange();
+ if(r.getStart() <= maxR.getStart() &&
+ r.getEnd() >= maxR.getEnd())
+ featuresContainedByRange.add(f);
}
+ return featuresContainedByRange;
}
/**
diff --git a/uk/ac/sanger/artemis/components/Splash.java b/uk/ac/sanger/artemis/components/Splash.java
index 34a6d38..7655608 100644
--- a/uk/ac/sanger/artemis/components/Splash.java
+++ b/uk/ac/sanger/artemis/components/Splash.java
@@ -418,7 +418,7 @@ abstract public class Splash extends JFrame
g.drawString(geneticCode,
left_margin, yPos+(font_height * 3));
- g.drawString("Copyright 1998 - 2014",
+ g.drawString("Copyright 1998 - 2016",
left_margin, yPos+(font_height * 9 / 2));
g.drawString("Genome Research Limited",
left_margin, yPos+(font_height * 11 / 2));
diff --git a/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java b/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java
index 075eb56..78a02e0 100644
--- a/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java
@@ -150,8 +150,17 @@ public class AbstractGraphPanel extends JPanel
*/
protected void drawMax(Graphics2D g2)
{
+ drawMax(g2, (float)max/(float)windowSize);
+ }
+
+ /**
+ * Draw maximum average value.
+ * @param g2
+ */
+ protected void drawMax(Graphics2D g2, float max)
+ {
DecimalFormat df = new DecimalFormat("0.#");
- String maxStr = df.format((float)max/(float)windowSize);
+ String maxStr = df.format(max);
FontMetrics fm = getFontMetrics(getFont());
g2.setColor(Color.black);
diff --git a/uk/ac/sanger/artemis/components/alignment/BamUtils.java b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
index c064061..f668011 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -28,12 +28,15 @@ import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
+import javax.swing.JProgressBar;
+
import net.sf.samtools.AlignmentBlock;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeatureSegmentVector;
+import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.io.Range;
class BamUtils
@@ -69,24 +72,21 @@ class BamUtils
* @return
*/
protected static float[] getCount(
+ final BamView bamView,
final int start,
final int end,
final String bam,
- final String refName,
- final Hashtable<String, SAMFileReader> samFileReaderHash,
- final Vector<String> seqNames,
- final HashMap<String, Integer> offsetLengths,
- final boolean concatSequences,
- final HashMap<String, Integer> seqLengths,
- final SAMRecordPredicate samRecordFlagPredicate,
- final SAMRecordMapQPredicate samRecordMapQPredicate,
final boolean contained,
final boolean useStrandTag)
{
+ final Vector<String> seqNames = bamView.getSeqNames();
+ final HashMap<String, Integer> offsetLengths = bamView.getOffsetLengths();
+ final HashMap<String, Integer> seqLengths = bamView.getSeqLengths();
+
int cnt[] = new int[2];
cnt[0] = 0;
cnt[1] = 0;
- if(concatSequences)
+ if(bamView.isConcatSequences())
{
int len = 0;
int lastLen = 1;
@@ -108,8 +108,7 @@ class BamUtils
if(thisEnd > thisLength)
thisEnd = thisLength;
- cnt = count(bam, samFileReaderHash, name, thisStart, thisEnd,
- samRecordFlagPredicate, samRecordMapQPredicate, contained, true, useStrandTag);
+ cnt = count(bamView, bam, thisStart, thisEnd, contained, true, useStrandTag);
}
lastLen = len;
@@ -117,8 +116,7 @@ class BamUtils
}
else
{
- cnt = count(bam, samFileReaderHash, refName, start, end,
- samRecordFlagPredicate, samRecordMapQPredicate, contained, true, useStrandTag);
+ cnt = count(bamView, bam, start, end, contained, true, useStrandTag);
}
float cntf[] = new float[2];
@@ -127,17 +125,20 @@ class BamUtils
return cntf;
}
- protected static int[] count(final String bam,
- final Hashtable<String, SAMFileReader> samFileReaderHash,
- final String refName,
- final int start,
- final int end,
- final SAMRecordPredicate samRecordFlagPredicate,
- final SAMRecordPredicate samRecordMapQPredicate,
- final boolean contained,
- final boolean byStrand,
- final boolean useStrandTag)
+ protected static int[] count(
+ final BamView bamView,
+ final String bam,
+ final int start,
+ final int end,
+ final boolean contained,
+ final boolean byStrand,
+ final boolean useStrandTag)
{
+ final String refName = (String) bamView.getCombo().getSelectedItem();
+ final Hashtable<String, SAMFileReader> samFileReaderHash = bamView.getSamFileReaderHash();
+ final SAMRecordPredicate samRecordFlagPredicate = bamView.getSamRecordFlagPredicate();
+ final SAMRecordPredicate samRecordMapQPredicate = bamView.getSamRecordMapQPredicate();
+
int cnt[] = new int[2];
cnt[0] = 0;
cnt[1] = 0;
@@ -164,29 +165,89 @@ class BamUtils
it.close();
return cnt;
}
+
+ protected static int[] calc(
+ final BamView bamView,
+ final String refName,
+ final int sequenceLength,
+ final boolean useStrandTag,
+ final JProgressBar progressBar)
+ {
+ int mappedReads[] = new int[bamView.bamList.size()];
+ int MAX_BASE_CHUNK = 2000 * 60;
+ boolean contained = false;
+ for (int i = 0; i < sequenceLength; i += MAX_BASE_CHUNK)
+ {
+ if(progressBar != null)
+ progressBar.setValue(i);
+ int sbegc = i;
+ int sendc = i + MAX_BASE_CHUNK - 1;
+
+ for (int j = 0; j < bamView.bamList.size(); j++)
+ {
+ String bam = bamView.bamList.get(j);
+ if (bamView.isConcatSequences())
+ {
+ int len = 0;
+ int lastLen = 1;
+ for (String name : bamView.getSeqNames())
+ {
+ int thisLength = bamView.getSeqLengths().get(name);
+ len += thisLength;
+
+ if ((lastLen >= sbegc && lastLen < sendc)
+ || (len >= sbegc && len < sendc)
+ || (sbegc >= lastLen && sbegc < len)
+ || (sendc >= lastLen && sendc < len))
+ {
+ int offset = bamView.getOffsetLengths().get(name);
+ int thisStart = sbegc - offset;
+ if (thisStart < 1)
+ thisStart = 1;
+ int thisEnd = sendc - offset;
+ if (thisEnd > thisLength)
+ thisEnd = thisLength;
+
+ mappedReads[j] += BamUtils.count(bamView, bam, thisStart, thisEnd,
+ contained, false, useStrandTag)[0];
+ }
+ lastLen = len;
+ }
+ }
+ else
+ {
+ mappedReads[j] += BamUtils.count(bamView, bam, sbegc, sendc,
+ contained, false, useStrandTag)[0];
+ }
+ }
+ }
+ return mappedReads;
+ }
/**
* Return the coverage for each base in a range for the forward and
* reverse strand.
+ * @param bamView
* @param bamFile
- * @param samFileReaderHash
- * @param refName
* @param start
* @param end
- * @param samRecordFlagPredicate
- * @param samRecordMapQPredicate
+ * @param concatShift
+ * @param cnt
* @return
*/
- protected static int[][] countOverRange(final String bamFile,
- final Hashtable<String, SAMFileReader> samFileReaderHash,
- final String refName,
- final int start,
- final int end,
- final int concatShift,
- final int cnt[][],
- final SAMRecordPredicate samRecordFlagPredicate,
- final SAMRecordPredicate samRecordMapQPredicate)
+ protected static int[][] countOverRange(
+ final BamView bamView,
+ final String bamFile,
+ final int start,
+ final int end,
+ final int concatShift,
+ final int cnt[][])
{
+ final String refName = (String) bamView.getCombo().getSelectedItem();
+ final Hashtable<String, SAMFileReader> samFileReaderHash = bamView.getSamFileReaderHash();
+ final SAMRecordPredicate samRecordFlagPredicate = bamView.getSamRecordFlagPredicate();
+ final SAMRecordPredicate samRecordMapQPredicate = bamView.getSamRecordMapQPredicate();
+
SAMFileReader inputSam = samFileReaderHash.get(bamFile);
final CloseableIterator<SAMRecord> it =
inputSam.query(refName, start, end, false);
@@ -226,5 +287,80 @@ class BamUtils
it.close();
return cnt;
}
+
+ /**
+ * For a list of features calculate the read count for each
+ * @param bamView
+ * @param features
+ * @param contained
+ * @param useIntrons
+ * @param useStrandTag
+ * @param mappedReads
+ * @param progressBar
+ * @return
+ */
+ protected static Hashtable<String, List<ReadCount>> calculateMappedReads(
+ final BamView bamView,
+ final FeatureVector features,
+ final boolean contained,
+ final boolean useIntrons,
+ final boolean useStrandTag,
+ final int mappedReads[],
+ final JProgressBar progressBar)
+ {
+ final Hashtable<String, List<ReadCount>> featureReadCount =
+ new Hashtable<String, List<ReadCount>>();
+ for (int i = 0; i < features.size(); i++)
+ {
+ final Feature f = features.elementAt(i);
+ if(progressBar != null)
+ progressBar.setValue(i);
+
+ int start = f.getRawFirstBase();
+ int end = f.getRawLastBase();
+ final float fLen = BamUtils.getFeatureLength(f);
+ List<ReadCount> sampleCounts = new Vector<ReadCount>();
+
+ for (int j = 0; j < bamView.bamList.size(); j++)
+ {
+ final String bam = bamView.bamList.get(j);
+ float cnt[] = new float[2];
+
+ cnt = BamUtils.getCount(bamView, start, end, bam, contained, useStrandTag);
+ if (!useIntrons && f.getSegments().size() > 1)
+ {
+ // remove reads contained by intron
+ for (int k = 0; k < f.getSegments().size()-1; k++)
+ {
+ int seg = k;
+ int nextSeg = k+1;
+ if(!f.isForwardFeature())
+ {
+ seg = f.getSegments().size()-k-1;
+ nextSeg = seg-1;
+ }
+
+ start = f.getSegments().elementAt(seg).getRawRange().getEnd();
+ end = f.getSegments().elementAt(nextSeg).getRawRange().getStart();
+
+ float tmpcnt[] = new float[2];
+ tmpcnt = BamUtils.getCount(bamView, start, end, bam, true, useStrandTag);
+ cnt[0] -= tmpcnt[0];
+ cnt[1] -= tmpcnt[1];
+ }
+ }
+
+ if (mappedReads != null)
+ {
+ cnt[0] = (cnt[0] / (((float) mappedReads[j] / 1000000.f) * (fLen / 1000.f)));
+ cnt[1] = (cnt[1] / (((float) mappedReads[j] / 1000000.f) * (fLen / 1000.f)));
+ }
+
+ sampleCounts.add( new ReadCount(cnt, f.isForwardFeature()) );
+ }
+ featureReadCount.put(ReadCountDialog.getFeatureName(f), sampleCounts);
+ }
+ return featureReadCount;
+ }
}
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 8dcac22..0228a84 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1837,9 +1837,13 @@ public class BamView extends JPanel
else
g2.setColor(Color.blue);
+ Color c = g2.getColor();
drawRead(g2, pr.sam1, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam1.sam), ydiff);
if(pr.sam2 != null)
+ {
+ g2.setColor(c);
drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam2.sam), ydiff);
+ }
}
}
@@ -1946,7 +1950,7 @@ public class BamView extends JPanel
coverageView.drawSelectionRange(g2, pixPerBase, start, end, getHeight(), Color.PINK);
coverageView.draw(g2, getWidth(), hgt, hideBamList);
if(!coverageView.isPlotHeatMap())
- coverageView.drawMax(g2);
+ coverageView.drawMax(g2, coverageView.getMaxCoverage());
}
/**
@@ -2582,9 +2586,7 @@ public class BamView extends JPanel
return;
//JOptionPane.showMessageDialog(null, yBox, "Read Count Option", JOptionPane.INFORMATION_MESSAGE);
- new MappedReads(features, (String)combo.getSelectedItem(), samFileReaderHash, bamList,
- seqNames, offsetLengths, concatSequences, seqLengths,
- samRecordFlagPredicate, samRecordMapQPredicate,
+ new MappedReads(BamView.this, features,
!overlap.isSelected(), spliced.isSelected(), colourByStrandTag.isSelected());
}
});
@@ -2622,16 +2624,12 @@ public class BamView extends JPanel
else if(bases != null)
seqlen = bases.getLength();
- new MappedReads(features, (String)combo.getSelectedItem(),
- samFileReaderHash, bamList, seqNames, offsetLengths, concatSequences,
- seqLengths, seqlen, samRecordFlagPredicate, samRecordMapQPredicate,
+ new MappedReads(BamView.this, features, seqlen,
!overlap.isSelected(), spliced.isSelected(), allRefSeqs.isSelected(),
colourByStrandTag.isSelected());
- }
+ }
});
-
-
-
+
final JMenuItem createFeatures = new JMenuItem("Create features from coverage peaks ...");
analyse.add(createFeatures);
if(feature_display == null)
@@ -2687,6 +2685,7 @@ public class BamView extends JPanel
if(cbStackView.isSelected())
logMenuItem.setEnabled(false);
getJspView().setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
+ setViewportBtm();
repaint();
}
});
@@ -3188,31 +3187,18 @@ public class BamView extends JPanel
public void mouseMoved(MouseEvent e)
{
lastMousePoint = e.getPoint();
-
int thisHgt = HEIGHT-2;
if (thisHgt < 5)
thisHgt = 15;
int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
- Point p = jspView.getViewport().getViewPosition();
- boolean isVis = topPanel.isVisible();
-
if (y < thisHgt)
- {
topPanel.setVisible(true);
- if(!isVis)
- p.y += topPanel.getHeight();
- }
else
{
- if (buttonAutoHide.isSelected())
+ if (buttonAutoHide.isSelected() && topPanel.isVisible())
topPanel.setVisible(false);
}
-
- if(!showBaseAlignment && topPanel.isVisible())
- jspView.getViewport().setViewPosition(p);
- mainPanel.repaint();
- //mainPanel.revalidate();
}
};
addMouseMotionListener(mouseMotionListener);
@@ -3396,18 +3382,17 @@ public class BamView extends JPanel
cbLastSelected.setSelected(true);
cbLastSelected = null;
}
-
+
jspView.setColumnHeaderView(null);
-
- if(!isStrandStackView())
+ if(isCoverageView(pixPerBase))
setViewportBtm();
- else
+ else if (isStrandStackView())
setViewportMidPoint();
showBaseAlignment = false;
baseQualityColour.setEnabled(false);
markInsertions.setEnabled(false);
}
-
+
if(scrollBar != null)
{
scrollBar.setValues(startValue, nbasesInView, 1,
@@ -3689,6 +3674,26 @@ public class BamView extends JPanel
return combo;
}
+ protected Hashtable<String, SAMFileReader> getSamFileReaderHash()
+ {
+ return samFileReaderHash;
+ }
+
+ protected Vector<String> getSeqNames()
+ {
+ return seqNames;
+ }
+
+ protected HashMap<String, Integer> getSeqLengths()
+ {
+ return seqLengths;
+ }
+
+ protected HashMap<String, Integer> getOffsetLengths()
+ {
+ return offsetLengths;
+ }
+
private String getVersion()
{
final ClassLoader cl = this.getClass().getClassLoader();
@@ -4288,8 +4293,7 @@ public class BamView extends JPanel
minBams.setValue(groupsFrame.getMaximumBamsInGroup());
}
- new MappedReads((String)combo.getSelectedItem(),BamView.this, samFileReaderHash,
- seqNames, offsetLengths, concatSequences, seqLengths,
+ new MappedReads(BamView.this,
(useGroup.isSelected() ? groupsFrame : null), threshold.getValue(),
minSize.getValue(), minBams.getValue(), cbOpposite.isSelected(), true);
}
diff --git a/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java b/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
index ae2fb2d..155be81 100644
--- a/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
+++ b/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
@@ -107,5 +107,8 @@ import uk.ac.sanger.artemis.util.OutOfRangeException;
public void reset()
{
}
-
- }
\ No newline at end of file
+
+ public void close()
+ {
+ }
+ }
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 64dbaa5..2d01720 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -47,6 +47,7 @@ import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.JSeparator;
import javax.swing.JTextField;
import uk.ac.sanger.artemis.components.Plot;
@@ -71,11 +72,14 @@ import net.sf.samtools.SAMRecord;
private List<String> selected = new Vector<String>();
private boolean showGrid = false;
private boolean logScale = false;
+ private int maxCoverage = Integer.MAX_VALUE;
+ private JCheckBox fixHgt = new JCheckBox("Fix the graph height to cut-off", false);
protected CoveragePanel(final BamView bamView)
{
this();
this.bamView = bamView;
+ setMaxBases = false;
createMenus(popup);
addMouseListener(new PopupListener());
}
@@ -129,7 +133,18 @@ import net.sf.samtools.SAMRecord;
if(!plotHeatMap)
drawSelectionRange(g2, pixPerBase, start, end, getHeight(), Color.PINK);
drawPlot(g2);
- drawMax(g2);
+ drawMax(g2, getMaxCoverage());
+ }
+
+ protected float getMaxCoverage()
+ {
+ return (useMaxCutOff() ? maxCoverage: (float)max/(float)windowSize);
+ }
+
+ private boolean useMaxCutOff()
+ {
+ return (maxCoverage < Integer.MAX_VALUE && maxCoverage < (float)max/(float)windowSize) ||
+ (maxCoverage < Integer.MAX_VALUE && fixHgt.isSelected());
}
protected void init(BamView bamView, float pixPerBase, int start, int end)
@@ -187,7 +202,7 @@ import net.sf.samtools.SAMRecord;
max = thisPlot[i][0];
}
}
-
+
draw(g2, getWidth(), getHeight(), null);
}
@@ -310,7 +325,12 @@ import net.sf.samtools.SAMRecord;
{
g2.setColor(line.getLineColour());
int hgt2 = hgt/2;
- float maxVal = getValue(max, logScale);
+ float maxVal;
+
+ if(useMaxCutOff())
+ maxVal = getValue((maxCoverage*windowSize), logScale);
+ else
+ maxVal = getValue(max, logScale);
if(line.getPlotType() == LineAttributes.PLOT_TYPES[0])
{
@@ -538,25 +558,45 @@ import net.sf.samtools.SAMRecord;
final GridBagConstraints c = new GridBagConstraints();
final JTextField newBaseMax = new JTextField(Integer.toString(bamView.getMaxBases()), 10);
- c.gridy = 0;
+ c.gridy+=1;
+ c.gridwidth = 1;
if(setMaxBases)
{
final JLabel labMax1 = new JLabel("Zoom level before switching");
final JLabel labMax2 = new JLabel("to coverage view (in bases):");
c.anchor = GridBagConstraints.WEST;
+ c.gridy+=1;
opts.add(labMax1, c);
- c.gridy = c.gridy+1;
+ c.gridy+=1;
opts.add(labMax2, c);
opts.add(newBaseMax, c);
+ addSeparator(c, opts);
}
+ // cut-off
+ final JTextField maxCutoff = new JTextField(
+ (maxCoverage < Integer.MAX_VALUE ? Integer.toString(maxCoverage) : ""), 10);
+ c.gridy+=1;
+ c.anchor = GridBagConstraints.WEST;
+ opts.add(new JLabel("Coverage cut-off:"), c);
+ c.anchor = GridBagConstraints.EAST;
+ opts.add(maxCutoff, c);
+
+ c.gridy+=1;
+ c.gridwidth = GridBagConstraints.REMAINDER;
+ c.anchor = GridBagConstraints.WEST;
+ opts.add(fixHgt, c);
+
+ addSeparator(c, opts);
+
+ // window size
final JTextField newWinSize = new JTextField(Integer.toString(userWinSize), 10);
final JLabel lab = new JLabel("Window size:");
lab.setEnabled(!autoWinSize);
newWinSize.setEnabled(!autoWinSize);
- c.gridy = c.gridy+1;
- c.anchor = GridBagConstraints.EAST;
+ c.gridy+=1;
+ c.anchor = GridBagConstraints.WEST;
opts.add(lab, c);
opts.add(newWinSize, c);
@@ -570,22 +610,24 @@ import net.sf.samtools.SAMRecord;
}
});
c.anchor = GridBagConstraints.WEST;
- c.gridy = c.gridy+1;
+ c.gridy+=1;
c.gridwidth = GridBagConstraints.REMAINDER;
opts.add(autoSet, c);
+ addSeparator(c, opts);
+
final JCheckBox showCombined = new JCheckBox("Show combined plot", includeCombined);
if(bamView.bamList.size() == 1)
showCombined.setEnabled(false);
- c.gridy = c.gridy+1;
+ c.gridy+=1;
opts.add(showCombined, c);
final JCheckBox byStrand = new JCheckBox("Plot by strand", plotByStrand);
- c.gridy = c.gridy+1;
+ c.gridy+=1;
opts.add(byStrand, c);
final JCheckBox logMenu = new JCheckBox("Log scale", logScale);
- c.gridy = c.gridy+1;
+ c.gridy+=1;
opts.add(logMenu, c);
String window_options[] = { "OK", "Cancel" };
@@ -601,10 +643,14 @@ import net.sf.samtools.SAMRecord;
includeCombined = showCombined.isSelected();
plotByStrand = byStrand.isSelected();
logScale = logMenu.isSelected();
-
+
try
{
userWinSize = Integer.parseInt(newWinSize.getText().trim());
+ if(maxCutoff.getText().length() > 0)
+ maxCoverage = Integer.parseInt(maxCutoff.getText().trim());
+ else
+ maxCoverage = Integer.MAX_VALUE;
if(setMaxBases)
bamView.setMaxBases(Integer.parseInt(newBaseMax.getText().trim()));
}
@@ -615,6 +661,22 @@ import net.sf.samtools.SAMRecord;
}
/**
+ * Add a separator
+ * @param c
+ * @param opts
+ */
+ private void addSeparator(GridBagConstraints c, final JPanel opts)
+ {
+ c.gridy+=1;
+ c.gridwidth = GridBagConstraints.REMAINDER;
+ final JSeparator sep = new JSeparator();
+ c.fill = GridBagConstraints.HORIZONTAL;
+ opts.add(sep, c);
+ c.gridwidth = 1;
+ c.fill = GridBagConstraints.NONE;
+ }
+
+ /**
* Click on heatmap
* @param y
*/
diff --git a/uk/ac/sanger/artemis/components/alignment/MappedReads.java b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
index 7b13366..d47b528 100644
--- a/uk/ac/sanger/artemis/components/alignment/MappedReads.java
+++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
@@ -9,7 +9,6 @@ import java.awt.event.ActionListener;
import java.io.File;
import java.text.DecimalFormat;
import java.util.Enumeration;
-import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
@@ -37,188 +36,93 @@ import uk.ac.sanger.artemis.sequence.MarkerRange;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.ReadOnlyException;
-import net.sf.samtools.SAMFileReader;
-
public class MappedReads
{
private JProgressBar progressBar;
private JLabel progressTxt = new JLabel();
private FeatureVector features;
- private String refName;
- private Hashtable<String, SAMFileReader> samFileReaderHash;
- private List<String> bamList;
- private List<Short> hideBamList;
- private Vector<String> seqNames;
- private HashMap<String, Integer> offsetLengths;
- private boolean concatSequences;
- private HashMap<String, Integer> seqLengths;
- private int sequenceLength;
- private SAMRecordPredicate samRecordFlagPredicate;
- private SAMRecordMapQPredicate samRecordMapQPredicate;
+ private BamView bamView;
+
private boolean contained;
private boolean useIntrons;
private boolean useStrandTag = false;
- private JDialog dialog = new JDialog((JFrame)null, "Calculating", true);;
-
- private int mappedReads[];
+ private JDialog dialog = new JDialog((JFrame)null, "Calculating", true);
/**
* Calculate the total number of mapped reads.
- * @param refName
- * @param samFileReaderHash
- * @param bamList
- * @param seqNames
- * @param offsetLengths
- * @param concatSequences
- * @param seqLengths
+ * @param bamView
+ * @param features
* @param sequenceLength
+ * @param contained
+ * @param useIntrons
+ * @param allRefSeqs
+ * @param useStrandTag
*/
public MappedReads(
+ final BamView bamView,
final FeatureVector features,
- final String refName,
- final Hashtable<String, SAMFileReader> samFileReaderHash,
- final List<String> bamList,
- final Vector<String> seqNames,
- final HashMap<String, Integer> offsetLengths,
- final boolean concatSequences,
- final HashMap<String, Integer> seqLengths,
final int sequenceLength,
- final SAMRecordPredicate samRecordFlagPredicate,
- SAMRecordMapQPredicate samRecordMapQPredicate,
final boolean contained,
final boolean useIntrons,
final boolean allRefSeqs,
final boolean useStrandTag)
{
this.features = features;
- this.refName = refName;
- this.samFileReaderHash = samFileReaderHash;
- this.bamList = bamList;
- this.seqNames = seqNames;
- this.offsetLengths = offsetLengths;
- this.concatSequences = concatSequences;
- this.seqLengths = seqLengths;
- this.sequenceLength = sequenceLength;
- this.samRecordFlagPredicate = samRecordFlagPredicate;
- this.samRecordMapQPredicate = samRecordMapQPredicate;
+ this.bamView = bamView;
this.contained = contained;
this.useIntrons = useIntrons;
this.useStrandTag = useStrandTag;
-
- progressBar = new JProgressBar(0, sequenceLength);
- progressBar.setValue(0);
- progressBar.setStringPainted(true);
- JPanel panel = new JPanel(new BorderLayout());
- progressTxt.setText("Total number of mapped reads");
- panel.add(progressTxt, BorderLayout.NORTH);
- panel.add(progressBar, BorderLayout.CENTER);
-
- dialog.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
- panel.setOpaque(true);
- dialog.setContentPane(panel);
- dialog.pack();
- centerDialog();
-
- CalculateTotalMappedReads cmr = new CalculateTotalMappedReads(allRefSeqs);
+ showProgress(sequenceLength, "Total number of mapped reads");
+ CalculateTotalMappedReads cmr = new CalculateTotalMappedReads(allRefSeqs, sequenceLength);
cmr.start();
dialog.setVisible(true);
}
/**
* Read count for selected features.
+ * @param bamView
* @param features
- * @param refName
- * @param samFileReaderHash
- * @param bamList
- * @param seqNames
- * @param offsetLengths
- * @param concatSequences
- * @param seqLengths
- * @param samRecordFlagPredicate
- * @param samRecordMapQPredicate
* @param contained
* @param useIntrons
+ * @param useStrandTag
*/
public MappedReads(
+ final BamView bamView,
final FeatureVector features,
- final String refName,
- final Hashtable<String, SAMFileReader> samFileReaderHash,
- final List<String> bamList,
- final Vector<String> seqNames,
- final HashMap<String, Integer> offsetLengths,
- final boolean concatSequences,
- final HashMap<String, Integer> seqLengths,
- final SAMRecordPredicate samRecordFlagPredicate,
- final SAMRecordMapQPredicate samRecordMapQPredicate,
final boolean contained,
final boolean useIntrons,
final boolean useStrandTag)
{
+ this.bamView = bamView;
this.features = features;
- this.refName = refName;
- this.samFileReaderHash = samFileReaderHash;
- this.bamList = bamList;
- this.seqNames = seqNames;
- this.offsetLengths = offsetLengths;
- this.concatSequences = concatSequences;
- this.seqLengths = seqLengths;
- this.samRecordFlagPredicate = samRecordFlagPredicate;
- this.samRecordMapQPredicate = samRecordMapQPredicate;
+ this.bamView = bamView;
this.contained = contained;
this.useIntrons = useIntrons;
this.useStrandTag = useStrandTag;
-
- progressBar = new JProgressBar(0, features.size());
- progressBar.setValue(0);
- progressBar.setStringPainted(true);
- JPanel panel = new JPanel(new BorderLayout());
- progressTxt.setText("Number of mapped reads for "+features.size()+" features");
- panel.add(progressTxt, BorderLayout.NORTH);
- panel.add(progressBar, BorderLayout.CENTER);
-
- panel.setOpaque(true);
- dialog.setContentPane(panel);
- dialog.pack();
- centerDialog();
-
- CalculateMappedReads cmr = new CalculateMappedReads();
+ showProgress(features.size(), "Number of mapped reads for "+features.size()+" features");
+ CalculateMappedReads cmr = new CalculateMappedReads(null);
cmr.start();
dialog.setVisible(true);
}
-
-
/**
* Search for new features based on a threshold of read counts in the intergenic
* and anti-sense regions of existing annotations. This should exclude rRNA and
* tRNA regions. If two or more BAM files are loaded it should create features
* based on the combined read peak span.
- * @param refName
* @param bamView
- * @param samFileReaderHash
- * @param bamList
- * @param seqNames
- * @param offsetLengths
- * @param concatSequences
- * @param seqLengths
* @param groupsFrame
* @param threshold
* @param minSize
* @param minBams
- * @param readsOnOppositeStrand assume reads are on the opposite strand if true.
+ * @param readsOnOppositeStrand
* @param contained
*/
public MappedReads(
- final String refName,
final BamView bamView,
- final Hashtable<String, SAMFileReader> samFileReaderHash,
- final Vector<String> seqNames,
- final HashMap<String, Integer> offsetLengths,
- final boolean concatSequences,
- final HashMap<String, Integer> seqLengths,
final GroupBamFrame groupsFrame,
final int threshold,
final int minSize,
@@ -226,26 +130,26 @@ public class MappedReads
final boolean readsOnOppositeStrand,
final boolean contained)
{
- this.refName = refName;
- this.samFileReaderHash = samFileReaderHash;
- this.bamList = bamView.bamList;
- this.hideBamList = bamView.hideBamList;
- this.seqNames = seqNames;
- this.offsetLengths = offsetLengths;
- this.concatSequences = concatSequences;
- this.seqLengths = seqLengths;
- this.samRecordFlagPredicate = bamView.getSamRecordFlagPredicate();
- this.samRecordMapQPredicate = bamView.getSamRecordMapQPredicate();
-
+ this.bamView = bamView;
this.contained = contained;
final FeatureDisplay feature_display = bamView.getFeatureDisplay();
- progressBar = new JProgressBar(0, feature_display.getSequenceLength());
+ showProgress(feature_display.getSequenceLength(), "");
+ final CalculateNewFeatures cmr = new CalculateNewFeatures(
+ feature_display, (String) bamView.getCombo().getSelectedItem(), groupsFrame,
+ threshold, minSize, minBams, readsOnOppositeStrand);
+ cmr.start();
+ dialog.setVisible(true);
+ }
+
+ private void showProgress(int progressBarMax, String txt)
+ {
+ progressBar = new JProgressBar(0, progressBarMax);
progressBar.setValue(0);
progressBar.setStringPainted(true);
JPanel panel = new JPanel(new BorderLayout());
- progressTxt.setText("");
+ progressTxt.setText(txt);
panel.add(progressTxt, BorderLayout.NORTH);
panel.add(progressBar, BorderLayout.CENTER);
@@ -254,11 +158,6 @@ public class MappedReads
dialog.setContentPane(panel);
dialog.pack();
centerDialog();
-
- final CalculateNewFeatures cmr = new CalculateNewFeatures(
- feature_display, refName, groupsFrame, threshold, minSize, minBams, readsOnOppositeStrand);
- cmr.start();
- dialog.setVisible(true);
}
private void centerDialog()
@@ -274,55 +173,18 @@ public class MappedReads
class CalculateMappedReads extends SwingWorker
{
- Hashtable<String, List<ReadCount>> featureReadCount;
+ private Hashtable<String, List<ReadCount>> featureReadCount;
+ private int mappedReads[];
+
+ public CalculateMappedReads(final int mappedReads[])
+ {
+ this.mappedReads = mappedReads;
+ }
+
public Object construct()
{
- featureReadCount = new Hashtable<String, List<ReadCount>>();
- for (int i = 0; i < features.size(); i++)
- {
- Feature f = features.elementAt(i);
- progressBar.setValue(i);
-
- int start = f.getRawFirstBase();
- int end = f.getRawLastBase();
- float fLen = BamUtils.getFeatureLength(f);
- List<ReadCount> sampleCounts = new Vector<ReadCount>();
-
- for (int j = 0; j < bamList.size(); j++)
- {
- String bam = bamList.get(j);
- float cnt[] = new float[2];
-
- if (!useIntrons && f.getSegments().size() > 1)
- {
- for (int k = 0; k < f.getSegments().size(); k++)
- {
- start = f.getSegments().elementAt(k).getRawRange().getStart();
- end = f.getSegments().elementAt(k).getRawRange().getEnd();
- float tmpcnt[] = new float[2];
- tmpcnt = BamUtils.getCount(start, end, bam, refName, samFileReaderHash,
- seqNames, offsetLengths, concatSequences, seqLengths,
- samRecordFlagPredicate, samRecordMapQPredicate, contained, useStrandTag);
- cnt[0] += tmpcnt[0];
- cnt[1] += tmpcnt[1];
- }
- }
- else
- cnt = BamUtils.getCount(start, end, bam, refName, samFileReaderHash, seqNames,
- offsetLengths, concatSequences, seqLengths,
- samRecordFlagPredicate, samRecordMapQPredicate, contained, useStrandTag);
-
- if (mappedReads != null)
- {
- cnt[0] = (cnt[0] / (((float) mappedReads[j] / 1000000.f) * (fLen / 1000.f)));
- cnt[1] = (cnt[1] / (((float) mappedReads[j] / 1000000.f) * (fLen / 1000.f)));
- }
-
- sampleCounts.add( new ReadCount(cnt, f.isForwardFeature()) );
- }
-
- featureReadCount.put(ReadCountDialog.getFeatureName(f), sampleCounts);
- }
+ featureReadCount = BamUtils.calculateMappedReads(bamView, features,
+ contained, useIntrons, useStrandTag, mappedReads, progressBar);
return null;
}
@@ -341,9 +203,9 @@ public class MappedReads
final StringBuilder titleToSave = new StringBuilder();
final StringBuilder body = new StringBuilder();
- for (int j = 0; j < bamList.size(); j++)
+ for (int j = 0; j < bamView.bamList.size(); j++)
{
- String bam = bamList.get(j);
+ String bam = bamView.bamList.get(j);
hdr.append("#BAM: " + bam);
if (mappedReads != null)
{
@@ -369,7 +231,7 @@ public class MappedReads
}
titleToSave.append("\t");
title.append("\t");
- for (String bam: bamList)
+ for (String bam: bamView.bamList)
{
String name = new File(bam).getName();
titleToSave.append(name+"\t");
@@ -409,7 +271,7 @@ public class MappedReads
}
title.append("\t");
titleToSave.append("\t");
- for (int j = 0; j < bamList.size(); j++)
+ for (int j = 0; j < bamView.bamList.size(); j++)
{
if(mappedReads != null)
{
@@ -481,88 +343,43 @@ public class MappedReads
class CalculateTotalMappedReads extends SwingWorker
{
private boolean useAllRefSeqs;
- CalculateTotalMappedReads(boolean useAllRefSeqs)
+ private int sequenceLength;
+
+ CalculateTotalMappedReads(boolean useAllRefSeqs, final int sequenceLength)
{
this.useAllRefSeqs = useAllRefSeqs;
+ this.sequenceLength = sequenceLength;
}
public Object construct()
{
- mappedReads = new int[bamList.size()];
- if(concatSequences || !useAllRefSeqs)
- calc(refName, sequenceLength);
+ int mappedReads[] = null;
+ if(bamView.isConcatSequences() || !useAllRefSeqs)
+ {
+ String refName = (String) bamView.getCombo().getSelectedItem();
+ mappedReads = BamUtils.calc(bamView, refName, sequenceLength,
+ useStrandTag, progressBar);
+ }
else
{
- for (String name : seqNames)
+ for (String name : bamView.getSeqNames())
{
progressTxt.setText(name);
- int thisLength = seqLengths.get(name);
+ int thisLength = bamView.getSeqLengths().get(name);
progressBar.setValue(0);
progressBar.setMaximum(thisLength);
- calc(name, thisLength);
+ mappedReads = BamUtils.calc(bamView, name, thisLength,
+ useStrandTag, progressBar);
}
}
progressBar.setValue(0);
progressBar.setMaximum(features.size());
progressTxt.setText("RPKM values for "+features.size()+" features");
- CalculateMappedReads cmr = new CalculateMappedReads();
+ CalculateMappedReads cmr = new CalculateMappedReads(mappedReads);
cmr.start();
return null;
}
-
- private void calc(final String refName, final int sequenceLength)
- {
- int MAX_BASE_CHUNK = 2000 * 60;
- boolean contained = false;
- for (int i = 0; i < sequenceLength; i += MAX_BASE_CHUNK)
- {
- progressBar.setValue(i);
- int sbegc = i;
- int sendc = i + MAX_BASE_CHUNK - 1;
-
- for (int j = 0; j < bamList.size(); j++)
- {
- String bam = bamList.get(j);
- if (concatSequences)
- {
- int len = 0;
- int lastLen = 1;
- for (String name : seqNames)
- {
- int thisLength = seqLengths.get(name);
- len += thisLength;
-
- if ((lastLen >= sbegc && lastLen < sendc)
- || (len >= sbegc && len < sendc)
- || (sbegc >= lastLen && sbegc < len)
- || (sendc >= lastLen && sendc < len))
- {
- int offset = offsetLengths.get(name);
- int thisStart = sbegc - offset;
- if (thisStart < 1)
- thisStart = 1;
- int thisEnd = sendc - offset;
- if (thisEnd > thisLength)
- thisEnd = thisLength;
-
- mappedReads[j] += BamUtils.count(bam, samFileReaderHash, name,
- thisStart, thisEnd, samRecordFlagPredicate,
- samRecordMapQPredicate, contained, false, useStrandTag)[0];
-
- }
- lastLen = len;
- }
- }
- else
- {
- mappedReads[j] += BamUtils.count(bam, samFileReaderHash, refName, sbegc,
- sendc, samRecordFlagPredicate, samRecordMapQPredicate,
- contained, false, useStrandTag)[0];
- }
- }
- }
- }
}
/**
@@ -572,7 +389,6 @@ public class MappedReads
{
private EntryGroup entryGroup;
private Bases bases;
- private String refSeq;
private int threshold;
private int minSize;
private int minBams;
@@ -589,7 +405,7 @@ public class MappedReads
{
entryGroup = feature_display.getEntryGroup();
bases = feature_display.getBases();
- this.refSeq = refSeq;
+
this.groupsFrame = groupsFrame;
this.threshold = threshold;
this.minSize = minSize;
@@ -620,14 +436,14 @@ public class MappedReads
int revStart = -1;
final List<MarkerObj> fwdMarkers = new Vector<MarkerObj>();
final List<MarkerObj> revMarkers = new Vector<MarkerObj>();
- for (short i = 0; i < bamList.size(); i++)
+ for (short i = 0; i < bamView.bamList.size(); i++)
{
- if(hideBamList.contains(i))
+ if(bamView.hideBamList.contains(i))
continue;
for(int j=beg; j<end; j+=MAX_BASE_CHUNK)
{
- progressBar.setValue((j + (i*end)) / bamList.size());
+ progressBar.setValue((j + (i*end)) / bamView.bamList.size());
if(j > end)
continue;
int start = j;
@@ -640,12 +456,12 @@ public class MappedReads
for (int col = 0; col < 2; col++)
cnt[row][col] = 0;
- if (concatSequences)
+ if (bamView.isConcatSequences())
{
- for (String name : seqNames)
+ for (String name : bamView.getSeqNames())
{
- int len = seqLengths.get(name);
- int offset = offsetLengths.get(name);
+ int len = bamView.getSeqLengths().get(name);
+ int offset = bamView.getOffsetLengths().get(name);
if( (start >= offset && start <= offset+len) ||
(stop >= offset && start <= offset+len) )
@@ -662,17 +478,15 @@ public class MappedReads
concatShift = offset-start;
cnt =
- BamUtils.countOverRange(bamList.get(i), samFileReaderHash,
- name, thisStart, thisEnd, concatShift, cnt,
- samRecordFlagPredicate, samRecordMapQPredicate);
+ BamUtils.countOverRange(bamView, bamView.bamList.get(i),
+ thisStart, thisEnd, concatShift, cnt);
}
}
}
else
cnt =
- BamUtils.countOverRange(bamList.get(i), samFileReaderHash,
- refSeq, start, stop, 0, cnt,
- samRecordFlagPredicate, samRecordMapQPredicate);
+ BamUtils.countOverRange(bamView, bamView.bamList.get(i),
+ start, stop, 0, cnt);
for(int k=0; k<cnt.length; k++)
{
@@ -741,7 +555,7 @@ public class MappedReads
Hashtable<String, Integer> groupCluster = new Hashtable<String, Integer>();
for(int j=0; j<bamIdxList.size(); j++)
{
- File f = new File(bamList.get(j));
+ File f = new File(bamView.bamList.get(j));
String grp = groupsFrame.getGroupName( f.getName() );
if(groupCluster.containsKey(grp))
{
@@ -894,23 +708,4 @@ public class MappedReads
dialog.dispose();
}
}
-
- class ReadCount
- {
- private float senseCnt = 0;
- private float antiCnt = 0;
- ReadCount(float[] cnt, boolean isFwd)
- {
- if(isFwd)
- {
- senseCnt = cnt[0];
- antiCnt = cnt[1];
- }
- else
- {
- senseCnt = cnt[1];
- antiCnt = cnt[0];
- }
- }
- }
}
diff --git a/uk/ac/sanger/artemis/components/alignment/ReadCount.java b/uk/ac/sanger/artemis/components/alignment/ReadCount.java
new file mode 100644
index 0000000..5d940ed
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/ReadCount.java
@@ -0,0 +1,40 @@
+/*
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2014 Genome Research Limited
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.components.alignment;
+
+class ReadCount
+{
+ protected float senseCnt = 0;
+ protected float antiCnt = 0;
+ ReadCount(float[] cnt, boolean isFwd)
+ {
+ if(isFwd)
+ {
+ senseCnt = cnt[0];
+ antiCnt = cnt[1];
+ }
+ else
+ {
+ senseCnt = cnt[1];
+ antiCnt = cnt[0];
+ }
+ }
+}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/ReadCountDialog.java b/uk/ac/sanger/artemis/components/alignment/ReadCountDialog.java
index 17861ff..35b5bc8 100644
--- a/uk/ac/sanger/artemis/components/alignment/ReadCountDialog.java
+++ b/uk/ac/sanger/artemis/components/alignment/ReadCountDialog.java
@@ -138,11 +138,14 @@ import uk.ac.sanger.artemis.util.StringVector;
if(qNames == null)
{
qNames = new StringVector();
- Object objs[] = systematicListSelectionPanel.getResultArray();
+ Object objs[];
+ if(systematicListSelectionPanel != null)
+ objs = systematicListSelectionPanel.getResultArray();
+ else
+ objs = Options.getOptions().getSystematicQualifierNames().toArray();
for(Object o: objs)
qNames.add((String)o);
}
-
return pickName(f, qNames);
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneEditorPanel.java b/uk/ac/sanger/artemis/components/genebuilder/GeneEditorPanel.java
index 5cf4c1d..2851efa 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneEditorPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneEditorPanel.java
@@ -40,7 +40,6 @@ import uk.ac.sanger.artemis.components.genebuilder.cv.CVPanel;
import uk.ac.sanger.artemis.components.genebuilder.gff.PropertiesPanel;
import uk.ac.sanger.artemis.components.genebuilder.ortholog.MatchPanel;
-
/**
* Panel for display controlled vocabulary terms for Chado
*/
@@ -92,22 +91,32 @@ public class GeneEditorPanel extends JPanel
coreButton = addOpenClosePanel("Core",qualifier_text_area, this, null);
add(qualifier_text_area);
- addDarkSeparator(this);
- refButton = addOpenClosePanel("References",refPanel, this, null);
- add(refPanel);
-
- addDarkSeparator(this);
- cvButton = addOpenClosePanel("Controlled Vocabulary", cvForm, this,
+ if(refPanel != null)
+ {
+ addDarkSeparator(this);
+ refButton = addOpenClosePanel("References",refPanel, this, null);
+ add(refPanel);
+ }
+
+ if(cvForm != null)
+ {
+ addDarkSeparator(this);
+ cvButton = addOpenClosePanel("Controlled Vocabulary", cvForm, this,
CVPanel.getDescription());
- add(cvForm);
-
- addDarkSeparator(this);
- matchButton = addOpenClosePanel("Match", matchForm, this,
+ add(cvForm);
+ }
+
+ if(matchForm != null)
+ {
+ addDarkSeparator(this);
+ matchButton = addOpenClosePanel("Match", matchForm, this,
MatchPanel.getDescription());
- add(matchForm);
-
+ add(matchForm);
+ }
+
add(Box.createVerticalGlue());
}
+
/**
* Open/close the sections if they contain elements or
@@ -116,9 +125,12 @@ public class GeneEditorPanel extends JPanel
public void updatePanelState()
{
coreButton.setOpen(!qualifier_text_area.getText().equals(""));
- cvButton.setOpen(!cvForm.isEmpty());
- refButton.setOpen(!refPanel.isEmpty());
- matchButton.setOpen(!matchForm.isEmpty());
+ if(cvForm != null)
+ cvButton.setOpen(!cvForm.isEmpty());
+ if(refPanel != null)
+ refButton.setOpen(!refPanel.isEmpty());
+ if(matchForm != null)
+ matchButton.setOpen(!matchForm.isEmpty());
propertiesButton.setOpen(!propertiesPanel.isEmpty());
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
index bee966d..7d8f160 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
@@ -61,6 +61,7 @@ import uk.ac.sanger.artemis.io.DatabaseInferredFeature;
import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.Feature;
+import uk.ac.sanger.artemis.io.GFF3Encoder;
import uk.ac.sanger.artemis.io.GFFDocumentEntry;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.InvalidRelationException;
@@ -126,7 +127,7 @@ public class GeneUtils
String value = featureSynonym.getSynonym().getName();
if(!featureSynonym.isCurrent())
- value.concat(GFFStreamFeature.encode(";current=false"));
+ value.concat(GFF3Encoder.encode(";current=false"));
Qualifier qualifier = feature.getQualifiers().getQualifierByName(name);
if(qualifier == null)
@@ -198,7 +199,7 @@ public class GeneUtils
final String qualifierString = new String(this_buff.getBytes());
int ind = qualifierString.indexOf('=');
final String name = qualifierString.substring(0, ind);
- final String value = GFFStreamFeature.decode(
+ final String value = GFF3Encoder.decode(
qualifierString.substring(ind+1, qualifierString.length()-1));
Qualifier qualifier = feature.getQualifiers().getQualifierByName(name);
diff --git a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java b/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
index a02fe75..03a72b4 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
@@ -34,7 +34,6 @@ import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Iterator;
import java.util.Set;
-import java.util.Vector;
import javax.swing.BorderFactory;
import javax.swing.Box;
@@ -184,7 +183,9 @@ public class PropertiesPanel extends JPanel
{
Qualifier idQualifier = gffQualifiers.getQualifierByName("ID");
Qualifier nameQualifier = gffQualifiers.getQualifierByName("Name");
-
+
+ if(idQualifier == null)
+ return;
final String uniquename = idQualifier.getValues().get(0);
uniquenameTextField = new JTextField(uniquename);
uniquenameTextField.setPreferredSize(calcPreferredMaxTextFieldWidth());
@@ -780,9 +781,13 @@ public class PropertiesPanel extends JPanel
private void addSynonym()
{
- final Vector<CvTerm> synonyms = DatabaseDocument.getCvterms("",
- ChadoTransactionManager.SYNONYM_TAG_CVNAME, false);
- final JExtendedComboBox list = new JExtendedComboBox(synonyms);
+ final JExtendedComboBox list;
+ if(GeneUtils.isDatabaseEntry(feature.getEmblFeature()))
+ list = new JExtendedComboBox(DatabaseDocument.getCvterms("",
+ ChadoTransactionManager.SYNONYM_TAG_CVNAME, false));
+ else
+ list = new JExtendedComboBox(ChadoTransactionManager.getSynonymTags());
+
final String options[] = { "CANCEL", "NEXT>"};
int select = JOptionPane.showOptionDialog(null, list,
@@ -790,12 +795,15 @@ public class PropertiesPanel extends JPanel
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE,
null, options, options[1]);
-
if(select == 0)
return;
-
+
Box xBox = Box.createHorizontalBox();
- final String synonymName = ((CvTerm)list.getSelectedItem()).getName();
+ final String synonymName;
+ if(list.getSelectedItem() instanceof CvTerm)
+ synonymName = ((CvTerm)list.getSelectedItem()).getName();
+ else
+ synonymName = (String) list.getSelectedItem();
final JLabel name = new JLabel( synonymName );
xBox.add(name);
diff --git a/uk/ac/sanger/artemis/io/DocumentEntryFactory.java b/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
index f530a08..a83b7b2 100644
--- a/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
+++ b/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
@@ -31,6 +31,8 @@ import uk.ac.sanger.artemis.util.LinePushBackReader;
import java.io.File;
import java.io.IOException;
+import javax.swing.JOptionPane;
+
/**
* This class contains the method makeDocumentEntry (), which creates a
@@ -79,7 +81,18 @@ abstract public class DocumentEntryFactory
document.getInputStream() instanceof net.sf.samtools.util.BlockCompressedInputStream)
{
if(IndexedGFFDocumentEntry.isIndexed( ((File)document.getLocation()) ))
- return new IndexedGFFDocumentEntry(document);
+ {
+ Object[] possibleValues = { "Use index", "Ignore index" };
+ int sel = JOptionPane.showOptionDialog(null,
+ "Use the GFF index file (to increase the performance)\n"+
+ "or concatenate the sequences together?",
+ "Indexed GFF",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, possibleValues, possibleValues[0]);
+
+ if(sel == 0)
+ return new IndexedGFFDocumentEntry(document);
+ }
}
final LinePushBackReader document_reader =
diff --git a/uk/ac/sanger/artemis/io/GFF3AttributeAggregator.java b/uk/ac/sanger/artemis/io/GFF3AttributeAggregator.java
new file mode 100644
index 0000000..4a8a737
--- /dev/null
+++ b/uk/ac/sanger/artemis/io/GFF3AttributeAggregator.java
@@ -0,0 +1,38 @@
+/* GFF3AttributeAggregator.java
+ * *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2014 Genome Research Limited
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+
+package uk.ac.sanger.artemis.io;
+
+import uk.ac.sanger.artemis.util.StringVector;
+
+/**
+ * Abstraction for processing various Artemis qualifiers into usable GFF3 strings.
+ */
+public interface GFF3AttributeAggregator {
+ /**
+ * Prepare a set of string values as a GFF attribute value.
+ * @param values the value set to convert to a <code>String</code>
+ * @return the <code>String</code> representation
+ */
+ public abstract String process(StringVector values);
+
+}
diff --git a/uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java b/uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java
new file mode 100644
index 0000000..b8bba7e
--- /dev/null
+++ b/uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java
@@ -0,0 +1,214 @@
+/* GFF3AttributeBuilder.java
+ * *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2014 Genome Research Limited
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+
+package uk.ac.sanger.artemis.io;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.lang.StringBuilder;
+
+import uk.ac.sanger.artemis.io.EntryInformationException;
+import uk.ac.sanger.artemis.io.GFF3AttributeAggregator;
+import uk.ac.sanger.artemis.util.StringVector;
+
+public class GFF3AttributeBuilder {
+ private HashMap<String, String> attrs = new HashMap<String, String>();
+ private HashMap<String, String> mappings = new HashMap<String, String>();
+ private HashMap<String, String> glue = new HashMap<String, String>();
+ private HashSet<String> ignores = new HashSet<String>();
+ private HashMap<String, String> clones = new HashMap<String, String>();
+ private HashMap<String, GFF3AttributeAggregator> aggs = new HashMap<String, GFF3AttributeAggregator>();
+ private HashSet<String> reserved = new HashSet<String>(
+ 13);
+ private static final GFF3AttributeAggregator defaultAgg = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ final String this_value = GFF3Encoder.encode(values.elementAt(value_index));
+ if (value_index > 0 && value_index < (values.size())) {
+ buffer.append(",");
+ }
+ buffer.append(this_value);
+ }
+ }
+ return buffer.toString();
+ }
+ };
+
+ final String reserved_a[] = { "ID",
+ "Name", "Alias", "Parent", "Derives_from", "Target", "Gap", "Note",
+ "Dbxref", "Ontology_term", "Start_range", "End_range", "Is_circular" };
+
+ public GFF3AttributeBuilder() {
+ for (String s : reserved_a) {
+ reserved.add(s);
+ }
+ }
+
+ public void setMapping(String attr, String mapsto) {
+ /* XXX: make sure only one level of mapping is used */
+ mappings.put(attr, mapsto);
+ }
+
+ public void unsetMapping(String attr, String mapsto) {
+ mappings.remove(attr);
+ }
+
+ public void setGlue(String attr, String glue_str) {
+ glue.put(attr, glue_str);
+ }
+
+ public void unsetGlue(String attr) {
+ glue.remove(attr);
+ }
+
+ public void setClone(String attr, String glue_str) {
+ clones.put(attr, glue_str);
+ }
+
+ public void unsetClone(String attr) {
+ clones.remove(attr);
+ }
+
+ public void setAggregator(String attr, GFF3AttributeAggregator agg) {
+ aggs.put(attr, agg);
+ }
+
+ public void unsetAggregator(String attr, GFF3AttributeAggregator agg) {
+ aggs.remove(attr);
+ }
+
+ public void ignore(String attr) {
+ ignores.add(attr);
+ }
+
+ public void unignore(String attr) {
+ ignores.remove(attr);
+ }
+
+ public void add(String attr, String val) {
+ StringVector v = new StringVector(val);
+ add(attr, v);
+ }
+
+ public void add(String attr, StringVector val) {
+ String origAttr = attr;
+ ArrayList<String> targetAttrs = new ArrayList<String>();
+ // expand attributes
+ if (clones.containsKey(attr))
+ targetAttrs.add(clones.get(attr));
+ if (mappings.containsKey(attr)) {
+ attr = mappings.get(attr);
+ targetAttrs.add(attr);
+ if (clones.containsKey(attr))
+ targetAttrs.add(clones.get(attr));
+ } else {
+ targetAttrs.add(attr);
+ }
+ // drop attributes with null or empty values
+ if (val == null || (val.size() == 1
+ && val.elementAt(0).replaceAll("\\s+", "").equals("")) )
+ return;
+ // process expanded list of attributes
+ for (String this_attr : targetAttrs) {
+ String aggregatedVal;
+ // do we have an aggregator for this type?
+ if (aggs.containsKey(origAttr)) {
+ GFF3AttributeAggregator agg = aggs.get(origAttr);
+ aggregatedVal = agg.process(val);
+ } else if (aggs.containsKey(this_attr)) {
+ GFF3AttributeAggregator agg = aggs.get(this_attr);
+ aggregatedVal = agg.process(val);
+ } else {
+ aggregatedVal = defaultAgg.process(val);
+ }
+ // do not add empty values
+ if (aggregatedVal == null)
+ return;
+ // append or set?
+ if (attrs.containsKey(this_attr)) {
+ String this_val = attrs.get(this_attr),
+ this_glue = " ";
+ if (glue.containsKey(this_attr))
+ this_glue = glue.get(this_attr);
+ this_val = this_val + this_glue + aggregatedVal;
+ attrs.put(this_attr, this_val);
+ } else {
+ attrs.put(this_attr, aggregatedVal);
+ }
+ }
+ }
+
+ private String decapitalize(String line) {
+ if (!reserved.contains(line)
+ && Character.toUpperCase(line.charAt(0)) == line.charAt(0)) {
+ return Character.toLowerCase(line.charAt(0)) + line.substring(1);
+ } else {
+ return line;
+ }
+ }
+
+ public String get(String attr) throws EntryInformationException {
+ if (mappings.containsKey(attr)) {
+ attr = mappings.get(attr);
+ }
+ if (attrs.containsKey(attr)) {
+ return attrs.get(attr);
+ } else {
+ throw new EntryInformationException("empty attribute value for " + attr);
+ }
+ }
+
+ private Comparator<String> comparator = new Comparator<String>() {
+ // make sure 'ID' is always at the beginning of the attribute list
+ public int compare(String o1, String o2) {
+ if (o1.equals("ID"))
+ return -1;
+ if (o2.equals("ID"))
+ return 1;
+ return o1.compareTo(o2);
+ }
+ };
+
+ public String toString() {
+ StringBuilder b = new StringBuilder();
+ int i = 0;
+ ArrayList<String> sortedAttrs = new ArrayList<String>(attrs.keySet());
+ Collections.sort(sortedAttrs, comparator);
+ for (String key : sortedAttrs) {
+ if (!ignores.contains(key)) {
+ String value = attrs.get(key);
+ if (value.length() > 0) {
+ if (i++ != 0)
+ b.append(";");
+ b.append(decapitalize(key) + "=" + value);
+ }
+ }
+ }
+ return b.toString();
+ }
+}
diff --git a/uk/ac/sanger/artemis/io/GFF3Encoder.java b/uk/ac/sanger/artemis/io/GFF3Encoder.java
new file mode 100644
index 0000000..49f5507
--- /dev/null
+++ b/uk/ac/sanger/artemis/io/GFF3Encoder.java
@@ -0,0 +1,38 @@
+/* GFF3Encoder.java
+ * *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2014 Genome Research Limited
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+
+package uk.ac.sanger.artemis.io;
+
+import org.apache.commons.lang.StringUtils;
+
+public class GFF3Encoder {
+ public static final String mapChars[] = { "%", "&", ",", ";", "=", "\t", "\n", "\r" };
+ public static final String mappedEscapes[] = { "%25", "%26", "%2C", "%3B", "%3D", "%09", "%0A", "%0D" };
+
+ public static String decode(String s) {
+ return StringUtils.replaceEach(s, mappedEscapes, mapChars);
+ }
+
+ public static String encode(String s) {
+ return StringUtils.replaceEach(s, mapChars, mappedEscapes);
+ }
+}
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 8e68ac3..7478608 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -25,11 +25,12 @@
package uk.ac.sanger.artemis.io;
-
import java.util.Hashtable;
import java.util.HashSet;
import java.util.Enumeration;
import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.Vector;
@@ -47,330 +48,273 @@ import uk.ac.sanger.artemis.util.LinePushBackReader;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.ReadOnlyException;
import uk.ac.sanger.artemis.util.StringVector;
-
+import uk.ac.sanger.artemis.io.GFF3Encoder;
/**
- * A StreamFeature that thinks it is a GFF feature.
- * @author Kim Rutherford
+ * A StreamFeature that thinks it is a GFF feature.
+ *
+ * @author Kim Rutherford
**/
-public class GFFStreamFeature extends SimpleDocumentFeature
- implements DocumentFeature, StreamFeature, ComparableFeature
-{
+public class GFFStreamFeature extends SimpleDocumentFeature implements
+ DocumentFeature, StreamFeature, ComparableFeature {
- private static org.apache.log4j.Logger logger4j =
- org.apache.log4j.Logger.getLogger(GFFStreamFeature.class);
+ private static org.apache.log4j.Logger logger4j = org.apache.log4j.Logger
+ .getLogger(GFFStreamFeature.class);
/** store for spliced features containing id and range of each segment */
- private Hashtable<String, Range> id_range_store;
+ private Hashtable<String, Range> id_range_store;
/** store a record of the new and old uniquenames that have been changed */
- private Hashtable<String, String> newIdMapToOldId;
+ private Hashtable<String, String> newIdMapToOldId;
/** store the Timestamp for the feature */
- private Timestamp timelastmodified;
+ private Timestamp timelastmodified;
- private ChadoCanonicalGene chadoGene;
+ private ChadoCanonicalGene chadoGene;
- private boolean visible = true;
+ private boolean visible = true;
/** combined feature_relationship.rank store for exons */
- private Hashtable<String, Integer> feature_relationship_rank_store;
+ private Hashtable<String, Integer> feature_relationship_rank_store;
- /** first tabbed parameter */
- private String gffSeqName;
+ /** first tabbed parameter */
+ private String gffSeqName;
/** second tabbed parameter */
- private String gffSource;
+ private String gffSource;
/** duplication count */
- private short duplicate = 0;
+ private short duplicate = 0;
protected static Hashtable<String, Range> contig_ranges;
- private boolean lazyLoaded = false;
- private org.gmod.schema.sequence.Feature chadoLazyFeature;
- private boolean readOnlyFeature = false;
-
-
- private static String MAP_DECODE[][] = {
- { " ", "%20" }, // white space
- { ",", "%2C" }, // comma
- { ";", "%3B" }, // semi-colon
- { "=", "%3D" }, // equals
- { "\t", "%09" }, // tab
- { " ", "+" }, // white space
- { "+", "%2B" },
- { "(", "%28" }, // left bracket
- { ")", "%29" }, // right bracket
- { "'", "\"" }
- };
-
- private static String MAP_ENCODE[][] = {
-// { " ", "%20" }, // white space
- { ",", "%2C" }, // comma
- { ";", "%3B" }, // semi-colon
- { "=", "%3D" }, // equals
- { "\t", "%09" }, // tab
- { "+", "%2B" },
- { " ", "+" }, // white space
- { "(", "%28" }, // left bracket
- { ")", "%29" }, // right bracket
- { "\n", "%5C" } // new-line
- };
-
- private static Set<String> attrs_to_filter = new HashSet<String>();
+ private boolean lazyLoaded = false;
+ private org.gmod.schema.sequence.Feature chadoLazyFeature;
+ private boolean readOnlyFeature = false;
+
+ private static Set<String> attrs_to_filter = new HashSet<String>();
/**
- * Registers an attribute not to be included in the GFF3 output for
- * GFFStreamFeatures
- * @param attr The GFF3 attribute to remove
+ * Registers an attribute not to be included in the GFF3 output for
+ * GFFStreamFeatures
+ *
+ * @param attr
+ * The GFF3 attribute to remove
**/
- public static void removeAttribute(String attr)
- {
+ public static void removeAttribute(String attr) {
attrs_to_filter.add(attr);
}
/**
- * Registers an attribute to be included in the GFF3 output for
- * GFFStreamFeatures
- * @param attr The GFF3 attribute to include
+ * Registers an attribute to be included in the GFF3 output for
+ * GFFStreamFeatures
+ *
+ * @param attr
+ * The GFF3 attribute to include
**/
- public static void includeAttribute(String attr)
- {
+ public static void includeAttribute(String attr) {
attrs_to_filter.remove(attr);
}
/**
- * Create a new GFFStreamFeature object. The feature should be added
- * to an Entry (with Entry.add()).
- * @param key The new feature key
- * @param location The Location object for the new feature
- * @param qualifiers The qualifiers for the new feature
+ * Create a new GFFStreamFeature object. The feature should be added to an
+ * Entry (with Entry.add()).
+ *
+ * @param key
+ * The new feature key
+ * @param location
+ * The Location object for the new feature
+ * @param qualifiers
+ * The qualifiers for the new feature
**/
public GFFStreamFeature(final Key key, final Location location,
- final QualifierVector qualifiers)
- {
+ final QualifierVector qualifiers) {
super(null);
- try
- {
+ try {
setKey(key);
setLocation(location);
setQualifiers(qualifiers);
- if(getQualifierByName("ID") == null)
- {
+ if (getQualifierByName("ID") == null) {
String idStr = null;
StringVector v = Options.getOptions().getSystematicQualifierNames();
- for(int i=0; i<v.size(); i++)
- {
- final String sysName = (String)v.get(i);
- if(getQualifierByName(sysName) != null)
- {
- idStr = (String)getQualifierByName(sysName).getValues().get(0);
+ for (int i = 0; i < v.size(); i++) {
+ final String sysName = (String) v.get(i);
+ if (getQualifierByName(sysName) != null) {
+ idStr = (String) getQualifierByName(sysName).getValues().get(0);
break;
}
}
// autogenerate ID
- if(idStr == null)
- idStr = key.getKeyString()+":"+location.toString();
+ if (idStr == null)
+ idStr = key.getKeyString() + ":" + location.toString();
setQualifier(new Qualifier("ID", idStr));
}
- }
- catch(EntryInformationException e)
- {
+ } catch (EntryInformationException e) {
// this should never happen because the feature will not be in an Entry
throw new Error("internal error - unexpected exception: " + e);
- }
- catch(ReadOnlyException e)
- {
+ } catch (ReadOnlyException e) {
// this should never happen because the feature will not be in an Entry
throw new Error("internal error - unexpected exception: " + e);
- }
- catch(OutOfRangeException e)
- {
+ } catch (OutOfRangeException e) {
// this should never happen because the feature will not be in an Entry
throw new Error("internal error - unexpected exception: " + e);
}
}
- public GFFStreamFeature(final Feature feature)
- {
+ public GFFStreamFeature(final Feature feature) {
this(feature, false);
}
/**
- * Create a new GFFStreamFeature with the same key, location and
- * qualifiers as the given feature. The feature should be added to an
- * Entry (with Entry.add()).
- * @param feature The feature to copy.
+ * Create a new GFFStreamFeature with the same key, location and qualifiers as
+ * the given feature. The feature should be added to an Entry (with
+ * Entry.add()).
+ *
+ * @param feature
+ * The feature to copy.
**/
- public GFFStreamFeature(final Feature feature, final boolean isDuplicatedInChado)
- {
+ @SuppressWarnings("unchecked")
+ public GFFStreamFeature(final Feature feature,
+ final boolean isDuplicatedInChado) {
this(feature.getKey(), feature.getLocation(), feature.getQualifiers());
- if(feature instanceof GFFStreamFeature)
- {
- if(((GFFStreamFeature)feature).id_range_store != null)
- this.id_range_store =
- (Hashtable)(((GFFStreamFeature)feature).id_range_store).clone();
+ if (feature instanceof GFFStreamFeature) {
+ if (((GFFStreamFeature) feature).id_range_store != null)
+ this.id_range_store = (Hashtable<String, Range>) (((GFFStreamFeature) feature).id_range_store)
+ .clone();
- if(((GFFStreamFeature)feature).feature_relationship_rank_store != null)
- this.feature_relationship_rank_store =
- (Hashtable)(((GFFStreamFeature)feature).feature_relationship_rank_store).clone();
+ if (((GFFStreamFeature) feature).feature_relationship_rank_store != null)
+ this.feature_relationship_rank_store = (Hashtable<String, Integer>) (((GFFStreamFeature) feature).feature_relationship_rank_store)
+ .clone();
- this.setGffSeqName(((GFFStreamFeature)feature).getGffSeqName());
- this.setGffSource(((GFFStreamFeature)feature).getGffSource());
+ this.setGffSeqName(((GFFStreamFeature) feature).getGffSeqName());
+ this.setGffSource(((GFFStreamFeature) feature).getGffSource());
- if(isDuplicatedInChado)
- {
- try
- {
+ if (isDuplicatedInChado) {
+ try {
final String uniquename;
final String duplicatePrefix;
- if(feature instanceof GFFStreamFeature)
- {
- ((GFFStreamFeature)feature).duplicate++;
- duplicatePrefix = "DUP"+Short.toString(((GFFStreamFeature)feature).duplicate)+"-";
- }
- else
+ if (feature instanceof GFFStreamFeature) {
+ ((GFFStreamFeature) feature).duplicate++;
+ duplicatePrefix = "DUP"
+ + Short.toString(((GFFStreamFeature) feature).duplicate) + "-";
+ } else
duplicatePrefix = "DUP";
- if(id_range_store != null)
- {
- final Hashtable<String, Range> new_id_range_store = new Hashtable<String, Range>(id_range_store.size());
+ if (id_range_store != null) {
+ final Hashtable<String, Range> new_id_range_store = new Hashtable<String, Range>(
+ id_range_store.size());
final Enumeration<String> enumIdRangeStore = id_range_store.keys();
- while(enumIdRangeStore.hasMoreElements())
- {
+ while (enumIdRangeStore.hasMoreElements()) {
final String keyId = enumIdRangeStore.nextElement();
- final Range range = id_range_store.get(keyId);
- new_id_range_store.put(duplicatePrefix+keyId, range);
+ final Range range = id_range_store.get(keyId);
+ new_id_range_store.put(duplicatePrefix + keyId, range);
}
id_range_store.clear();
- this.id_range_store = (Hashtable) new_id_range_store.clone();
+ this.id_range_store = (Hashtable<String, Range>) new_id_range_store
+ .clone();
-
- if(getLocation().getRanges().size() > 1)
+ if (getLocation().getRanges().size() > 1)
uniquename = getSegmentID(getLocation().getRanges());
- else
- {
- if( ((String)getQualifierByName("ID").getValues().get(0)).endsWith("}") )
+ else {
+ if (((String) getQualifierByName("ID").getValues().get(0))
+ .endsWith("}"))
uniquename = id_range_store.keys().nextElement();
else
- uniquename = duplicatePrefix+ (String)getQualifierByName("ID").getValues().get(0);
+ uniquename = duplicatePrefix
+ + (String) getQualifierByName("ID").getValues().get(0);
}
- }
- else
- uniquename = duplicatePrefix+ (String)getQualifierByName("ID").getValues().get(0);
+ } else
+ uniquename = duplicatePrefix
+ + (String) getQualifierByName("ID").getValues().get(0);
setQualifier(new Qualifier("ID", uniquename));
- if(getQualifierByName("Parent") != null)
- {
- final String parent =
- (String) getQualifierByName("Parent").getValues().get(0);
- setQualifier(new Qualifier("Parent", duplicatePrefix+parent));
+ if (getQualifierByName("Parent") != null) {
+ final String parent = (String) getQualifierByName("Parent")
+ .getValues().get(0);
+ setQualifier(new Qualifier("Parent", duplicatePrefix + parent));
}
- if(getQualifierByName("Derives_from") != null)
- {
- final String derives_from =
- (String) getQualifierByName("Derives_from").getValues().get(0);
- setQualifier(new Qualifier("Derives_from", duplicatePrefix+derives_from));
+ if (getQualifierByName("Derives_from") != null) {
+ final String derives_from = (String) getQualifierByName(
+ "Derives_from").getValues().get(0);
+ setQualifier(new Qualifier("Derives_from", duplicatePrefix
+ + derives_from));
}
// remove qualifiers that don't get transferred to duplicate
- final String removeQualifierNames[] =
- { "feature_id",
- "timelastmodified",
- "feature_relationship_rank",
- ProteinMapPanel.POLYPEPTIDE_DOMAIN,
- ProteinMapPanel.TMHMM[0],
- ProteinMapPanel.TMHMM[1],
- ProteinMapPanel.TMHMM[2],
- ProteinMapPanel.TMHMM[3],
- MatchPanel.ORTHOLOG,
- MatchPanel.ORTHOLOG
- };
-
- for(int i=0;i<removeQualifierNames.length; i++)
+ final String removeQualifierNames[] = { "feature_id",
+ "timelastmodified", "feature_relationship_rank",
+ ProteinMapPanel.POLYPEPTIDE_DOMAIN, ProteinMapPanel.TMHMM[0],
+ ProteinMapPanel.TMHMM[1], ProteinMapPanel.TMHMM[2],
+ ProteinMapPanel.TMHMM[3], MatchPanel.ORTHOLOG,
+ MatchPanel.ORTHOLOG };
+
+ for (int i = 0; i < removeQualifierNames.length; i++)
removeQualifierByName(removeQualifierNames[i]);
+ } catch (ReadOnlyException e) {
+ } catch (EntryInformationException e) {
}
- catch(ReadOnlyException e){}
- catch(EntryInformationException e){}
- }
- else
- {
- chadoGene = ((GFFStreamFeature)feature).chadoGene;
+ } else {
+ chadoGene = ((GFFStreamFeature) feature).chadoGene;
}
}
}
/**
- * Create a new GFFStreamFeature from the given line. The String should be
- * in gene finder format.
+ * Create a new GFFStreamFeature from the given line. The String should be in
+ * gene finder format.
**/
- public GFFStreamFeature(final String line)
- throws ReadFormatException
- {
+ public GFFStreamFeature(final String line) throws ReadFormatException {
super(null);
final StringVector line_bits = StringVector.getStrings(line, "\t", true);
- if(line_bits.size() < 8)
- throw new ReadFormatException("invalid GFF line: 8 fields needed " +
- "(got " + line_bits.size () +
- " fields) from: " + line);
+ if (line_bits.size() < 8)
+ throw new ReadFormatException("invalid GFF line: 8 fields needed "
+ + "(got " + line_bits.size() + " fields) from: " + line);
final String start_base_str = line_bits.elementAt(3).trim();
- final String end_base_str = line_bits.elementAt(4).trim();
+ final String end_base_str = line_bits.elementAt(4).trim();
final int start_base;
final int end_base;
- try
- {
+ try {
start_base = Integer.parseInt(start_base_str);
- end_base = Integer.parseInt(end_base_str);
- }
- catch(NumberFormatException e)
- {
- throw new ReadFormatException("Could not understand the start or end base " +
- "of a GFF feature: " + start_base_str +
- " " + end_base_str);
+ end_base = Integer.parseInt(end_base_str);
+ } catch (NumberFormatException e) {
+ throw new ReadFormatException(
+ "Could not understand the start or end base " + "of a GFF feature: "
+ + start_base_str + " " + end_base_str);
}
// start of qualifier parsing and setting
- try
- {
+ try {
final boolean complement_flag;
- if(line_bits.elementAt(6).equals("+"))
+ if (line_bits.elementAt(6).equals("+"))
complement_flag = false;
- else if(line_bits.elementAt(6).equals("-"))
+ else if (line_bits.elementAt(6).equals("-"))
complement_flag = true;
- else
- {
+ else {
// must be unstranded
complement_flag = false;
}
- if(line_bits.size() == 9)
- {
+ if (line_bits.size() == 9) {
final String rest_of_line = line_bits.elementAt(8);
final Hashtable<String, StringVector> attributes = parseAttributes(rest_of_line);
- for(final Enumeration<String> attribute_enum = attributes.keys();
- attribute_enum.hasMoreElements();)
- {
+ for (final Enumeration<String> attribute_enum = attributes.keys(); attribute_enum
+ .hasMoreElements();) {
String name = attribute_enum.nextElement();
final StringVector values = attributes.get(name);
- if(MatchPanel.isClusterTag(name))
- {
+ if (MatchPanel.isClusterTag(name)) {
List<ClusterLazyQualifierValue> lazyValues = new Vector<ClusterLazyQualifierValue>();
- for(int i=0; i<values.size(); i++)
- lazyValues.add(
- new ClusterLazyQualifierValue( (String)values.get(i), name,
- this ));
+ for (int i = 0; i < values.size(); i++)
+ lazyValues.add(new ClusterLazyQualifierValue((String) values
+ .get(i), name, this));
setQualifier(new QualifierLazyLoading(name, lazyValues));
- }
- else
- {
- if(values.size() == 0)
+ } else {
+ if (values.size() == 0)
setQualifier(new Qualifier(name));
else
setQualifier(new Qualifier(name, values));
@@ -378,200 +322,175 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
}
- if( !line_bits.elementAt(0).equals("null") )
- setGffSeqName( decode(line_bits.elementAt(0)) );
+ if (!line_bits.elementAt(0).equals("null"))
+ setGffSeqName(GFF3Encoder.decode(line_bits.elementAt(0)));
setKey(new Key(line_bits.elementAt(2)));
setGffSource(line_bits.elementAt(1));
- if( !line_bits.elementAt(5).equals(".") )
- {
- final Qualifier score_qualifier =
- new Qualifier("score", line_bits.elementAt(5));
+ if (!line_bits.elementAt(5).equals(".")) {
+ final Qualifier score_qualifier = new Qualifier("score",
+ line_bits.elementAt(5));
setQualifier(score_qualifier);
}
String frame = line_bits.elementAt(7);
- if(frame.equals ("0"))
+ if (frame.equals("0"))
frame = "1";
- else if(frame.equals("1"))
+ else if (frame.equals("1"))
frame = "2";
- else if(frame.equals("2"))
+ else if (frame.equals("2"))
frame = "3";
else
frame = ".";
- if(!frame.equals("."))
- {
- final Qualifier codon_start_qualifier =
- new Qualifier("codon_start", frame);
+ if (!frame.equals(".")) {
+ final Qualifier codon_start_qualifier = new Qualifier("codon_start",
+ frame);
setQualifier(codon_start_qualifier);
}
- if(start_base > end_base)
- throw new ReadFormatException("start position is greater than end " +
- "position: " + start_base + " > " +
- end_base+"\n"+line);
+ if (start_base > end_base)
+ throw new ReadFormatException("start position is greater than end "
+ + "position: " + start_base + " > " + end_base + "\n" + line);
- if(start_base < 0)
- throw new ReadFormatException("start position must be positive: " +
- start_base);
+ if (start_base < 0)
+ throw new ReadFormatException("start position must be positive: "
+ + start_base);
final Range location_range = new Range(start_base, end_base);
final RangeVector location_ranges = new RangeVector(location_range);
setLocation(new Location(location_ranges, complement_flag));
- }
- catch(ReadOnlyException e)
- {
+ } catch (ReadOnlyException e) {
throw new Error("internal error - unexpected exception: " + e);
- }
- catch(EntryInformationException e)
- {
+ } catch (EntryInformationException e) {
throw new Error("internal error - unexpected exception: " + e);
- }
- catch(OutOfRangeException e)
- {
+ } catch (OutOfRangeException e) {
throw new Error("internal error - unexpected exception: " + e);
}
- //this.gff_lines = new StringVector(line);
+ // this.gff_lines = new StringVector(line);
}
/**
- *
- * Store for spliced regions of segments ID's and ranges.
- *
- */
- public void setSegmentRangeStore(Hashtable<String, Range> id_range_store)
- {
+ *
+ * Store for spliced regions of segments ID's and ranges.
+ *
+ */
+ public void setSegmentRangeStore(Hashtable<String, Range> id_range_store) {
this.id_range_store = id_range_store;
}
- public Hashtable<String, Range> getSegmentRangeStore()
- {
- if(id_range_store == null)
- {
+ public Hashtable<String, Range> getSegmentRangeStore() {
+ if (id_range_store == null) {
id_range_store = new Hashtable<String, Range>();
- id_range_store.put((String)this.getQualifierByName("ID").getValues().get(0),
- this.getLocation().getTotalRange());
+ id_range_store.put((String) this.getQualifierByName("ID").getValues()
+ .get(0), this.getLocation().getTotalRange());
}
return id_range_store;
}
- public Hashtable<String, String> getNewIdMapToOldId()
- {
+ public Hashtable<String, String> getNewIdMapToOldId() {
return newIdMapToOldId;
}
/**
* Used when changing spliced feature uniquenames
+ *
* @param newIdMapToOldId
*/
- public void setNewIdMapToOldId(Hashtable<String, String> newIdMapToOldId)
- {
+ public void setNewIdMapToOldId(Hashtable<String, String> newIdMapToOldId) {
this.newIdMapToOldId = newIdMapToOldId;
}
/**
* Store for ID's and CHADO feature_relationship.rank
+ *
* @param feature_relationship_rank_store
*/
public void setFeature_relationship_rank_store(
- Hashtable<String, Integer> feature_relationship_rank_store)
- {
+ Hashtable<String, Integer> feature_relationship_rank_store) {
this.feature_relationship_rank_store = feature_relationship_rank_store;
}
/**
* Store for ID's and CHADO feature_relationship.rank
+ *
* @return
*/
- public Hashtable<String, Integer> getFeature_relationship_rank_store()
- {
+ public Hashtable<String, Integer> getFeature_relationship_rank_store() {
return feature_relationship_rank_store;
}
-
/**
* Get the chado uniquename
+ *
* @param r
* @return
*/
- public String getSegmentID(final Range r)
- {
- if(id_range_store != null)
- {
+ public String getSegmentID(final Range r) {
+ if ( id_range_store != null &&
+ getKey().getKeyString().indexOf("gene") == -1 &&
+ getKey().getKeyString().indexOf("RNA") == -1 ) {
int offset = 0;
- if(getGffSeqName() != null && contig_ranges != null &&
- contig_ranges.containsKey(getGffSeqName()))
- {
+ if (getGffSeqName() != null && contig_ranges != null
+ && contig_ranges.containsKey(getGffSeqName())) {
// adjust for coordinates in multi-sequence GFF
Range offset_range = contig_ranges.get(getGffSeqName());
- offset = offset_range.getStart()-1;
+ offset = offset_range.getStart() - 1;
}
Enumeration<String> enum_ranges = id_range_store.keys();
- while(enum_ranges.hasMoreElements())
- {
- String key = enum_ranges.nextElement();
+ while (enum_ranges.hasMoreElements()) {
+ String key = enum_ranges.nextElement();
Range range = id_range_store.get(key);
- if(range.getStart() == r.getStart()-offset &&
- range.getEnd() == r.getEnd()-offset)
+ if (range.getStart() == r.getStart() - offset
+ && range.getEnd() == r.getEnd() - offset)
return key;
}
- }
- else if (getQualifierByName("ID") != null)
- {
- return (String)getQualifierByName("ID").getValues().get(0);
+ } else if (getQualifierByName("ID") != null) {
+ return (String) getQualifierByName("ID").getValues().get(0);
}
- logger4j.warn("RANGE NOT FOUND "+r.toString());
+ logger4j.warn("RANGE NOT FOUND " + r.toString());
return null;
}
/**
- * Get the feature ID based on the segments chado
- * uniquename's.
+ * Get the feature ID based on the segments chado uniquename's.
+ *
* @param rv
* @return
*/
- public String getSegmentID(final RangeVector rv)
- {
+ public String getSegmentID(final RangeVector rv) {
String id = "";
- if(id_range_store != null)
- {
+ if (id_range_store != null) {
String id_new;
Range range;
int index;
- for(int i=0; i<rv.size(); i++)
- {
- range = (Range)rv.get(i);
+ for (int i = 0; i < rv.size(); i++) {
+ range = (Range) rv.get(i);
id_new = getSegmentID(range);
String prefix[] = getPrefix(id_new, ':');
- if(prefix[0] != null)
- {
+ if (prefix[0] != null) {
index = id.indexOf(prefix[0]);
- if(id.equals("") || index < 0)
- {
- if(!id.equals(""))
- id = id +",";
- id = id+prefix[0] + "{" + prefix[1] + "}";
+ if (id.equals("") || index < 0) {
+ if (!id.equals(""))
+ id = id + ",";
+ id = id + prefix[0] + "{" + prefix[1] + "}";
continue;
}
index = id.indexOf('}', index);
- id = id.substring(0,index) + "," +
- prefix[1] + id.substring(index);
- }
- else if(id_new != null)
- {
- if(!id.equals(""))
- id = id +",";
- id = id+id_new;
+ id = id.substring(0, index) + "," + prefix[1] + id.substring(index);
+ } else if (id_new != null) {
+ if (!id.equals(""))
+ id = id + ",";
+ id = id + id_new;
}
}
}
@@ -580,204 +499,149 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
/**
- * Get the ID prefix, e.g. for SPAC1556.06.1:exon:2
- * returns SPAC1556.06.1:exon as the prefix and 2 as the
- * index.
+ * Get the ID prefix, e.g. for SPAC1556.06.1:exon:2 returns SPAC1556.06.1:exon
+ * as the prefix and 2 as the index.
+ *
* @param id
* @return
*/
- public String[] getPrefix(final String id,
- final char separator)
- {
+ public String[] getPrefix(final String id, final char separator) {
String prefix[] = new String[2];
int index = id.lastIndexOf(separator);
- if(index > -1)
- {
- prefix[0] = id.substring(0,index);
- prefix[1] = id.substring(index+1);
+ if (index > -1) {
+ prefix[0] = id.substring(0, index);
+ prefix[1] = id.substring(index + 1);
}
return prefix;
}
/**
* Used to automatically generate
+ *
* @param prefix
* @return
*/
- public int getAutoNumber(final String prefix,
- final char separator)
- {
- int auto = 1;
+ public int getAutoNumber(final String prefix, final char separator) {
+ int auto = 1;
String val = prefix + separator + auto;
- while(id_range_store.containsKey(val))
- {
+ while (id_range_store.containsKey(val)) {
auto++;
val = prefix + separator + auto;
}
return auto;
}
-
- /**
- * For gff-version 3:
- * http://www.sequenceontology.org/gff3.shtml
- * Remove URL escaping rule (e.g. space="%20" or "+")
- */
- public static String decode(String s)
- {
- int ind;
- String enc;
- String dec;
-
- for(int i=0; i<MAP_DECODE.length; i++)
- {
- enc = MAP_DECODE[i][1];
- dec = MAP_DECODE[i][0];
- while( (ind = s.indexOf(enc)) > -1)
- s = s.substring(0,ind) + dec + s.substring(ind+enc.length());
- }
- return s;
- }
-
-
/**
- * For gff-version 3:
- * http://www.sequenceontology.org/gff3.shtml
- * Add URL escaping rule (e.g. space="%20" or "+")
- */
- public static String encode(String s)
- {
- int ind;
- String enc;
- String dec;
-
- for(int i=0; i<MAP_ENCODE.length; i++)
- {
- enc = MAP_ENCODE[i][1];
- dec = MAP_ENCODE[i][0];
- while( (ind = s.indexOf(dec)) > -1 )
- s = s.substring(0,ind) + enc + s.substring(ind+1);
- }
- return s;
- }
-
-
- /**
- * Return the reference of a new copy of this Feature.
+ * Return the reference of a new copy of this Feature.
**/
- public Feature copy()
- {
+ public Feature copy() {
final Feature return_value = new GFFStreamFeature(this);
return return_value;
}
/**
- * Read and return a GFFStreamFeature from a stream. A feature must be the
- * next thing in the stream.
- * @param stream the Feature is read from this stream
- * @exception IOException thrown if there is a problem reading the Feature -
- * most likely ReadFormatException.
- * @exception InvalidRelationException Thrown if this Feature cannot contain
- * the given Qualifier.
- * @return null if in_stream is at the end of file when the method is
- * called
+ * Read and return a GFFStreamFeature from a stream. A feature must be the
+ * next thing in the stream.
+ *
+ * @param stream
+ * the Feature is read from this stream
+ * @exception IOException
+ * thrown if there is a problem reading the Feature - most likely
+ * ReadFormatException.
+ * @exception InvalidRelationException
+ * Thrown if this Feature cannot contain the given Qualifier.
+ * @return null if in_stream is at the end of file when the method is called
*/
protected static GFFStreamFeature readFromStream(LinePushBackReader stream)
- throws IOException, InvalidRelationException
- {
+ throws IOException, InvalidRelationException {
final String line = stream.readLine();
- if(line == null)
+ if (line == null)
return null;
- try
- {
+ try {
return new GFFStreamFeature(line);
- }
- catch(ReadFormatException exception)
- {
+ } catch (ReadFormatException exception) {
// re-throw the exception with the line number added
final String new_error_string = exception.getMessage();
- throw new ReadFormatException(new_error_string,
- stream.getLineNumber());
+ throw new ReadFormatException(new_error_string, stream.getLineNumber());
}
}
/**
- * Read the details of a feature from an EMBL stream into the current
- * object.
- * @param entry_information The EntryInformation object of the Entry that
- * will contain the Feature.
- * @param in_stream the Feature is read from this stream
- * @exception IOException thrown if there is a problem reading the Feature -
- * most likely ReadFormatException if the stream does not contain GFF
- * feature.
+ * Read the details of a feature from an EMBL stream into the current object.
+ *
+ * @param entry_information
+ * The EntryInformation object of the Entry that will contain the
+ * Feature.
+ * @param in_stream
+ * the Feature is read from this stream
+ * @exception IOException
+ * thrown if there is a problem reading the Feature - most likely
+ * ReadFormatException if the stream does not contain GFF
+ * feature.
**/
public void setFromStream(final EntryInformation entry_information,
- final LinePushBackReader in_stream)
- throws IOException, InvalidRelationException, ReadOnlyException
- {
+ final LinePushBackReader in_stream) throws IOException,
+ InvalidRelationException, ReadOnlyException {
throw new ReadOnlyException();
}
/**
- * Write this Feature to the given stream.
- * @param writer The stream to write to.
- * @exception IOException thrown if there is an io problem while writing
- * the Feature.
+ * Write this Feature to the given stream.
+ *
+ * @param writer
+ * The stream to write to.
+ * @exception IOException
+ * thrown if there is an io problem while writing the Feature.
**/
- public void writeToStream(final Writer writer)
- throws IOException
- {
+ public void writeToStream(final Writer writer) throws IOException {
final RangeVector ranges = getLocation().getRanges();
final int ranges_size = ranges.size();
-// final Hashtable contig_ranges = SimpleDocumentEntry.getContigRanges();
- for(int i = 0; i < ranges_size; ++i)
- {
- Range this_range = (Range)ranges.elementAt(i);
+ // final Hashtable contig_ranges = SimpleDocumentEntry.getContigRanges();
+ for (int i = 0; i < ranges_size; ++i) {
+ Range this_range = (Range) ranges.elementAt(i);
String seqname = getGffSeqName();
- String source = getGffSource();
- Qualifier score = getQualifierByName("score");
- Qualifier group = getQualifierByName("group");
+ String source = getGffSource();
+ Qualifier score = getQualifierByName("score");
+ Qualifier group = getQualifierByName("group");
// source becomes a Dbxref in chado
String source_str = null;
- if(getQualifierByName("Dbxref") != null)
- {
+ if (getQualifierByName("Dbxref") != null) {
source_str = getDbxrefGFFSource(getQualifierByName("Dbxref"));
}
int start = this_range.getStart();
- int end = this_range.getEnd();
+ int end = this_range.getEnd();
- if(seqname == null && ((GFFDocumentEntry)getEntry()).getDocument() != null)
- seqname = ((GFFDocumentEntry)getEntry()).getDocument().getName();
- if(seqname == null)
+ if (seqname == null
+ && ((GFFDocumentEntry) getEntry()).getDocument() != null)
+ seqname = ((GFFDocumentEntry) getEntry()).getDocument().getName();
+ if (seqname == null)
seqname = deriveSeqName(start);
- if(source == null)
+ if (source == null)
source = "artemis";
- if(score == null)
+ if (score == null)
score = new Qualifier("score", ".");
- if(seqname != null && contig_ranges != null &&
- contig_ranges.containsKey(seqname))
- {
+ if (seqname != null && contig_ranges != null
+ && contig_ranges.containsKey(seqname)) {
Range offset_range = contig_ranges.get(seqname);
- start = start-offset_range.getStart()+1;
- end = end-offset_range.getStart()+1;
+ start = start - offset_range.getStart() + 1;
+ end = end - offset_range.getStart() + 1;
}
- if(group == null || group.getValues() == null ||
- group.getValues().elementAt(0).equals(""))
- {
+ if (group == null || group.getValues() == null
+ || group.getValues().elementAt(0).equals("")) {
final Qualifier gene = getQualifierByName("gene");
- if(gene == null)
+ if (gene == null)
group = new Qualifier("group", "");
else
group = gene;
@@ -786,333 +650,402 @@ public class GFFStreamFeature extends SimpleDocumentFeature
String frame = ".";
final Qualifier codon_start = getQualifierByName("codon_start");
- if(codon_start != null)
- {
- frame = (String)(codon_start.getValues()).elementAt(0);
+ if (codon_start != null) {
+ frame = (String) (codon_start.getValues()).elementAt(0);
- if(frame.equals ("1"))
+ if (frame.equals("1"))
frame = "0";
- else if(frame.equals("2"))
+ else if (frame.equals("2"))
frame = "1";
- else if(frame.equals("3"))
+ else if (frame.equals("3"))
frame = "2";
else
frame = ".";
}
// phase is REQUIRED for all CDS features
- if(getKey().equals("CDS") && frame.equals("."))
+ if (getKey().equals("CDS") && frame.equals("."))
frame = "0";
final String myId = getSegmentID(this_range);
String attribute_string = unParseAttributes(myId);
- if(source_str == null && source != null)
- source_str = source;
+ if (source_str == null && source != null)
+ source_str = source;
final String translation = getTranslation();
- if(translation != null)
+ if (translation != null)
attribute_string = attribute_string + ";" + translation;
- writer.write(seqname + "\t" +
- source_str + "\t" +
- getKey().getKeyString() + "\t" +
- start + "\t" +
- end + "\t" +
- score.getValues() .elementAt(0)+ "\t" +
- (getLocation().isComplement() ? "-\t" : "+\t") +
- frame + "\t" +
- attribute_string + "\n");
+ writer.write(seqname + "\t" + source_str + "\t" + getKey().getKeyString()
+ + "\t" + start + "\t" + end + "\t" + score.getValues().elementAt(0)
+ + "\t" + (getLocation().isComplement() ? "-\t" : "+\t") + frame
+ + "\t" + attribute_string + "\n");
}
}
/**
- * If the seqname is not set for this feature try to derive the contig/chromosome
- * it is located on
+ * If the seqname is not set for this feature try to derive the
+ * contig/chromosome it is located on
+ *
* @param start
* @return
*/
- private String deriveSeqName(int start)
- {
+ private String deriveSeqName(int start) {
String seqname = null;
- if(contig_ranges != null)
- {
+ if (contig_ranges != null) {
final Enumeration<String> contigEnum = contig_ranges.keys();
- while(contigEnum.hasMoreElements())
- {
+ while (contigEnum.hasMoreElements()) {
final String key = contigEnum.nextElement();
final Range r = contig_ranges.get(key);
- if(r.getStart() > start)
+ if (r.getStart() > start)
continue;
- if(r.getEnd() > start)
+ if (r.getEnd() > start)
return key;
}
- }
- else
- {
- try
- {
- seqname = ((GFFStreamFeature)(getEntry().getAllFeatures().elementAt(0))).getGffSeqName();
+ } else {
+ try {
+ seqname = ((GFFStreamFeature) (getEntry().getAllFeatures().elementAt(0)))
+ .getGffSeqName();
+ } catch (Exception e) {
}
- catch(Exception e) {}
}
- if(seqname == null)
+ if (seqname == null)
seqname = "gff_seqname";
return seqname;
}
/**
- * Return a String containing the qualifiers of this feature in a form
- * suitable for using as the last field of a GFF line. The codon_start
- * attribute is not included since GFF has a frame field. gff_seqname,
- * gff_source and score aren't included since they have corresponding
- * fields.
+ * Return a String containing the qualifiers of this feature in a form
+ * suitable for using as the last field of a GFF line.
**/
- private String unParseAttributes(final String myId)
- {
- final StringBuffer buffer = new StringBuffer();
+ private String unParseAttributes(final String myId) {
final QualifierVector qualifiers = getQualifiers();
+ GFF3AttributeBuilder abuf = new GFF3AttributeBuilder();
+ prepareProcessors(abuf);
- final String names[] = { "ID", "Name", "Alias", "Parent",
- "Derives_from",
- "Target", "Gap", "Note",
- "Dbxref", "Ontology_term",
- "Start_range", "End_range",
- "Is_circular"};
- int count = 0;
- final int names_length = names.length;
-
- if(myId != null)
- {
- buffer.append("ID=");
- buffer.append(encode(myId));
- count++;
+ for (String attr : attrs_to_filter) {
+ abuf.ignore(attr);
}
- for(int i=1; i<names_length; i++)
- {
- Qualifier this_qualifier = qualifiers.getQualifierByName(names[i]);
+ final int names_length = abuf.reserved_a.length;
- if(this_qualifier == null)
- continue;
+ // add ID attribute
+ if (myId != null) {
+ abuf.add("ID", myId);
+ }
+
+ // build reserved attributes
+ for (int i = 1; i < names_length; i++) {
+ Qualifier this_qualifier = qualifiers.getQualifierByName(abuf.reserved_a[i]);
- final String this_qualifier_str = getQualifierString(this_qualifier, true);
- if(this_qualifier_str == null)
+ if (this_qualifier == null)
continue;
- if(count != 0)
- buffer.append(";");
- buffer.append(this_qualifier_str);
- count++;
+ abuf.add(this_qualifier.getName(), this_qualifier.getValues());
}
+ // build remaining attributes
boolean lname;
- for(Qualifier this_qualifier: qualifiers)
- {
+ for (Qualifier this_qualifier : qualifiers) {
lname = false;
- for(int j=0; j<names_length; j++)
- if(this_qualifier.getName().equals(names[j]))
- lname = true;
-
- if(lname)
- continue;
-
- if(attrs_to_filter.contains(this_qualifier.getName()))
- continue;
- if( (this_qualifier.getName().equals("private") && System.getProperty("noprivate") != null) ||
- (this_qualifier.getName().equals("history") && System.getProperty("nohistory") != null) )
+ // skip reserved names
+ for (int j = 0; j < names_length; j++)
+ if (this_qualifier.getName().equals(abuf.reserved_a[j]))
+ lname = true;
+ if (lname)
continue;
- final String this_qualifier_str = getQualifierString(this_qualifier, false);
-
- if(this_qualifier_str == null)
+ // skip internal qualifiers
+ if ( (this_qualifier.getName().equals("private") &&
+ System.getProperty("noprivate") != null) ||
+ (this_qualifier.getName().equals("history") &&
+ System.getProperty("nohistory") != null) ||
+ this_qualifier.getName().equals("codon_start"))
continue;
- if(count != 0)
- buffer.append(";");
- buffer.append(this_qualifier_str);
+ abuf.add(this_qualifier.getName(), this_qualifier.getValues());
}
- return buffer.toString();
+ return abuf.toString();
}
-
- /**
- * Get the translation qualifier string for polypeptide features.
- */
- private String getTranslation()
- {
- if (! getKey().getKeyString().equals("polypeptide"))
- return null;
- if (chadoGene != null)
- {
- if(getUserData() == null)
- new uk.ac.sanger.artemis.Feature(this);
- // the above line constructs the appropriate userData within this current GFFStreamFeature object,
- // which is required by the following GeneUtils.deriveResidues()
- String residues = GeneUtils.deriveResidues(this);
- if (residues != null)
- return "translation="+residues;
+ private static String strJoin(String[] aArr, String sSep) {
+ StringBuilder sbStr = new StringBuilder();
+ for (int i = 0, il = aArr.length; i < il; i++) {
+ if (i > 0)
+ sbStr.append(sSep);
+ sbStr.append(aArr[i]);
}
- return null;
+ return sbStr.toString();
}
- /**
- * Used to write out the GFF attributes.
- * @param q the qualifier to represent as a <code>String</code>
- * @param reserved indicate if this is one of the reserved tags or not
- * @return the <code>String</code> representation
- */
- private String getQualifierString(Qualifier q, boolean reserved )
- {
- StringBuffer buffer = new StringBuffer();
- final String name = q.getName();
-
- if(name.equals("codon_start") || name.equals("gff_source") ||
- name.equals("gff_seqname") || name.equals("score"))
- return null;
-
- final StringVector values = q.getValues();
-
- /* ignore qualifiers with just one empty value, will mess up GFF3 output */
- if(values != null && values.size() == 1)
- {
- if (values.elementAt(0).replaceAll("\\s+","").equals(""))
- return null;
- }
-
- /*
- * GSV :
- * The Bio::FeatureIO perl module falls over if there are Uppercased
- * attribute names for tags which aren't part of the standard reserved
- * set. So we lowercase these, since in the specification it says :
- *
- * "All attributes that begin with an uppercase letter are reserved for
- * later use. Attributes that begin with a lowercase letter can be used
- * freely by applications."
- * see http://www.sequenceontology.org/gff3.shtml
- */
- String nameToBuffer = encode(name);
-
- if (! reserved)
- nameToBuffer = Character.toLowerCase(nameToBuffer.charAt(0)) + nameToBuffer.substring(1);
- buffer.append(nameToBuffer);
-
- if(values != null && values.size() > 0)
- {
- buffer.append('=');
- for(int value_index = 0; value_index < values.size();
- ++value_index)
- {
- final String this_value;
- if(name.equals("class"))
- {
- int index = values.elementAt(value_index).indexOf("::");
- if(index > -1)
- this_value = encode(values.elementAt(value_index).substring(0,index));
- else
- this_value = encode(values.elementAt(value_index));
+ void prepareProcessors(GFF3AttributeBuilder abuf) {
+ GFF3AttributeAggregator productProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ String this_value = GFF3Encoder.encode(values.elementAt(value_index));
+ if (value_index > 0 && value_index < (values.size())) {
+ buffer.append(",");
+ }
+ buffer.append(this_value);
+ }
}
- else
- this_value = encode(values.elementAt(value_index));
-
- if(value_index>0)
- buffer.append("%2C");
-
- if(name.equals("Parent"))
- buffer.append(this_value);
- else
- {
- try
- {
- buffer.append(Integer.valueOf(this_value));
+ return buffer.toString();
+ }
+ };
+
+ GFF3AttributeAggregator ecProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ final String this_value = "EC:"
+ + GFF3Encoder.encode(values.elementAt(value_index));
+ if (value_index > 0 && value_index < (values.size())) {
+ buffer.append(",");
+ }
+ buffer.append(this_value);
+ }
+ }
+ return buffer.toString();
+ }
+ };
+
+ GFF3AttributeAggregator psysIDProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ final String this_value;
+ int index = values.elementAt(value_index).indexOf(";current=");
+ if (index > -1)
+ this_value = GFF3Encoder.encode(values.elementAt(value_index)
+ .substring(0, index));
+ else
+ this_value = GFF3Encoder.encode(values.elementAt(value_index));
+ if (value_index > 0 && value_index < (values.size())) {
+ buffer.append(",");
+ }
+ buffer.append(this_value);
+ }
+ }
+ return buffer.toString();
+ }
+ };
+
+ GFF3AttributeAggregator classProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ final String this_value;
+ int index = values.elementAt(value_index).indexOf("::");
+ if (index > -1)
+ this_value = GFF3Encoder.encode(values.elementAt(value_index)
+ .substring(0, index));
+ else
+ this_value = GFF3Encoder.encode(values.elementAt(value_index));
+ if (value_index > 0 && value_index < (values.size())) {
+ buffer.append(",");
+ }
+ buffer.append(this_value);
}
- catch(NumberFormatException _)
- {
- // not an integer
- try
- {
- buffer.append(Double.valueOf(this_value));
+ }
+ return buffer.toString();
+ }
+ };
+
+ GFF3AttributeAggregator startEndRangeProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ if (value_index > 0 && value_index < (values.size())) {
+ buffer.append(",");
}
- catch (NumberFormatException __)
- {
- // not a double or integer so quote it
- buffer.append(this_value);
+ buffer.append(values.elementAt(value_index));
+ }
+ }
+ return buffer.toString();
+ }
+ };
+
+ GFF3AttributeAggregator goProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ int goindex = values.elementAt(value_index).indexOf("GOid=");
+ int termindex = values.elementAt(value_index).indexOf(";term=");
+ if (goindex > -1 && termindex > -1) {
+ buffer.append(GFF3Encoder.encode(values.elementAt(value_index)
+ .substring(goindex + 5, termindex)));
+ if (value_index < (values.size()) - 1)
+ buffer.append(",");
}
}
}
+ return buffer.toString();
}
+ };
+
+ GFF3AttributeAggregator ucProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ Set<String> set = new HashSet<String>();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ String regex = "eupathdb_uc[:=]\"?([a-zA-Z0-9]+)";
+ Pattern pattern = Pattern.compile(regex, Pattern.CASE_INSENSITIVE);
+ Matcher matcher = pattern.matcher(values.elementAt(value_index));
+ while (matcher.find()) {
+ set.add(GFF3Encoder.encode(matcher.group(1)));
+ }
+ }
+ }
+ return strJoin(set.toArray(new String[set.size()]), ",");
+ }
+ };
+
+ GFF3AttributeAggregator curcomProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ buffer.append(GFF3Encoder.encode(values.elementAt(value_index)));
+ if (value_index < (values.size()) - 1)
+ buffer.append(" ");
+ }
+ }
+ return buffer.toString();
+ }
+ };
+
+ // map GO -> full_GO
+ abuf.setMapping("GO", "full_GO");
+ abuf.setGlue("full_GO", ",");
+
+ // merge curation and comment
+ abuf.setMapping("curation", "comment");
+ abuf.setGlue("comment", " ");
+ abuf.setAggregator("comment", curcomProc);
+
+ // also put GOs in Ontology_term
+ abuf.setClone("full_GO", "Ontology_term");
+ abuf.setAggregator("Ontology_term", goProc);
+ abuf.setGlue("Ontology_term", ",");
+
+ // also put EuPathDB UC numbers into separate attribute
+ abuf.setClone("history", "eupathdb_uc");
+ abuf.setAggregator("eupathdb_uc", ucProc);
+ abuf.setGlue("eupathdb_uc", ",");
+
+ // class
+ abuf.setAggregator("class", classProc);
+
+ // EC numbers go into Dbxref
+ abuf.setMapping("EC_number", "Dbxref");
+ abuf.setAggregator("EC_number", ecProc);
+ abuf.setGlue("Dbxref", ",");
+
+ // start/end ranges
+ abuf.setAggregator("Start_range", startEndRangeProc);
+ abuf.setAggregator("End_range", startEndRangeProc);
+
+ // previous_systematic_id
+ abuf.setAggregator("previous_systematic_id", psysIDProc);
+
+ // product
+ abuf.setAggregator("product", productProc);
+ }
+
+ /**
+ * Get the translation qualifier string for polypeptide features.
+ */
+ private String getTranslation() {
+ if (!getKey().getKeyString().equals("polypeptide"))
+ return null;
+ if (chadoGene != null) {
+ if (getUserData() == null)
+ new uk.ac.sanger.artemis.Feature(this);
+ // the above line constructs the appropriate userData within this current
+ // GFFStreamFeature object,
+ // which is required by the following GeneUtils.deriveResidues()
+ String residues = GeneUtils.deriveResidues(this);
+ if (residues != null)
+ return "translation=" + residues;
}
- if (buffer.toString().charAt(buffer.toString().length()-1) == '=')
- System.out.println(buffer.toString() + " ----- values length was " + values.size() + ": '" + values.elementAt(0) + "'");
- return buffer.toString();
+ return null;
}
/**
- * Parse the given String as ACeDB format attributes.
- * Adapted from code by Matthew Pocock for the BioJava project.
+ * Parse the given String as ACeDB format attributes. Adapted from code by
+ * Matthew Pocock for the BioJava project.
+ *
+ * Modified for gff-version 3.
*
- * Modified for gff-version 3.
- * @return Return a Hashtable. Each key is an attribute name and each value
- * of the Hashtable is a StringVector containing the attribute values.
- * If the attribute has no value then the Hashtable value will be a zero
- * length vector.
+ * @return Return a Hashtable. Each key is an attribute name and each value of
+ * the Hashtable is a StringVector containing the attribute values. If
+ * the attribute has no value then the Hashtable value will be a zero
+ * length vector.
**/
- private Hashtable<String, StringVector> parseAttributes(final String att_val_list)
- {
+ private Hashtable<String, StringVector> parseAttributes(
+ final String att_val_list) {
final Hashtable<String, StringVector> attr = new Hashtable<String, StringVector>();
int ind_start = 0;
int ind_end;
- while( (ind_end = att_val_list.indexOf(";",ind_start)) > -1 ||
- ind_start < att_val_list.length() )
- {
- if(ind_end < 0)
+ while ((ind_end = att_val_list.indexOf(";", ind_start)) > -1
+ || ind_start < att_val_list.length()) {
+ if (ind_end < 0)
ind_end = att_val_list.length();
- final String this_token = decode(att_val_list.substring(ind_start, ind_end).trim());
- ind_start = ind_end+1;
+ final String this_token = GFF3Encoder.decode(att_val_list.substring(ind_start,
+ ind_end).trim());
+ ind_start = ind_end + 1;
int index_of_first_space = this_token.indexOf(" ");
final String att_name;
StringVector att_values = new StringVector();
- if( this_token.indexOf("=") > -1 &&
- (this_token.indexOf("=") < index_of_first_space ||
- index_of_first_space == -1) )
- {
+ if (this_token.indexOf("=") > -1
+ && (this_token.indexOf("=") < index_of_first_space || index_of_first_space == -1)) {
index_of_first_space = this_token.indexOf("=");
att_name = this_token.substring(0, index_of_first_space);
- att_values.add(this_token.substring(index_of_first_space+1).trim());
- }
- else if(index_of_first_space == -1)
+ att_values.add(this_token.substring(index_of_first_space + 1).trim());
+ } else if (index_of_first_space == -1)
att_name = this_token;
- else
- {
+ else {
att_name = this_token.substring(0, index_of_first_space);
- String rest_of_token =
- this_token.substring(index_of_first_space+1).trim();
+ String rest_of_token = this_token.substring(index_of_first_space + 1)
+ .trim();
- while(rest_of_token.length() > 0)
- {
- if(rest_of_token.startsWith("\""))
- {
+ while (rest_of_token.length() > 0) {
+ if (rest_of_token.startsWith("\"")) {
int quote_index = 0;
- do
- {
+ do {
quote_index++;
quote_index = rest_of_token.indexOf("\"", quote_index);
- } while(quote_index > -1 &&
- rest_of_token.charAt(quote_index - 1) == '\\');
+ } while (quote_index > -1
+ && rest_of_token.charAt(quote_index - 1) == '\\');
- if(quote_index < 0)
- {
+ if (quote_index < 0) {
// no closing quote - panic
- final Hashtable<String, StringVector> panic_attributes =
- new Hashtable<String, StringVector>();
+ final Hashtable<String, StringVector> panic_attributes = new Hashtable<String, StringVector>();
final StringVector notes = new StringVector();
notes.add(att_val_list);
panic_attributes.put("note", notes);
@@ -1123,60 +1056,52 @@ public class GFFStreamFeature extends SimpleDocumentFeature
final String next_bit = rest_of_token.substring(1, quote_index);
att_values.add(next_bit);
rest_of_token = rest_of_token.substring(quote_index + 1).trim();
- }
- else
- {
+ } else {
final int index_of_next_space = rest_of_token.indexOf(" ");
- if(index_of_next_space == -1)
- {
+ if (index_of_next_space == -1) {
att_values.add(rest_of_token);
rest_of_token = "";
- }
- else
- {
- final String next_bit =
- rest_of_token.substring(0, index_of_next_space);
+ } else {
+ final String next_bit = rest_of_token.substring(0,
+ index_of_next_space);
att_values.add(next_bit);
- rest_of_token =
- rest_of_token.substring(index_of_next_space).trim();
+ rest_of_token = rest_of_token.substring(index_of_next_space)
+ .trim();
}
}
}
- if(!rest_of_token.equals(""))
+ if (!rest_of_token.equals(""))
att_values.add(rest_of_token);
}
- if(att_name.equals("Dbxref") || att_name.equals("Alias")) // convert to multi-line
+ if (att_name.equals("Dbxref") || att_name.equals("Alias")) // convert to
+ // multi-line
{
- StringTokenizer stok =
- new StringTokenizer((String)att_values.get(0), ",");
+ StringTokenizer stok = new StringTokenizer((String) att_values.get(0),
+ ",");
StringVector str_values = new StringVector();
- while(stok.hasMoreTokens())
+ while (stok.hasMoreTokens())
str_values.add(stok.nextToken());
att_values = str_values;
}
- if(att_name.equals("timelastmodified"))
- {
- try
- {
- this.timelastmodified =
- new Timestamp( Long.parseLong((String)att_values.get(0)) );
- SimpleDateFormat date_format =
- new SimpleDateFormat("dd.MM.yyyy hh:mm:ss z");
- att_values.set(0,date_format.format(timelastmodified));
- }
- catch(NumberFormatException e)
- {
- att_values.set(0,(String)att_values.get(0));
+ if (att_name.equals("timelastmodified")) {
+ try {
+ this.timelastmodified = new Timestamp(
+ Long.parseLong((String) att_values.get(0)));
+ SimpleDateFormat date_format = new SimpleDateFormat(
+ "dd.MM.yyyy hh:mm:ss z");
+ att_values.set(0, date_format.format(timelastmodified));
+ } catch (NumberFormatException e) {
+ att_values.set(0, (String) att_values.get(0));
}
}
- if(attr.get(att_name) != null)
+ if (attr.get(att_name) != null)
attr.get(att_name).add(att_values);
else
attr.put(att_name, att_values);
@@ -1187,32 +1112,30 @@ public class GFFStreamFeature extends SimpleDocumentFeature
/**
* Get the feature time last modified timestamp.
+ *
* @return
*/
- public Timestamp getLastModified()
- {
+ public Timestamp getLastModified() {
return timelastmodified;
}
/**
* Get the GFF_source value of a Dbxref qualifier.
+ *
* @param qualifier
- * @return the gff_source value or NULL
+ * @return the gff_source value or NULL
*/
- private String getDbxrefGFFSource(final Qualifier qualifier)
- {
- StringVector qualifier_strings =
- StreamQualifier.toStringVector(null, qualifier);
+ private String getDbxrefGFFSource(final Qualifier qualifier) {
+ StringVector qualifier_strings = StreamQualifier.toStringVector(null,
+ qualifier);
- for(int i=0; i<qualifier_strings.size(); i++)
- {
- String qualifier_string = (String)qualifier_strings.elementAt(i);
+ for (int i = 0; i < qualifier_strings.size(); i++) {
+ String qualifier_string = (String) qualifier_strings.elementAt(i);
- if(qualifier_string.indexOf("GFF_source:") >-1)
- {
- int index = qualifier_string.indexOf(":")+1;
+ if (qualifier_string.indexOf("GFF_source:") > -1) {
+ int index = qualifier_string.indexOf(":") + 1;
int len = qualifier_string.length();
- if(qualifier_string.endsWith("\""))
+ if (qualifier_string.endsWith("\""))
len--;
return qualifier_string.substring(index, len);
}
@@ -1222,136 +1145,112 @@ public class GFFStreamFeature extends SimpleDocumentFeature
/**
* Set the feature time last modified timestamp.
+ *
* @param timelastmodified
*/
- public void setLastModified(final Timestamp timelastmodified)
- {
+ public void setLastModified(final Timestamp timelastmodified) {
this.timelastmodified = timelastmodified;
// now update the qualifier value itself
QualifierVector qualifiers = getQualifiers();
Qualifier qualifier = qualifiers.getQualifierByName("timelastmodified");
- SimpleDateFormat date_format =
- new SimpleDateFormat("dd.MM.yyyy hh:mm:ss z");
-
- if(qualifier != null)
- qualifier.removeValue((String)qualifier.getValues().get(0));
- else
- {
- try
- {
+ SimpleDateFormat date_format = new SimpleDateFormat("dd.MM.yyyy hh:mm:ss z");
+
+ if (qualifier != null)
+ qualifier.removeValue((String) qualifier.getValues().get(0));
+ else {
+ try {
qualifier = new Qualifier("timelastmodified",
- date_format.format(timelastmodified));
+ date_format.format(timelastmodified));
setQualifier(qualifier);
return;
+ } catch (EntryInformationException eie) {
+ } catch (ReadOnlyException roe) {
}
- catch(EntryInformationException eie)
- {}
- catch(ReadOnlyException roe)
- {}
}
qualifier.addValue(date_format.format(timelastmodified));
}
/**
- * Returns true if and only if this Feature can't be changed or can't be
- * removed from it's entry.
+ * Returns true if and only if this Feature can't be changed or can't be
+ * removed from it's entry.
**/
- public boolean isReadOnly ()
- {
- if(readOnlyFeature)
+ public boolean isReadOnly() {
+ if (readOnlyFeature)
return true;
return super.isReadOnly();
}
- public void setReadOnlyFeature(boolean readOnlyFeature)
- {
+ public void setReadOnlyFeature(boolean readOnlyFeature) {
this.readOnlyFeature = readOnlyFeature;
}
- public ChadoCanonicalGene getChadoGene()
- {
+ public ChadoCanonicalGene getChadoGene() {
return chadoGene;
}
- public void setChadoGene(ChadoCanonicalGene chadoGene)
- {
+ public void setChadoGene(ChadoCanonicalGene chadoGene) {
this.chadoGene = chadoGene;
}
- public boolean isVisible()
- {
+ public boolean isVisible() {
return visible;
}
- public void setVisible(boolean visible)
- {
+ public void setVisible(boolean visible) {
this.visible = visible;
}
- public String getGffSeqName()
- {
+ public String getGffSeqName() {
return gffSeqName;
}
- public void setGffSeqName(String gffSeqName)
- {
+ public void setGffSeqName(String gffSeqName) {
this.gffSeqName = gffSeqName;
}
- public String getGffSource()
- {
+ public String getGffSource() {
return gffSource;
}
- public void setGffSource(String gffSource)
- {
+ public void setGffSource(String gffSource) {
this.gffSource = gffSource;
}
- public boolean isLazyLoaded()
- {
+ public boolean isLazyLoaded() {
return lazyLoaded;
}
- public void setLazyLoaded(boolean lazyLoaded)
- {
+ public void setLazyLoaded(boolean lazyLoaded) {
this.lazyLoaded = lazyLoaded;
}
- public org.gmod.schema.sequence.Feature getChadoLazyFeature()
- {
+ public org.gmod.schema.sequence.Feature getChadoLazyFeature() {
return chadoLazyFeature;
}
public void setChadoLazyFeature(
- org.gmod.schema.sequence.Feature chadoLazyFeature)
- {
+ org.gmod.schema.sequence.Feature chadoLazyFeature) {
this.chadoLazyFeature = chadoLazyFeature;
}
- protected static boolean isGTF(Feature feature)
- {
- if(!(feature instanceof GFFStreamFeature))
+ protected static boolean isGTF(Feature feature) {
+ if (!(feature instanceof GFFStreamFeature))
return false;
- final String names[] = { "ID", "Name", "Alias", "Parent",
- "Derives_from",
- "Target", "Gap", "Note",
- "Dbxref", "Ontology_term" };
+ final String names[] = { "ID", "Name", "Alias", "Parent", "Derives_from",
+ "Target", "Gap", "Note", "Dbxref", "Ontology_term" };
- for(String name: names)
- {
- if(feature.getQualifiers().getQualifierByName(name) != null)
+ for (String name : names) {
+ if (feature.getQualifiers().getQualifierByName(name) != null)
return false;
}
- if(feature.getQualifiers().getQualifierByName("gene_id") != null &&
- feature.getQualifiers().getQualifierByName("transcript_id") != null)
- {
- if(feature.getEntry() != null)
- logger4j.debug(feature.getEntry().getName()+" is in GTF format");
+ if (feature.getQualifiers().getQualifierByName("gene_id") != null
+ && feature.getQualifiers().getQualifierByName("transcript_id") != null) {
+ if (feature.getEntry() != null)
+ logger4j.debug(feature.getEntry().getName() + " is in GTF format");
return true;
}
return false;
diff --git a/uk/ac/sanger/artemis/io/GenbankTblOutputStream.java b/uk/ac/sanger/artemis/io/GenbankTblOutputStream.java
index 82ae21e..4083fac 100644
--- a/uk/ac/sanger/artemis/io/GenbankTblOutputStream.java
+++ b/uk/ac/sanger/artemis/io/GenbankTblOutputStream.java
@@ -38,14 +38,12 @@ import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.util.FileDocument;
import uk.ac.sanger.artemis.util.StringVector;
-
/**
* Handle writing tbl format:
* http://www.ncbi.nlm.nih.gov/Sequin/table.html
*/
public class GenbankTblOutputStream
{
-
/**
* Write out an entry as tbl format.
* @param entry
@@ -76,10 +74,9 @@ public class GenbankTblOutputStream
{
final Writer writer = fileDocument.getWriter();
writer.write(">Feature "+entry.getName()+"\n");
-
+
final FeatureVector features = entry.getAllFeatures();
final EntryInformation entry_information = entry.getEntryInformation ();
-
int count = 0;
for(int i=0; i<features.size(); i++)
{
@@ -88,7 +85,7 @@ public class GenbankTblOutputStream
continue;
if(count > 0)
writer.write("\n");
-
+
count++;
writeRanges(feature, writer);
writeQualifiers(feature, entry_information, writer);
@@ -113,27 +110,94 @@ public class GenbankTblOutputStream
final RangeVector ranges = feature.getLocation().getRanges();
if(!feature.isForwardFeature() && ranges.size() > 1)
ranges.reverse();
-
- Range r = (Range)ranges.elementAt(0);
- if(feature.isForwardFeature())
- writer.write(r.getStart()+"\t"+r.getEnd());
+
+ boolean isStartPartial = false;
+ boolean isEndPartial = false;
+ if(feature.getEmblFeature() instanceof GFFStreamFeature)
+ {
+ try
+ {
+ if(feature.getQualifierByName("Start_range") != null)
+ isStartPartial = true;
+ if(feature.getQualifierByName("End_range") != null)
+ isEndPartial = true;
+ }
+ catch (InvalidRelationException e){}
+ }
else
- writer.write(r.getEnd()+"\t"+r.getStart());
-
+ {
+ if(feature.getLocation().isPartial(true)) // 5prime
+ {
+ if(feature.isForwardFeature())
+ isStartPartial = true;
+ else
+ isEndPartial = true;
+ }
+ if(feature.getLocation().isPartial(false)) // 3prime
+ {
+ if(feature.isForwardFeature())
+ isEndPartial = true;
+ else
+ isStartPartial = true;
+ }
+ }
+
+ writer.write( getPositionsStr(feature, ranges.elementAt(0),
+ isStartPartial, isEndPartial) );
writer.write("\t"+feature.getKey().getKeyString());
for(int j=1; j<ranges.size(); j++)
{
writer.write("\n");
- r = (Range)ranges.elementAt(j);
- if(feature.isForwardFeature())
- writer.write(r.getStart()+"\t"+r.getEnd());
- else
- writer.write(r.getEnd()+"\t"+r.getStart());
+ writer.write( getPositionsStr(feature, ranges.elementAt(j),
+ isStartPartial, isEndPartial) );
}
}
/**
+ * Get the start and end positions as a tab delimited string
+ * @param feature
+ * @param r
+ * @param isStartRangePartial
+ * @param isEndRangePartial
+ * @return
+ */
+ private static String getPositionsStr(
+ final Feature feature,
+ final Range r,
+ final boolean isStartPartial,
+ final boolean isEndPartial)
+ {
+ boolean firstBase;
+ boolean lastBase;
+ final int low_marker = feature.getFirstBaseMarker().getPosition();
+ final int high_marker = feature.getLastBaseMarker().getPosition();
+ String low_pos;
+ String high_pos;
+ if(feature.isForwardFeature())
+ {
+ firstBase = (r.getStart() == low_marker);
+ lastBase = (r.getEnd() == high_marker);
+ low_pos = Integer.toString(r.getStart());
+ high_pos = Integer.toString(r.getEnd());
+ }
+ else
+ {
+ firstBase = (r.getEnd() == high_marker);
+ lastBase = (r.getStart() == low_marker);
+ low_pos = Integer.toString(r.getEnd());
+ high_pos = Integer.toString(r.getStart());
+ }
+
+ // set partials
+ if(firstBase && isStartPartial)
+ low_pos = (feature.isForwardFeature() ? "<" : ">")+low_pos;
+ if(lastBase && isEndPartial)
+ high_pos = (feature.isForwardFeature() ? ">" : "<")+high_pos;
+ return low_pos+"\t"+high_pos;
+ }
+
+ /**
* Write out qualifiers
* @param feature
* @param entry_information
diff --git a/uk/ac/sanger/artemis/io/GffToEMBL.java b/uk/ac/sanger/artemis/io/GffToEMBL.java
index 838247b..cb62d11 100644
--- a/uk/ac/sanger/artemis/io/GffToEMBL.java
+++ b/uk/ac/sanger/artemis/io/GffToEMBL.java
@@ -224,7 +224,7 @@ class GffToEMBL
(args == null || args.length < 1))
{
System.out.println("-h\tshow help");
- System.out.println("-s\tspace separated list of sequences to read and write out");
+ System.out.println("-s\tspace separated list of GFF files to read and write out");
System.out.println("-o\toutput directory");
System.out.println("-f\t[y|n] flatten the gene model, default is y");
System.out.println("-z\t[y|n] gzip output, default is y");
diff --git a/uk/ac/sanger/artemis/io/KeyVector.java b/uk/ac/sanger/artemis/io/KeyVector.java
index 95aa455..b5b8993 100644
--- a/uk/ac/sanger/artemis/io/KeyVector.java
+++ b/uk/ac/sanger/artemis/io/KeyVector.java
@@ -3,19 +3,19 @@
* created: Fri Apr 16 1999
*
* This file is part of Artemis
- *
+ *
* Copyright (C) 1999 Genome Research Limited
- *
+ *
* 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 2
* 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, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -39,13 +39,13 @@ public class KeyVector extends FastVector
public KeyVector ()
{
- super();
+ super();
}
-
+
/**
* Create a new vector which contains only the given Key.
**/
- public KeyVector (final Key new_key)
+ public KeyVector (final Key new_key)
{
super();
add (new_key);
@@ -54,7 +54,7 @@ public class KeyVector extends FastVector
/**
* Return a new copy of this object.
**/
- public KeyVector copy ()
+ public KeyVector copy ()
{
final KeyVector new_key_vector = (KeyVector)clone();
@@ -65,21 +65,21 @@ public class KeyVector extends FastVector
* Sorts the elements of the vector using a simple O(n^2) selection
* sort.
*/
- public void sort()
+ public void mysort()
{
int smallest;
- for (int i = 0; i < size (); ++i)
+ for (int i = 0; i < size (); ++i)
{
//find smallest remaining element
smallest = i;
- for(int j = i + 1 ; j < size () ; ++j)
+ for(int j = i + 1 ; j < size () ; ++j)
{
- if(((Key)get(j)).compareTo( (Key)get(smallest)) < 0)
+ if(((Key)get(j)).compareTo( (Key)get(smallest)) < 0)
smallest = j;
}
//exchange smallest and i
- if (smallest != i)
+ if (smallest != i)
{
final Key tmp = (Key)get(i);
setElementAt (get(smallest), i);
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index 11284b4..1c1756f 100644
--- a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
@@ -473,27 +473,31 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
{
final StringVector values = productQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
- for(int j=0; j<values.size(); j++)
+ for(String val: values)
{
- String val = (String)values.get(j);
-
int ind = 0;
-
if((ind=val.indexOf(";db_xref="))>-1 && this instanceof EmblDocumentEntry)
val = val.substring(0,ind);
-
+
if((ind=val.indexOf(";evidence="))>-1 && this instanceof EmblDocumentEntry)
val = val.substring(0,ind);
-
+
if((ind=val.indexOf(";with="))>-1 && this instanceof EmblDocumentEntry)
val = val.substring(0,ind);
-
+
+ if((ind=val.indexOf("rank="))>-1 && this instanceof EmblDocumentEntry)
+ {
+ int ind2 = val.indexOf(";", ind);
+ if(ind == 0 && ind2 > -1)
+ val = val.substring(ind2+1);
+ }
+
if(val.startsWith("term="))
val = val.substring(5, val.length());
-
+
if(val.endsWith(";"))
val = val.substring(0, val.length()-1);
-
+
tmpNewValues.add(val);
}
return tmpNewValues;
@@ -741,7 +745,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
Enumeration qualifiersenum = qualifierMapProperties.propertyNames();
n = 0;
- Vector qualifiersToRemove = new Vector();
+ Vector<String> qualifiersToRemove = new Vector<String>();
while(qualifiersenum.hasMoreElements())
{
String current_map_name = (String) qualifiersenum.nextElement();
diff --git a/uk/ac/sanger/artemis/io/SimpleEntryInformation.java b/uk/ac/sanger/artemis/io/SimpleEntryInformation.java
index 81cdcb0..db4dde0 100644
--- a/uk/ac/sanger/artemis/io/SimpleEntryInformation.java
+++ b/uk/ac/sanger/artemis/io/SimpleEntryInformation.java
@@ -175,7 +175,7 @@ public class SimpleEntryInformation
return null;
}
- return_vector.sort ();
+ return_vector.mysort ();
return return_vector;
}
@@ -187,11 +187,11 @@ public class SimpleEntryInformation
if (isValidKey (misc_feature_key))
return misc_feature_key;
-
+
misc_feature_key = new Key ("region");
if (isValidKey (misc_feature_key))
return misc_feature_key;
-
+
return (Key)getValidKeys ().get (0);
}
@@ -397,7 +397,7 @@ public class SimpleEntryInformation
return getQualifierInfoHash ().copy ();
}
}
-
+
/**
* Fix this EntryInformation so that the given exception won't happen
* again.
diff --git a/uk/ac/sanger/artemis/io/StreamQualifier.java b/uk/ac/sanger/artemis/io/StreamQualifier.java
index 5cb78f2..9afa821 100644
--- a/uk/ac/sanger/artemis/io/StreamQualifier.java
+++ b/uk/ac/sanger/artemis/io/StreamQualifier.java
@@ -106,10 +106,14 @@ class StreamQualifier {
buffer.append ('/');
buffer.append (qualifier.getName ());
if (values.elementAt (i) != null) {
+ /* Escape double quotes */
+ String processedValue = (String)values.elementAt (i).replaceAll("(^|[^\"])\"([^\"]|$)","$1\"\"$2");
+ /* Mask line breaks in entries (e.g. notes/history) */
+ processedValue = processedValue.replaceAll("\n", " ");
buffer.append ('=');
- buffer.append (quotedValue (qualifier_info,
- qualifier.getName (),
- (String)values.elementAt (i)));
+ buffer.append (quotedValue(qualifier_info,
+ qualifier.getName(),
+ processedValue));
}
}
@@ -140,10 +144,14 @@ class StreamQualifier {
buffer.append ('/');
buffer.append (qualifier.getName ());
if (values.elementAt (i) != null) {
+ /* Escape double quotes */
+ String processedValue = (String)values.elementAt (i).replaceAll("(^|[^\"])\"([^\"]|$)","$1\"\"$2");
+ /* Mask line breaks in entries (e.g. notes/history) */
+ processedValue = processedValue.replaceAll("\n", " ");
buffer.append ('=');
buffer.append (quotedValue (qualifier_info,
qualifier.getName (),
- (String)values.elementAt (i)));
+ processedValue));
}
return_vector.add (buffer.toString ());
}
diff --git a/uk/ac/sanger/artemis/plot/Algorithm.java b/uk/ac/sanger/artemis/plot/Algorithm.java
index 1ffeb9e..a160d2f 100644
--- a/uk/ac/sanger/artemis/plot/Algorithm.java
+++ b/uk/ac/sanger/artemis/plot/Algorithm.java
@@ -51,7 +51,7 @@ public abstract class Algorithm {
/**
* Set by disableMaxAndMin () and enableMaxAndMin ().
**/
- private boolean max_min_disabled = false;
+ protected boolean max_min_disabled = false;
/**
* Set by the constructor by looking at the options with this name:
diff --git a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
index fb4b8b0..6767966 100644
--- a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
@@ -21,6 +21,7 @@
package uk.ac.sanger.artemis.plot;
import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.sequence.Strand;
import uk.ac.sanger.artemis.util.Document;
@@ -183,6 +184,18 @@ public class UserDataAlgorithm extends BaseAlgorithm
readWiggle(pushback_reader);
pushback_reader.close();
doc_reader.close();
+
+ max_min_disabled = Options.getOptions ().getPropertyTruthValue(
+ getAlgorithmShortName () + "_scaling_on");
+
+ String propStr = getAlgorithmShortName () + "_data_max";
+ if(Options.getOptions ().getProperty(propStr) != null)
+ data_max = Float.valueOf(
+ Options.getOptions ().getProperty(propStr));
+ propStr = getAlgorithmShortName () + "_data_min";
+ if(Options.getOptions ().getProperty(propStr) != null)
+ data_min = Float.valueOf(
+ Options.getOptions ().getProperty(propStr));
}
/**
@@ -211,6 +224,13 @@ public class UserDataAlgorithm extends BaseAlgorithm
final int seqLength = getStrand ().getSequenceLength ();
final Pattern patt = Pattern.compile("\\s+");
+ final boolean useEstimate =
+ Options.getOptions ().getIntegerProperty (getAlgorithmShortName () +
+ "_default_window_size") == null;
+ if(!useEstimate)
+ default_window_size = Options.getOptions ().getIntegerProperty (getAlgorithmShortName () +
+ "_default_window_size");
+
while ((line = pushback_reader.readLine ()) != null)
{
if (count >= seqLength)
@@ -278,7 +298,7 @@ public class UserDataAlgorithm extends BaseAlgorithm
else
{
average_value = average_value/countAll;
- if(estimate_window_size != Integer.MAX_VALUE)
+ if(estimate_window_size != Integer.MAX_VALUE && useEstimate)
default_window_size = estimate_window_size;
}
}
@@ -782,7 +802,11 @@ public class UserDataAlgorithm extends BaseAlgorithm
**/
public Integer getDefaultMaxWindowSize ()
{
- return new Integer (100);
+ if(Options.getOptions ().getIntegerProperty (getAlgorithmShortName () +
+ "_default_max_window") == null)
+ return new Integer (100);
+ else
+ return super.getDefaultMaxWindowSize ();
}
/**
@@ -792,7 +816,11 @@ public class UserDataAlgorithm extends BaseAlgorithm
**/
public Integer getDefaultMinWindowSize ()
{
- return new Integer (1);
+ if(Options.getOptions ().getIntegerProperty (getAlgorithmShortName () +
+ "_default_min_window") == null)
+ return new Integer (1);
+ else
+ return super.getDefaultMinWindowSize();
}
/**
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 6cba75d..d3ff19c 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -27,11 +27,11 @@ package uk.ac.sanger.artemis.util;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.DocumentEntry;
+import uk.ac.sanger.artemis.io.GFF3Encoder;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.PartialSequence;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.ReadFormatException;
-
import uk.ac.sanger.artemis.chado.ArtemisUtils;
import uk.ac.sanger.artemis.chado.ChadoCvTermView;
import uk.ac.sanger.artemis.chado.ChadoTransactionManager;
@@ -67,10 +67,12 @@ import org.postgresql.largeobject.LargeObjectManager;
import com.ibatis.common.jdbc.SimpleDataSource;
import java.sql.*;
+import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.io.*;
import java.net.ConnectException;
import java.net.InetAddress;
+import java.util.Calendar;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashSet;
@@ -551,7 +553,11 @@ public class DatabaseDocument extends Document
ByteBuffer entryBuffer = new ByteBuffer();
try
{
+ DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
+ Calendar cal = Calendar.getInstance();
+
entryBuffer.append("##gff-version 3\n");
+ entryBuffer.append("#created " + dateFormat.format(cal.getTime()) + "\n");
ByteBuffer sequenceBuffer = new ByteBuffer();
if(dao instanceof IBatisDAO)
@@ -1301,7 +1307,7 @@ public class DatabaseDocument extends Document
// ortholog/paralog/cluster data
int orthologueFeature = fr.getFeatureByObjectId().getFeatureId();
clusterOrthoParalog.append(cvTermName+"="+
- GFFStreamFeature.encode("object_id="+orthologueFeature+"; rank="+fr.getRank())+";");
+ GFF3Encoder.encode("object_id="+orthologueFeature+"; rank="+fr.getRank())+";");
}
}
}
@@ -1393,10 +1399,10 @@ public class DatabaseDocument extends Document
if(qualifier_name == null)
continue;
if(featprop.getValue() != null)
- this_buff.append(GFFStreamFeature.encode(qualifier_name)+ "=" +
- GFFStreamFeature.encode(featprop.getValue())+";");
+ this_buff.append(GFF3Encoder.encode(qualifier_name)+ "=" +
+ GFF3Encoder.encode(featprop.getValue())+";");
else
- this_buff.append(GFFStreamFeature.encode(qualifier_name)+";");
+ this_buff.append(GFF3Encoder.encode(qualifier_name)+";");
}
}
@@ -1408,7 +1414,7 @@ public class DatabaseDocument extends Document
if(feat.getDbXRef() != null)
{
this_buff.append("Dbxref=");
- this_buff.append(GFFStreamFeature.encode(
+ this_buff.append(GFF3Encoder.encode(
feat.getDbXRef().getDb().getName()+":"+feat.getDbXRef().getAccession()));
foundPrimaryDbXRef = true;
if(dbxref == null || dbxref.size() == 0)
@@ -1423,7 +1429,7 @@ public class DatabaseDocument extends Document
this_buff.append("Dbxref=");
for(int j=0; j<dbxref.size(); j++)
{
- this_buff.append(GFFStreamFeature.encode(dbxref.get(j)));
+ this_buff.append(GFF3Encoder.encode(dbxref.get(j)));
if(j<dbxref.size()-1)
this_buff.append(",");
}
@@ -1442,7 +1448,7 @@ public class DatabaseDocument extends Document
this_buff.append(alias.getSynonym().getName());
if(!alias.isCurrent())
- this_buff.append(GFFStreamFeature.encode(";current=false"));
+ this_buff.append(GFF3Encoder.encode(";current=false"));
//if(j<v_synonyms.size()-1)
this_buff.append(";");
@@ -1511,9 +1517,9 @@ public class DatabaseDocument extends Document
attr_buff.append("controlled_curation=");
attr_buff.append("term="+
- GFFStreamFeature.encode(feature_cvterm.getCvTerm().getName())+"%3B");
+ GFF3Encoder.encode(feature_cvterm.getCvTerm().getName())+"%3B");
attr_buff.append("cv="+
- GFFStreamFeature.encode(feature_cvterm.getCvTerm().getCv().getName())+"%3B");
+ GFF3Encoder.encode(feature_cvterm.getCvTerm().getCv().getName())+"%3B");
// N.B. the db_xref may be a FeatureCvTermDbXRef or a Pub for /controlled_curation
int nfound_dbxref = 0;
@@ -1584,7 +1590,7 @@ public class DatabaseDocument extends Document
attr_buff.append(getCvtermName(feature_cvtermprop.getCvTerm()
.getCvTermId(), dao, gene_builder));
attr_buff.append("=");
- attr_buff.append(GFFStreamFeature.encode(feature_cvtermprop.getValue()));
+ attr_buff.append(GFF3Encoder.encode(feature_cvtermprop.getValue()));
if(i < feature_cvtermprops.size()-1)
attr_buff.append("%3B");
}
@@ -1655,10 +1661,10 @@ public class DatabaseDocument extends Document
if(showDbId)
attr_buff.append("GOid="+dbXRef.getDb().getName() + ":"
+ dbXRef.getAccession() + "%3B");
-
+
attr_buff.append("term="+
- GFFStreamFeature.encode(feature_cvterm.getCvTerm().getName())+"%3B");
-
+ GFF3Encoder.encode(feature_cvterm.getCvTerm().getName())+"%3B");
+
// PMID
int nfound_pub = 0;
if(feature_cvterm.getPub() != null &&
@@ -1666,62 +1672,68 @@ public class DatabaseDocument extends Document
!feature_cvterm.getPub().getUniqueName().equalsIgnoreCase("NULL"))
{
Pub pub = feature_cvterm.getPub();
- attr_buff.append("db_xref="+
- pub.getUniqueName());
+ attr_buff.append("db_xref="+pub.getUniqueName());
nfound_pub++;
}
-
- if(featureCvTermPubs != null &&
- featureCvTermPubs.size() > 0)
+
+ if(featureCvTermPubs != null && featureCvTermPubs.size() > 0)
{
for(FeatureCvTermPub featureCvTermPub: featureCvTermPubs)
{
if(feature_cvterm.getFeatureCvTermId() !=
featureCvTermPub.getFeatureCvTerm().getFeatureCvTermId())
continue;
-
- if(nfound_pub == 0)
- attr_buff.append("db_xref=");
- else if(nfound_pub > 0)
- attr_buff.append("|");
+ attr_buff.append((nfound_pub == 0 ? "db_xref=" : "|"));
attr_buff.append(featureCvTermPub.getPub().getUniqueName());
nfound_pub++;
}
}
-
+
+ // GO_REF is stored as a dbxref and displayed in the dbxref column
+ if(featureCvTermDbXRefs != null && featureCvTermDbXRefs.size() > 0 )
+ {
+ for(FeatureCvTermDbXRef featureCvTermDbXRef: featureCvTermDbXRefs)
+ {
+ if(feature_cvterm.getFeatureCvTermId() !=
+ featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId())
+ continue;
+
+ DbXRef fc_dbXRef = featureCvTermDbXRef.getDbXRef();
+ if(!fc_dbXRef.getDb().getName().equals("GO_REF"))
+ continue;
+ attr_buff.append((nfound_pub == 0 ? "db_xref=" : "|"));
+ attr_buff.append(fc_dbXRef.getDb().getName()+":");
+ attr_buff.append(fc_dbXRef.getAccession());
+ nfound_pub++;
+ }
+ }
if(nfound_pub > 0)
attr_buff.append("%3B");
-
- if(featureCvTermDbXRefs != null &&
- featureCvTermDbXRefs.size() > 0 )
+
+ if(featureCvTermDbXRefs != null && featureCvTermDbXRefs.size() > 0 )
{
int nfound = 0;
for(FeatureCvTermDbXRef featureCvTermDbXRef : featureCvTermDbXRefs)
{
if(feature_cvterm.getFeatureCvTermId() !=
featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId())
- {
continue;
- }
- if(nfound == 0)
- attr_buff.append("with=");
- else if(nfound > 0)
- attr_buff.append("|");
-
DbXRef fc_dbXRef = featureCvTermDbXRef.getDbXRef();
+ if(fc_dbXRef.getDb().getName().equals("GO_REF"))
+ continue;
+ attr_buff.append((nfound == 0 ? "with=" : "|"));
attr_buff.append(fc_dbXRef.getDb().getName()+":");
attr_buff.append(fc_dbXRef.getAccession());
nfound++;
}
-
if(nfound > 0)
attr_buff.append("%3B");
-
}
- List<FeatureCvTermProp> feature_cvtermprops = (List<FeatureCvTermProp>)feature_cvterm.getFeatureCvTermProps();
+ List<FeatureCvTermProp> feature_cvtermprops =
+ (List<FeatureCvTermProp>)feature_cvterm.getFeatureCvTermProps();
for(int i = 0; i < feature_cvtermprops.size(); i++)
{
FeatureCvTermProp feature_cvtermprop = feature_cvtermprops.get(i);
@@ -1731,11 +1743,10 @@ public class DatabaseDocument extends Document
attr_buff.append(getCvtermName(feature_cvtermprop.getCvTerm()
.getCvTermId(), dao, gene_builder));
attr_buff.append("=");
- attr_buff.append(GFFStreamFeature.encode(feature_cvtermprop.getValue()));
+ attr_buff.append(GFF3Encoder.encode(feature_cvtermprop.getValue()));
if(i < feature_cvtermprops.size()-1)
attr_buff.append("%3B");
}
-
attr_buff.append(";");
}
diff --git a/uk/ac/sanger/artemis/util/FastVector.java b/uk/ac/sanger/artemis/util/FastVector.java
index b9d1712..d79dc47 100644
--- a/uk/ac/sanger/artemis/util/FastVector.java
+++ b/uk/ac/sanger/artemis/util/FastVector.java
@@ -3,19 +3,19 @@
* created: Sun Feb 20 2000
*
* This file is part of Artemis
- *
+ *
* Copyright (C) 2000 Genome Research Limited
- *
+ *
* 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 2
* 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, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -43,9 +43,9 @@ public class FastVector extends ArrayList
/**
* Performs the same function as Vector.addElement()
*/
- public boolean add(Object object)
+ public boolean add(Object object)
{
- if(object == null)
+ if(object == null)
throw new Error("internal error - adding a null object");
else if(contains(object))
throw new Error("internal error - object added a second time");
@@ -56,24 +56,24 @@ public class FastVector extends ArrayList
/**
* Performs the same function as Vector.lastElement()
**/
- public Object lastElement()
+ public Object lastElement()
{
return (Object)get(size() - 1);
}
-
+
/**
* Insert an Object after another.
* @param old_object The new_object will be inserted after this object
* or at the start if old_object isn't in the vector.
* @param new_object The new object to insert.
**/
- public void insertElementAfter(Object old_object, Object new_object)
+ public void insertElementAfter(Object old_object, Object new_object)
{
final int old_object_index = indexOf(old_object);
- if(old_object_index == -1)
+ if(old_object_index == -1)
add(0, new_object);
- else
+ else
add(old_object_index + 1, new_object);
}
@@ -81,7 +81,7 @@ public class FastVector extends ArrayList
* Replace the Object at the given index. (Performs the same function as
* Vector.elementAt())
**/
- public void setElementAt(final Object object, final int index)
+ public void setElementAt(final Object object, final int index)
{
remove(index);
add(index, object);
@@ -91,7 +91,7 @@ public class FastVector extends ArrayList
* Return a sorted copy of this vector.
* @param cmp The returned vector will be sorted with this Comparator.
**/
- public FastVector sort(final Comparator cmp)
+ public FastVector mysort(final Comparator cmp)
{
final FastVector return_vector = (FastVector)clone();
Collections.sort(return_vector, cmp);
diff --git a/uk/ac/sanger/artemis/util/StringVector.java b/uk/ac/sanger/artemis/util/StringVector.java
index 95f560d..ce3495b 100644
--- a/uk/ac/sanger/artemis/util/StringVector.java
+++ b/uk/ac/sanger/artemis/util/StringVector.java
@@ -51,11 +51,11 @@ public class StringVector extends Vector<String>
/**
* Create a new vector which contains the given Strings.
**/
- public StringVector(final String[] new_strings)
+ public StringVector(final String[] new_strings)
{
super(new_strings.length);
int len = new_strings.length;
- for(int i = 0; i < len; ++i)
+ for(int i = 0; i < len; ++i)
add(new_strings[i]);
}
@@ -68,7 +68,7 @@ public class StringVector extends Vector<String>
/**
* Create a new vector which contains the given Strings.
**/
- public StringVector(final StringVector new_strings)
+ public StringVector(final StringVector new_strings)
{
super(new_strings);
}
@@ -76,7 +76,7 @@ public class StringVector extends Vector<String>
/**
* Call add() on each of the String objects in the given StringVector.
**/
- public void add(final StringVector new_strings)
+ public void add(final StringVector new_strings)
{
for (int i = 0; i < new_strings.size(); ++i)
add (new_strings.elementAt(i));
@@ -87,19 +87,19 @@ public class StringVector extends Vector<String>
* package.
*/
public void sort()
- {
+ {
final Comparator<String> comparator = new Comparator<String>()
{
- public int compare(String fst, String snd)
+ public int compare(String fst, String snd)
{
- if(fst == null)
+ if(fst == null)
{
if(snd == null)
return 0;
else
return -1;
- }
- else
+ }
+ else
{
if(snd == null)
return 1;
@@ -114,7 +114,7 @@ public class StringVector extends Vector<String>
/**
* Return a new copy of this object.
**/
- public StringVector copy()
+ public StringVector copy()
{
return new StringVector(this);
}
@@ -132,7 +132,7 @@ public class StringVector extends Vector<String>
**/
public static StringVector getStrings(final String argument,
final String delim,
- final boolean keep_zero_char_toks)
+ final boolean keep_zero_char_toks)
{
final StringVector strVector = new StringVector();
@@ -153,23 +153,23 @@ public class StringVector extends Vector<String>
if(idx2 < 0)
idx2 = argLen;
-
+
tok = argument.substring(idx1,idx2);
idx1 = idx2+1;
if(tok.length() == 1 &&
- delim.indexOf(tok.charAt(0)) != -1)
+ delim.indexOf(tok.charAt(0)) != -1)
{
// ignore the split characters
if(keep_zero_char_toks &&
(lastTok == null ||
lastTok != null && lastTok.length () == 1 &&
- delim.indexOf (lastTok) != -1))
+ delim.indexOf (lastTok) != -1))
{
// add a space because of two split_characters in a row
strVector.add("");
}
- }
+ }
else
strVector.add(tok);
@@ -186,7 +186,7 @@ public class StringVector extends Vector<String>
* vector will be zero length.
**/
public static StringVector getStrings(final String argument,
- final String split_characters)
+ final String split_characters)
{
return getStrings(argument, split_characters, false);
}
@@ -198,7 +198,7 @@ public class StringVector extends Vector<String>
* String is zero length or it consists only of whitespace, the return
* vector will be zero length.
**/
- public static StringVector getStrings(final String argument)
+ public static StringVector getStrings(final String argument)
{
return getStrings(argument, " ", false);
}
--
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