<classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
- <classpathentry kind="lib" path="lib/VAqua4.jar"/>
+ <classpathentry kind="lib" path="lib/VAqua5-patch.jar"/>
+ <classpathentry kind="lib" path="utils/classgraph-4.1.6.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
<classpathentry kind="lib" path="lib/xml-apis.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
The people listed below are 'The Jalview Authors', who collectively
own the copyright to the Jalview source code and permit it to be released under GPL.
-This is the authoritative list. It was correct on 23rd November 2016.
+This is the authoritative list: it was correct on 5th September 2018 (or the last commit date!)
+
If you are releasing a version of Jalview, please make sure any
statement of authorship in the GUI reflects the list shown here.
In particular, check the resources/authors.props file !
Jim Procter
Mungo Carstairs
-Tochukwu 'Charles' Ofoegbu
+Ben Soares
Kira Mourao
+Tochukwu 'Charles' Ofoegbu
Andrew Waterhouse
Jan Engelhardt
Lauren Lui
##################
-To run application:
+To run application...
+[ NOTE: when using the -classpath option with the '*' wildcard, the argument must be quoted to avoid shell expansion of the wildcard,
+ ALSO, the wildcard MUST be as DIR/* and not DIR/*.jar etc or it will not be interpreted correctly ]
-java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview
+on Windows use:
+ java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+and on MacOS or Linux:
+ java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
-java -Djava.ext.dirs=JALVIEW_BUILD/dist -cp JALVIEW_BUILD/dist/jalview.jar jalview.bin.Jalview
+ java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
##################
quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
-vaqua: v4 (latest stable) by Alan Snyder et al. GPLv2 with Classpathe xception, also includes contributions from Quaqua: ownloaded from http://violetlib.org/vaqua/overview.html
+vaqua5-patch: This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
-lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
+lib/htsjdk-2.12.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
+Libraries for Test Suite
+
+utils/classgraph-4.1.6.jar: BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview
+ version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6
+
+
Additional dependencies
examples/javascript/deployJava.js : http://java.com/js/deployJava.js
<property name="reportDir" value="test-reports" />
<property name="testDir" value="test" />
<property name="testOutputDir" value="tests" />
+ <property name="cloverOutputDir" value="clover" if:set="clover.jar" />
<!-- switch to indicate if we should obfuscate jalviewLite -->
<!-- <property name="donotobfuscate" value="true"/> -->
<!-- switch to exclude associations from generated jnlp files -->
<include name="**/*.*" />
</fileset>
</copy>
+ <mkdir dir="${cloverOutputDir}" if:set="clover.jar"/>
</target>
<target name="build" depends="prepare">
</jar>
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
+ <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
<param name="inih" value="10M" />
<param name="maxh" value="256M" />
</antcall>
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
+ <param name="inih" value="800M" />
+ <param name="maxh" value="1024M" />
+ </antcall>
<antcall target="writejnlpf">
<param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
<antcall target="writejnlpf">
<param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
- <param name="inih" value="256M" />
+ <param name="inih" value="800M" />
<param name="maxh" value="1024M" />
</antcall>
<association mime-type="application-x/ext-file" extensions="jar"/>-->
</target>
- <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
+ <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
<fileset dir="${packageDir}">
</fileset>
</signjar>
</target>
- <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
+ <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
<fileset dir="${packageDir}">
<include name="*.jar" />
<include name="ap_${jsonSimple}" />
</fileset>
</target>
-<target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
+<target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
<fileset refid="signappletjarset" />
</signjar>
</target>
-<target name="-signapplettsa" if="timestamp" depends="-signapplet">
+<target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
<fileset refid="signappletjarset" />
</signjar>
--- /dev/null
+VAqua5-patched.jar - how the patch was created
+
+1. Download VAqua5 source from https://violetlib.org/release/vaqua/5/VAqua5Source.zip
+2. Unzip to a directory and apply this patch
+
+diff --git a/src/org/violetlib/aqua/fc/AquaFileChooserUI.java b/src/org/violetlib/aqua/fc/AquaFileChooserUI.java
+index 833366d..61f66e5 100644
+--- a/src/org/violetlib/aqua/fc/AquaFileChooserUI.java
++++ b/src/org/violetlib/aqua/fc/AquaFileChooserUI.java
+@@ -1171,7 +1171,8 @@ public class AquaFileChooserUI extends BasicFileChooserUI {
+ goToFolderCancelButtonText = getString("FileChooser.goToFolderCancelButtonText", l, "Cancel");
+ goToFolderAcceptButtonText = getString("FileChooser.goToFolderAcceptButtonText", l, "Accept");
+ goToFolderErrorText = getString("FileChooser.goToFolderErrorText", l, "The folder can\u2019t be found.");
+- defaultInitialSaveFileName = getString("FileChooser.defaultSaveFileName", l, "Untitled");
++ // Don't set an initial filename for saving (or loading) !
++ // defaultInitialSaveFileName = getString("FileChooser.defaultSaveFileName", l, "Untitled");
+ }
+
+ /**
+
+3. Ensure XCode is installed, along with command line tools and the OSX developer packs
+ - you should have /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
+
+4. Download the VAqua rendering library from violetlib.org and save to the VAqua source's lib folder as lib/VAquaRendering.jar
+
+5. change to the release directory and execute 'ant' - a few warnings are generated but providing a final jar is created, all is good!
+
--- /dev/null
+# STOCKHOLM 1.0
+#=GF ID RNA.SS.TEST
+#=GF TP RNA;
+Test.sequence GUACAAAAAAAAAA
+#=GC SS_cons <(EHBheb(E)e)>
+//
SEQUENCE_GROUP Group_B 1 351 2-5
SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
-PROPERTIES Group_B outlineColour=red colour=None
+PROPERTIES Group_B outlineColour=green colour=None
PROPERTIES Group_C colour=Clustal
provided by InstallAnywhere any output from the application will be
sent to output.txt, not standard out.<br> The Jalview
application also requires a number of additional libraries on the
- class path. The command line below adds the Jalview installation's
- 'lib' directory to the list of directories that are searched for
- jars to be added to the classpath:
+ class path. The command line below adds all the jar files in the
+ Jalview installation's 'lib' directory to the classpath, as well as
+ the Jalview application jar file:
</p>
- <pre>java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] </pre>
+ <pre>java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE] </pre>
<p>
Use '-help' to get more information on the <a
href="clarguments.html">command line arguments</a> that
! <string>-Xms2M</string>
! <string>-Xmx64M</string>
</array>
-</pre> Exchange the above two string tags for : <pre>
+</pre>Exchange the above two string tags for : <pre>
<string>-Xms500M</string>
<string>-Xmx1000M</string>
</pre>
the file and try to start Jalview in the normal way. If it doesn't
start, see below...</li>
</ul>
+ <p>
+ <em>Please Note:</em> We do modify the default memory settings in
+ Jalview from time to time, so you may find different numbers to
+ those shown in the examples above.
+ </p>
<font size="3"><em>Jalview doesn't start... What do the
memory settings mean ?<a name="memsetting"></a>
</em></font>
enlighten us if you know better!). Our experiments found 1000m to be
the biggest setting that could be used on a 1GB machine. Just try
reducing the sizes until Jalview starts up properly!</p>
+ <p>
+ We increased the default memory in Jalview 2.10.5 to 1G. To launch
+ Jalview with the pre 2.10.5 default memory allocation, use the <a
+ href="http://www.jalview.org/webstart/jalview_256MB.jnlp">Jalview
+ 256MB JNLP</a>.
+ </p>
<p> </p>
</body>
</html>
</div></td>
</tr>
<tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-3101 -->Default memory for Jalview webstart and
+ InstallAnywhere increased to 1G.
+ </li>
+ <li>
+ <!-- JAL-247 -->Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. <em>Display is configured via the
+ Format menu, or for command-line use via a jalview
+ properties file.</em>
+ </li>
+ <li>
+ <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
+ API and sequence data now imported as JSON.
+ </li>
+ <li>
+ <!-- JAL-3065 -->Change in recommended way of starting
+ Jalview via a Java command line: add jars in lib directory
+ to CLASSPATH, rather than via the deprecated java.ext.dirs
+ property.
+ </li>
+ </ul>
+ <em>Development</em>
+ <ul>
+ <li>
+ <!-- JAL-3047 -->Support added to execute test suite
+ instrumented with <a href="http://openclover.org/">Open
+ Clover</a>
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-3104 -->Poorly scaled bar in quality annotation
+ row shown in Feredoxin Structure alignment view of example
+ alignment.
+ </li>
+ <li>
+ <!-- JAL-2854 -->Annotation obscures sequences if lots of
+ annotation displayed.
+ </li>
+ <li>
+ <!-- JAL-3107 -->Group conservation/consensus not shown
+ for newly created group when 'Apply to all groups'
+ selected
+ </li>
+ <li>
+ <!-- JAL-3087 -->Corrupted display when switching to
+ wrapped mode when sequence panel's vertical scrollbar is
+ visible.
+ </li>
+ <li>
+ <!-- JAL-3003 -->Alignment is black in exported EPS file
+ when sequences are selected in exported view.</em>
+ </li>
+ <li>
+ <!-- JAL-3059 -->Groups with different coloured borders
+ aren't rendered with correct colour.
+ </li>
+ <li>
+ <!-- JAL-3092 -->Jalview could hang when importing certain
+ types of knotted RNA secondary structure.
+ </li>
+ <li>
+ <!-- JAL-3095 -->Sequence highlight and selection in
+ trimmed VARNA 2D structure is incorrect for sequences that
+ do not start at 1.
+ </li>
+ <li>
+ <!-- JAL-3061 -->'.' inserted into RNA secondary structure
+ annotation when columns are inserted into an alignment,
+ and when exporting as Stockholm flatfile.
+ </li>
+ <li>
+ <!-- JAL-3053 -->Jalview annotation rows containing upper
+ and lower-case 'E' and 'H' do not automatically get
+ treated as RNA secondary structure.
+ </li>
+ <li>
+ <!-- JAL-3106 -->.jvp should be used as default extension
+ (not .jar) when saving a jalview project file.
+ </li>
+ <li>
+ <!-- JAL-3105 -->Mac Users: closing a window correctly
+ transfers focus to previous window on OSX
+ </li>
+ </ul>
+ <em>Java 10 Issues Resolved</em>
+ <ul>
+ <li>
+ <!-- JAL-2988 -->OSX - Can't save new files via the File
+ or export menus by typing in a name into the Save dialog
+ box.
+ </li>
+ <li>
+ <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
+ of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
+ 'look and feel' which has improved compatibility with the
+ latest version of OSX.
+ </li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
- <em>27/05/2018</em></strong>
+ <em>7/06/2018</em></strong>
</div>
</td>
<td><div align="left">
<em></em>
<ul>
<li>
+ <!-- JAL-2920 -->Use HGVS nomenclature for variant
+ annotation retrieved from Uniprot
+ </li>
+ <li>
<!-- JAL-1460 -->Windows File Shortcuts can be dragged
onto the Jalview Desktop
</li>
<em></em>
<ul>
<li>
+ <!-- JAL-3017 -->Cannot import features with multiple
+ variant elements (blocks import of some Uniprot records)
+ </li>
+ <li>
<!-- JAL-2997 -->Clustal files with sequence positions in
right-hand column parsed correctly
</li>
<li>
+ <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
+ not alignment area in exported graphic
+ </li>
+ <li>
<!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
window has input focus
</li>
<li>
- <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
- not alignment area in exported graphic
+ <!-- JAL-2992 -->Annotation panel set too high when
+ annotation added to view (Windows)
+ </li>
+ <li>
+ <!-- JAL-3009 -->Jalview Desktop is slow to start up when
+ network connectivity is poor
</li>
<li>
<!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
- Jalview desktop on Windows doesn't open file<br />
- <em>Dragging the currently open URL and links from a page viewed in Firefox or Chrome on
- Windows is now fully supported. If you are using Edge, only
- links in the page can be dragged, and with Internet Explorer, only
- the currently open URL in the browser can be dropped onto
- Jalview.</em>
- </li>
- <li>
- <!-- JAL-2992 -->
+ Jalview desktop on Windows doesn't open file<br /> <em>Dragging
+ the currently open URL and links from a page viewed in
+ Firefox or Chrome on Windows is now fully supported. If
+ you are using Edge, only links in the page can be
+ dragged, and with Internet Explorer, only the currently
+ open URL in the browser can be dropped onto Jalview.</em>
</li>
</ul>
</div></td>
</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.4 ?</strong>
- </p>
- <p>
- This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
+ <strong>What's new in Jalview 2.10.5 ?</strong>
</p>
+ <p>Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, RNA secondary structure
+ annotation, and those running Jalview on OSX with Java 10.</p>
<ul>
- <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
- <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
- <li>Critical patches for running Jalview on OSX with Java 10</li>
- <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
- <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
- <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
- <li>New buttons on the Structure Chooser for adding structures
- to an existing view, and disabling automatic superposition
- according to linked alignments</li>
- <li>Annotation transfer between Chimera and Jalview <em>(formerly only
- available in 'Experimental' mode)</em></li>
+ <li>Jalview's default memory limit increased to 1G. <br/>If you have
+ problems starting Jalview 2.10.5 and you have 1G or less
+ physical memory on your machine, you will need to <a
+ href="memory.html#memsetting">reduce the memory</a> allocated to
+ Jalview.
+ </li>
+ <li>EPS, PNG and SVG export now includes hidden sequence
+ markers, and representative sequences are marked in bold.</li>
+ <li>Ensembl Client updated for Ensembl Rest API v7.<br />The
+ latest Ensembl API is not backwards compatible with earlier
+ versions of Jalview, so if you require Ensembl functionality you
+ will need to install this release.
+ </li>
+ <li>Improved support for VIENNA extended dot-bracket notation
+ for RNA secondary structure.</li>
+ <li>Positional and selected region highlighting in VARNA
+ 'trimmed sequence' view made more reliable.</li>
</ul>
<p>
- The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
- Release Notes</a>.
+ The full list of bugs fixed in this release can be found in the <a
+ href="releases.html#Jalview.2.10.5">2.10.5 Release Notes</a>. The
+ majority of bug fixes and improvements in 2.10.5 are due to Jalview users
+ contacting us via the jalview-discuss email list. Thanks to everyone
+ who took the time to help make Jalview better !
+ </p>
+ <p>
+ <strong>Jalview and Java 10</strong>
</p>
+ <p>This release addresses a critical bug for OSX users who are
+ running Jalview with Java 10 which can prevent files being saved
+ correctly through the 'Save As' dialog box.</p>
+ <em>Known Issues</em>
+ <ul>
+ <li>OSX: The 'Open File' dialog for Jalview's Groovy Console
+ appears with the title 'Save As', and attempting to select a file to load yields a FileNotFound exception.</br>The workaround is to first clear the 'Untitled' filename before selecting the file you wish to load.
+ </li>
+ <li>OSX: Links don't open when clicked on or via the Sequence or Alignment window popup menu.</li>
+ <li>OSX (Webstart): Jalview only displays old news feed items</li>
+ </ul>
</body>
</html>
-YEAR=2016
-AUTHORS=J Procter, M Carstairs, TC Ofoegbu, K Mourao, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
-AUTHORFNAMES=Jim Procter, Mungo Carstairs, Tochukwu 'Charles' Ofoegbu, Kira Mourao, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+YEAR=2018
+AUTHORS=J Procter, M Carstairs, B Soares, K Mourao, TC Ofoegbu, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
+AUTHORFNAMES=Jim Procter, Mungo Carstairs, Ben Soares, Kira Mourao, Tochukwu 'Charles' Ofoegbu, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0"?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<mapping>
- <class name="jalview.datamodel.xdb.uniprot.UniprotFile">
- <map-to xml="uniprot"/>
- <field name="UniprotEntries" type="jalview.datamodel.xdb.uniprot.UniprotEntry" collection="vector">
- <bind-xml name="entry"/>
- </field>
- </class>
-
- <class name="jalview.datamodel.xdb.uniprot.UniprotEntry">
- <field name="name" type="string" collection="vector"/>
- <field name="accession" type="string" collection="vector"/>
- <field name="protein" type="jalview.datamodel.xdb.uniprot.UniprotProteinName"/>
- <field name="UniprotSequence" type="jalview.datamodel.xdb.uniprot.UniprotSequence">
- <bind-xml name="sequence"/>
- </field>
- <field name="feature" type="jalview.datamodel.xdb.uniprot.UniprotFeature" collection="vector"/>
- <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
-
- </class>
- <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
- <field name="name" collection="vector" type="string">
- <bind-xml name="fullName" location="recommendedName" node="element"/>
- </field>
- </class>
- <!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot
- record. This means this doesn't exist anymore...
- <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
- <field name="name" type="string" collection="vector">
- <bind-xml name="name"/>
- </field>
- </class>
- -->
-
- <class name="jalview.datamodel.xdb.uniprot.UniprotFeature">
- <field name="type">
- <bind-xml node="attribute"/>
- </field>
- <field name="description">
- <bind-xml node="attribute"/>
- </field>
- <field name="status">
- <bind-xml node="attribute"/>
- </field>
- <field name="position">
- <bind-xml name="position" node="attribute" location="location/position"/>
- </field>
- <field name="begin">
- <bind-xml name="position" node="attribute" location="location/begin"/>
- </field>
- <field name="end">
- <bind-xml name="position" node="attribute" location="location/end"/>
- </field>
- <field name="variation">
- <bind-xml name="variation"/>
- </field>
- <field name="original">
- <bind-xml name="original"/>
- </field>
- </class>
-
- <class name="jalview.datamodel.xdb.uniprot.UniprotSequence">
- <field name="content" type="string">
- <bind-xml name="sequence" node="text"/>
- </field>
- </class>
-
- <class name="jalview.datamodel.PDBEntry">
- <field name="type"><bind-xml node="attribute"/></field>
- <field name="id"><bind-xml node="attribute"/></field>
- <field name="props" collection="hashtable">
- <bind-xml name="property">
- <class name="org.exolab.castor.mapping.MapItem">
- <field name="key">
- <bind-xml name="type" node="attribute"/>
- </field>
- <field name="value">
- <bind-xml node="attribute"/>
- </field>
- </class>
- </bind-xml>
- </field>
- </class>
-
-</mapping>
You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
+<!--
+ Java JAXB binding classes are generated by running command line tool xjc:
+ xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ Note this also generates code for included schemas
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:jalview="www.jalview.org/colours" targetNamespace="www.jalview.org/colours">
+ <xs:element name="JalviewUserColours" type="jalview:JalviewUserColours" />
<xs:complexType name="JalviewUserColours">
<xs:sequence>
<xs:element name="Version" maxOccurs="1" minOccurs="0" type="xs:string">
<xs:attribute name="RGB" type="xs:string" use="required"/>
<xs:attribute name="minRGB" type="xs:string" use="optional"/>
<xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
- <xs:attribute name="threshType" use="optional">
- <xs:simpleType>
- <xs:restriction base="xs:string">
- <xs:enumeration value="NONE" />
- <xs:enumeration value="ABOVE" />
- <xs:enumeration value="BELOW" />
- </xs:restriction>
- </xs:simpleType>
- </xs:attribute>
+ <xs:attribute name="threshType" use="optional" type="jalview:ThresholdType" />
<xs:attribute name="threshold" type="xs:float" use="optional"/>
<xs:attribute name="max" type="xs:float" use="optional"/>
<xs:attribute name="min" type="xs:float" use="optional"/>
<xs:element name="condition" type="xs:string" />
<xs:element name="value" type="xs:string" />
</xs:sequence>
- <xs:attribute name="by">
- <xs:simpleType>
- <xs:restriction base="xs:string">
- <xs:enumeration value="byLabel" />
- <xs:enumeration value="byScore" />
- <xs:enumeration value="byAttribute" />
- </xs:restriction>
- </xs:simpleType>
- </xs:attribute>
- </xs:complexType>
+ <xs:attribute name="by" type="jalview:FilterBy" />
+ </xs:complexType>
+
+ <xs:simpleType name="ThresholdType">
+ <xs:annotation>
+ <xs:documentation>Whether filter has a threshold, and if so is it
+ above or below
+ </xs:documentation>
+ </xs:annotation>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="NONE" />
+ <xs:enumeration value="ABOVE" />
+ <xs:enumeration value="BELOW" />
+ </xs:restriction>
+ </xs:simpleType>
+
+ <xs:simpleType name="FilterBy">
+ <xs:annotation>
+ <xs:documentation>Filter may apply to label, score or some feature attribute</xs:documentation>
+ </xs:annotation>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="byLabel" />
+ <xs:enumeration value="byScore" />
+ <xs:enumeration value="byAttribute" />
+ </xs:restriction>
+ </xs:simpleType>
<xs:simpleType name="NoValueColour">
<xs:annotation>
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
+<!--
+ Java JAXB binding classes are generated by running command line tool xjc:
+ xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ Note this also generates code for included schemas
+-->
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:wsparams="www.jalview.org/xml/wsparamset"
targetNamespace="www.jalview.org/xml/wsparamset">
+ <xs:element name="WebServiceParameterSet" type="wsparams:WebServiceParameterSet" />
<xs:complexType name="WebServiceParameterSet">
<xs:sequence>
<xs:element name="Version" maxOccurs="1" minOccurs="0"
--- /dev/null
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!--
+ Retrieved for Jalview 14-Sep-2018 from ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd
+ Modified to match ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.root.xsd with only ENA.embl.xsd included
+ root element "ROOT" contains a <choice> of "entry" (single accession) or "entrySet" (one or more accessions)
+ Java binding classes are generated by
+ xjc schemas/embl.xsd -b schemas/embl_bindings.xml -d src -p jalview.xml.binding.embl
+-->
+<xs:schema xmlns:ebi="http://www.ebi.ac.uk/embl/schema"
+ xmlns:xs="http://www.w3.org/2001/XMLSchema"
+ attributeFormDefault="unqualified" elementFormDefault="qualified"
+ version="1.1">
+ <xs:complexType name="XrefType">
+ <xs:annotation>
+ <xs:documentation>Database cross-reference.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="db" type="xs:string" use="required" />
+ <xs:attribute name="id" type="xs:string" use="required" />
+ <xs:attribute name="secondaryId" type="xs:string"
+ use="optional" />
+ </xs:complexType>
+ <xs:complexType name="EntrySetType">
+ <xs:sequence minOccurs="1" maxOccurs="unbounded">
+ <xs:element name="entry" type="EntryType" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="EntryType">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="secondaryAccession" type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="projectAccession" type="xs:string" />
+ <xs:element maxOccurs="1" minOccurs="1" name="description"
+ type="xs:string" />
+ <xs:element maxOccurs="1" minOccurs="0" name="comment"
+ type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="keyword" type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="reference">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="1" minOccurs="0" name="title"
+ type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="author" type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="applicant" type="xs:string">
+ <xs:annotation>
+ <xs:documentation>Patent applicant.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="consortium" type="xs:string" />
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="submissionDate" type="xs:date">
+ <xs:annotation>
+ <xs:documentation>The submission date (used only for submission
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="journal"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The journal name (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="year"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The publication year (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="volume"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The volume number (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="issue"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The issue number (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="firstPage" type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The first page (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="lastPage"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The last page (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="comment"
+ type="xs:string" />
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="referenceLocation" type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="xref" type="XrefType" />
+ </xs:sequence>
+ <xs:attribute name="type" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="submission" />
+ <xs:enumeration value="book" />
+ <xs:enumeration value="article" />
+ <xs:enumeration value="patent" />
+ <xs:enumeration value="thesis" />
+ <xs:enumeration value="unpublished" />
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="number" type="xs:integer"
+ use="required" />
+ <xs:attribute name="location" type="xs:string" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="xref" type="XrefType" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="feature">
+ <xs:annotation>
+ <xs:documentation>Sequence feature.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="1" minOccurs="0" name="taxon">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="lineage">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="1"
+ name="taxon">
+ <xs:complexType>
+ <xs:attribute name="scientificName"
+ type="xs:string" use="required" />
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="scientificName"
+ type="xs:string" use="required" />
+ <xs:attribute name="commonName" type="xs:string"
+ use="optional" />
+ <xs:attribute name="taxId" type="xs:integer"
+ use="optional" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="xref" type="XrefType" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="qualifier">
+ <xs:annotation>
+ <xs:documentation>Sequence feature qualifier.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="1" minOccurs="0" name="value"
+ type="xs:string" />
+ </xs:sequence>
+ <xs:attribute name="name" type="xs:string"
+ use="required" />
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="name" type="xs:string"
+ use="required" />
+ <xs:attribute name="location" type="xs:string"
+ use="required" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="assembly">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="1"
+ name="range">
+ <xs:complexType>
+ <xs:attribute name="begin" type="xs:integer"
+ use="required" />
+ <xs:attribute name="end" type="xs:integer"
+ use="required" />
+ <xs:attribute name="primaryBegin" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="primaryEnd" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="accession" type="xs:string"
+ use="required" />
+ <xs:attribute name="version" type="xs:integer"
+ use="required" />
+ <xs:attribute default="false" name="complement"
+ type="xs:boolean" use="optional" />
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="contig">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:choice maxOccurs="unbounded" minOccurs="0">
+ <xs:element maxOccurs="1" minOccurs="1" name="range">
+ <xs:complexType>
+ <xs:attribute name="begin" type="xs:integer"
+ use="required" />
+ <xs:attribute name="end" type="xs:integer"
+ use="required" />
+ <xs:attribute name="primaryBegin"
+ type="xs:integer" use="optional" />
+ <xs:attribute name="primaryEnd" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="accession" type="xs:string"
+ use="required" />
+ <xs:attribute name="version" type="xs:integer"
+ use="required" />
+ <xs:attribute default="false" name="complement"
+ type="xs:boolean" use="optional" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="1" name="gap">
+ <xs:complexType>
+ <xs:attribute name="begin" type="xs:integer"
+ use="required" />
+ <xs:attribute name="end" type="xs:integer"
+ use="required" />
+ <xs:attribute name="length" type="xs:integer"
+ use="required" />
+ <xs:attribute default="false" name="unknownLength"
+ type="xs:boolean" use="optional" />
+ </xs:complexType>
+ </xs:element>
+ </xs:choice>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="sequence"
+ type="xs:string" />
+ </xs:sequence>
+ <xs:attribute name="accession" type="xs:string"
+ use="required" />
+ <xs:attribute name="version" type="xs:integer"
+ use="required" />
+ <xs:attribute name="entryVersion" type="xs:integer">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="dataClass" type="xs:string"
+ use="required" />
+ <xs:attribute name="taxonomicDivision" type="xs:string"
+ use="required" />
+ <xs:attribute name="moleculeType" type="xs:string"
+ use="required" />
+ <xs:attribute name="sequenceLength" type="xs:integer"
+ use="required" />
+ <xs:attribute name="topology" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="circular" />
+ <xs:enumeration value="linear" />
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="firstPublic" type="xs:date">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="firstPublicRelease" type="xs:integer">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="lastUpdated" type="xs:date">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="lastUpdatedRelease" type="xs:integer">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:element name="ROOT">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element name="entrySet" type="EntrySetType" />
+ <xs:element name="entry" type="EntryType" />
+ </xs:choice>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
--- /dev/null
+<!--
+ Binding file stops the nested 'taxon' elements generating invalid Java (nested type hiding enclosing type).
+ The binding converts EntryType/feature/taxon to EntryType$Feature$FeatureTaxon.
+ EntryType/feature/taxon/lineage/taxon generates EntryType$Feature$FeatureTaxon$Lineage$Taxon.
+-->
+<jaxb:bindings
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+ xmlns:jaxb="http://java.sun.com/xml/ns/jaxb" version="2.1">
+ <jaxb:bindings schemaLocation="embl.xsd">
+ <jaxb:bindings
+ node="/xsd:schema/xsd:complexType[@name='EntryType']/xsd:sequence/xsd:element[@name='feature']/xsd:complexType/xsd:sequence/xsd:element[@name='taxon']/xsd:complexType">
+ <jaxb:class name="FeatureTaxon" />
+ </jaxb:bindings>
+ </jaxb:bindings>
+</jaxb:bindings>
\ No newline at end of file
Public License for more details. * * You should have received a copy of the
GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file. -->
+<!--
+ Java JAXB binding classes are generated by running command line tool xjc:
+ xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ Note this also generates code for included schemas
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours"
xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset"
schemaLocation="JalviewUserColours.xsd" />
<xs:import namespace="www.jalview.org/xml/wsparamset"
schemaLocation="JalviewWsParamSet.xsd" />
+ <xs:element name="JalviewModel" type="jv:JalviewModel" />
<xs:complexType name="JalviewModel">
<xs:sequence>
<xs:element name="creationDate" type="xs:dateTime" />
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- *****************************************************************************
+ UniProt Knowledgebase
+ Version: $Revision: 1.3 $
+ Date: $Date: 2015/04/07 15:00:57 $
+
+ Copyright (c) 2011 UniProt consortium
+ All rights reserved.
+*******************************************************************************-->
+<xs:schema targetNamespace="http://uniprot.org/uniprot" xmlns:xs="http://www.w3.org/2001/XMLSchema"
+ xmlns="http://uniprot.org/uniprot" elementFormDefault="qualified">
+<!--
+ Retrieved for Jalview 13-Sep-2018 from https://www.uniprot.org/docs/uniprot.xsd
+ Java binding classes are generated by
+ xjc schemas/uniprot.xsd -d src -p jalview.xml.binding.uniprot
+-->
+ <!-- XML Schema definition for the UniProtKB XML format
+ Tested with:
+ -XSV (XML Schema Validator), http://www.w3.org/2001/03/webdata/xsv
+ -->
+ <!-- Root element definition begins -->
+ <xs:element name="uniprot">
+ <xs:annotation>
+ <xs:documentation>Describes a collection of UniProtKB entries.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="entry" maxOccurs="unbounded"/>
+ <xs:element ref="copyright" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <!-- Root element definition ends -->
+
+ <!-- Entry definition begins -->
+ <xs:element name="entry">
+ <xs:annotation>
+ <xs:documentation>Describes a UniProtKB entry.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="accession" type="xs:string" maxOccurs="unbounded"/>
+ <xs:element name="name" type="xs:string" maxOccurs="unbounded"/>
+ <xs:element name="protein" type="proteinType"/>
+ <xs:element name="gene" type="geneType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="organism" type="organismType" />
+ <xs:element name="organismHost" type="organismType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="geneLocation" type="geneLocationType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="reference" type="referenceType" maxOccurs="unbounded"/>
+ <xs:element name="comment" type="commentType" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="dbReference" type="dbReferenceType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="proteinExistence" type="proteinExistenceType"/>
+ <xs:element name="keyword" type="keywordType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="feature" type="featureType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="evidence" type="evidenceType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="sequence" type="sequenceType"/>
+ </xs:sequence>
+ <xs:attribute name="dataset" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="Swiss-Prot"/>
+ <xs:enumeration value="TrEMBL"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="created" type="xs:date" use="required"/>
+ <xs:attribute name="modified" type="xs:date" use="required"/>
+ <xs:attribute name="version" type="xs:int" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <!-- Entry definition ends -->
+
+ <xs:element name="copyright" type="xs:string"/>
+
+ <!-- Protein names definition begins -->
+ <xs:complexType name="proteinType">
+ <xs:annotation>
+ <xs:documentation>Describes the names for the protein and parts thereof.
+ Equivalent to the flat file DE-line.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:group ref="proteinNameGroup"/>
+ <xs:element name="domain" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes names of "domains".
+ Equivalent to the flat file DE-line Includes: section.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:group ref="proteinNameGroup"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="component" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes names of processed products.
+ Equivalent to the flat file DE-line Contains: section.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:group ref="proteinNameGroup"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:group name="proteinNameGroup">
+ <xs:sequence>
+ <xs:element name="recommendedName" minOccurs="0">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="fullName" type="evidencedStringType"/>
+ <xs:element name="shortName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="ecNumber" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <!-- xs:attribute name="ref" type="xs:string" use="optional"/ -->
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="alternativeName" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="fullName" type="evidencedStringType" minOccurs="0"/>
+ <xs:element name="shortName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="ecNumber" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <!-- xs:attribute name="ref" type="xs:string" use="optional"/ -->
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="submittedName" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="fullName" type="evidencedStringType"/>
+ <xs:element name="ecNumber" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <!-- xs:attribute name="ref" type="xs:string" use="optional"/ -->
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="allergenName" type="evidencedStringType" minOccurs="0"/>
+ <xs:element name="biotechName" type="evidencedStringType" minOccurs="0"/>
+ <xs:element name="cdAntigenName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="innName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:group>
+ <!-- Protein names definition ends -->
+
+ <!-- Gene names definition begins -->
+ <xs:complexType name="geneType">
+ <xs:annotation>
+ <xs:documentation>Describes a gene.
+ Equivalent to the flat file GN-line.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="name" type="geneNameType" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="geneNameType">
+ <xs:annotation>
+ <xs:documentation>Describes different types of gene designations.
+ Equivalent to the flat file GN-line.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ <xs:attribute name="type" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="primary"/>
+ <xs:enumeration value="synonym"/>
+ <xs:enumeration value="ordered locus"/>
+ <xs:enumeration value="ORF"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <!-- Gene names definition ends -->
+
+ <!-- Organism definition begins -->
+ <xs:complexType name="organismType">
+ <xs:annotation>
+ <xs:documentation>Describes the source organism.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="name" type="organismNameType" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes the names of the source organism.
+ Equivalent to the flat file OS-line.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="dbReference" type="dbReferenceType" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes a cross-reference to the NCBI taxonomy database.
+ Equivalent to the flat file OX-line.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="lineage" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Describes the lineage of the source organism.
+ Equivalent to the flat file OC-line.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="taxon" type="xs:string" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:complexType>
+ <xs:complexType name="organismNameType">
+ <xs:annotation>
+ <xs:documentation>Describes different types of source organism names.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="type" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="common"/>
+ <xs:enumeration value="full"/>
+ <xs:enumeration value="scientific"/>
+ <xs:enumeration value="synonym"/>
+ <xs:enumeration value="abbreviation"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <!-- Organism definition ends -->
+
+ <!-- Gene location definition begins -->
+ <xs:complexType name="geneLocationType">
+ <xs:annotation>
+ <xs:documentation>Describes non-nuclear gene locations (organelles and plasmids).
+ Equivalent to the flat file OG-line.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="name" type="statusType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="type" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="apicoplast"/>
+ <xs:enumeration value="chloroplast"/>
+ <xs:enumeration value="organellar chromatophore"/>
+ <xs:enumeration value="cyanelle"/>
+ <xs:enumeration value="hydrogenosome"/>
+ <xs:enumeration value="mitochondrion"/>
+ <xs:enumeration value="non-photosynthetic plastid"/>
+ <xs:enumeration value="nucleomorph"/>
+ <xs:enumeration value="plasmid"/>
+ <xs:enumeration value="plastid"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:complexType>
+ <xs:complexType name="statusType">
+ <xs:annotation>
+ <xs:documentation>Indicates whether the name of a plasmid is known or unknown.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="status" use="optional" default="known">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="known"/>
+ <xs:enumeration value="unknown"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <!-- Gene location definition ends -->
+
+ <!-- Reference definition begins -->
+ <xs:complexType name="referenceType">
+ <xs:annotation>
+ <xs:documentation>Describes a citation and a summary of its content.
+ Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="citation" type="citationType"/>
+ <xs:group ref="sptrCitationGroup"/>
+ </xs:sequence>
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ <xs:attribute name="key" type="xs:string" use="required"/>
+ </xs:complexType>
+ <!-- Reference definition ends -->
+
+ <!-- Citation definition begins -->
+ <xs:complexType name="citationType">
+ <xs:annotation>
+ <xs:documentation>Describes different types of citations.
+ Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="title" type="xs:string" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Describes the title of a citation.
+ Equivalent to the flat file RT-line.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="editorList" type="nameListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Describes the editors of a book (only used for books).
+ Equivalent to part of the flat file RL-line of books.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="authorList" type="nameListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Describes the authors of a citation.
+ Equivalent to the flat file RA-line.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="locator" type="xs:string" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Describes the location (URL) of an online journal article.
+ No flat file equivalent.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="dbReference" type="dbReferenceType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes cross-references to bibliography databases (MEDLINE, PubMed, AGRICOLA) or other online resources (DOI).
+ Equivalent to the flat file RX-line.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="type" use="required">
+ <xs:annotation>
+ <xs:documentation>Describes the type of a citation.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="book"/>
+ <xs:enumeration value="journal article"/>
+ <xs:enumeration value="online journal article"/>
+ <xs:enumeration value="patent"/>
+ <xs:enumeration value="submission"/>
+ <xs:enumeration value="thesis"/>
+ <xs:enumeration value="unpublished observations"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="date" use="optional">
+ <xs:simpleType>
+ <xs:union memberTypes="xs:date xs:gYearMonth xs:gYear"/>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="name" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the name of an (online) journal or book.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="volume" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the volume of a journal or book.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="first" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the first page of an article.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="last" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the last page of an article.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="publisher" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the publisher of a book.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="city" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the city where a book was published.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="db" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the database name of submissions.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="number" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes a patent number.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="institute" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the institute where a thesis was made.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="country" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the country where a thesis was made.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:complexType name="consortiumType">
+ <xs:annotation>
+ <xs:documentation>Describes the authors of a citation when these are represented by a consortium.
+ Equivalent to the flat file RG-line.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="name" type="xs:string" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="personType">
+ <xs:attribute name="name" type="xs:string" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="nameListType">
+ <xs:choice maxOccurs="unbounded">
+ <xs:element name="consortium" type="consortiumType"/>
+ <xs:element name="person" type="personType"/>
+ </xs:choice>
+ </xs:complexType>
+ <!-- Citation definition ends -->
+
+ <!-- Citation summary definition begins -->
+ <xs:group name="sptrCitationGroup">
+ <xs:annotation>
+ <xs:documentation>Groups a citation's scope and source descriptions.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="scope" type="xs:string" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes the scope of a citation.
+ Equivalent to the flat file RP-line.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="source" type="sourceDataType" minOccurs="0"/>
+ </xs:sequence>
+ </xs:group>
+ <xs:complexType name="sourceDataType">
+ <xs:annotation>
+ <xs:documentation>Describes the source of the sequence according to the citation.
+ Equivalent to the flat file RC-line.</xs:documentation>
+ </xs:annotation>
+ <xs:choice maxOccurs="unbounded">
+ <xs:element name="strain">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plasmid">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="transposon">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tissue">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:choice>
+ </xs:complexType>
+ <!-- Citation summary definition ends -->
+
+ <!-- Comment definition begins -->
+ <xs:complexType name="commentType">
+ <xs:annotation>
+ <xs:documentation>Describes different types of general annotations.
+ Equivalent to the flat file CC-line.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="molecule" type="moleculeType" minOccurs="0"/>
+ <xs:choice minOccurs="0">
+ <xs:group ref="bpcCommentGroup"/>
+
+ <xs:sequence>
+ <xs:annotation>
+ <xs:documentation>Used in 'cofactor' annotations.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="cofactor" type="cofactorType" maxOccurs="unbounded"/>
+ </xs:sequence>
+
+ <xs:sequence>
+ <xs:annotation>
+ <xs:documentation>Used in 'subcellular location' annotations.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="subcellularLocation" type="subcellularLocationType" maxOccurs="unbounded"/>
+ </xs:sequence>
+
+ <xs:element name="conflict">
+ <xs:annotation>
+ <xs:documentation>Used in 'sequence caution' annotations.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="sequence" minOccurs="0">
+ <xs:complexType>
+ <xs:attribute name="resource" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="EMBL-CDS"/>
+ <xs:enumeration value="EMBL"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="id" type="xs:string" use="required"/>
+ <xs:attribute name="version" type="xs:int" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="type" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="frameshift"/>
+ <xs:enumeration value="erroneous initiation"/>
+ <xs:enumeration value="erroneous termination"/>
+ <xs:enumeration value="erroneous gene model prediction"/>
+ <xs:enumeration value="erroneous translation"/>
+ <xs:enumeration value="miscellaneous discrepancy"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="ref" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Refers to the 'key' attribute of a 'reference' element.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ </xs:element>
+
+ <xs:sequence>
+ <xs:element name="link" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Used in 'online information' annotations.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="uri" type="xs:anyURI" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+
+ <xs:sequence>
+ <xs:annotation>
+ <xs:documentation>Used in 'alternative products' annotations.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="event" type="eventType" maxOccurs="4"/>
+ <xs:element name="isoform" type="isoformType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+
+ <xs:sequence>
+ <xs:annotation>
+ <xs:documentation>Used in 'interaction' annotations.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="interactant" type="interactantType" minOccurs="2" maxOccurs="2"/>
+ <xs:element name="organismsDiffer" type="xs:boolean" default="false"/>
+ <xs:element name="experiments" type="xs:int"/>
+ </xs:sequence>
+
+ <xs:element name="disease">
+ <xs:annotation>
+ <xs:documentation>Used in 'disease' annotations.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="name" type="xs:string"/>
+ <xs:element name="acronym" type="xs:string"/>
+ <xs:element name="description" type="xs:string"/>
+ <xs:element name="dbReference" type="dbReferenceType"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:string" use="required"/>
+ </xs:complexType>
+ </xs:element>
+
+ </xs:choice>
+
+ <xs:element name="location" type="locationType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Used in 'mass spectrometry' and 'sequence caution' annotations.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+
+ <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+
+ </xs:sequence>
+
+ <xs:attribute name="type" use="required">
+ <xs:annotation>
+ <xs:documentation>Describes the type of a general annotation.
+ Equivalent to the flat file CC comment topics (except for "DATABASE" which is translated to "online information").</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="allergen"/>
+ <xs:enumeration value="alternative products"/>
+ <xs:enumeration value="biotechnology"/>
+ <xs:enumeration value="biophysicochemical properties"/>
+ <xs:enumeration value="catalytic activity"/>
+ <xs:enumeration value="caution"/>
+ <xs:enumeration value="cofactor"/>
+ <xs:enumeration value="developmental stage"/>
+ <xs:enumeration value="disease"/>
+ <xs:enumeration value="domain"/>
+ <xs:enumeration value="disruption phenotype"/>
+ <xs:enumeration value="activity regulation"/>
+ <xs:enumeration value="function"/>
+ <xs:enumeration value="induction"/>
+ <xs:enumeration value="miscellaneous"/>
+ <xs:enumeration value="pathway"/>
+ <xs:enumeration value="pharmaceutical"/>
+ <xs:enumeration value="polymorphism"/>
+ <xs:enumeration value="PTM"/>
+ <xs:enumeration value="RNA editing"/>
+ <xs:enumeration value="similarity"/>
+ <xs:enumeration value="subcellular location"/>
+ <xs:enumeration value="sequence caution"/>
+ <xs:enumeration value="subunit"/>
+ <xs:enumeration value="tissue specificity"/>
+ <xs:enumeration value="toxic dose"/>
+ <xs:enumeration value="online information"/>
+ <xs:enumeration value="mass spectrometry"/>
+ <xs:enumeration value="interaction"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+
+ <xs:attribute name="locationType" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the type of sequence location in 'RNA editing' annotations. Common values are "Not_applicable" and "Undetermined".</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+
+ <xs:attribute name="name" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes an optional name for an 'online information'.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+
+ <xs:attribute name="mass" type="xs:float" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the molecular mass in 'mass spectrometry' annotations.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="error" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the error of the mass measurement in 'mass spectrometry' annotations.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="method" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Describes the experimental method in 'mass spectrometry' annotations.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:complexType>
+
+ <xs:group name="bpcCommentGroup">
+ <xs:annotation>
+ <xs:documentation>Describes different types of biophysicochemical properties.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="absorption" minOccurs="0">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="max" type="evidencedStringType" minOccurs="0"/>
+ <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="kinetics" minOccurs="0">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="KM" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="Vmax" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="phDependence" minOccurs="0">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="text" type="evidencedStringType" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="redoxPotential" minOccurs="0">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="text" type="evidencedStringType" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="temperatureDependence" minOccurs="0">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="text" type="evidencedStringType" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:group>
+
+ <xs:complexType name="cofactorType">
+ <xs:annotation>
+ <xs:documentation>Describes a cofactor.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="name" type="xs:string"/>
+ <xs:element name="dbReference" type="dbReferenceType"/>
+ </xs:sequence>
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:complexType>
+
+ <xs:complexType name="subcellularLocationType">
+ <xs:annotation>
+ <xs:documentation>Describes the subcellular location and optionally the topology and orientation of a molecule.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="location" type="evidencedStringType" maxOccurs="unbounded"/>
+ <xs:element name="topology" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="orientation" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="eventType">
+ <xs:annotation>
+ <xs:documentation>Describes the type of events that cause alternative products.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="type" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="alternative splicing"/>
+ <xs:enumeration value="alternative initiation"/>
+ <xs:enumeration value="alternative promoter"/>
+ <xs:enumeration value="ribosomal frameshifting"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:complexType>
+
+ <xs:complexType name="isoformType">
+ <xs:annotation>
+ <xs:documentation>Describes isoforms in 'alternative products' annotations.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="id" type="xs:string" maxOccurs="unbounded"/>
+ <xs:element name="name" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="sequence">
+ <xs:complexType>
+ <xs:attribute name="type" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="not described"/>
+ <xs:enumeration value="described"/>
+ <xs:enumeration value="displayed"/>
+ <xs:enumeration value="external"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="ref" type="xs:string" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:group name="interactantGroup">
+ <xs:sequence>
+ <xs:element name="id" type="xs:string"/>
+ <xs:element name="label" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:group>
+ <xs:complexType name="interactantType">
+ <xs:group ref="interactantGroup" minOccurs="0"/>
+ <xs:attribute name="intactId" type="xs:string" use="required"/>
+ </xs:complexType>
+ <!-- Comment definition ends -->
+
+ <!-- Database cross-reference definition begins -->
+ <xs:complexType name="dbReferenceType">
+ <xs:annotation>
+ <xs:documentation>Describes a database cross-reference.
+ Equivalent to the flat file DR-line.
+ </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="molecule" type="moleculeType" minOccurs="0"/>
+ <xs:element name="property" type="propertyType" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="type" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation>Describes the name of the database.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="id" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation>Describes a unique database identifier.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ <!-- xs:attribute name="key" type="xs:string" use="optional"/ -->
+ </xs:complexType>
+
+ <xs:complexType name="propertyType">
+ <xs:attribute name="type" type="xs:string" use="required"/>
+ <xs:attribute name="value" type="xs:string" use="required"/>
+ </xs:complexType>
+ <!-- Database cross-reference definition ends -->
+
+ <!-- Protein existence definition begins -->
+ <xs:complexType name="proteinExistenceType">
+ <xs:annotation>
+ <xs:documentation>Describes the evidence for the protein's existence.
+ Equivalent to the flat file PE-line.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="type" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="evidence at protein level"/>
+ <xs:enumeration value="evidence at transcript level"/>
+ <xs:enumeration value="inferred from homology"/>
+ <xs:enumeration value="predicted"/>
+ <xs:enumeration value="uncertain"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:complexType>
+ <!-- Protein existence definition ends -->
+
+ <!-- Keyword definition begins -->
+ <xs:complexType name="keywordType">
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ <xs:attribute name="id" type="xs:string" use="required"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <!-- Keyword definition ends -->
+
+ <!-- Feature definition begins -->
+ <xs:complexType name="featureType">
+ <xs:annotation>
+ <xs:documentation>Describes different types of sequence annotations.
+ Equivalent to the flat file FT-line.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="original" type="xs:string" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Describes the original sequence in annotations that describe natural or artifical sequence variations.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="variation" type="xs:string" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes the variant sequence in annotations that describe natural or artifical sequence variations.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="location" type="locationType">
+ <xs:annotation>
+ <xs:documentation>Describes the sequence coordinates of the annotation.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="type" use="required">
+ <xs:annotation>
+ <xs:documentation>Describes the type of a sequence annotation.
+ Equivalent to the flat file FT feature keys, but using full terms instead of acronyms.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="active site"/>
+ <xs:enumeration value="binding site"/>
+ <xs:enumeration value="calcium-binding region"/>
+ <xs:enumeration value="chain"/>
+ <xs:enumeration value="coiled-coil region"/>
+ <xs:enumeration value="compositionally biased region"/>
+ <xs:enumeration value="cross-link"/>
+ <xs:enumeration value="disulfide bond"/>
+ <xs:enumeration value="DNA-binding region"/>
+ <xs:enumeration value="domain"/>
+ <xs:enumeration value="glycosylation site"/>
+ <xs:enumeration value="helix"/>
+ <xs:enumeration value="initiator methionine"/>
+ <xs:enumeration value="lipid moiety-binding region"/>
+ <xs:enumeration value="metal ion-binding site"/>
+ <xs:enumeration value="modified residue"/>
+ <xs:enumeration value="mutagenesis site"/>
+ <xs:enumeration value="non-consecutive residues"/>
+ <xs:enumeration value="non-terminal residue"/>
+ <xs:enumeration value="nucleotide phosphate-binding region"/>
+ <xs:enumeration value="peptide"/>
+ <xs:enumeration value="propeptide"/>
+ <xs:enumeration value="region of interest"/>
+ <xs:enumeration value="repeat"/>
+ <xs:enumeration value="non-standard amino acid"/>
+ <xs:enumeration value="sequence conflict"/>
+ <xs:enumeration value="sequence variant"/>
+ <xs:enumeration value="short sequence motif"/>
+ <xs:enumeration value="signal peptide"/>
+ <xs:enumeration value="site"/>
+ <xs:enumeration value="splice variant"/>
+ <xs:enumeration value="strand"/>
+ <xs:enumeration value="topological domain"/>
+ <xs:enumeration value="transit peptide"/>
+ <xs:enumeration value="transmembrane region"/>
+ <xs:enumeration value="turn"/>
+ <xs:enumeration value="unsure residue"/>
+ <xs:enumeration value="zinc finger region"/>
+ <xs:enumeration value="intramembrane region"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="status" use="optional">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="by similarity"/>
+ <xs:enumeration value="probable"/>
+ <xs:enumeration value="potential"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="id" type="xs:string" use="optional"/>
+ <xs:attribute name="description" type="xs:string" use="optional"/>
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ <xs:attribute name="ref" type="xs:string" use="optional"/>
+ </xs:complexType>
+
+ <xs:complexType name="locationType">
+ <xs:annotation>
+ <xs:documentation>Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry.</xs:documentation>
+ </xs:annotation>
+ <xs:choice>
+ <xs:sequence>
+ <xs:element name="begin" type="positionType"/>
+ <xs:element name="end" type="positionType"/>
+ </xs:sequence>
+ <xs:element name="position" type="positionType"/>
+ </xs:choice>
+ <xs:attribute name="sequence" type="xs:string" use="optional"/>
+ </xs:complexType>
+
+ <xs:complexType name="positionType">
+ <xs:attribute name="position" type="xs:unsignedLong" use="optional"/>
+ <xs:attribute name="status" use="optional" default="certain">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="certain"/>
+ <xs:enumeration value="uncertain"/>
+ <xs:enumeration value="less than"/>
+ <xs:enumeration value="greater than"/>
+ <xs:enumeration value="unknown"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ </xs:complexType>
+ <!-- Feature definition ends -->
+
+ <!-- Sequence definition begins -->
+ <xs:complexType name="sequenceType">
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="length" type="xs:int" use="required"/>
+ <xs:attribute name="mass" type="xs:int" use="required"/>
+ <xs:attribute name="checksum" type="xs:string" use="required"/>
+ <xs:attribute name="modified" type="xs:date" use="required"/>
+ <xs:attribute name="version" type="xs:int" use="required"/>
+ <xs:attribute name="precursor" type="xs:boolean" use="optional"/>
+ <xs:attribute name="fragment" use="optional">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="single"/>
+ <xs:enumeration value="multiple"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <!-- Sequence definition ends -->
+
+ <!-- Molecule definition begins -->
+ <xs:complexType name="moleculeType">
+ <xs:annotation>
+ <xs:documentation>Describes a molecule by name or unique identifier.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="id" type="xs:string" use="optional"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <!-- Molecule definition ends -->
+
+ <!-- Evidence definition begins -->
+ <xs:complexType name="evidenceType">
+ <xs:annotation>
+ <xs:documentation>Describes the evidence for an annotation.
+ No flat file equivalent.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="source" type="sourceType" minOccurs="0"/>
+ <xs:element name="importedFrom" type="importedFromType" minOccurs="0"/>
+ </xs:sequence>
+ <xs:attribute name="type" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation>Describes the type of an evidence using the Evidence Code Ontology (http://www.obofoundry.org/cgi-bin/detail.cgi?id=evidence_code).</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="key" type="xs:integer" use="required">
+ <xs:annotation>
+ <xs:documentation>A unique key to link annotations (via 'evidence' attributes) to evidences.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:complexType name="sourceType">
+ <xs:annotation>
+ <xs:documentation>Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="dbReference" type="dbReferenceType" minOccurs="0"/>
+ </xs:sequence>
+ <xs:attribute name="ref" type="xs:integer" use="optional"/>
+ </xs:complexType>
+ <xs:complexType name="importedFromType">
+ <xs:annotation>
+ <xs:documentation>Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="dbReference" type="dbReferenceType"/>
+ </xs:sequence>
+ </xs:complexType>
+ <!-- Evidence definition ends -->
+
+ <xs:complexType name="evidencedStringType">
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="evidence" type="intListType" use="optional"/>
+ <xs:attribute name="status" use="optional">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="by similarity"/>
+ <xs:enumeration value="probable"/>
+ <xs:enumeration value="potential"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+
+ <xs:simpleType name="intListType">
+ <xs:list itemType="xs:int"/>
+ </xs:simpleType>
+</xs:schema>
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
+<!--
+ Java JAXB binding classes are generated by running command line tool xjc:
+ xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ Note this also generates code for included schemas
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:complexType name="VAMSAS">
<xs:sequence>
/**
* Complete the given consensus and quuality annotation rows. Note: currently
- * this method will enlarge the given annotation row if it is too small,
- * otherwise will leave its length unchanged.
+ * this method will reallocate the given annotation row if it is different to
+ * the calculated width, otherwise will leave its length unchanged.
*
* @param conservation
* conservation annotation row
float qmax = 0f;
if (conservation != null && conservation.annotations != null
- && conservation.annotations.length < alWidth)
+ && conservation.annotations.length != alWidth)
{
conservation.annotations = new Annotation[alWidth];
}
{
quality2.graphMax = (float) qualityMaximum;
if (quality2.annotations != null
- && quality2.annotations.length < alWidth)
+ && quality2.annotations.length != alWidth)
{
quality2.annotations = new Annotation[alWidth];
}
/*
* catch things like <<..<<..>>..<<..>>>> |
*/
- int j = bps.size() - 1;
- while (j >= 0)
+ int j = bps.size();
+ while (--j >= 0)
{
int popen = bps.get(j).getBP5();
break;
}
}
- j -= 1;
}
// Put positions and helix information into the hashtable
/**
* Main class for Jalview Application <br>
* <br>
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview
+ *
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ *
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
*
* @author $author$
* @version $Revision$
{
error.printStackTrace();
System.out.println("\nEssential logging libraries not found."
- + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
System.exit(0);
}
import jalview.analysis.WUSSParseException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
}
/**
+ * Get the RNA Secondary Structure SequenceFeature Array if present
+ */
+ public SequenceFeature[] getRnaSecondaryStructure()
+ {
+ return this._rnasecstr;
+ }
+
+ /**
+ * Check the RNA Secondary Structure is equivalent to one in given
+ * AlignmentAnnotation param
+ */
+ public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that)
+ {
+ return rnaSecondaryStructureEquivalent(that, true);
+ }
+
+ public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType)
+ {
+ SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
+ SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
+ if (thisSfArray == null || thatSfArray == null)
+ {
+ return thisSfArray == null && thatSfArray == null;
+ }
+ if (thisSfArray.length != thatSfArray.length)
+ {
+ return false;
+ }
+ Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
+ // like this
+ Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
+ // like this
+ for (int i=0; i < thisSfArray.length; i++) {
+ SequenceFeature thisSf = thisSfArray[i];
+ SequenceFeature thatSf = thatSfArray[i];
+ if (compareType) {
+ if (thisSf.getType() == null || thatSf.getType() == null) {
+ if (thisSf.getType() == null && thatSf.getType() == null) {
+ continue;
+ } else {
+ return false;
+ }
+ }
+ if (! thisSf.getType().equals(thatSf.getType())) {
+ return false;
+ }
+ }
+ if (!(thisSf.getBegin() == thatSf.getBegin()
+ && thisSf.getEnd() == thatSf.getEnd()))
+ {
+ return false;
+ }
+ }
+ return true;
+
+ }
+
+ /**
* map of positions in the associated annotation
*/
private Map<Integer, Annotation> sequenceMapping;
char firstChar = 0;
for (int i = 0; i < annotations.length; i++)
{
+ // DEBUG System.out.println(i + ": " + annotations[i]);
if (annotations[i] == null)
{
continue;
if (annotations[i].secondaryStructure == 'H'
|| annotations[i].secondaryStructure == 'E')
{
+ // DEBUG System.out.println( "/H|E/ '" +
+ // annotations[i].secondaryStructure + "'");
hasIcons |= true;
}
else
// Check for RNA secondary structure
{
- // System.out.println(annotations[i].secondaryStructure);
+ // DEBUG System.out.println( "/else/ '" +
+ // annotations[i].secondaryStructure + "'");
// TODO: 2.8.2 should this ss symbol validation check be a function in
// RNA/ResidueProperties ?
if (annotations[i].secondaryStructure == '('
|| annotations[i].secondaryStructure == 'B'
|| annotations[i].secondaryStructure == 'C'
|| annotations[i].secondaryStructure == 'D'
- || annotations[i].secondaryStructure == 'E'
+ // || annotations[i].secondaryStructure == 'E' // ambiguous on
+ // its own -- already checked above
|| annotations[i].secondaryStructure == 'F'
|| annotations[i].secondaryStructure == 'G'
- || annotations[i].secondaryStructure == 'H'
+ // || annotations[i].secondaryStructure == 'H' // ambiguous on
+ // its own -- already checked above
|| annotations[i].secondaryStructure == 'I'
|| annotations[i].secondaryStructure == 'J'
|| annotations[i].secondaryStructure == 'K'
// &&
// annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
- && firstChar != '(' && firstChar != '[' && firstChar != '>'
+ && firstChar != '(' && firstChar != '[' && firstChar != '<'
&& firstChar != '{' && firstChar != 'A' && firstChar != 'B'
&& firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
&& firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
}
return aa;
}
+
}
return ((value == 0f)
&& ((description == null) || (description.trim().length() == 0))
&& ((displayCharacter == null)
- || (displayCharacter.trim().length() == 0))
+ || (displayCharacter.trim().length() == 0)
+ || (displayCharacter.equals(" ."))) // RNA Stockholm blank
+ // displayCharacter can
+ // end up like this
&& (secondaryStructure == '\0' || (secondaryStructure == ' '))
&& colour == null);
}
import jalview.datamodel.features.FeatureSources;
import jalview.util.StringUtils;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
source = theSource;
}
}
+
+class SFSortByEnd implements Comparator<SequenceFeature>
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getEnd() - b.getEnd();
+ }
+}
+
+class SFSortByBegin implements Comparator<SequenceFeature>
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getBegin() - b.getBegin();
+ }
+}
*/
// featureStore = Collections
// .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
- featureStore = new TreeMap<String, FeatureStore>();
+ featureStore = new TreeMap<>();
}
/**
}
/**
- * Answers true if the given type is one of the specified sequence ontology
- * terms (or a sub-type of one), or if no terms are supplied. Answers false if
- * filter terms are specified and the given term does not match any of them.
+ * Answers true if the given type matches one of the specified terms (or is a
+ * sub-type of one in the Sequence Ontology), or if no terms are supplied.
+ * Answers false if filter terms are specified and the given term does not
+ * match any of them.
*
* @param type
* @param soTerm
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
for (String term : soTerm)
{
- if (so.isA(type, term))
+ if (type.equals(term) || so.isA(type, term))
{
return true;
}
String group, String... type);
/**
- * Answers a list of all features stored, whose type either matches one of the
- * given ontology terms, or is a specialisation of a term in the Sequence
- * Ontology. Results are returned in no particular guaranteed order.
+ * Answers a list of all features stored, whose type either matches, or is a
+ * specialisation (in the Sequence Ontology) of, one of the given terms.
+ * Results are returned in no particular order.
*
* @param ontologyTerm
* @return
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import jalview.analysis.SequenceIdMatcher;
-import jalview.bin.Cache;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.FeatureProperties;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.util.DBRefUtils;
-import jalview.util.DnaUtils;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-import jalview.util.StringUtils;
-
-import java.text.ParseException;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Vector;
-import java.util.regex.Pattern;
-
-/**
- * Data model for one entry returned from an EMBL query, as marshalled by a
- * Castor binding file
- *
- * For example: http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
- *
- * @see embl_mapping.xml
- */
-public class EmblEntry
-{
- private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
-
- String accession;
-
- String entryVersion;
-
- String sequenceVersion;
-
- String dataClass;
-
- String moleculeType;
-
- String topology;
-
- String sequenceLength;
-
- String taxonomicDivision;
-
- String description;
-
- String firstPublicDate;
-
- String firstPublicRelease;
-
- String lastUpdatedDate;
-
- String lastUpdatedRelease;
-
- Vector<String> keywords;
-
- Vector<DBRefEntry> dbRefs;
-
- Vector<EmblFeature> features;
-
- EmblSequence sequence;
-
- /**
- * @return the accession
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * @param accession
- * the accession to set
- */
- public void setAccession(String accession)
- {
- this.accession = accession;
- }
-
- /**
- * @return the dbRefs
- */
- public Vector<DBRefEntry> getDbRefs()
- {
- return dbRefs;
- }
-
- /**
- * @param dbRefs
- * the dbRefs to set
- */
- public void setDbRefs(Vector<DBRefEntry> dbRefs)
- {
- this.dbRefs = dbRefs;
- }
-
- /**
- * @return the features
- */
- public Vector<EmblFeature> getFeatures()
- {
- return features;
- }
-
- /**
- * @param features
- * the features to set
- */
- public void setFeatures(Vector<EmblFeature> features)
- {
- this.features = features;
- }
-
- /**
- * @return the keywords
- */
- public Vector<String> getKeywords()
- {
- return keywords;
- }
-
- /**
- * @param keywords
- * the keywords to set
- */
- public void setKeywords(Vector<String> keywords)
- {
- this.keywords = keywords;
- }
-
- /**
- * @return the sequence
- */
- public EmblSequence getSequence()
- {
- return sequence;
- }
-
- /**
- * @param sequence
- * the sequence to set
- */
- public void setSequence(EmblSequence sequence)
- {
- this.sequence = sequence;
- }
-
- /**
- * Recover annotated sequences from EMBL file
- *
- * @param sourceDb
- * @param peptides
- * a list of protein products found so far (to add to)
- * @return dna dataset sequence with DBRefs and features
- */
- public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
- {
- SequenceI dna = makeSequence(sourceDb);
- if (dna == null)
- {
- return null;
- }
- dna.setDescription(description);
- DBRefEntry retrievedref = new DBRefEntry(sourceDb, getSequenceVersion(),
- accession);
- dna.addDBRef(retrievedref);
- // add map to indicate the sequence is a valid coordinate frame for the
- // dbref
- retrievedref
- .setMap(new Mapping(null, new int[]
- { 1, dna.getLength() }, new int[] { 1, dna.getLength() }, 1,
- 1));
-
- /*
- * transform EMBL Database refs to canonical form
- */
- if (dbRefs != null)
- {
- for (DBRefEntry dbref : dbRefs)
- {
- dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
- dna.addDBRef(dbref);
- }
- }
-
- SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
- try
- {
- for (EmblFeature feature : features)
- {
- if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
- {
- parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
- }
- }
- } catch (Exception e)
- {
- System.err.println("EMBL Record Features parsing error!");
- System.err
- .println("Please report the following to help@jalview.org :");
- System.err.println("EMBL Record " + accession);
- System.err.println("Resulted in exception: " + e.getMessage());
- e.printStackTrace(System.err);
- }
-
- return dna;
- }
-
- /**
- * @param sourceDb
- * @return
- */
- SequenceI makeSequence(String sourceDb)
- {
- if (sequence == null)
- {
- System.err.println(
- "No sequence was returned for ENA accession " + accession);
- return null;
- }
- SequenceI dna = new Sequence(sourceDb + "|" + accession,
- sequence.getSequence());
- return dna;
- }
-
- /**
- * Extracts coding region and product from a CDS feature and properly decorate
- * it with annotations.
- *
- * @param feature
- * coding feature
- * @param sourceDb
- * source database for the EMBLXML
- * @param dna
- * parent dna sequence for this record
- * @param peptides
- * list of protein product sequences for Embl entry
- * @param matcher
- * helper to match xrefs in already retrieved sequences
- */
- void parseCodingFeature(EmblFeature feature, String sourceDb,
- SequenceI dna, List<SequenceI> peptides,
- SequenceIdMatcher matcher)
- {
- boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
-
- int[] exons = getCdsRanges(feature);
-
- String translation = null;
- String proteinName = "";
- String proteinId = null;
- Map<String, String> vals = new Hashtable<>();
-
- /*
- * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
- * (phase is required for CDS features in GFF3 format)
- */
- int codonStart = 1;
-
- /*
- * parse qualifiers, saving protein translation, protein id,
- * codon start position, product (name), and 'other values'
- */
- if (feature.getQualifiers() != null)
- {
- for (Qualifier q : feature.getQualifiers())
- {
- String qname = q.getName();
- if (qname.equals("translation"))
- {
- // remove all spaces (precompiled String.replaceAll(" ", ""))
- translation = SPACE_PATTERN.matcher(q.getValues()[0])
- .replaceAll("");
- }
- else if (qname.equals("protein_id"))
- {
- proteinId = q.getValues()[0].trim();
- }
- else if (qname.equals("codon_start"))
- {
- try
- {
- codonStart = Integer.parseInt(q.getValues()[0].trim());
- } catch (NumberFormatException e)
- {
- System.err.println("Invalid codon_start in XML for " + accession
- + ": " + e.getMessage());
- }
- }
- else if (qname.equals("product"))
- {
- // sometimes name is returned e.g. for V00488
- proteinName = q.getValues()[0].trim();
- }
- else
- {
- // throw anything else into the additional properties hash
- String[] qvals = q.getValues();
- if (qvals != null)
- {
- String commaSeparated = StringUtils.arrayToSeparatorList(qvals,
- ",");
- vals.put(qname, commaSeparated);
- }
- }
- }
- }
-
- DBRefEntry proteinToEmblProteinRef = null;
- exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
-
- SequenceI product = null;
- Mapping dnaToProteinMapping = null;
- if (translation != null && proteinName != null && proteinId != null)
- {
- int translationLength = translation.length();
-
- /*
- * look for product in peptides list, if not found, add it
- */
- product = matcher.findIdMatch(proteinId);
- if (product == null)
- {
- product = new Sequence(proteinId, translation, 1,
- translationLength);
- product.setDescription(((proteinName.length() == 0)
- ? "Protein Product from " + sourceDb
- : proteinName));
- peptides.add(product);
- matcher.add(product);
- }
-
- // we have everything - create the mapping and perhaps the protein
- // sequence
- if (exons == null || exons.length == 0)
- {
- /*
- * workaround until we handle dna location for CDS sequence
- * e.g. location="X53828.1:60..1058" correctly
- */
- System.err.println(
- "Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
- + sourceDb + ":" + getAccession() + ")");
- int dnaLength = dna.getLength();
- if (translationLength * 3 == (1 - codonStart + dnaLength))
- {
- System.err.println(
- "Not allowing for additional stop codon at end of cDNA fragment... !");
- // this might occur for CDS sequences where no features are marked
- exons = new int[] { dna.getStart() + (codonStart - 1),
- dna.getEnd() };
- dnaToProteinMapping = new Mapping(product, exons,
- new int[]
- { 1, translationLength }, 3, 1);
- }
- if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
- {
- System.err.println(
- "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
- exons = new int[] { dna.getStart() + (codonStart - 1),
- dna.getEnd() - 3 };
- dnaToProteinMapping = new Mapping(product, exons,
- new int[]
- { 1, translationLength }, 3, 1);
- }
- }
- else
- {
- // Trim the exon mapping if necessary - the given product may only be a
- // fragment of a larger protein. (EMBL:AY043181 is an example)
-
- if (isEmblCdna)
- {
- // TODO: Add a DbRef back to the parent EMBL sequence with the exon
- // map
- // if given a dataset reference, search dataset for parent EMBL
- // sequence if it exists and set its map
- // make a new feature annotating the coding contig
- }
- else
- {
- // final product length truncation check
- int[] cdsRanges = adjustForProteinLength(translationLength,
- exons);
- dnaToProteinMapping = new Mapping(product, cdsRanges,
- new int[]
- { 1, translationLength }, 3, 1);
- if (product != null)
- {
- /*
- * make xref with mapping from protein to EMBL dna
- */
- DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
- getSequenceVersion(), proteinId,
- new Mapping(dnaToProteinMapping.getMap().getInverse()));
- product.addDBRef(proteinToEmblRef);
-
- /*
- * make xref from protein to EMBLCDS; we assume here that the
- * CDS sequence version is same as dna sequence (?!)
- */
- MapList proteinToCdsMapList = new MapList(
- new int[]
- { 1, translationLength },
- new int[]
- { 1 + (codonStart - 1),
- (codonStart - 1) + 3 * translationLength },
- 1, 3);
- DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
- DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
- new Mapping(proteinToCdsMapList));
- product.addDBRef(proteinToEmblCdsRef);
-
- /*
- * make 'direct' xref from protein to EMBLCDSPROTEIN
- */
- proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
- proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
- proteinToEmblProteinRef.setMap(null);
- product.addDBRef(proteinToEmblProteinRef);
- }
- }
- }
-
- /*
- * add cds features to dna sequence
- */
- String cds = feature.getName(); // "CDS"
- for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2)
- {
- int exonStart = exons[xint];
- int exonEnd = exons[xint + 1];
- int begin = Math.min(exonStart, exonEnd);
- int end = Math.max(exonStart, exonEnd);
- int exonNumber = xint / 2 + 1;
- String desc = String.format("Exon %d for protein '%s' EMBLCDS:%s",
- exonNumber, proteinName, proteinId);
-
- SequenceFeature sf = makeCdsFeature(cds, desc, begin, end,
- sourceDb, vals);
-
- sf.setEnaLocation(feature.getLocation());
- boolean forwardStrand = exonStart <= exonEnd;
- sf.setStrand(forwardStrand ? "+" : "-");
- sf.setPhase(String.valueOf(codonStart - 1));
- sf.setValue(FeatureProperties.EXONPOS, exonNumber);
- sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
-
- dna.addSequenceFeature(sf);
- }
- }
-
- /*
- * add feature dbRefs to sequence, and mappings for Uniprot xrefs
- */
- boolean hasUniprotDbref = false;
- if (feature.dbRefs != null)
- {
- boolean mappingUsed = false;
- for (DBRefEntry ref : feature.dbRefs)
- {
- /*
- * ensure UniProtKB/Swiss-Prot converted to UNIPROT
- */
- String source = DBRefUtils.getCanonicalName(ref.getSource());
- ref.setSource(source);
- DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(),
- ref.getVersion(), ref.getAccessionId());
- if (source.equals(DBRefSource.UNIPROT))
- {
- String proteinSeqName = DBRefSource.UNIPROT + "|"
- + ref.getAccessionId();
- if (dnaToProteinMapping != null
- && dnaToProteinMapping.getTo() != null)
- {
- if (mappingUsed)
- {
- /*
- * two or more Uniprot xrefs for the same CDS -
- * each needs a distinct Mapping (as to a different sequence)
- */
- dnaToProteinMapping = new Mapping(dnaToProteinMapping);
- }
- mappingUsed = true;
-
- /*
- * try to locate the protein mapped to (possibly by a
- * previous CDS feature); if not found, construct it from
- * the EMBL translation
- */
- SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
- if (proteinSeq == null)
- {
- proteinSeq = new Sequence(proteinSeqName,
- product.getSequenceAsString());
- matcher.add(proteinSeq);
- peptides.add(proteinSeq);
- }
- dnaToProteinMapping.setTo(proteinSeq);
- dnaToProteinMapping.setMappedFromId(proteinId);
- proteinSeq.addDBRef(proteinDbRef);
- ref.setMap(dnaToProteinMapping);
- }
- hasUniprotDbref = true;
- }
- if (product != null)
- {
- /*
- * copy feature dbref to our protein product
- */
- DBRefEntry pref = proteinDbRef;
- pref.setMap(null); // reference is direct
- product.addDBRef(pref);
- // Add converse mapping reference
- if (dnaToProteinMapping != null)
- {
- Mapping pmap = new Mapping(dna,
- dnaToProteinMapping.getMap().getInverse());
- pref = new DBRefEntry(sourceDb, getSequenceVersion(),
- this.getAccession());
- pref.setMap(pmap);
- if (dnaToProteinMapping.getTo() != null)
- {
- dnaToProteinMapping.getTo().addDBRef(pref);
- }
- }
- }
- dna.addDBRef(ref);
- }
- }
-
- /*
- * if we have a product (translation) but no explicit Uniprot dbref
- * (example: EMBL AAFI02000057 protein_id EAL65544.1)
- * then construct mappings to an assumed EMBLCDSPROTEIN accession
- */
- if (!hasUniprotDbref && product != null)
- {
- if (proteinToEmblProteinRef == null)
- {
- // assuming CDSPROTEIN sequence version = dna version (?!)
- proteinToEmblProteinRef = new DBRefEntry(DBRefSource.EMBLCDSProduct,
- getSequenceVersion(), proteinId);
- }
- product.addDBRef(proteinToEmblProteinRef);
-
- if (dnaToProteinMapping != null
- && dnaToProteinMapping.getTo() != null)
- {
- DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
- DBRefSource.EMBLCDSProduct, getSequenceVersion(),
- proteinId);
- dnaToEmblProteinRef.setMap(dnaToProteinMapping);
- dnaToProteinMapping.setMappedFromId(proteinId);
- dna.addDBRef(dnaToEmblProteinRef);
- }
- }
- }
-
- /**
- * Helper method to construct a SequenceFeature for one cds range
- *
- * @param type
- * feature type ("CDS")
- * @param desc
- * description
- * @param begin
- * start position
- * @param end
- * end position
- * @param group
- * feature group
- * @param vals
- * map of 'miscellaneous values' for feature
- * @return
- */
- protected SequenceFeature makeCdsFeature(String type, String desc,
- int begin, int end, String group, Map<String, String> vals)
- {
- SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
- if (!vals.isEmpty())
- {
- StringBuilder sb = new StringBuilder();
- boolean first = true;
- for (Entry<String, String> val : vals.entrySet())
- {
- if (!first)
- {
- sb.append(";");
- }
- sb.append(val.getKey()).append("=").append(val.getValue());
- first = false;
- sf.setValue(val.getKey(), val.getValue());
- }
- sf.setAttributes(sb.toString());
- }
- return sf;
- }
-
- /**
- * Returns the CDS positions as a single array of [start, end, start, end...]
- * positions. If on the reverse strand, these will be in descending order.
- *
- * @param feature
- * @return
- */
- protected int[] getCdsRanges(EmblFeature feature)
- {
- if (feature.location == null)
- {
- return new int[] {};
- }
-
- try
- {
- List<int[]> ranges = DnaUtils.parseLocation(feature.location);
- return listToArray(ranges);
- } catch (ParseException e)
- {
- Cache.log.warn(
- String.format("Not parsing inexact CDS location %s in ENA %s",
- feature.location, this.accession));
- return new int[] {};
- }
- }
-
- /**
- * Converts a list of [start, end] ranges to a single array of [start, end,
- * start, end ...]
- *
- * @param ranges
- * @return
- */
- int[] listToArray(List<int[]> ranges)
- {
- int[] result = new int[ranges.size() * 2];
- int i = 0;
- for (int[] range : ranges)
- {
- result[i++] = range[0];
- result[i++] = range[1];
- }
- return result;
- }
-
- /**
- * Truncates (if necessary) the exon intervals to match 3 times the length of
- * the protein; also accepts 3 bases longer (for stop codon not included in
- * protein)
- *
- * @param proteinLength
- * @param exon
- * an array of [start, end, start, end...] intervals
- * @return the same array (if unchanged) or a truncated copy
- */
- static int[] adjustForProteinLength(int proteinLength, int[] exon)
- {
- if (proteinLength <= 0 || exon == null)
- {
- return exon;
- }
- int expectedCdsLength = proteinLength * 3;
- int exonLength = MappingUtils.getLength(Arrays.asList(exon));
-
- /*
- * if exon length matches protein, or is shorter, or longer by the
- * length of a stop codon (3 bases), then leave it unchanged
- */
- if (expectedCdsLength >= exonLength
- || expectedCdsLength == exonLength - 3)
- {
- return exon;
- }
-
- int origxon[];
- int sxpos = -1;
- int endxon = 0;
- origxon = new int[exon.length];
- System.arraycopy(exon, 0, origxon, 0, exon.length);
- int cdspos = 0;
- for (int x = 0; x < exon.length; x += 2)
- {
- cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
- if (expectedCdsLength <= cdspos)
- {
- // advanced beyond last codon.
- sxpos = x;
- if (expectedCdsLength != cdspos)
- {
- // System.err
- // .println("Truncating final exon interval on region by "
- // + (cdspos - cdslength));
- }
-
- /*
- * shrink the final exon - reduce end position if forward
- * strand, increase it if reverse
- */
- if (exon[x + 1] >= exon[x])
- {
- endxon = exon[x + 1] - cdspos + expectedCdsLength;
- }
- else
- {
- endxon = exon[x + 1] + cdspos - expectedCdsLength;
- }
- break;
- }
- }
-
- if (sxpos != -1)
- {
- // and trim the exon interval set if necessary
- int[] nxon = new int[sxpos + 2];
- System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
- nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
- // set
- exon = nxon;
- }
- return exon;
- }
-
- public String getSequenceVersion()
- {
- return sequenceVersion;
- }
-
- public void setSequenceVersion(String sequenceVersion)
- {
- this.sequenceVersion = sequenceVersion;
- }
-
- public String getSequenceLength()
- {
- return sequenceLength;
- }
-
- public void setSequenceLength(String sequenceLength)
- {
- this.sequenceLength = sequenceLength;
- }
-
- public String getEntryVersion()
- {
- return entryVersion;
- }
-
- public void setEntryVersion(String entryVersion)
- {
- this.entryVersion = entryVersion;
- }
-
- public String getMoleculeType()
- {
- return moleculeType;
- }
-
- public void setMoleculeType(String moleculeType)
- {
- this.moleculeType = moleculeType;
- }
-
- public String getTopology()
- {
- return topology;
- }
-
- public void setTopology(String topology)
- {
- this.topology = topology;
- }
-
- public String getTaxonomicDivision()
- {
- return taxonomicDivision;
- }
-
- public void setTaxonomicDivision(String taxonomicDivision)
- {
- this.taxonomicDivision = taxonomicDivision;
- }
-
- public String getDescription()
- {
- return description;
- }
-
- public void setDescription(String description)
- {
- this.description = description;
- }
-
- public String getFirstPublicDate()
- {
- return firstPublicDate;
- }
-
- public void setFirstPublicDate(String firstPublicDate)
- {
- this.firstPublicDate = firstPublicDate;
- }
-
- public String getFirstPublicRelease()
- {
- return firstPublicRelease;
- }
-
- public void setFirstPublicRelease(String firstPublicRelease)
- {
- this.firstPublicRelease = firstPublicRelease;
- }
-
- public String getLastUpdatedDate()
- {
- return lastUpdatedDate;
- }
-
- public void setLastUpdatedDate(String lastUpdatedDate)
- {
- this.lastUpdatedDate = lastUpdatedDate;
- }
-
- public String getLastUpdatedRelease()
- {
- return lastUpdatedRelease;
- }
-
- public void setLastUpdatedRelease(String lastUpdatedRelease)
- {
- this.lastUpdatedRelease = lastUpdatedRelease;
- }
-
- public String getDataClass()
- {
- return dataClass;
- }
-
- public void setDataClass(String dataClass)
- {
- this.dataClass = dataClass;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-/**
- * Data model mapped from any <error> elements returned from an EMBL query
- *
- * @see embl_mapping.xml
- */
-public class EmblError
-{
- String accession;
-
- /**
- * @return the accession
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * @param accession
- * the accession to set
- */
- public void setAccession(String accession)
- {
- this.accession = accession;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import jalview.datamodel.DBRefEntry;
-
-import java.util.Vector;
-
-/**
- * Data model for a <feature> element returned from an EMBL query reply
- *
- * @see embl_mapping.xml
- */
-public class EmblFeature
-{
- String name;
-
- Vector<DBRefEntry> dbRefs;
-
- Vector<Qualifier> qualifiers;
-
- String location;
-
- /**
- * @return the dbRefs
- */
- public Vector<DBRefEntry> getDbRefs()
- {
- return dbRefs;
- }
-
- /**
- * @param dbRefs
- * the dbRefs to set
- */
- public void setDbRefs(Vector<DBRefEntry> dbRefs)
- {
- this.dbRefs = dbRefs;
- }
-
- /**
- * @return the location
- */
- public String getLocation()
- {
- return location;
- }
-
- /**
- * @param loc
- */
- public void setLocation(String loc)
- {
- this.location = loc;
- }
-
- /**
- * @return the name
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- */
- public void setName(String name)
- {
- this.name = name;
- }
-
- /**
- * @return the qualifiers
- */
- public Vector<Qualifier> getQualifiers()
- {
- return qualifiers;
- }
-
- /**
- * @param qualifiers
- * the qualifiers to set
- */
- public void setQualifiers(Vector<Qualifier> qualifiers)
- {
- this.qualifiers = qualifiers;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import jalview.datamodel.DBRefEntry;
-import jalview.ws.dbsources.Uniprot;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.PrintWriter;
-import java.io.Reader;
-import java.util.Vector;
-
-import org.exolab.castor.mapping.Mapping;
-import org.exolab.castor.xml.Unmarshaller;
-
-/**
- * Data model for entries returned from an EMBL query, as marshalled by a Castor
- * binding file
- *
- * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
- *
- * @see embl_mapping.xml
- */
-public class EmblFile
-{
- Vector<EmblEntry> entries;
-
- Vector<EmblError> errors;
-
- String text;
-
- /**
- * @return the entries
- */
- public Vector<EmblEntry> getEntries()
- {
- return entries;
- }
-
- /**
- * @param entries
- * the entries to set
- */
- public void setEntries(Vector<EmblEntry> entries)
- {
- this.entries = entries;
- }
-
- /**
- * @return the errors
- */
- public Vector<EmblError> getErrors()
- {
- return errors;
- }
-
- /**
- * @param errors
- * the errors to set
- */
- public void setErrors(Vector<EmblError> errors)
- {
- this.errors = errors;
- }
-
- /**
- * Parse an EmblXML file into an EmblFile object
- *
- * @param file
- * @return parsed EmblXML or null if exceptions were raised
- */
- public static EmblFile getEmblFile(File file)
- {
- if (file == null)
- {
- return null;
- }
- try
- {
- return EmblFile.getEmblFile(new FileReader(file));
- } catch (Exception e)
- {
- System.err.println("Exception whilst reading EMBLfile from " + file);
- e.printStackTrace(System.err);
- }
- return null;
- }
-
- public static EmblFile getEmblFile(Reader file)
- {
- EmblFile record = new EmblFile();
- try
- {
- // 1. Load the mapping information from the file
- Mapping map = new Mapping(record.getClass().getClassLoader());
-
- java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
- map.loadMapping(url);
-
- // 2. Unmarshal the data
- Unmarshaller unmar = new Unmarshaller(record);
- try
- {
- // uncomment to DEBUG EMBLFile reading
- if (jalview.bin.Cache
- .getDefault(jalview.bin.Cache.CASTORLOGLEVEL, "debug")
- .equalsIgnoreCase("DEBUG"))
- {
- unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
- }
- } catch (Exception e)
- {
- }
- unmar.setIgnoreExtraElements(true);
- unmar.setIgnoreExtraAttributes(true);
- unmar.setMapping(map);
- unmar.setLogWriter(new PrintWriter(System.out));
- record = (EmblFile) unmar.unmarshal(file);
-
- canonicaliseDbRefs(record);
- } catch (Exception e)
- {
- e.printStackTrace(System.err);
- record = null;
- }
-
- return record;
- }
-
- /**
- * Change blank version to "0" in any DBRefEntry, to ensure consistent
- * comparison with other DBRefEntry in Jalview
- *
- * @param record
- * @see Uniprot#getDbVersion
- */
- static void canonicaliseDbRefs(EmblFile record)
- {
- if (record.getEntries() == null)
- {
- return;
- }
- for (EmblEntry entry : record.getEntries())
- {
- if (entry.getDbRefs() != null)
- {
- for (DBRefEntry dbref : entry.getDbRefs())
- {
- if ("".equals(dbref.getVersion()))
- {
- dbref.setVersion("0");
- }
- }
- }
-
- if (entry.getFeatures() != null)
- {
- for (EmblFeature feature : entry.getFeatures())
- {
- if (feature.getDbRefs() != null)
- {
- for (DBRefEntry dbref : feature.getDbRefs())
- {
- if ("".equals(dbref.getVersion()))
- {
- dbref.setVersion("0");
- }
- }
- }
- }
- }
- }
- }
-
- public String getText()
- {
- return text;
- }
-
- public void setText(String text)
- {
- this.text = text;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-/**
- * Data model for the sequence extracted from an EMBL query reply
- *
- * @see embl_mapping.xml
- */
-public class EmblSequence
-{
- String sequence;
-
- /**
- * @return the sequence
- */
- public String getSequence()
- {
- return sequence;
- }
-
- /**
- * @param sequence
- * the sequence to set
- */
- public void setSequence(String sequence)
- {
- // remove spaces introduced by unmarshalling of newline characters
- this.sequence = sequence.replace(" ", "");
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-/**
- * Data model for a <qualifier> child element of a <feature> read
- * from an EMBL query reply
- *
- * @see embl_mapping.xml
- */
-public class Qualifier
-{
- String name;
-
- String[] values;
-
- String[] evidence;
-
- /**
- * @return the name
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- */
- public void setName(String name)
- {
- this.name = name;
- }
-
- /**
- * @return the values
- */
- public String[] getValues()
- {
- return values;
- }
-
- /**
- * @param values
- * the values to set
- */
- public void setValues(String[] values)
- {
- this.values = values;
- }
-
- public void addEvidence(String qevidence)
- {
- // TODO - not used? can remove?
- if (evidence == null)
- {
- evidence = new String[1];
- }
- else
- {
- String[] temp = new String[evidence.length + 1];
- System.arraycopy(evidence, 0, temp, 0, evidence.length);
- evidence = temp;
- }
- evidence[evidence.length - 1] = qevidence;
- }
-
- public void addValues(String value)
- {
- // TODO - not used? can remove?
- if (values == null)
- {
- values = new String[1];
- }
- else
- {
- String[] temp = new String[values.length + 1];
- System.arraycopy(values, 0, temp, 0, values.length);
- values = temp;
- }
- values[values.length - 1] = value;
- }
-
- /**
- * @return the evidence
- */
- public String[] getEvidence()
- {
- return evidence;
- }
-
- /**
- * @param evidence
- * the evidence to set
- */
- public void setEvidence(String[] evidence)
- {
- this.evidence = evidence;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.uniprot;
-
-import jalview.datamodel.PDBEntry;
-
-import java.util.Vector;
-
-/**
- * Data model for an entry returned from a Uniprot query
- *
- * @see uniprot_mapping.xml
- */
-public class UniprotEntry
-{
-
- UniprotSequence sequence;
-
- Vector<String> name;
-
- Vector<String> accession;
-
- Vector<UniprotFeature> feature;
-
- Vector<PDBEntry> dbrefs;
-
- UniprotProteinName protName;
-
- public void setAccession(Vector<String> items)
- {
- accession = items;
- }
-
- public void setFeature(Vector<UniprotFeature> items)
- {
- feature = items;
- }
-
- public Vector<UniprotFeature> getFeature()
- {
- return feature;
- }
-
- public Vector<String> getAccession()
- {
- return accession;
- }
-
- public void setProtein(UniprotProteinName names)
- {
- protName = names;
- }
-
- public UniprotProteinName getProtein()
- {
- return protName;
- }
-
- public void setName(Vector<String> na)
- {
- name = na;
- }
-
- public Vector<String> getName()
- {
- return name;
- }
-
- public UniprotSequence getUniprotSequence()
- {
- return sequence;
- }
-
- public void setUniprotSequence(UniprotSequence seq)
- {
- sequence = seq;
- }
-
- public Vector<PDBEntry> getDbReference()
- {
- return dbrefs;
- }
-
- public void setDbReference(Vector<PDBEntry> dbref)
- {
- this.dbrefs = dbref;
- }
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.uniprot;
-
-/**
- * A data model class for binding from Uniprot XML via uniprot_mapping.xml
- */
-public class UniprotFeature
-{
- private String type;
-
- private String description = null;
-
- private String original = null;
-
- private String variation = null;
-
- private String status;
-
- private int begin;
-
- private int end;
-
- public String getType()
- {
- return type;
- }
-
- public void setType(String t)
- {
- this.type = t;
- }
-
- public String getDescription()
- {
- if (description == null && variation == null && original == null)
- {
- return null;
- }
- return (description == null ? "" : description)
- + (variation != null
- ? (description != null ? " " : "") + "Variation: '"
- + variation + "'"
- : "")
- + (original != null
- ? ((description != null || variation != null) ? " "
- : "") + "Original: '" + original + "'"
- : "");
- }
-
- public void setDescription(String d)
- {
- this.description = d;
- }
-
- public String getStatus()
- {
- return status;
- }
-
- public void setStatus(String s)
- {
- this.status = s;
- }
-
- public int getBegin()
- {
- return begin;
- }
-
- public void setBegin(int b)
- {
- this.begin = b;
- }
-
- public int getEnd()
- {
- return end;
- }
-
- public void setEnd(int e)
- {
- this.end = e;
- }
-
- public int getPosition()
- {
- return begin;
- }
-
- public void setPosition(int p)
- {
- this.begin = p;
- this.end = p;
- }
-
- public String getOriginal()
- {
- return original;
- }
-
- public void setOriginal(String original)
- {
- this.original = original;
- }
-
- public String getVariation()
- {
- return variation;
- }
-
- public void setVariation(String variant)
- {
- this.variation = variant;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.uniprot;
-
-import java.util.Vector;
-
-/**
- * Data model of a retrieved Uniprot entry, as unmarshalled by Castor using a
- * binding file (uniprot_mapping.xml)
- */
-public class UniprotFile
-{
- Vector<UniprotEntry> _items;
-
- public void setUniprotEntries(Vector<UniprotEntry> items)
- {
- _items = items;
- }
-
- public Vector<UniprotEntry> getUniprotEntries()
- {
- return _items;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.uniprot;
-
-import java.util.Vector;
-
-/**
- * Data model for protein name returned from a Uniprot query
- *
- * Protein names are read from the Uniprot XML element
- * uniprot/entry/protein/recommendedName/fullName
- *
- * @see uniprot_mapping.xml
- */
-public class UniprotProteinName
-{
- private Vector<String> names;
-
- public void setName(Vector<String> names)
- {
- this.names = names;
- }
-
- public Vector<String> getName()
- {
- return names;
- }
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.uniprot;
-
-/**
- * Data model for the sequence returned by a Uniprot query
- *
- * @see uniprot_mapping.xml
- */
-public class UniprotSequence
-{
- private String _content = "";
-
- /**
- * Sets the content string, omitting any space characters
- *
- * @param seq
- */
- public void setContent(String seq)
- {
- if (seq != null)
- {
- StringBuilder sb = new StringBuilder(seq.length());
- for (int i = 0; i < seq.length(); i++)
- {
- if (seq.charAt(i) != ' ')
- {
- sb.append(seq.charAt(i));
- }
- }
- _content = sb.toString();
- }
- }
-
- public String getContent()
- {
- return _content;
- }
-
-}
package jalview.ext.ensembl;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
+import java.util.ArrayList;
+import java.util.List;
+
import com.stevesoft.pat.Regex;
/**
}
/**
- * Answers true if the sequence feature type is 'exon' (or a subtype of exon
- * in the Sequence Ontology), and the Parent of the feature is the transcript
- * we are retrieving
+ * Answers a list of sequence features (if any) whose type is 'exon' (or a
+ * subtype of exon in the Sequence Ontology), and whose Parent is the
+ * transcript we are retrieving
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
- SequenceOntologyI.EXON))
+ List<SequenceFeature> result = new ArrayList<>();
+ List<SequenceFeature> sfs = seq.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.EXON);
+ for (SequenceFeature sf : sfs)
{
String parentFeature = (String) sf.getValue(PARENT);
if (("transcript:" + accId).equals(parentFeature))
{
- return true;
+ result.add(sf);
}
}
- return false;
+
+ return result;
}
/**
}
/**
- * Answers true if the sequence feature type is 'CDS' (or a subtype of CDS in
- * the Sequence Ontology), and the Parent of the feature is the transcript we
- * are retrieving
+ * Answers a list of sequence features (if any) whose type is 'CDS' (or a
+ * subtype of CDS in the Sequence Ontology), and whose Parent is the
+ * transcript we are retrieving
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
- SequenceOntologyI.CDS))
+ List<SequenceFeature> result = new ArrayList<>();
+ List<SequenceFeature> sfs = seq.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.CDS);
+ for (SequenceFeature sf : sfs)
{
String parentFeature = (String) sf.getValue(PARENT);
if (("transcript:" + accId).equals(parentFeature))
{
- return true;
+ result.add(sf);
}
}
- return false;
+ return result;
}
/**
protected List<int[]> getCdsRanges(SequenceI dnaSeq)
{
int len = dnaSeq.getLength();
- List<int[]> ranges = new ArrayList<int[]>();
+ List<int[]> ranges = new ArrayList<>();
ranges.add(new int[] { 1, len });
return ranges;
}
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.io.FileParse;
+import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
// TODO: use a vararg String... for getSequenceRecords instead?
List<String> queries = new ArrayList<>();
queries.add(query);
- FileParse fp = getSequenceReader(queries);
- if (fp == null || !fp.isValid())
+ BufferedReader fp = getSequenceReader(queries);
+ if (fp == null)
{
return null;
}
- FeaturesFile fr = new FeaturesFile(fp);
+ FeaturesFile fr = new FeaturesFile(
+ new FileParse(fp, null, DataSourceType.URL));
return new Alignment(fr.getSeqsAsArray());
}
* describes the required encoding of the response.
*/
@Override
- protected String getRequestMimeType(boolean multipleIds)
+ protected String getRequestMimeType()
{
return "text/x-gff3";
}
/**
- * Returns the MIME type for GFF3.
+ * Returns the MIME type for GFF3
*/
@Override
protected String getResponseMimeType()
}
/**
- * Answers true for a feature of type 'gene' (or a sub-type of gene in the
- * Sequence Ontology), whose ID is the accession we are retrieving
+ * Answers a list of sequence features (if any) whose type is 'gene' (or a
+ * subtype of gene in the Sequence Ontology), and whose ID is the accession we
+ * are retrieving
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
- SequenceOntologyI.GENE))
+ List<SequenceFeature> result = new ArrayList<>();
+ List<SequenceFeature> sfs = seq.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.GENE);
+ for (SequenceFeature sf : sfs)
{
// NB features as gff use 'ID'; rest services return as 'id'
String id = (String) sf.getValue("ID");
if ((GENE_PREFIX + accId).equalsIgnoreCase(id))
{
- return true;
+ result.add(sf);
}
}
- return false;
+ return result;
}
/**
}
/**
- * Answers false. This allows an optimisation - a single 'gene' feature is all
- * that is needed to identify the positions of the gene on the genomic
- * sequence.
- */
- @Override
- protected boolean isSpliceable()
- {
- return false;
- }
-
- /**
* Override to do nothing as Ensembl doesn't return a protein sequence for a
* gene identifier
*/
package jalview.ext.ensembl;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+
+import java.util.ArrayList;
+import java.util.List;
/**
* A client to fetch genomic sequence from Ensembl
}
/**
- * Answers true if the sequence feature type is 'transcript' (or a subtype of
- * transcript in the Sequence Ontology), and the ID of the feature is the
- * transcript we are retrieving
+ * Answers a list of sequence features (if any) whose type is 'transcript' (or
+ * a subtype of transcript in the Sequence Ontology), and whose ID is the
+ * accession we are retrieving.
+ * <p>
+ * Note we also include features of type "NMD_transcript_variant", although
+ * not strictly 'transcript' in the SO, as they used in Ensembl as if they
+ * were.
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- if (isTranscript(sf.getType()))
+ List<SequenceFeature> result = new ArrayList<>();
+ List<SequenceFeature> sfs = seq.getFeatures().getFeaturesByOntology(
+ SequenceOntologyI.TRANSCRIPT,
+ SequenceOntologyI.NMD_TRANSCRIPT_VARIANT);
+ for (SequenceFeature sf : sfs)
{
+ // NB features as gff use 'ID'; rest services return as 'id'
String id = (String) sf.getValue("ID");
if (("transcript:" + accId).equals(id))
{
- return true;
+ result.add(sf);
}
}
- return false;
+ return result;
}
}
return true;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return "application/json";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "application/json";
- }
-
/**
* Answers the domain (http://rest.ensembl.org or
* http://rest.ensemblgenomes.org) for the given division, or null if not
return true;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return "application/json";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "application/json";
- }
-
/**
* Returns the gene id related to the given identifier (which may be for a
* gene, transcript or protein), or null if none is found
}
@Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return "application/json";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "application/json";
- }
-
- @Override
protected URL getUrl(List<String> ids) throws MalformedURLException
{
return null; // not used
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.List;
import com.stevesoft.pat.Regex;
}
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- // not applicable - protein sequence is not a 'subset' of genomic sequence
- return false;
+ return new ArrayList<>();
}
@Override
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
* @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "6.3";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "7.0";
- private static final String LATEST_ENSEMBL_REST_VERSION = "6.3";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "7.0";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
protected abstract boolean useGetRequest();
/**
- * Return the desired value for the Content-Type request header
- *
- * @param multipleIds
+ * Returns the desired value for the Content-Type request header. Default is
+ * application/json, override if required to vary this.
*
* @return
* @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
*/
- protected abstract String getRequestMimeType(boolean multipleIds);
+ protected String getRequestMimeType()
+ {
+ return "application/json";
+ }
/**
- * Return the desired value for the Accept request header
+ * Return the desired value for the Accept request header. Default is
+ * application/json, override if required to vary this.
*
* @return
* @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
*/
- protected abstract String getResponseMimeType();
+ protected String getResponseMimeType()
+ {
+ return "application/json";
+ }
/**
* Checks Ensembl's REST 'ping' endpoint, and returns true if response
}
/**
- * returns a reader to a Fasta response from the Ensembl sequence endpoint
+ * Returns a reader to a (Json) response from the Ensembl sequence endpoint.
+ * If the request failed the return value may be null.
*
* @param ids
* @return
* @throws IOException
*/
- protected FileParse getSequenceReader(List<String> ids) throws IOException
+ protected BufferedReader getSequenceReader(List<String> ids)
+ throws IOException
{
URL url = getUrl(ids);
BufferedReader reader = getHttpResponse(url, ids);
- if (reader == null)
- {
- // request failed
- return null;
- }
- FileParse fp = new FileParse(reader, url.toString(),
- DataSourceType.URL);
- return fp;
+ return reader;
}
/**
boolean multipleIds = ids != null && ids.size() > 1;
connection.setRequestMethod(
multipleIds ? HttpMethod.POST : HttpMethod.GET);
- connection.setRequestProperty("Content-Type",
- getRequestMimeType(multipleIds));
+ connection.setRequestProperty("Content-Type", getRequestMimeType());
connection.setRequestProperty("Accept", getResponseMimeType());
connection.setDoInput(true);
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.exceptions.JalviewException;
-import jalview.io.FastaFile;
-import jalview.io.FileParse;
import jalview.io.gff.Gff3Helper;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.IntRangeComparator;
import jalview.util.MapList;
+import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Collections;
import java.util.List;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
/**
* Base class for Ensembl sequence fetchers
*
inProgress = false;
throw new JalviewException("ENSEMBL Rest API not available.");
}
- FileParse fp = getSequenceReader(ids);
- if (fp == null)
+ BufferedReader br = getSequenceReader(ids);
+ if (br == null)
{
return alignment;
}
- FastaFile fr = new FastaFile(fp);
- if (fr.hasWarningMessage())
+ List<SequenceI> seqs = parseSequenceJson(br);
+
+ if (seqs.isEmpty())
{
- System.out.println(
- String.format("Warning when retrieving %d ids %s\n%s",
- ids.size(), ids.toString(), fr.getWarningMessage()));
+ throw new IOException("No data returned for " + ids);
}
- else if (fr.getSeqs().size() != ids.size())
+
+ if (seqs.size() != ids.size())
{
System.out.println(String.format(
"Only retrieved %d sequences for %d query strings",
- fr.getSeqs().size(), ids.size()));
+ seqs.size(), ids.size()));
}
- if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0)
+ if (!seqs.isEmpty())
{
- /*
- * POST request has returned an empty FASTA file e.g. for invalid id
- */
- throw new IOException("No data returned for " + ids);
- }
-
- if (fr.getSeqs().size() > 0)
- {
- AlignmentI seqal = new Alignment(fr.getSeqsAsArray());
- for (SequenceI sq : seqal.getSequences())
+ AlignmentI seqal = new Alignment(
+ seqs.toArray(new SequenceI[seqs.size()]));
+ for (SequenceI seq : seqs)
{
- if (sq.getDescription() == null)
+ if (seq.getDescription() == null)
{
- sq.setDescription(getDbName());
+ seq.setDescription(getDbName());
}
- String name = sq.getName();
+ String name = seq.getName();
if (ids.contains(name)
|| ids.contains(name.replace("ENSP", "ENST")))
{
- DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(),
+ // TODO JAL-3077 use true accession version in dbref
+ DBRefEntry dbref = DBRefUtils.parseToDbRef(seq, getDbSource(),
getEnsemblDataVersion(), name);
- sq.addDBRef(dbref);
+ seq.addDBRef(dbref);
}
}
if (alignment == null)
}
/**
+ * Parses a JSON response for a single sequence ID query
+ *
+ * @param br
+ * @return a single jalview.datamodel.Sequence
+ * @see http://rest.ensembl.org/documentation/info/sequence_id
+ */
+ protected List<SequenceI> parseSequenceJson(BufferedReader br)
+ {
+ JSONParser jp = new JSONParser();
+ List<SequenceI> result = new ArrayList<>();
+ try
+ {
+ /*
+ * for now, assumes only one sequence returned; refactor if needed
+ * in future to handle a JSONArray with more than one
+ */
+ final JSONObject val = (JSONObject) jp.parse(br);
+ Object s = val.get("desc");
+ String desc = s == null ? null : s.toString();
+ s = val.get("id");
+ String id = s == null ? null : s.toString();
+ s = val.get("seq");
+ String seq = s == null ? null : s.toString();
+ Sequence sequence = new Sequence(id, seq);
+ if (desc != null)
+ {
+ sequence.setDescription(desc);
+ }
+ // todo JAL-3077 make a DBRefEntry with true accession version
+ // s = val.get("version");
+ // String version = s == null ? "0" : s.toString();
+ // DBRefEntry dbref = new DBRefEntry(getDbSource(), version, id);
+ // sequence.addDBRef(dbref);
+ result.add(sequence);
+ } catch (ParseException | IOException e)
+ {
+ System.err.println("Error processing JSON response: " + e.toString());
+ // ignore
+ }
+ return result;
+ }
+
+ /**
* Returns the URL for the REST call
*
* @return
}
// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
urlstring.append("?type=").append(getSourceEnsemblType().getType());
- urlstring.append(("&Accept=text/x-fasta"));
+ urlstring.append(("&Accept=application/json"));
+ urlstring.append(("&Content-Type=application/json"));
String objectType = getObjectType();
if (objectType != null)
return false;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return multipleIds ? "application/json" : "text/x-fasta";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "text/x-fasta";
- }
-
/**
*
* @return the configured sequence return type for this source
protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
String accId, int start)
{
- List<SequenceFeature> sfs = sourceSequence.getFeatures()
- .getPositionalFeatures();
+ List<SequenceFeature> sfs = getIdentifyingFeatures(sourceSequence,
+ accId);
if (sfs.isEmpty())
{
return null;
for (SequenceFeature sf : sfs)
{
+ int strand = sf.getStrand();
+ strand = strand == 0 ? 1 : strand; // treat unknown as forward
+
+ if (directionSet && strand != direction)
+ {
+ // abort - mix of forward and backward
+ System.err
+ .println("Error: forward and backward strand for " + accId);
+ return null;
+ }
+ direction = strand;
+ directionSet = true;
+
/*
- * accept the target feature type or a specialisation of it
- * (e.g. coding_exon for exon)
+ * add to CDS ranges, semi-sorted forwards/backwards
*/
- if (identifiesSequence(sf, accId))
+ if (strand < 0)
{
- int strand = sf.getStrand();
- strand = strand == 0 ? 1 : strand; // treat unknown as forward
-
- if (directionSet && strand != direction)
- {
- // abort - mix of forward and backward
- System.err.println(
- "Error: forward and backward strand for " + accId);
- return null;
- }
- direction = strand;
- directionSet = true;
-
- /*
- * add to CDS ranges, semi-sorted forwards/backwards
- */
- if (strand < 0)
- {
- regions.add(0, new int[] { sf.getEnd(), sf.getBegin() });
- }
- else
- {
- regions.add(new int[] { sf.getBegin(), sf.getEnd() });
- }
- mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1);
-
- if (!isSpliceable())
- {
- /*
- * 'gene' sequence is contiguous so we can stop as soon as its
- * identifying feature has been found
- */
- break;
- }
+ regions.add(0, new int[] { sf.getEnd(), sf.getBegin() });
+ }
+ else
+ {
+ regions.add(new int[] { sf.getBegin(), sf.getEnd() });
}
+ mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1);
}
if (regions.isEmpty())
}
/**
- * Answers true if the sequence being retrieved may occupy discontiguous
- * regions on the genomic sequence.
- */
- protected boolean isSpliceable()
- {
- return true;
- }
-
- /**
- * Returns true if the sequence feature marks positions of the genomic
+ * Answers a list of sequence features that mark positions of the genomic
* sequence feature which are within the sequence being retrieved. For
* example, an 'exon' feature whose parent is the target transcript marks the
- * cdna positions of the transcript.
+ * cdna positions of the transcript. For a gene sequence, this is trivially
+ * just the 'gene' feature with matching gene id.
*
- * @param sf
+ * @param seq
* @param accId
* @return
*/
- protected abstract boolean identifiesSequence(SequenceFeature sf,
- String accId);
+ protected abstract List<SequenceFeature> getIdentifyingFeatures(
+ SequenceI seq, String accId);
/**
* Transfers the sequence feature to the target sequence, locating its start
return true;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return "application/json";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "application/json";
- }
-
/**
* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
* ("primary_id") for the given identifier (Ensembl accession id) and database
*/
public List<DBRefEntry> getCrossReferences(String identifier)
{
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
- List<String> ids = new ArrayList<String>();
+ List<DBRefEntry> result = new ArrayList<>();
+ List<String> ids = new ArrayList<>();
ids.add(identifier);
BufferedReader br = null;
throws IOException
{
JSONParser jp = new JSONParser();
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> result = new ArrayList<>();
try
{
JSONArray responses = (JSONArray) jp.parse(br);
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
- if (aSize == 1 && ap.av.viewName == null)
+ if (aSize == 1 && ap.av.getViewName() == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName, ap);
+ tabbedPane.addTab(ap.av.getViewName(), ap);
ap.setVisible(false);
}
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
- tabbedPane.addTab(first.av.viewName, first);
+ tabbedPane.addTab(first.av.getViewName(), first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
* @param av
* AlignViewport
*/
- void setMenusFromViewport(AlignViewport av)
+ public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
shortName = shortName.substring(
shortName.lastIndexOf(File.separatorChar) + 1);
}
- lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
+ lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file,
shortName);
+
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { fileName, format }));
+
return;
}
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+ AlignmentPanel newap = new jalview.project.Jalview2XML()
+ .copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
newap.av.setGatherViewsHere(false);
- if (viewport.viewName == null)
+ if (viewport.getViewName() == null)
{
- viewport.viewName = MessageManager
- .getString("label.view_name_original");
+ viewport.setViewName(MessageManager
+ .getString("label.view_name_original"));
}
/*
newap.refresh(true); // adjust layout of annotations
}
- newap.av.viewName = getNewViewName(viewTitle);
+ newap.av.setViewName(getNewViewName(viewTitle));
addAlignmentPanel(newap, true);
newap.alignmentChanged();
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
- if (!existingNames.contains(ap.av.viewName))
+ if (!existingNames.contains(ap.av.getViewName()))
{
- existingNames.add(ap.av.viewName);
+ existingNames.add(ap.av.getViewName());
}
}
}
frameTitle += " from ";
- if (viewport.viewName != null)
+ if (viewport.getViewName() != null)
{
- frameTitle += viewport.viewName + " of ";
+ frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
if (reply != null)
{
- viewport.viewName = reply;
+ viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
{
if (avc.createGroup())
{
+ if (applyAutoAnnotationSettings.isSelected())
+ {
+ alignPanel.updateAnnotation(true, false);
+ }
alignPanel.alignmentChanged();
}
}
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ // alignPanels is never null
+ // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ return alignPanels;
}
/**
private Rectangle explodedGeometry;
- String viewName;
+ private String viewName;
/*
* Flag set true on the view that should 'gather' multiple views of the same
}
fr.setTransparency(featureSettings.getTransparency());
}
+
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
+ }
}
import jalview.util.Comparison;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
-import jalview.util.Platform;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
protected void validateAnnotationDimensions(boolean adjustPanelHeight)
{
int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ annotationHeight = getAnnotationPanel()
+ .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
- if (adjustPanelHeight)
- {
- int rowHeight = av.getCharHeight();
- int alignmentHeight = rowHeight * av.getAlignment().getHeight();
-
- /*
- * Estimate available height in the AlignFrame for alignment +
- * annotations. Deduct an estimate for title bar, menu bar, scale panel,
- * hscroll, status bar, insets.
- */
- int stuff = Platform.isAMac() ? 120 : 140;
- int availableHeight = alignFrame.getHeight() - stuff;
-
- /*
- * If not enough vertical space, maximize annotation height while keeping
- * at least two rows of alignment visible
- */
- if (annotationHeight + alignmentHeight > availableHeight)
- {
- annotationHeight = Math.min(annotationHeight,
- availableHeight - 2 * rowHeight);
- }
- }
- else
- {
- // maintain same window layout whilst updating sliders
- annotationHeight = annotationScroller.getSize().height;
- }
hscroll.addNotify();
-
annotationScroller.setPreferredSize(
new Dimension(annotationScroller.getWidth(), annotationHeight));
{
annotationScroller.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
+ validateAnnotationDimensions(false);
}
int canvasWidth = getSeqPanel().seqCanvas.getWidth();
@Override
public String getViewName()
{
- return av.viewName;
+ return av.getViewName();
}
/**
import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
@Override
public Dimension getPreferredScrollableViewportSize()
{
- return getPreferredSize();
+ Dimension ps = getPreferredSize();
+ return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
}
@Override
repaint();
}
}
+
+ /**
+ * computes the visible height of the annotation panel
+ *
+ * @param adjustPanelHeight
+ * - when false, just adjust existing height according to other
+ * windows
+ * @param annotationHeight
+ * @return height to use for the ScrollerPreferredVisibleSize
+ */
+ public int adjustForAlignFrame(boolean adjustPanelHeight,
+ int annotationHeight)
+ {
+ /*
+ * Estimate available height in the AlignFrame for alignment +
+ * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+ * hscroll, status bar, insets.
+ */
+ int stuff = (ap.getViewName() != null ? 30 : 0)
+ + (Platform.isAMac() ? 120 : 140);
+ int availableHeight = ap.alignFrame.getHeight() - stuff;
+ int rowHeight = av.getCharHeight();
+
+ if (adjustPanelHeight)
+ {
+ int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+ /*
+ * If not enough vertical space, maximize annotation height while keeping
+ * at least two rows of alignment visible
+ */
+ if (annotationHeight + alignmentHeight > availableHeight)
+ {
+ annotationHeight = Math.min(annotationHeight,
+ availableHeight - 2 * rowHeight);
+ }
+ }
+ else
+ {
+ // maintain same window layout whilst updating sliders
+ annotationHeight = Math.min(ap.annotationScroller.getSize().height,
+ availableHeight - 2 * rowHeight);
+ }
+ return annotationHeight;
+ }
}
}
}
+ /**
+ * highlight a region from start to end (inclusive) on rna
+ *
+ * @param rna
+ * @param start
+ * - first base pair index (from 0)
+ * @param end
+ * - last base pair index (from 0)
+ */
public void highlightRegion(RNA rna, int start, int end)
{
clearLastSelection();
RnaModel rnaModel = models.get(rna);
if (rnaModel.seq == sequence)
{
- int highlightPos = rnaModel.gapped ? index : position - 1;
+ int highlightPos = rnaModel.gapped ? index
+ : position - sequence.getStart();
mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos);
vab.updateSelectedRNA(rna);
}
{
return;
}
- if (seqsel != null && seqsel.getSize() > 0)
+
+ RnaModel rnaModel = models.get(rna);
+
+ if (seqsel != null && seqsel.getSize() > 0
+ && seqsel.contains(rnaModel.seq))
{
int start = seqsel.getStartRes(), end = seqsel.getEndRes();
- ShiftList shift = offsets.get(rna);
- if (shift != null)
+ if (rnaModel.gapped)
{
- start = shift.shift(start);
- end = shift.shift(end);
+ ShiftList shift = offsets.get(rna);
+ if (shift != null)
+ {
+ start = shift.shift(start);
+ end = shift.shift(end);
+ }
}
+ else
+ {
+ start = rnaModel.seq.findPosition(start) - rnaModel.seq.getStart();
+ end = rnaModel.seq.findPosition(end) - rnaModel.seq.getStart();
+ }
+
selectionHighlighter.highlightRegion(rna, start, end);
selectionHighlighter.getLastHighlight()
.setOutlineColor(seqsel.getOutlineColour());
super.activateFrame(f);
}
- // If this is the first activation, add to child list.
- if (fChildFrames.indexOf(f) == -1)
+ // add or relocate to top of stack
+ if (fChildFrames.indexOf(f) != -1)
{
- fChildFrames.addElement(f);
+ fChildFrames.remove(f);
}
+ fChildFrames.addElement(f);
if (fCurrentFrame != null && f != fCurrentFrame)
{
setMinimumSize(new Dimension(325, height - 10));
String title = MessageManager.getString("label.choose_calculation");
- if (af.getViewport().viewName != null)
+ if (af.getViewport().getViewName() != null)
{
- title = title + " (" + af.getViewport().viewName + ")";
+ title = title + " (" + af.getViewport().getViewName() + ")";
}
Desktop.addInternalFrame(frame, title, width, height, false);
{
final Desktop me = this;
// Thread off the news reader, in case there are connection problems.
- addDialogThread(new Runnable()
+ new Thread(new Runnable()
{
@Override
public void run()
showNews.setVisible(true);
Cache.log.debug("Completed news thread.");
}
- });
+ }).start();
}
public void getIdentifiersOrgData()
{
// Thread off the identifiers fetcher
- addDialogThread(new Runnable()
+ new Thread(new Runnable()
{
@Override
public void run()
+ e.getMessage());
}
}
- });
+ }).start();
+ ;
}
@Override
* Jalview project file
*/
@Override
- public void saveState_actionPerformed()
+ public void saveState_actionPerformed(boolean asCastor)
{
- JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ asCastor ? "jvp" : "jvx",
"Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_state"));
-
+ // TODO: JAL-3048 Dialog runner refactoring here
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- new Jalview2XML().saveState(choice);
+ if (asCastor)
+ {
+ new Jalview2XML().saveState(choice);
+ }
+ else
+ {
+ new jalview.project.Jalview2XML().saveState(choice);
+ }
} catch (OutOfMemoryError oom)
{
new OOMWarning(
* Prompts the user to choose a file and loads in as a Jalview project file
*/
@Override
- public void loadState_actionPerformed()
- {
+ public void loadState_actionPerformed(boolean asCastor)
+ {
+ // TODO: GET RID OF .JVX BEFORE RELEASE JIM!
+ final String[] suffix = asCastor ? new String[] { "jvp", "jar" }
+ : new String[]
+ { "jvx" };
+ final String[] desc = asCastor
+ ? new String[]
+ { "Jalview Project", "Jalview Project (old)" }
+ : new String[]
+ { "Jalview Project" };
JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jvp", "jar" },
- new String[]
- { "Jalview Project", "Jalview Project (old)" },
+ Cache.getProperty("LAST_DIRECTORY"), suffix,
+ desc,
"Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
{ choice }), choice.hashCode());
try
{
- new Jalview2XML().loadJalviewAlign(choice);
+ if (asCastor)
+ {
+ new Jalview2XML().loadJalviewAlign(choice);
+ }
+ else
+ {
+ new jalview.project.Jalview2XML().loadJalviewAlign(choice);
+ }
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst loading project from " + choice, oom);
import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
-import jalview.schemabinding.version2.Filter;
-import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.MatcherSet;
import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.JalviewUserColours.Filter;
+import jalview.xml.binding.jalview.ObjectFactory;
import java.awt.BorderLayout;
import java.awt.Color;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
InputStreamReader in = new InputStreamReader(
new FileInputStream(file), "UTF-8");
- JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(in);
+ JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+ JalviewUserColours.class);
+ JalviewUserColours jucs = jbe.getValue();
+
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
/*
* load feature colours
*/
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
{
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+ Colour newcol = jucs.getColour().get(i);
+ FeatureColourI colour = jalview.project.Jalview2XML
+ .parseColour(newcol);
fr.setColour(newcol.getName(), colour);
- fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
+ fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
}
/*
* load feature filters; loaded filters will replace any that are
* currently defined, other defined filters are left unchanged
*/
- for (int i = 0; i < jucs.getFilterCount(); i++)
+ for (int i = 0; i < jucs.getFilter().size(); i++)
{
- jalview.schemabinding.version2.Filter filterModel = jucs
- .getFilter(i);
+ Filter filterModel = jucs.getFilter().get(i);
String featureType = filterModel.getFeatureType();
- FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
- filterModel.getMatcherSet());
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
for (String featureType : sortedTypes)
{
FeatureColourI fcol = fr.getFeatureStyle(featureType);
- jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
- featureType, fcol);
- ucs.addColour(col);
+ Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+ fcol);
+ ucs.getColour().add(col);
}
/*
{
Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
+ jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
+ .marshalFilter(firstMatcher, iterator,
filter.isAnded());
Filter filterModel = new Filter();
filterModel.setFeatureType(featureType);
filterModel.setMatcherSet(ms);
- ucs.addFilter(filterModel);
+ ucs.getFilter().add(filterModel);
}
}
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
+
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ out.flush();
- ucs.marshal(out);
+ // ucs.marshal(out);
out.close();
} catch (Exception ex)
{
public FontChooser(TreePanel treePanel)
{
this.tp = treePanel;
- ap = treePanel.treeCanvas.ap;
+ ap = treePanel.getTreeCanvas().getAssociatedPanel();
oldFont = treePanel.getTreeFont();
defaultButton.setVisible(false);
smoothFont.setEnabled(false);
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.treeCanvas.av.getAlignment() == jal)
+ if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
tree.setNewick(tp.getTree().print());
- tree.setThreshold(tp.treeCanvas.threshold);
+ tree.setThreshold(tp.getTreeCanvas().getThreshold());
tree.setFitToWindow(tp.fitToWindow.getState());
tree.setFontName(tp.getTreeFont().getName());
{
view.setComplementId(av.getCodingComplement().getViewId());
}
- view.setViewName(av.viewName);
+ view.setViewName(av.getViewName());
view.setGatheredViews(av.isGatherViewsHere());
Rectangle size = ap.av.getExplodedGeometry();
tp.setTitle(tree.getTitle());
tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
tree.getWidth(), tree.getHeight()));
- tp.av = av; // af.viewport; // TODO: verify 'associate with all
+ tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all
// views'
// works still
- tp.treeCanvas.av = av; // af.viewport;
- tp.treeCanvas.ap = ap; // af.alignPanel;
+ tp.getTreeCanvas().setViewport(av); // af.viewport;
+ tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
}
if (tp == null)
tp.showBootstrap(tree.getShowBootstrap());
tp.showDistances(tree.getShowDistances());
- tp.treeCanvas.threshold = tree.getThreshold();
+ tp.getTreeCanvas().setThreshold(tree.getThreshold());
if (tree.getCurrentTree())
{
if (view.getViewName() != null)
{
- af.viewport.viewName = view.getViewName();
+ af.viewport.setViewName(view.getViewName());
af.setInitialTabVisible();
}
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
tp.showBootstrap(tree.getShowBootstrap());
tp.showDistances(tree.getShowDistances());
- tp.treeCanvas.threshold = tree.getThreshold();
+ tp.getTreeCanvas().setThreshold(tree.getThreshold());
if (tree.getCurrentTree())
{
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
+ item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av);
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
width -= (width % charWidth);
height -= (height % charHeight);
+
if ((img != null) && (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
|| (getVisibleRect().height != g.getClipBounds().height)))
topFrame.setDisplayedView(newTopPanel);
}
- newBottomPanel.av.viewName = newTopPanel.av.viewName;
+ newBottomPanel.av.setViewName(newTopPanel.av.getViewName());
newTopPanel.av.setCodingComplement(newBottomPanel.av);
/*
import java.util.List;
import java.util.Vector;
-import javax.swing.JColorChooser;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
TreePanel tp;
- AlignViewport av;
+ private AlignViewport av;
- AlignmentPanel ap;
+ private AlignmentPanel ap;
Font font;
int offy;
- float threshold;
+ private float threshold;
String longestName;
{
this.tp = tp;
this.av = ap.av;
- this.ap = ap;
+ this.setAssociatedPanel(ap);
font = av.getFont();
scrollPane = scroller;
addMouseListener(this);
if (ob instanceof SequenceI)
{
treeSelectionChanged((Sequence) ob);
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
repaint();
av.sendSelection();
return;
}
}
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
repaint();
}
}
else
{
- return new AlignmentPanel[] { ap };
+ return new AlignmentPanel[] { getAssociatedPanel() };
}
}
+
+ public AlignmentPanel getAssociatedPanel()
+ {
+ return ap;
+ }
+
+ public void setAssociatedPanel(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public float getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setThreshold(float threshold)
+ {
+ this.threshold = threshold;
+ }
}
SimilarityParamsI similarityParams;
- TreeCanvas treeCanvas;
+ private TreeCanvas treeCanvas;
TreeModel tree;
- AlignViewport av;
+ private AlignViewport av;
/**
* Creates a new TreePanel object.
public AlignmentI getAlignment()
{
- return treeCanvas.av.getAlignment();
+ return getTreeCanvas().getViewport().getAlignment();
}
public AlignmentViewport getViewPort()
{
- return treeCanvas.av;
+ // @Mungo - Why don't we return our own viewport ???
+ return getTreeCanvas().getViewport();
}
void initTreePanel(AlignmentPanel ap, String type, String modelName,
{
AlignmentPanel[] aps = PaintRefresher
.getAssociatedPanels(av.getSequenceSetId());
- if (aps.length == 1 && treeCanvas.ap == aps[0])
+ if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
{
associateLeavesMenu.setVisible(false);
return;
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+ item = new JRadioButtonMenuItem(ap.av.getViewName(),
+ ap == treeCanvas.getAssociatedPanel());
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = false;
- treeCanvas.ap = ap;
- treeCanvas.av = ap.av;
+ treeCanvas.setAssociatedPanel(ap);
+ treeCanvas.setViewport(ap.av);
PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
}
});
else
{
ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName, treeCanvas.ap);
+ .getScoreModel(scoreModelName,
+ treeCanvas.getAssociatedPanel());
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
? new NJTree(av, sm, similarityParams)
: new AverageDistanceTree(av, sm, similarityParams);
}
else
{
- treeCanvas.ap.alignFrame
- .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+ treeCanvas.getAssociatedPanel().alignFrame
+ .addHistoryItem(
+ sortAlignmentIn(treeCanvas.getAssociatedPanel()));
}
}
ex.printStackTrace();
}
}
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public TreeCanvas getTreeCanvas()
+ {
+ return treeCanvas;
+ }
}
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GUserDefinedColours;
-import jalview.schemabinding.version2.Colour;
-import jalview.schemabinding.version2.JalviewUserColours;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.util.ColorUtils;
import jalview.util.Format;
import jalview.util.MessageManager;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.ObjectFactory;
import java.awt.Color;
import java.awt.Font;
import javax.swing.JInternalFrame;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Marshaller;
/**
* This panel allows the user to assign colours to Amino Acid residue codes, and
Colour col = new Colour();
col.setName(button.getText());
col.setRGB(Format.getHexString(button.getBackground()));
- ucs.addColour(col);
+ ucs.getColour().add(col);
}
- ucs.marshal(out);
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
+ // ucs.marshal(out);
out.close();
} catch (Exception ex)
{
errorsDuringUpdate = true;
Cache.log.error("Exception synchronizing " + af.getTitle()
+ " "
- + (af.getViewport().viewName == null ? ""
- : " view " + af.getViewport().viewName)
+ + (af.getViewport().getViewName() == null ? ""
+ : " view " + af.getViewport().getViewName())
+ " to document.", e);
stored = false;
}
import jalview.ws.params.ParamDatastoreI;
import jalview.ws.params.ParamManager;
import jalview.ws.params.WsParamSetI;
+import jalview.xml.binding.jalview.ObjectFactory;
+import jalview.xml.binding.jalview.WebServiceParameterSet;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.List;
import java.util.StringTokenizer;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
+
/**
* store and retrieve web service parameter sets.
*
*/
public class WsParamSetManager implements ParamManager
{
- Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<String, ParamDatastoreI>();
+ Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<>();
@Override
public WsParamSetI[] getParameterSet(String name, String serviceUrl,
}
StringTokenizer st = new StringTokenizer(files, "|");
String pfile = null;
- ArrayList<WsParamSetI> params = new ArrayList<WsParamSetI>();
+ List<WsParamSetI> params = new ArrayList<>();
while (st.hasMoreTokens())
{
pfile = st.nextToken();
private WsParamSetI[] parseParamFile(String filename) throws IOException
{
- List<WsParamSetI> psets = new ArrayList<WsParamSetI>();
+ List<WsParamSetI> psets = new ArrayList<>();
InputStreamReader is = new InputStreamReader(
- new java.io.FileInputStream(new File(filename)), "UTF-8");
-
- jalview.schemabinding.version2.WebServiceParameterSet wspset = new jalview.schemabinding.version2.WebServiceParameterSet();
+ new FileInputStream(new File(filename)), "UTF-8");
- org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
- wspset);
- unmar.setWhitespacePreserve(true);
+ WebServiceParameterSet wspset = null;
try
{
- wspset = (jalview.schemabinding.version2.WebServiceParameterSet) unmar
- .unmarshal(is);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(is);
+ JAXBElement<WebServiceParameterSet> jbe = um.unmarshal(streamReader,
+ WebServiceParameterSet.class);
+ wspset = jbe.getValue();
} catch (Exception ex)
{
throw new IOException(ex);
}
+
if (wspset != null && wspset.getParameters().length() > 0)
{
- for (String url : wspset.getServiceURL())
+ List<String> urls = wspset.getServiceURL();
+ final String[] urlArray = urls.toArray(new String[urls.size()]);
+
+ for (String url : urls)
{
ParamDatastoreI parser = paramparsers.get(url);
if (parser != null)
{
WsParamSetI pset = parser.parseServiceParameterFile(
wspset.getName(), wspset.getDescription(),
- wspset.getServiceURL(), wspset.getParameters());
+ urlArray, wspset.getParameters());
if (pset != null)
{
pset.setSourceFile(filename);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
outfile = chooser.getSelectedFile();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- outfile.getParent());
+ Cache.setProperty("LAST_DIRECTORY", outfile.getParent());
filename = outfile.getAbsolutePath();
if (!filename.endsWith(".wsparams"))
{
}
paramFiles = paramFiles.concat(filename);
}
- jalview.bin.Cache.setProperty("WS_PARAM_FILES", paramFiles);
+ Cache.setProperty("WS_PARAM_FILES", paramFiles);
- jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet();
+ WebServiceParameterSet paramxml = new WebServiceParameterSet();
paramxml.setName(parameterSet.getName());
paramxml.setDescription(parameterSet.getDescription());
- paramxml.setServiceURL(parameterSet.getApplicableUrls().clone());
+ for (String url : parameterSet.getApplicableUrls())
+ {
+ paramxml.getServiceURL().add(url);
+ }
paramxml.setVersion("1.0");
try
{
parser.generateServiceParameterFile(parameterSet));
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(outfile), "UTF-8"));
- paramxml.marshal(out);
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(WebServiceParameterSet.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createWebServiceParameterSet(paramxml),
+ out);
out.close();
parameterSet.setSourceFile(filename);
} catch (Exception e)
return true;
}
},
- Jalview("Jalview", "jar,jvp", true, true)
+ Jalview("Jalview", "jvp, jar", true, true)
{
@Override
public AlignmentFileReaderI getReader(FileParse source)
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
-import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
+import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
}
return null;
}
+
+ File ourselectedFile = null;
+
+ @Override
+ public File getSelectedFile()
+ {
+ File selfile = super.getSelectedFile();
+ if (selfile == null && ourselectedFile != null)
+ {
+ return ourselectedFile;
+ }
+ return selfile;
+ }
Component saveparent;
RunResponse overwriteCheck = new RunResponse(
@Override
public void run()
{
+ ourselectedFile = getSelectedFile();
+
+ if (getSelectedFile() == null)
+ {
+ // Workaround for Java 9,10 on OSX - no selected file, but there is a
+ // filename typed in
+ try
+ {
+ String filename = ((BasicFileChooserUI) getUI()).getFileName();
+ if (filename != null && filename.length() > 0)
+ {
+ ourselectedFile = new File(getCurrentDirectory(), filename);
+ }
+ } catch (Throwable x)
+ {
+ System.err.println(
+ "Unexpected exception when trying to get filename.");
+ x.printStackTrace();
+ }
+ }
+ if (ourselectedFile == null)
+ {
+ returned = new Response(JalviewFileChooser.CANCEL_OPTION);
+ return;
+ }
// JBP Note - this code was executed regardless of 'SAVE' being pressed
// need to see if there were side effects
if (getFileFilter() instanceof JalviewFileFilter)
}
setDialogType(SAVE_DIALOG);
+
+ // Java 9,10,11 on OSX - clear selected file so name isn't auto populated
+ this.setSelectedFile(null);
+
saveparent = parent;
int value = showDialog(parent, MessageManager.getString("action.save"));
package jalview.io;
import java.io.File;
-import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.Map;
import java.util.StringTokenizer;
import javax.swing.filechooser.FileFilter;
{
public static Hashtable suffixHash = new Hashtable();
- private Hashtable filters = null;
+ private Map<String, JalviewFileFilter> filters = null;
private String description = "no description";
public String getAcceptableExtension()
{
- return filters.keys().nextElement().toString();
+ return filters.keySet().iterator().next().toString();
}
// takes account of the fact that database is a directory
+ @Override
public boolean accept(File f)
{
if (f != null)
return true;
}
- if ((extension != null) && (filters.get(getExtension(f)) != null))
+ if ((extension != null) && (filters.get(extension) != null))
{
return true;
}
{
if (filters == null)
{
- filters = new Hashtable(5);
+ filters = new LinkedHashMap<>(5);
}
filters.put(extension.toLowerCase(), this);
fullDescription = null;
}
+ @Override
public String getDescription()
{
if (fullDescription == null)
: (description + " (");
// build the description from the extension list
- Enumeration extensions = filters.keys();
+ Iterator<String> extensions = filters.keySet().iterator();
if (extensions != null)
{
- fullDescription += ("." + (String) extensions.nextElement());
+ fullDescription += ("." + extensions.next());
- while (extensions.hasMoreElements())
+ while (extensions.hasNext())
{
- fullDescription += (", " + (String) extensions.nextElement());
+ fullDescription += (", " + extensions.next());
}
}
private void loadExtensions()
{
- extensions = new HashMap<String, String>();
+ extensions = new HashMap<>();
for (FileFormatI ff : FileFormats.getInstance().getFormats())
{
String desc = ff.getName() + " file";
String exts = ff.getExtensions();
for (String ext : exts.split(","))
{
- extensions.put(ext.trim().toLowerCase(),
+ ext = ext.trim().toLowerCase();
+ extensions.put(ext,
desc + ("jar".equals(ext) ? " (old)" : ""));
}
}
{
if (icons == null)
{
- icons = new HashMap<String, ImageIcon>();
+ icons = new HashMap<>();
}
if (!icons.containsKey(filePath))
{
public static final Regex DETECT_BRACKETS = new Regex(
"(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
+ // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
+ public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
+
+ // use the following regex to decide an annotations (whole) line is NOT an RNA
+ // SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
+ private static final Regex NOT_RNASS = new Regex(
+ "^[^<>[\\](){}A-DF-Za-df-z]*$");
+
StringBuffer out; // output buffer
AlignmentI al;
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
strucAnn = new Hashtable();
}
- Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+ Vector<AlignmentAnnotation> newStruc = new Vector<>();
parseAnnotationRow(newStruc, type, ns);
for (AlignmentAnnotation alan : newStruc)
{
private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
{
DBRefEntry dbrf = null;
- List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> dbrs = new ArrayList<>();
String seqdb = "Unknown", sdbac = "" + dbr;
int st = -1, en = -1, p;
if ((st = sdbac.indexOf("/")) > -1)
}
boolean ss = false, posterior = false;
type = id2type(type);
+
+ boolean isrnass = false;
if (type.equalsIgnoreCase("secondary structure"))
{
ss = true;
+ isrnass = !NOT_RNASS.search(annots); // sorry about the double negative
+ // here (it's easier for dealing with
+ // other non-alpha-non-brace chars)
}
if (type.equalsIgnoreCase("posterior probability"))
{
{
// if (" .-_".indexOf(pos) == -1)
{
- if (DETECT_BRACKETS.search(pos))
+ if (isrnass && RNASS_BRACKETS.indexOf(pos) >= 0)
{
ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
ann.displayCharacter = "" + pos.charAt(0);
String ch = (annot == null)
? ((sequenceI == null) ? "-"
: Character.toString(sequenceI.getCharAt(k)))
- : annot.displayCharacter;
+ : (annot.displayCharacter == null
+ ? String.valueOf(annot.secondaryStructure)
+ : annot.displayCharacter);
+ if (ch == null)
+ {
+ ch = " ";
+ }
if (key != null && key.equals("SS"))
{
+ char ssannotchar = ' ';
+ boolean charset = false;
if (annot == null)
{
// sensible gap character
- return ' ';
+ ssannotchar = ' ';
+ charset = true;
}
else
{
// valid secondary structure AND no alternative label (e.g. ' B')
if (annot.secondaryStructure > ' ' && ch.length() < 2)
{
- return annot.secondaryStructure;
+ ssannotchar = annot.secondaryStructure;
+ charset = true;
}
}
+ if (charset)
+ {
+ return (ssannotchar == ' ' && isrna) ? '.' : ssannotchar;
+ }
}
if (ch.length() == 0)
{
seq = ch.charAt(1);
}
- return seq;
+
+ return (seq == ' ' && key != null && key.equals("SS") && isrna) ? '.'
+ : seq;
}
public String print()
@Override
public void actionPerformed(ActionEvent e)
{
- saveState_actionPerformed();
+ saveState_actionPerformed(true);
+ }
+ });
+ JMenuItem saveAsJaxb = new JMenuItem("Save Project as JAXB");
+ saveAsJaxb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ saveState_actionPerformed(false);
}
});
loadState.setText(MessageManager.getString("action.load_project"));
@Override
public void actionPerformed(ActionEvent e)
{
- loadState_actionPerformed();
+ loadState_actionPerformed(true);
+ }
+ });
+ JMenuItem loadAsJaxb = new JMenuItem("Load Project as JAXB");
+ loadAsJaxb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadState_actionPerformed(false);
}
});
inputMenu.setText(MessageManager.getString("label.input_alignment"));
FileMenu.add(saveState);
FileMenu.add(loadState);
}
+
+ FileMenu.add(saveAsJaxb);
+ FileMenu.add(loadAsJaxb);
FileMenu.addSeparator();
FileMenu.add(quit);
HelpMenu.add(aboutMenuItem);
{
}
- public void saveState_actionPerformed()
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void saveState_actionPerformed(boolean asCastor)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void loadState_actionPerformed(boolean asCastor)
{
}
- public void loadState_actionPerformed()
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void loadJalviewAlign_actionPerformed(ActionEvent e)
{
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.project;
+
+import jalview.analysis.Conservation;
+import jalview.api.FeatureColourI;
+import jalview.api.ViewStyleI;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.ext.varna.RnaModel;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.AppVarna;
+import jalview.gui.ChimeraViewFrame;
+import jalview.gui.Desktop;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.Jalview2XML_V1;
+import jalview.gui.JvOptionPane;
+import jalview.gui.OOMWarning;
+import jalview.gui.PaintRefresher;
+import jalview.gui.SplitFrame;
+import jalview.gui.StructureViewer;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.gui.StructureViewerBase;
+import jalview.gui.TreePanel;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.NewickFile;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.StringUtils;
+import jalview.util.jarInputStreamProvider;
+import jalview.util.matcher.Condition;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.AutoCalcSetting;
+import jalview.ws.params.WsParamSetI;
+import jalview.xml.binding.jalview.AlcodonFrame;
+import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
+import jalview.xml.binding.jalview.Annotation;
+import jalview.xml.binding.jalview.Annotation.ThresholdLine;
+import jalview.xml.binding.jalview.AnnotationColourScheme;
+import jalview.xml.binding.jalview.AnnotationElement;
+import jalview.xml.binding.jalview.Feature;
+import jalview.xml.binding.jalview.Feature.OtherData;
+import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
+import jalview.xml.binding.jalview.FilterBy;
+import jalview.xml.binding.jalview.JalviewModel;
+import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
+import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
+import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
+import jalview.xml.binding.jalview.JalviewModel.JGroup;
+import jalview.xml.binding.jalview.JalviewModel.JSeq;
+import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
+import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
+import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
+import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
+import jalview.xml.binding.jalview.JalviewModel.Tree;
+import jalview.xml.binding.jalview.JalviewModel.UserColours;
+import jalview.xml.binding.jalview.JalviewModel.Viewport;
+import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
+import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.MapListType.MapListFrom;
+import jalview.xml.binding.jalview.MapListType.MapListTo;
+import jalview.xml.binding.jalview.Mapping;
+import jalview.xml.binding.jalview.NoValueColour;
+import jalview.xml.binding.jalview.ObjectFactory;
+import jalview.xml.binding.jalview.Pdbentry.Property;
+import jalview.xml.binding.jalview.Sequence;
+import jalview.xml.binding.jalview.Sequence.DBRef;
+import jalview.xml.binding.jalview.SequenceSet;
+import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
+import jalview.xml.binding.jalview.ThresholdType;
+import jalview.xml.binding.jalview.VAMSAS;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.math.BigInteger;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.GregorianCalendar;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.SwingUtilities;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeFactory;
+import javax.xml.datatype.XMLGregorianCalendar;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
+
+/**
+ * Write out the current jalview desktop state as a Jalview XML stream.
+ *
+ * Note: the vamsas objects referred to here are primitive versions of the
+ * VAMSAS project schema elements - they are not the same and most likely never
+ * will be :)
+ *
+ * @author $author$
+ * @version $Revision: 1.134 $
+ */
+public class Jalview2XML
+{
+
+ // BH 2018 we add the .jvp binary extension to J2S so that
+ // it will declare that binary when we do the file save from the browser
+
+ private static void addJ2SBinaryType(String ext)
+ {
+ ext = "." + ext + "?";
+
+ /**
+ * @j2sNative
+ *
+ * J2S._binaryTypes.push(ext);
+ *
+ */
+ }
+
+ static
+ {
+ addJ2SBinaryType(".jvp?");
+ }
+
+ private static final String VIEWER_PREFIX = "viewer_";
+
+ private static final String RNA_PREFIX = "rna_";
+
+ private static final String UTF_8 = "UTF-8";
+
+ // use this with nextCounter() to make unique names for entities
+ private int counter = 0;
+
+ /*
+ * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
+ * of sequence objects are created.
+ */
+ IdentityHashMap<SequenceI, String> seqsToIds = null;
+
+ /**
+ * jalview XML Sequence ID to jalview sequence object reference (both dataset
+ * and alignment sequences. Populated as XML reps of sequence objects are
+ * created.)
+ */
+ Map<String, SequenceI> seqRefIds = null;
+
+ Map<String, SequenceI> incompleteSeqs = null;
+
+ List<SeqFref> frefedSequence = null;
+
+ boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+
+ /*
+ * Map of reconstructed AlignFrame objects that appear to have come from
+ * SplitFrame objects (have a dna/protein complement view).
+ */
+ private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
+
+ /*
+ * Map from displayed rna structure models to their saved session state jar
+ * entry names
+ */
+ private Map<RnaModel, String> rnaSessions = new HashMap<>();
+
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the boolean value, or false
+ * if null.
+ *
+ * @param b
+ * @return
+ */
+ public static boolean safeBoolean(Boolean b)
+ {
+ return b == null ? false : b.booleanValue();
+ }
+
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the integer value, or zero
+ * if null.
+ *
+ * @param i
+ * @return
+ */
+ public static int safeInt(Integer i)
+ {
+ return i == null ? 0 : i.intValue();
+ }
+
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the float value, or zero if
+ * null.
+ *
+ * @param f
+ * @return
+ */
+ public static float safeFloat(Float f)
+ {
+ return f == null ? 0f : f.floatValue();
+ }
+
+ /**
+ * create/return unique hash string for sq
+ *
+ * @param sq
+ * @return new or existing unique string for sq
+ */
+ String seqHash(SequenceI sq)
+ {
+ if (seqsToIds == null)
+ {
+ initSeqRefs();
+ }
+ if (seqsToIds.containsKey(sq))
+ {
+ return seqsToIds.get(sq);
+ }
+ else
+ {
+ // create sequential key
+ String key = "sq" + (seqsToIds.size() + 1);
+ key = makeHashCode(sq, key); // check we don't have an external reference
+ // for it already.
+ seqsToIds.put(sq, key);
+ return key;
+ }
+ }
+
+ void initSeqRefs()
+ {
+ if (seqsToIds == null)
+ {
+ seqsToIds = new IdentityHashMap<>();
+ }
+ if (seqRefIds == null)
+ {
+ seqRefIds = new HashMap<>();
+ }
+ if (incompleteSeqs == null)
+ {
+ incompleteSeqs = new HashMap<>();
+ }
+ if (frefedSequence == null)
+ {
+ frefedSequence = new ArrayList<>();
+ }
+ }
+
+ public Jalview2XML()
+ {
+ }
+
+ public Jalview2XML(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ }
+
+ /**
+ * base class for resolving forward references to sequences by their ID
+ *
+ * @author jprocter
+ *
+ */
+ abstract class SeqFref
+ {
+ String sref;
+
+ String type;
+
+ public SeqFref(String _sref, String type)
+ {
+ sref = _sref;
+ this.type = type;
+ }
+
+ public String getSref()
+ {
+ return sref;
+ }
+
+ public SequenceI getSrefSeq()
+ {
+ return seqRefIds.get(sref);
+ }
+
+ public boolean isResolvable()
+ {
+ return seqRefIds.get(sref) != null;
+ }
+
+ public SequenceI getSrefDatasetSeq()
+ {
+ SequenceI sq = seqRefIds.get(sref);
+ if (sq != null)
+ {
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ }
+ return sq;
+ }
+
+ /**
+ * @return true if the forward reference was fully resolved
+ */
+ abstract boolean resolve();
+
+ @Override
+ public String toString()
+ {
+ return type + " reference to " + sref;
+ }
+ }
+
+ /**
+ * create forward reference for a mapping
+ *
+ * @param sref
+ * @param _jmap
+ * @return
+ */
+ public SeqFref newMappingRef(final String sref,
+ final jalview.datamodel.Mapping _jmap)
+ {
+ SeqFref fref = new SeqFref(sref, "Mapping")
+ {
+ public jalview.datamodel.Mapping jmap = _jmap;
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ jmap.setTo(seq);
+ return true;
+ }
+ };
+ return fref;
+ }
+
+ public SeqFref newAlcodMapRef(final String sref,
+ final AlignedCodonFrame _cf,
+ final jalview.datamodel.Mapping _jmap)
+ {
+
+ SeqFref fref = new SeqFref(sref, "Codon Frame")
+ {
+ AlignedCodonFrame cf = _cf;
+
+ public jalview.datamodel.Mapping mp = _jmap;
+
+ @Override
+ public boolean isResolvable()
+ {
+ return super.isResolvable() && mp.getTo() != null;
+ };
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ cf.addMap(seq, mp.getTo(), mp.getMap());
+ return true;
+ }
+ };
+ return fref;
+ }
+
+ public void resolveFrefedSequences()
+ {
+ Iterator<SeqFref> nextFref = frefedSequence.iterator();
+ int toresolve = frefedSequence.size();
+ int unresolved = 0, failedtoresolve = 0;
+ while (nextFref.hasNext())
+ {
+ SeqFref ref = nextFref.next();
+ if (ref.isResolvable())
+ {
+ try
+ {
+ if (ref.resolve())
+ {
+ nextFref.remove();
+ }
+ else
+ {
+ failedtoresolve++;
+ }
+ } catch (Exception x)
+ {
+ System.err.println(
+ "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+ + ref.getSref());
+ x.printStackTrace();
+ failedtoresolve++;
+ }
+ }
+ else
+ {
+ unresolved++;
+ }
+ }
+ if (unresolved > 0)
+ {
+ System.err.println("Jalview Project Import: There were " + unresolved
+ + " forward references left unresolved on the stack.");
+ }
+ if (failedtoresolve > 0)
+ {
+ System.err.println("SERIOUS! " + failedtoresolve
+ + " resolvable forward references failed to resolve.");
+ }
+ if (incompleteSeqs != null && incompleteSeqs.size() > 0)
+ {
+ System.err.println(
+ "Jalview Project Import: There are " + incompleteSeqs.size()
+ + " sequences which may have incomplete metadata.");
+ if (incompleteSeqs.size() < 10)
+ {
+ for (SequenceI s : incompleteSeqs.values())
+ {
+ System.err.println(s.toString());
+ }
+ }
+ else
+ {
+ System.err.println(
+ "Too many to report. Skipping output of incomplete sequences.");
+ }
+ }
+ }
+
+ /**
+ * This maintains a map of viewports, the key being the seqSetId. Important to
+ * set historyItem and redoList for multiple views
+ */
+ Map<String, AlignViewport> viewportsAdded = new HashMap<>();
+
+ Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
+
+ String uniqueSetSuffix = "";
+
+ /**
+ * List of pdbfiles added to Jar
+ */
+ List<String> pdbfiles = null;
+
+ // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
+ public void saveState(File statefile)
+ {
+ FileOutputStream fos = null;
+ try
+ {
+ fos = new FileOutputStream(statefile);
+ JarOutputStream jout = new JarOutputStream(fos);
+ saveState(jout);
+
+ } catch (Exception e)
+ {
+ // TODO: inform user of the problem - they need to know if their data was
+ // not saved !
+ if (errorMessage == null)
+ {
+ errorMessage = "Couldn't write Jalview Archive to output file '"
+ + statefile + "' - See console error log for details";
+ }
+ else
+ {
+ errorMessage += "(output file was '" + statefile + "')";
+ }
+ e.printStackTrace();
+ } finally
+ {
+ if (fos != null)
+ {
+ try
+ {
+ fos.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ reportErrors();
+ }
+
+ /**
+ * Writes a jalview project archive to the given Jar output stream.
+ *
+ * @param jout
+ */
+ public void saveState(JarOutputStream jout)
+ {
+ AlignFrame[] frames = Desktop.getAlignFrames();
+
+ if (frames == null)
+ {
+ return;
+ }
+ saveAllFrames(Arrays.asList(frames), jout);
+ }
+
+ /**
+ * core method for storing state for a set of AlignFrames.
+ *
+ * @param frames
+ * - frames involving all data to be exported (including containing
+ * splitframes)
+ * @param jout
+ * - project output stream
+ */
+ private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
+ {
+ Hashtable<String, AlignFrame> dsses = new Hashtable<>();
+
+ /*
+ * ensure cached data is clear before starting
+ */
+ // todo tidy up seqRefIds, seqsToIds initialisation / reset
+ rnaSessions.clear();
+ splitFrameCandidates.clear();
+
+ try
+ {
+
+ // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+ // //////////////////////////////////////////////////
+
+ List<String> shortNames = new ArrayList<>();
+ List<String> viewIds = new ArrayList<>();
+
+ // REVERSE ORDER
+ for (int i = frames.size() - 1; i > -1; i--)
+ {
+ AlignFrame af = frames.get(i);
+ // skip ?
+ if (skipList != null && skipList
+ .containsKey(af.getViewport().getSequenceSetId()))
+ {
+ continue;
+ }
+
+ String shortName = makeFilename(af, shortNames);
+
+ int apSize = af.getAlignPanels().size();
+
+ for (int ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
+ .get(ap);
+ String fileName = apSize == 1 ? shortName : ap + shortName;
+ if (!fileName.endsWith(".xml"))
+ {
+ fileName = fileName + ".xml";
+ }
+
+ saveState(apanel, fileName, jout, viewIds);
+
+ String dssid = getDatasetIdRef(
+ af.getViewport().getAlignment().getDataset());
+ if (!dsses.containsKey(dssid))
+ {
+ dsses.put(dssid, af);
+ }
+ }
+ }
+
+ writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
+ jout);
+
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
+ jout.close();
+ } catch (Exception ex)
+ {
+ // TODO: inform user of the problem - they need to know if their data was
+ // not saved !
+ if (errorMessage == null)
+ {
+ errorMessage = "Couldn't write Jalview Archive - see error output for details";
+ }
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * Generates a distinct file name, based on the title of the AlignFrame, by
+ * appending _n for increasing n until an unused name is generated. The new
+ * name (without its extension) is added to the list.
+ *
+ * @param af
+ * @param namesUsed
+ * @return the generated name, with .xml extension
+ */
+ protected String makeFilename(AlignFrame af, List<String> namesUsed)
+ {
+ String shortName = af.getTitle();
+
+ if (shortName.indexOf(File.separatorChar) > -1)
+ {
+ shortName = shortName
+ .substring(shortName.lastIndexOf(File.separatorChar) + 1);
+ }
+
+ int count = 1;
+
+ while (namesUsed.contains(shortName))
+ {
+ if (shortName.endsWith("_" + (count - 1)))
+ {
+ shortName = shortName.substring(0, shortName.lastIndexOf("_"));
+ }
+
+ shortName = shortName.concat("_" + count);
+ count++;
+ }
+
+ namesUsed.add(shortName);
+
+ if (!shortName.endsWith(".xml"))
+ {
+ shortName = shortName + ".xml";
+ }
+ return shortName;
+ }
+
+ // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
+ public boolean saveAlignment(AlignFrame af, String jarFile,
+ String fileName)
+ {
+ try
+ {
+ FileOutputStream fos = new FileOutputStream(jarFile);
+ JarOutputStream jout = new JarOutputStream(fos);
+ List<AlignFrame> frames = new ArrayList<>();
+
+ // resolve splitframes
+ if (af.getViewport().getCodingComplement() != null)
+ {
+ frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
+ }
+ else
+ {
+ frames.add(af);
+ }
+ saveAllFrames(frames, jout);
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
+ jout.close();
+ return true;
+ } catch (Exception ex)
+ {
+ errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
+ ex.printStackTrace();
+ return false;
+ }
+ }
+
+ private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
+ String fileName, JarOutputStream jout)
+ {
+
+ for (String dssids : dsses.keySet())
+ {
+ AlignFrame _af = dsses.get(dssids);
+ String jfileName = fileName + " Dataset for " + _af.getTitle();
+ if (!jfileName.endsWith(".xml"))
+ {
+ jfileName = jfileName + ".xml";
+ }
+ saveState(_af.alignPanel, jfileName, true, jout, null);
+ }
+ }
+
+ /**
+ * create a JalviewModel from an alignment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param jout
+ * jar output stream
+ * @param viewIds
+ * @param out
+ * jar entry name
+ */
+ public JalviewModel saveState(AlignmentPanel ap, String fileName,
+ JarOutputStream jout, List<String> viewIds)
+ {
+ return saveState(ap, fileName, false, jout, viewIds);
+ }
+
+ /**
+ * create a JalviewModel from an alignment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param storeDS
+ * when true, only write the dataset for the alignment, not the data
+ * associated with the view.
+ * @param jout
+ * jar output stream
+ * @param out
+ * jar entry name
+ */
+ public JalviewModel saveState(AlignmentPanel ap, String fileName,
+ boolean storeDS, JarOutputStream jout, List<String> viewIds)
+ {
+ if (viewIds == null)
+ {
+ viewIds = new ArrayList<>();
+ }
+
+ initSeqRefs();
+
+ List<UserColourScheme> userColours = new ArrayList<>();
+
+ AlignViewport av = ap.av;
+ ViewportRanges vpRanges = av.getRanges();
+
+ final ObjectFactory objectFactory = new ObjectFactory();
+ JalviewModel object = objectFactory.createJalviewModel();
+ object.setVamsasModel(new VAMSAS());
+
+ // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
+ try
+ {
+ GregorianCalendar c = new GregorianCalendar();
+ DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
+ XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
+ object.setCreationDate(now);
+ } catch (DatatypeConfigurationException e)
+ {
+ System.err.println("error writing date: " + e.toString());
+ }
+ object.setVersion(
+ jalview.bin.Cache.getDefault("VERSION", "Development Build"));
+
+ /**
+ * rjal is full height alignment, jal is actual alignment with full metadata
+ * but excludes hidden sequences.
+ */
+ jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
+
+ if (av.hasHiddenRows())
+ {
+ rjal = jal.getHiddenSequences().getFullAlignment();
+ }
+
+ SequenceSet vamsasSet = new SequenceSet();
+ Sequence vamsasSeq;
+ // JalviewModelSequence jms = new JalviewModelSequence();
+
+ vamsasSet.setGapChar(jal.getGapCharacter() + "");
+
+ if (jal.getDataset() != null)
+ {
+ // dataset id is the dataset's hashcode
+ vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
+ if (storeDS)
+ {
+ // switch jal and the dataset
+ jal = jal.getDataset();
+ rjal = jal;
+ }
+ }
+ if (jal.getProperties() != null)
+ {
+ Enumeration en = jal.getProperties().keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ SequenceSetProperties ssp = new SequenceSetProperties();
+ ssp.setKey(key);
+ ssp.setValue(jal.getProperties().get(key).toString());
+ // vamsasSet.addSequenceSetProperties(ssp);
+ vamsasSet.getSequenceSetProperties().add(ssp);
+ }
+ }
+
+ JSeq jseq;
+ Set<String> calcIdSet = new HashSet<>();
+ // record the set of vamsas sequence XML POJO we create.
+ HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
+ // SAVE SEQUENCES
+ for (final SequenceI jds : rjal.getSequences())
+ {
+ final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
+ : jds.getDatasetSequence();
+ String id = seqHash(jds);
+ if (vamsasSetIds.get(id) == null)
+ {
+ if (seqRefIds.get(id) != null && !storeDS)
+ {
+ // This happens for two reasons: 1. multiple views are being
+ // serialised.
+ // 2. the hashCode has collided with another sequence's code. This
+ // DOES
+ // HAPPEN! (PF00072.15.stk does this)
+ // JBPNote: Uncomment to debug writing out of files that do not read
+ // back in due to ArrayOutOfBoundExceptions.
+ // System.err.println("vamsasSeq backref: "+id+"");
+ // System.err.println(jds.getName()+"
+ // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(jds));
+ // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+ // System.err.println(rsq.getName()+"
+ // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(rsq));
+ }
+ else
+ {
+ vamsasSeq = createVamsasSequence(id, jds);
+// vamsasSet.addSequence(vamsasSeq);
+ vamsasSet.getSequence().add(vamsasSeq);
+ vamsasSetIds.put(id, vamsasSeq);
+ seqRefIds.put(id, jds);
+ }
+ }
+ jseq = new JSeq();
+ jseq.setStart(jds.getStart());
+ jseq.setEnd(jds.getEnd());
+ jseq.setColour(av.getSequenceColour(jds).getRGB());
+
+ jseq.setId(id); // jseq id should be a string not a number
+ if (!storeDS)
+ {
+ // Store any sequences this sequence represents
+ if (av.hasHiddenRows())
+ {
+ // use rjal, contains the full height alignment
+ jseq.setHidden(
+ av.getAlignment().getHiddenSequences().isHidden(jds));
+
+ if (av.isHiddenRepSequence(jds))
+ {
+ jalview.datamodel.SequenceI[] reps = av
+ .getRepresentedSequences(jds).getSequencesInOrder(rjal);
+
+ for (int h = 0; h < reps.length; h++)
+ {
+ if (reps[h] != jds)
+ {
+ // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
+ jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
+ }
+ }
+ }
+ }
+ // mark sequence as reference - if it is the reference for this view
+ if (jal.hasSeqrep())
+ {
+ jseq.setViewreference(jds == jal.getSeqrep());
+ }
+ }
+
+ // TODO: omit sequence features from each alignment view's XML dump if we
+ // are storing dataset
+ List<SequenceFeature> sfs = jds.getSequenceFeatures();
+ for (SequenceFeature sf : sfs)
+ {
+ // Features features = new Features();
+ Feature features = new Feature();
+
+ features.setBegin(sf.getBegin());
+ features.setEnd(sf.getEnd());
+ features.setDescription(sf.getDescription());
+ features.setType(sf.getType());
+ features.setFeatureGroup(sf.getFeatureGroup());
+ features.setScore(sf.getScore());
+ if (sf.links != null)
+ {
+ for (int l = 0; l < sf.links.size(); l++)
+ {
+ OtherData keyValue = new OtherData();
+ keyValue.setKey("LINK_" + l);
+ keyValue.setValue(sf.links.elementAt(l).toString());
+ // features.addOtherData(keyValue);
+ features.getOtherData().add(keyValue);
+ }
+ }
+ if (sf.otherDetails != null)
+ {
+ /*
+ * save feature attributes, which may be simple strings or
+ * map valued (have sub-attributes)
+ */
+ for (Entry<String, Object> entry : sf.otherDetails.entrySet())
+ {
+ String key = entry.getKey();
+ Object value = entry.getValue();
+ if (value instanceof Map<?, ?>)
+ {
+ for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
+ .entrySet())
+ {
+ OtherData otherData = new OtherData();
+ otherData.setKey(key);
+ otherData.setKey2(subAttribute.getKey());
+ otherData.setValue(subAttribute.getValue().toString());
+ // features.addOtherData(otherData);
+ features.getOtherData().add(otherData);
+ }
+ }
+ else
+ {
+ OtherData otherData = new OtherData();
+ otherData.setKey(key);
+ otherData.setValue(value.toString());
+ // features.addOtherData(otherData);
+ features.getOtherData().add(otherData);
+ }
+ }
+ }
+
+ // jseq.addFeatures(features);
+ jseq.getFeatures().add(features);
+ }
+
+ if (jdatasq.getAllPDBEntries() != null)
+ {
+ Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
+ while (en.hasMoreElements())
+ {
+ Pdbids pdb = new Pdbids();
+ jalview.datamodel.PDBEntry entry = en.nextElement();
+
+ String pdbId = entry.getId();
+ pdb.setId(pdbId);
+ pdb.setType(entry.getType());
+
+ /*
+ * Store any structure views associated with this sequence. This
+ * section copes with duplicate entries in the project, so a dataset
+ * only view *should* be coped with sensibly.
+ */
+ // This must have been loaded, is it still visible?
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ String matchedFile = null;
+ for (int f = frames.length - 1; f > -1; f--)
+ {
+ if (frames[f] instanceof StructureViewerBase)
+ {
+ StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
+ matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
+ matchedFile, viewFrame);
+ /*
+ * Only store each structure viewer's state once in the project
+ * jar. First time through only (storeDS==false)
+ */
+ String viewId = viewFrame.getViewId();
+ if (!storeDS && !viewIds.contains(viewId))
+ {
+ viewIds.add(viewId);
+ try
+ {
+ String viewerState = viewFrame.getStateInfo();
+ writeJarEntry(jout, getViewerJarEntryName(viewId),
+ viewerState.getBytes());
+ } catch (IOException e)
+ {
+ System.err.println(
+ "Error saving viewer state: " + e.getMessage());
+ }
+ }
+ }
+ }
+
+ if (matchedFile != null || entry.getFile() != null)
+ {
+ if (entry.getFile() != null)
+ {
+ // use entry's file
+ matchedFile = entry.getFile();
+ }
+ pdb.setFile(matchedFile); // entry.getFile());
+ if (pdbfiles == null)
+ {
+ pdbfiles = new ArrayList<>();
+ }
+
+ if (!pdbfiles.contains(pdbId))
+ {
+ pdbfiles.add(pdbId);
+ copyFileToJar(jout, matchedFile, pdbId);
+ }
+ }
+
+ Enumeration<String> props = entry.getProperties();
+ if (props.hasMoreElements())
+ {
+ // PdbentryItem item = new PdbentryItem();
+ while (props.hasMoreElements())
+ {
+ Property prop = new Property();
+ String key = props.nextElement();
+ prop.setName(key);
+ prop.setValue(entry.getProperty(key).toString());
+ // item.addProperty(prop);
+ pdb.getProperty().add(prop);
+ }
+ // pdb.addPdbentryItem(item);
+ }
+
+ // jseq.addPdbids(pdb);
+ jseq.getPdbids().add(pdb);
+ }
+ }
+
+ saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
+
+ // jms.addJSeq(jseq);
+ object.getJSeq().add(jseq);
+ }
+
+ if (!storeDS && av.hasHiddenRows())
+ {
+ jal = av.getAlignment();
+ }
+ // SAVE MAPPINGS
+ // FOR DATASET
+ if (storeDS && jal.getCodonFrames() != null)
+ {
+ List<AlignedCodonFrame> jac = jal.getCodonFrames();
+ for (AlignedCodonFrame acf : jac)
+ {
+ AlcodonFrame alc = new AlcodonFrame();
+ if (acf.getProtMappings() != null
+ && acf.getProtMappings().length > 0)
+ {
+ boolean hasMap = false;
+ SequenceI[] dnas = acf.getdnaSeqs();
+ jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
+ for (int m = 0; m < pmaps.length; m++)
+ {
+ AlcodMap alcmap = new AlcodMap();
+ alcmap.setDnasq(seqHash(dnas[m]));
+ alcmap.setMapping(
+ createVamsasMapping(pmaps[m], dnas[m], null, false));
+ // alc.addAlcodMap(alcmap);
+ alc.getAlcodMap().add(alcmap);
+ hasMap = true;
+ }
+ if (hasMap)
+ {
+ // vamsasSet.addAlcodonFrame(alc);
+ vamsasSet.getAlcodonFrame().add(alc);
+ }
+ }
+ // TODO: delete this ? dead code from 2.8.3->2.9 ?
+ // {
+ // AlcodonFrame alc = new AlcodonFrame();
+ // vamsasSet.addAlcodonFrame(alc);
+ // for (int p = 0; p < acf.aaWidth; p++)
+ // {
+ // Alcodon cmap = new Alcodon();
+ // if (acf.codons[p] != null)
+ // {
+ // // Null codons indicate a gapped column in the translated peptide
+ // // alignment.
+ // cmap.setPos1(acf.codons[p][0]);
+ // cmap.setPos2(acf.codons[p][1]);
+ // cmap.setPos3(acf.codons[p][2]);
+ // }
+ // alc.addAlcodon(cmap);
+ // }
+ // if (acf.getProtMappings() != null
+ // && acf.getProtMappings().length > 0)
+ // {
+ // SequenceI[] dnas = acf.getdnaSeqs();
+ // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
+ // for (int m = 0; m < pmaps.length; m++)
+ // {
+ // AlcodMap alcmap = new AlcodMap();
+ // alcmap.setDnasq(seqHash(dnas[m]));
+ // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
+ // false));
+ // alc.addAlcodMap(alcmap);
+ // }
+ // }
+ }
+ }
+
+ // SAVE TREES
+ // /////////////////////////////////
+ if (!storeDS && av.getCurrentTree() != null)
+ {
+ // FIND ANY ASSOCIATED TREES
+ // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
+ if (Desktop.desktop != null)
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof TreePanel)
+ {
+ TreePanel tp = (TreePanel) frames[t];
+
+ if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
+ {
+ JalviewModel.Tree tree = new JalviewModel.Tree();
+ tree.setTitle(tp.getTitle());
+ tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
+ tree.setNewick(tp.getTree().print());
+ tree.setThreshold(tp.getTreeCanvas().getThreshold());
+
+ tree.setFitToWindow(tp.fitToWindow.getState());
+ tree.setFontName(tp.getTreeFont().getName());
+ tree.setFontSize(tp.getTreeFont().getSize());
+ tree.setFontStyle(tp.getTreeFont().getStyle());
+ tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+
+ tree.setShowBootstrap(tp.bootstrapMenu.getState());
+ tree.setShowDistances(tp.distanceMenu.getState());
+
+ tree.setHeight(tp.getHeight());
+ tree.setWidth(tp.getWidth());
+ tree.setXpos(tp.getX());
+ tree.setYpos(tp.getY());
+ tree.setId(makeHashCode(tp, null));
+ // jms.addTree(tree);
+ object.getTree().add(tree);
+ }
+ }
+ }
+ }
+ }
+
+ // SAVE ANNOTATIONS
+ /**
+ * store forward refs from an annotationRow to any groups
+ */
+ IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
+ if (storeDS)
+ {
+ for (SequenceI sq : jal.getSequences())
+ {
+ // Store annotation on dataset sequences only
+ AlignmentAnnotation[] aa = sq.getAnnotation();
+ if (aa != null && aa.length > 0)
+ {
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
+ }
+ }
+ }
+ else
+ {
+ if (jal.getAlignmentAnnotation() != null)
+ {
+ // Store the annotation shown on the alignment.
+ AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
+ }
+ }
+ // SAVE GROUPS
+ if (jal.getGroups() != null)
+ {
+ JGroup[] groups = new JGroup[jal.getGroups().size()];
+ int i = -1;
+ for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
+ {
+ JGroup jGroup = new JGroup();
+ groups[++i] = jGroup;
+
+ jGroup.setStart(sg.getStartRes());
+ jGroup.setEnd(sg.getEndRes());
+ jGroup.setName(sg.getName());
+ if (groupRefs.containsKey(sg))
+ {
+ // group has references so set its ID field
+ jGroup.setId(groupRefs.get(sg));
+ }
+ ColourSchemeI colourScheme = sg.getColourScheme();
+ if (colourScheme != null)
+ {
+ ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
+ if (groupColourScheme.conservationApplied())
+ {
+ jGroup.setConsThreshold(groupColourScheme.getConservationInc());
+
+ if (colourScheme instanceof jalview.schemes.UserColourScheme)
+ {
+ jGroup.setColour(
+ setUserColourScheme(colourScheme, userColours,
+ object));
+ }
+ else
+ {
+ jGroup.setColour(colourScheme.getSchemeName());
+ }
+ }
+ else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
+ {
+ jGroup.setColour("AnnotationColourGradient");
+ jGroup.setAnnotationColours(constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) colourScheme,
+ userColours, object));
+ }
+ else if (colourScheme instanceof jalview.schemes.UserColourScheme)
+ {
+ jGroup.setColour(
+ setUserColourScheme(colourScheme, userColours, object));
+ }
+ else
+ {
+ jGroup.setColour(colourScheme.getSchemeName());
+ }
+
+ jGroup.setPidThreshold(groupColourScheme.getThreshold());
+ }
+
+ jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
+ jGroup.setDisplayBoxes(sg.getDisplayBoxes());
+ jGroup.setDisplayText(sg.getDisplayText());
+ jGroup.setColourText(sg.getColourText());
+ jGroup.setTextCol1(sg.textColour.getRGB());
+ jGroup.setTextCol2(sg.textColour2.getRGB());
+ jGroup.setTextColThreshold(sg.thresholdTextColour);
+ jGroup.setShowUnconserved(sg.getShowNonconserved());
+ jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+ jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
+ jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
+ jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
+ for (SequenceI seq : sg.getSequences())
+ {
+ // jGroup.addSeq(seqHash(seq));
+ jGroup.getSeq().add(seqHash(seq));
+ }
+ }
+
+ //jms.setJGroup(groups);
+ Object group;
+ for (JGroup grp : groups)
+ {
+ object.getJGroup().add(grp);
+ }
+ }
+ if (!storeDS)
+ {
+ // /////////SAVE VIEWPORT
+ Viewport view = new Viewport();
+ view.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(
+ makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
+ view.setId(av.getViewId());
+ if (av.getCodingComplement() != null)
+ {
+ view.setComplementId(av.getCodingComplement().getViewId());
+ }
+ view.setViewName(av.getViewName());
+ view.setGatheredViews(av.isGatherViewsHere());
+
+ Rectangle size = ap.av.getExplodedGeometry();
+ Rectangle position = size;
+ if (size == null)
+ {
+ size = ap.alignFrame.getBounds();
+ if (av.getCodingComplement() != null)
+ {
+ position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
+ .getBounds();
+ }
+ else
+ {
+ position = size;
+ }
+ }
+ view.setXpos(position.x);
+ view.setYpos(position.y);
+
+ view.setWidth(size.width);
+ view.setHeight(size.height);
+
+ view.setStartRes(vpRanges.getStartRes());
+ view.setStartSeq(vpRanges.getStartSeq());
+
+ if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
+ userColours, object));
+ }
+ else if (av
+ .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
+ {
+ AnnotationColourScheme ac = constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme(),
+ userColours, object);
+
+ view.setAnnotationColours(ac);
+ view.setBgColour("AnnotationColourGradient");
+ }
+ else
+ {
+ view.setBgColour(ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
+ }
+
+ ResidueShaderI vcs = av.getResidueShading();
+ ColourSchemeI cs = av.getGlobalColourScheme();
+
+ if (cs != null)
+ {
+ if (vcs.conservationApplied())
+ {
+ view.setConsThreshold(vcs.getConservationInc());
+ if (cs instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(setUserColourScheme(cs, userColours, object));
+ }
+ }
+ view.setPidThreshold(vcs.getThreshold());
+ }
+
+ view.setConservationSelected(av.getConservationSelected());
+ view.setPidSelected(av.getAbovePIDThreshold());
+ final Font font = av.getFont();
+ view.setFontName(font.getName());
+ view.setFontSize(font.getSize());
+ view.setFontStyle(font.getStyle());
+ view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
+ view.setRenderGaps(av.isRenderGaps());
+ view.setShowAnnotation(av.isShowAnnotation());
+ view.setShowBoxes(av.getShowBoxes());
+ view.setShowColourText(av.getColourText());
+ view.setShowFullId(av.getShowJVSuffix());
+ view.setRightAlignIds(av.isRightAlignIds());
+ view.setShowSequenceFeatures(av.isShowSequenceFeatures());
+ view.setShowText(av.getShowText());
+ view.setShowUnconserved(av.getShowUnconserved());
+ view.setWrapAlignment(av.getWrapAlignment());
+ view.setTextCol1(av.getTextColour().getRGB());
+ view.setTextCol2(av.getTextColour2().getRGB());
+ view.setTextColThreshold(av.getThresholdTextColour());
+ view.setShowConsensusHistogram(av.isShowConsensusHistogram());
+ view.setShowSequenceLogo(av.isShowSequenceLogo());
+ view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
+ view.setShowGroupConsensus(av.isShowGroupConsensus());
+ view.setShowGroupConservation(av.isShowGroupConservation());
+ view.setShowNPfeatureTooltip(av.isShowNPFeats());
+ view.setShowDbRefTooltip(av.isShowDBRefs());
+ view.setFollowHighlight(av.isFollowHighlight());
+ view.setFollowSelection(av.followSelection);
+ view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
+ if (av.getFeaturesDisplayed() != null)
+ {
+ FeatureSettings fs = new FeatureSettings();
+
+ FeatureRenderer fr = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+ String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
+
+ Vector<String> settingsAdded = new Vector<>();
+ if (renderOrder != null)
+ {
+ for (String featureType : renderOrder)
+ {
+ FeatureSettings.Setting setting = new FeatureSettings.Setting();
+ setting.setType(featureType);
+
+ /*
+ * save any filter for the feature type
+ */
+ FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
+ if (filter != null) {
+ Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
+ FeatureMatcherI firstFilter = filters.next();
+ setting.setMatcherSet(Jalview2XML.marshalFilter(
+ firstFilter, filters, filter.isAnded()));
+ }
+
+ /*
+ * save colour scheme for the feature type
+ */
+ FeatureColourI fcol = fr.getFeatureStyle(featureType);
+ if (!fcol.isSimpleColour())
+ {
+ setting.setColour(fcol.getMaxColour().getRGB());
+ setting.setMincolour(fcol.getMinColour().getRGB());
+ setting.setMin(fcol.getMin());
+ setting.setMax(fcol.getMax());
+ setting.setColourByLabel(fcol.isColourByLabel());
+ if (fcol.isColourByAttribute())
+ {
+ String[] attName = fcol.getAttributeName();
+ setting.getAttributeName().add(attName[0]);
+ if (attName.length > 1)
+ {
+ setting.getAttributeName().add(attName[1]);
+ }
+ }
+ setting.setAutoScale(fcol.isAutoScaled());
+ setting.setThreshold(fcol.getThreshold());
+ Color noColour = fcol.getNoColour();
+ if (noColour == null)
+ {
+ setting.setNoValueColour(NoValueColour.NONE);
+ }
+ else if (noColour.equals(fcol.getMaxColour()))
+ {
+ setting.setNoValueColour(NoValueColour.MAX);
+ }
+ else
+ {
+ setting.setNoValueColour(NoValueColour.MIN);
+ }
+ // -1 = No threshold, 0 = Below, 1 = Above
+ setting.setThreshstate(fcol.isAboveThreshold() ? 1
+ : (fcol.isBelowThreshold() ? 0 : -1));
+ }
+ else
+ {
+ setting.setColour(fcol.getColour().getRGB());
+ }
+
+ setting.setDisplay(
+ av.getFeaturesDisplayed().isVisible(featureType));
+ float rorder = fr
+ .getOrder(featureType);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ /// fs.addSetting(setting);
+ fs.getSetting().add(setting);
+ settingsAdded.addElement(featureType);
+ }
+ }
+
+ // is groups actually supposed to be a map here ?
+ Iterator<String> en = fr.getFeatureGroups().iterator();
+ Vector<String> groupsAdded = new Vector<>();
+ while (en.hasNext())
+ {
+ String grp = en.next();
+ if (groupsAdded.contains(grp))
+ {
+ continue;
+ }
+ Group g = new Group();
+ g.setName(grp);
+ g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
+ .booleanValue());
+ // fs.addGroup(g);
+ fs.getGroup().add(g);
+ groupsAdded.addElement(grp);
+ }
+ // jms.setFeatureSettings(fs);
+ object.setFeatureSettings(fs);
+ }
+
+ if (av.hasHiddenColumns())
+ {
+ jalview.datamodel.HiddenColumns hidden = av.getAlignment()
+ .getHiddenColumns();
+ if (hidden == null)
+ {
+ warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+ }
+ else
+ {
+ Iterator<int[]> hiddenRegions = hidden.iterator();
+ while (hiddenRegions.hasNext())
+ {
+ int[] region = hiddenRegions.next();
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ // view.addHiddenColumns(hc);
+ view.getHiddenColumns().add(hc);
+ }
+ }
+ }
+ if (calcIdSet.size() > 0)
+ {
+ for (String calcId : calcIdSet)
+ {
+ if (calcId.trim().length() > 0)
+ {
+ CalcIdParam cidp = createCalcIdParam(calcId, av);
+ // Some calcIds have no parameters.
+ if (cidp != null)
+ {
+ // view.addCalcIdParam(cidp);
+ view.getCalcIdParam().add(cidp);
+ }
+ }
+ }
+ }
+
+ // jms.addViewport(view);
+ object.getViewport().add(view);
+ }
+ // object.setJalviewModelSequence(jms);
+ // object.getVamsasModel().addSequenceSet(vamsasSet);
+ object.getVamsasModel().getSequenceSet().add(vamsasSet);
+
+ if (jout != null && fileName != null)
+ {
+ // We may not want to write the object to disk,
+ // eg we can copy the alignViewport to a new view object
+ // using save and then load
+ try
+ {
+ System.out.println("Writing jar entry " + fileName);
+ JarEntry entry = new JarEntry(fileName);
+ jout.putNextEntry(entry);
+ PrintWriter pout = new PrintWriter(
+ new OutputStreamWriter(jout, UTF_8));
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewModel.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+
+ // output pretty printed
+ // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewModel(object), pout);
+
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ pout.flush();
+ jout.closeEntry();
+ } catch (Exception ex)
+ {
+ // TODO: raise error in GUI if marshalling failed.
+ System.err.println("Error writing Jalview project");
+ ex.printStackTrace();
+ }
+ }
+ return object;
+ }
+
+ /**
+ * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
+ * for each viewer, with
+ * <ul>
+ * <li>viewer geometry (position, size, split pane divider location)</li>
+ * <li>index of the selected structure in the viewer (currently shows gapped
+ * or ungapped)</li>
+ * <li>the id of the annotation holding RNA secondary structure</li>
+ * <li>(currently only one SS is shown per viewer, may be more in future)</li>
+ * </ul>
+ * Varna viewer state is also written out (in native Varna XML) to separate
+ * project jar entries. A separate entry is written for each RNA structure
+ * displayed, with the naming convention
+ * <ul>
+ * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
+ * </ul>
+ *
+ * @param jout
+ * @param jseq
+ * @param jds
+ * @param viewIds
+ * @param ap
+ * @param storeDataset
+ */
+ protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
+ final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
+ boolean storeDataset)
+ {
+ if (Desktop.desktop == null)
+ {
+ return;
+ }
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int f = frames.length - 1; f > -1; f--)
+ {
+ if (frames[f] instanceof AppVarna)
+ {
+ AppVarna varna = (AppVarna) frames[f];
+ /*
+ * link the sequence to every viewer that is showing it and is linked to
+ * its alignment panel
+ */
+ if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
+ {
+ String viewId = varna.getViewId();
+ RnaViewer rna = new RnaViewer();
+ rna.setViewId(viewId);
+ rna.setTitle(varna.getTitle());
+ rna.setXpos(varna.getX());
+ rna.setYpos(varna.getY());
+ rna.setWidth(varna.getWidth());
+ rna.setHeight(varna.getHeight());
+ rna.setDividerLocation(varna.getDividerLocation());
+ rna.setSelectedRna(varna.getSelectedIndex());
+ // jseq.addRnaViewer(rna);
+ jseq.getRnaViewer().add(rna);
+
+ /*
+ * Store each Varna panel's state once in the project per sequence.
+ * First time through only (storeDataset==false)
+ */
+ // boolean storeSessions = false;
+ // String sequenceViewId = viewId + seqsToIds.get(jds);
+ // if (!storeDataset && !viewIds.contains(sequenceViewId))
+ // {
+ // viewIds.add(sequenceViewId);
+ // storeSessions = true;
+ // }
+ for (RnaModel model : varna.getModels())
+ {
+ if (model.seq == jds)
+ {
+ /*
+ * VARNA saves each view (sequence or alignment secondary
+ * structure, gapped or trimmed) as a separate XML file
+ */
+ String jarEntryName = rnaSessions.get(model);
+ if (jarEntryName == null)
+ {
+
+ String varnaStateFile = varna.getStateInfo(model.rna);
+ jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
+ copyFileToJar(jout, varnaStateFile, jarEntryName);
+ rnaSessions.put(model, jarEntryName);
+ }
+ SecondaryStructure ss = new SecondaryStructure();
+ String annotationId = varna.getAnnotation(jds).annotationId;
+ ss.setAnnotationId(annotationId);
+ ss.setViewerState(jarEntryName);
+ ss.setGapped(model.gapped);
+ ss.setTitle(model.title);
+ // rna.addSecondaryStructure(ss);
+ rna.getSecondaryStructure().add(ss);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Copy the contents of a file to a new entry added to the output jar
+ *
+ * @param jout
+ * @param infilePath
+ * @param jarEntryName
+ */
+ protected void copyFileToJar(JarOutputStream jout, String infilePath,
+ String jarEntryName)
+ {
+ DataInputStream dis = null;
+ try
+ {
+ File file = new File(infilePath);
+ if (file.exists() && jout != null)
+ {
+ dis = new DataInputStream(new FileInputStream(file));
+ byte[] data = new byte[(int) file.length()];
+ dis.readFully(data);
+ writeJarEntry(jout, jarEntryName, data);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (dis != null)
+ {
+ try
+ {
+ dis.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+ /**
+ * Write the data to a new entry of given name in the output jar file
+ *
+ * @param jout
+ * @param jarEntryName
+ * @param data
+ * @throws IOException
+ */
+ protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
+ byte[] data) throws IOException
+ {
+ if (jout != null)
+ {
+ System.out.println("Writing jar entry " + jarEntryName);
+ jout.putNextEntry(new JarEntry(jarEntryName));
+ DataOutputStream dout = new DataOutputStream(jout);
+ dout.write(data, 0, data.length);
+ dout.flush();
+ jout.closeEntry();
+ }
+ }
+
+ /**
+ * Save the state of a structure viewer
+ *
+ * @param ap
+ * @param jds
+ * @param pdb
+ * the archive XML element under which to save the state
+ * @param entry
+ * @param viewIds
+ * @param matchedFile
+ * @param viewFrame
+ * @return
+ */
+ protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
+ Pdbids pdb, PDBEntry entry, List<String> viewIds,
+ String matchedFile, StructureViewerBase viewFrame)
+ {
+ final AAStructureBindingModel bindingModel = viewFrame.getBinding();
+
+ /*
+ * Look for any bindings for this viewer to the PDB file of interest
+ * (including part matches excluding chain id)
+ */
+ for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
+ {
+ final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
+ final String pdbId = pdbentry.getId();
+ if (!pdbId.equals(entry.getId())
+ && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
+ .startsWith(pdbId.toLowerCase())))
+ {
+ /*
+ * not interested in a binding to a different PDB entry here
+ */
+ continue;
+ }
+ if (matchedFile == null)
+ {
+ matchedFile = pdbentry.getFile();
+ }
+ else if (!matchedFile.equals(pdbentry.getFile()))
+ {
+ Cache.log.warn(
+ "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + pdbentry.getFile());
+ }
+ // record the
+ // file so we
+ // can get at it if the ID
+ // match is ambiguous (e.g.
+ // 1QIP==1qipA)
+
+ for (int smap = 0; smap < viewFrame.getBinding()
+ .getSequence()[peid].length; smap++)
+ {
+ // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+ if (jds == viewFrame.getBinding().getSequence()[peid][smap])
+ {
+ StructureState state = new StructureState();
+ state.setVisible(true);
+ state.setXpos(viewFrame.getX());
+ state.setYpos(viewFrame.getY());
+ state.setWidth(viewFrame.getWidth());
+ state.setHeight(viewFrame.getHeight());
+ final String viewId = viewFrame.getViewId();
+ state.setViewId(viewId);
+ state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
+ state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
+ state.setColourByJmol(viewFrame.isColouredByViewer());
+ state.setType(viewFrame.getViewerType().toString());
+ // pdb.addStructureState(state);
+ pdb.getStructureState().add(state);
+ }
+ }
+ }
+ return matchedFile;
+ }
+
+ /**
+ * Populates the AnnotationColourScheme xml for save. This captures the
+ * settings of the options in the 'Colour by Annotation' dialog.
+ *
+ * @param acg
+ * @param userColours
+ * @param jm
+ * @return
+ */
+ private AnnotationColourScheme constructAnnotationColours(
+ AnnotationColourGradient acg, List<UserColourScheme> userColours,
+ JalviewModel jm)
+ {
+ AnnotationColourScheme ac = new AnnotationColourScheme();
+ ac.setAboveThreshold(acg.getAboveThreshold());
+ ac.setThreshold(acg.getAnnotationThreshold());
+ // 2.10.2 save annotationId (unique) not annotation label
+ ac.setAnnotation(acg.getAnnotation().annotationId);
+ if (acg.getBaseColour() instanceof UserColourScheme)
+ {
+ ac.setColourScheme(
+ setUserColourScheme(acg.getBaseColour(), userColours, jm));
+ }
+ else
+ {
+ ac.setColourScheme(
+ ColourSchemeProperty.getColourName(acg.getBaseColour()));
+ }
+
+ ac.setMaxColour(acg.getMaxColour().getRGB());
+ ac.setMinColour(acg.getMinColour().getRGB());
+ ac.setPerSequence(acg.isSeqAssociated());
+ ac.setPredefinedColours(acg.isPredefinedColours());
+ return ac;
+ }
+
+ private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
+ IdentityHashMap<SequenceGroup, String> groupRefs,
+ AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
+ SequenceSet vamsasSet)
+ {
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ Annotation an = new Annotation();
+
+ AlignmentAnnotation annotation = aa[i];
+ if (annotation.annotationId != null)
+ {
+ annotationIds.put(annotation.annotationId, annotation);
+ }
+
+ an.setId(annotation.annotationId);
+
+ an.setVisible(annotation.visible);
+
+ an.setDescription(annotation.description);
+
+ if (annotation.sequenceRef != null)
+ {
+ // 2.9 JAL-1781 xref on sequence id rather than name
+ an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
+ }
+ if (annotation.groupRef != null)
+ {
+ String groupIdr = groupRefs.get(annotation.groupRef);
+ if (groupIdr == null)
+ {
+ // make a locally unique String
+ groupRefs.put(annotation.groupRef,
+ groupIdr = ("" + System.currentTimeMillis()
+ + annotation.groupRef.getName()
+ + groupRefs.size()));
+ }
+ an.setGroupRef(groupIdr.toString());
+ }
+
+ // store all visualization attributes for annotation
+ an.setGraphHeight(annotation.graphHeight);
+ an.setCentreColLabels(annotation.centreColLabels);
+ an.setScaleColLabels(annotation.scaleColLabel);
+ an.setShowAllColLabels(annotation.showAllColLabels);
+ an.setBelowAlignment(annotation.belowAlignment);
+
+ if (annotation.graph > 0)
+ {
+ an.setGraph(true);
+ an.setGraphType(annotation.graph);
+ an.setGraphGroup(annotation.graphGroup);
+ if (annotation.getThreshold() != null)
+ {
+ ThresholdLine line = new ThresholdLine();
+ line.setLabel(annotation.getThreshold().label);
+ line.setValue(annotation.getThreshold().value);
+ line.setColour(annotation.getThreshold().colour.getRGB());
+ an.setThresholdLine(line);
+ }
+ }
+ else
+ {
+ an.setGraph(false);
+ }
+
+ an.setLabel(annotation.label);
+
+ if (annotation == av.getAlignmentQualityAnnot()
+ || annotation == av.getAlignmentConservationAnnotation()
+ || annotation == av.getAlignmentConsensusAnnotation()
+ || annotation.autoCalculated)
+ {
+ // new way of indicating autocalculated annotation -
+ an.setAutoCalculated(annotation.autoCalculated);
+ }
+ if (annotation.hasScore())
+ {
+ an.setScore(annotation.getScore());
+ }
+
+ if (annotation.getCalcId() != null)
+ {
+ calcIdSet.add(annotation.getCalcId());
+ an.setCalcId(annotation.getCalcId());
+ }
+ if (annotation.hasProperties())
+ {
+ for (String pr : annotation.getProperties())
+ {
+ jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
+ prop.setName(pr);
+ prop.setValue(annotation.getProperty(pr));
+ // an.addProperty(prop);
+ an.getProperty().add(prop);
+ }
+ }
+
+ AnnotationElement ae;
+ if (annotation.annotations != null)
+ {
+ an.setScoreOnly(false);
+ for (int a = 0; a < annotation.annotations.length; a++)
+ {
+ if ((annotation == null) || (annotation.annotations[a] == null))
+ {
+ continue;
+ }
+
+ ae = new AnnotationElement();
+ if (annotation.annotations[a].description != null)
+ {
+ ae.setDescription(annotation.annotations[a].description);
+ }
+ if (annotation.annotations[a].displayCharacter != null)
+ {
+ ae.setDisplayCharacter(
+ annotation.annotations[a].displayCharacter);
+ }
+
+ if (!Float.isNaN(annotation.annotations[a].value))
+ {
+ ae.setValue(annotation.annotations[a].value);
+ }
+
+ ae.setPosition(a);
+ if (annotation.annotations[a].secondaryStructure > ' ')
+ {
+ ae.setSecondaryStructure(
+ annotation.annotations[a].secondaryStructure + "");
+ }
+
+ if (annotation.annotations[a].colour != null
+ && annotation.annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(annotation.annotations[a].colour.getRGB());
+ }
+
+ // an.addAnnotationElement(ae);
+ an.getAnnotationElement().add(ae);
+ if (annotation.autoCalculated)
+ {
+ // only write one non-null entry into the annotation row -
+ // sufficient to get the visualization attributes necessary to
+ // display data
+ continue;
+ }
+ }
+ }
+ else
+ {
+ an.setScoreOnly(true);
+ }
+ if (!storeDS || (storeDS && !annotation.autoCalculated))
+ {
+ // skip autocalculated annotation - these are only provided for
+ // alignments
+ // vamsasSet.addAnnotation(an);
+ vamsasSet.getAnnotation().add(an);
+ }
+ }
+
+ }
+
+ private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
+ {
+ AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
+ if (settings != null)
+ {
+ CalcIdParam vCalcIdParam = new CalcIdParam();
+ vCalcIdParam.setCalcId(calcId);
+ // vCalcIdParam.addServiceURL(settings.getServiceURI());
+ vCalcIdParam.getServiceURL().add(settings.getServiceURI());
+ // generic URI allowing a third party to resolve another instance of the
+ // service used for this calculation
+ for (String url : settings.getServiceURLs())
+ {
+ // vCalcIdParam.addServiceURL(urls);
+ vCalcIdParam.getServiceURL().add(url);
+ }
+ vCalcIdParam.setVersion("1.0");
+ if (settings.getPreset() != null)
+ {
+ WsParamSetI setting = settings.getPreset();
+ vCalcIdParam.setName(setting.getName());
+ vCalcIdParam.setDescription(setting.getDescription());
+ }
+ else
+ {
+ vCalcIdParam.setName("");
+ vCalcIdParam.setDescription("Last used parameters");
+ }
+ // need to be able to recover 1) settings 2) user-defined presets or
+ // recreate settings from preset 3) predefined settings provided by
+ // service - or settings that can be transferred (or discarded)
+ vCalcIdParam.setParameters(
+ settings.getWsParamFile().replace("\n", "|\\n|"));
+ vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
+ // todo - decide if updateImmediately is needed for any projects.
+
+ return vCalcIdParam;
+ }
+ return null;
+ }
+
+ private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
+ AlignViewport av)
+ {
+ if (calcIdParam.getVersion().equals("1.0"))
+ {
+ final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
+ Jws2Instance service = Jws2Discoverer.getDiscoverer()
+ .getPreferredServiceFor(calcIds);
+ if (service != null)
+ {
+ WsParamSetI parmSet = null;
+ try
+ {
+ parmSet = service.getParamStore().parseServiceParameterFile(
+ calcIdParam.getName(), calcIdParam.getDescription(),
+ calcIds,
+ calcIdParam.getParameters().replace("|\\n|", "\n"));
+ } catch (IOException x)
+ {
+ warn("Couldn't parse parameter data for "
+ + calcIdParam.getCalcId(), x);
+ return false;
+ }
+ List<ArgumentI> argList = null;
+ if (calcIdParam.getName().length() > 0)
+ {
+ parmSet = service.getParamStore()
+ .getPreset(calcIdParam.getName());
+ if (parmSet != null)
+ {
+ // TODO : check we have a good match with settings in AACon -
+ // otherwise we'll need to create a new preset
+ }
+ }
+ else
+ {
+ argList = parmSet.getArguments();
+ parmSet = null;
+ }
+ AAConSettings settings = new AAConSettings(
+ calcIdParam.isAutoUpdate(), service, parmSet, argList);
+ av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
+ calcIdParam.isNeedsUpdate());
+ return true;
+ }
+ else
+ {
+ warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ return false;
+ }
+ }
+ throw new Error(MessageManager.formatMessage(
+ "error.unsupported_version_calcIdparam", new Object[]
+ { calcIdParam.toString() }));
+ }
+
+ /**
+ * External mapping between jalview objects and objects yielding a valid and
+ * unique object ID string. This is null for normal Jalview project IO, but
+ * non-null when a jalview project is being read or written as part of a
+ * vamsas session.
+ */
+ IdentityHashMap jv2vobj = null;
+
+ /**
+ * Construct a unique ID for jvobj using either existing bindings or if none
+ * exist, the result of the hashcode call for the object.
+ *
+ * @param jvobj
+ * jalview data object
+ * @return unique ID for referring to jvobj
+ */
+ private String makeHashCode(Object jvobj, String altCode)
+ {
+ if (jv2vobj != null)
+ {
+ Object id = jv2vobj.get(jvobj);
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // check string ID mappings
+ if (jvids2vobj != null && jvobj instanceof String)
+ {
+ id = jvids2vobj.get(jvobj);
+ }
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // give up and warn that something has gone wrong
+ warn("Cannot find ID for object in external mapping : " + jvobj);
+ }
+ return altCode;
+ }
+
+ /**
+ * return local jalview object mapped to ID, if it exists
+ *
+ * @param idcode
+ * (may be null)
+ * @return null or object bound to idcode
+ */
+ private Object retrieveExistingObj(String idcode)
+ {
+ if (idcode != null && vobj2jv != null)
+ {
+ return vobj2jv.get(idcode);
+ }
+ return null;
+ }
+
+ /**
+ * binding from ID strings from external mapping table to jalview data model
+ * objects.
+ */
+ private Hashtable vobj2jv;
+
+ private Sequence createVamsasSequence(String id, SequenceI jds)
+ {
+ return createVamsasSequence(true, id, jds, null);
+ }
+
+ private Sequence createVamsasSequence(boolean recurse, String id,
+ SequenceI jds, SequenceI parentseq)
+ {
+ Sequence vamsasSeq = new Sequence();
+ vamsasSeq.setId(id);
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
+ jalview.datamodel.DBRefEntry[] dbrefs = null;
+ if (jds.getDatasetSequence() != null)
+ {
+ vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
+ }
+ else
+ {
+ // seqId==dsseqid so we can tell which sequences really are
+ // dataset sequences only
+ vamsasSeq.setDsseqid(id);
+ dbrefs = jds.getDBRefs();
+ if (parentseq == null)
+ {
+ parentseq = jds;
+ }
+ }
+ if (dbrefs != null)
+ {
+ for (int d = 0; d < dbrefs.length; d++)
+ {
+ DBRef dbref = new DBRef();
+ dbref.setSource(dbrefs[d].getSource());
+ dbref.setVersion(dbrefs[d].getVersion());
+ dbref.setAccessionId(dbrefs[d].getAccessionId());
+ if (dbrefs[d].hasMap())
+ {
+ Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ jds, recurse);
+ dbref.setMapping(mp);
+ }
+ // vamsasSeq.addDBRef(dbref);
+ vamsasSeq.getDBRef().add(dbref);
+ }
+ }
+ return vamsasSeq;
+ }
+
+ private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
+ SequenceI parentseq, SequenceI jds, boolean recurse)
+ {
+ Mapping mp = null;
+ if (jmp.getMap() != null)
+ {
+ mp = new Mapping();
+
+ jalview.util.MapList mlst = jmp.getMap();
+ List<int[]> r = mlst.getFromRanges();
+ for (int[] range : r)
+ {
+ MapListFrom mfrom = new MapListFrom();
+ mfrom.setStart(range[0]);
+ mfrom.setEnd(range[1]);
+ // mp.addMapListFrom(mfrom);
+ mp.getMapListFrom().add(mfrom);
+ }
+ r = mlst.getToRanges();
+ for (int[] range : r)
+ {
+ MapListTo mto = new MapListTo();
+ mto.setStart(range[0]);
+ mto.setEnd(range[1]);
+ // mp.addMapListTo(mto);
+ mp.getMapListTo().add(mto);
+ }
+ mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
+ mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
+ if (jmp.getTo() != null)
+ {
+ // MappingChoice mpc = new MappingChoice();
+
+ // check/create ID for the sequence referenced by getTo()
+
+ String jmpid = "";
+ SequenceI ps = null;
+ if (parentseq != jmp.getTo()
+ && parentseq.getDatasetSequence() != jmp.getTo())
+ {
+ // chaining dbref rather than a handshaking one
+ jmpid = seqHash(ps = jmp.getTo());
+ }
+ else
+ {
+ jmpid = seqHash(ps = parentseq);
+ }
+ // mpc.setDseqFor(jmpid);
+ mp.setDseqFor(jmpid);
+ if (!seqRefIds.containsKey(jmpid))
+ {
+ jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ seqRefIds.put(jmpid, ps);
+ }
+ else
+ {
+ jalview.bin.Cache.log.debug("reusing DseqFor ID");
+ }
+
+ // mp.setMappingChoice(mpc);
+ }
+ }
+ return mp;
+ }
+
+ String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
+ List<UserColourScheme> userColours, JalviewModel jm)
+ {
+ String id = null;
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
+ boolean newucs = false;
+ if (!userColours.contains(ucs))
+ {
+ userColours.add(ucs);
+ newucs = true;
+ }
+ id = "ucs" + userColours.indexOf(ucs);
+ if (newucs)
+ {
+ // actually create the scheme's entry in the XML model
+ java.awt.Color[] colours = ucs.getColours();
+ UserColours uc = new UserColours();
+ // UserColourScheme jbucs = new UserColourScheme();
+ JalviewUserColours jbucs = new JalviewUserColours();
+
+ for (int i = 0; i < colours.length; i++)
+ {
+ Colour col = new Colour();
+ col.setName(ResidueProperties.aa[i]);
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ // jbucs.addColour(col);
+ jbucs.getColour().add(col);
+ }
+ if (ucs.getLowerCaseColours() != null)
+ {
+ colours = ucs.getLowerCaseColours();
+ for (int i = 0; i < colours.length; i++)
+ {
+ Colour col = new Colour();
+ col.setName(ResidueProperties.aa[i].toLowerCase());
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ // jbucs.addColour(col);
+ jbucs.getColour().add(col);
+ }
+ }
+
+ uc.setId(id);
+ uc.setUserColourScheme(jbucs);
+ // jm.addUserColours(uc);
+ jm.getUserColours().add(uc);
+ }
+
+ return id;
+ }
+
+ jalview.schemes.UserColourScheme getUserColourScheme(
+ JalviewModel jm, String id)
+ {
+ List<UserColours> uc = jm.getUserColours();
+ UserColours colours = null;
+/*
+ for (int i = 0; i < uc.length; i++)
+ {
+ if (uc[i].getId().equals(id))
+ {
+ colours = uc[i];
+ break;
+ }
+ }
+*/
+ for (UserColours c : uc)
+ {
+ if (c.getId().equals(id))
+ {
+ colours = c;
+ break;
+ }
+ }
+
+ java.awt.Color[] newColours = new java.awt.Color[24];
+
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ // colours.getUserColourScheme().getColour(i).getRGB(), 16));
+ colours.getUserColourScheme().getColour().get(i).getRGB(),
+ 16));
+ }
+
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ newColours);
+
+ if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
+ {
+ newColours = new java.awt.Color[23];
+ for (int i = 0; i < 23; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ colours.getUserColourScheme().getColour().get(i + 24)
+ .getRGB(),
+ 16));
+ }
+ ucs.setLowerCaseColours(newColours);
+ }
+
+ return ucs;
+ }
+
+ /**
+ * contains last error message (if any) encountered by XML loader.
+ */
+ String errorMessage = null;
+
+ /**
+ * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+ * exceptions are raised during project XML parsing
+ */
+ public boolean attemptversion1parse = false;
+
+ /**
+ * Load a jalview project archive from a jar file
+ *
+ * @param file
+ * - HTTP URL or filename
+ */
+ public AlignFrame loadJalviewAlign(final String file)
+ {
+
+ jalview.gui.AlignFrame af = null;
+
+ try
+ {
+ // create list to store references for any new Jmol viewers created
+ newStructureViewers = new Vector<>();
+ // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+ // Workaround is to make sure caller implements the JarInputStreamProvider
+ // interface
+ // so we can re-open the jar input stream for each entry.
+
+ jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
+ af = loadJalviewAlign(jprovider);
+ if (af != null)
+ {
+ af.setMenusForViewport();
+ }
+ } catch (MalformedURLException e)
+ {
+ errorMessage = "Invalid URL format for '" + file + "'";
+ reportErrors();
+ } finally
+ {
+ try
+ {
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ setLoadingFinishedForNewStructureViewers();
+ };
+ });
+ } catch (Exception x)
+ {
+ System.err.println("Error loading alignment: " + x.getMessage());
+ }
+ }
+ return af;
+ }
+
+ private jarInputStreamProvider createjarInputStreamProvider(
+ final String file) throws MalformedURLException
+ {
+ URL url = null;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded.clear();
+ frefedSequence = null;
+
+ if (file.startsWith("http://"))
+ {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider()
+ {
+
+ @Override
+ public JarInputStream getJarInputStream() throws IOException
+ {
+ if (_url != null)
+ {
+ return new JarInputStream(_url.openStream());
+ }
+ else
+ {
+ return new JarInputStream(new FileInputStream(file));
+ }
+ }
+
+ @Override
+ public String getFilename()
+ {
+ return file;
+ }
+ };
+ }
+
+ /**
+ * Recover jalview session from a jalview project archive. Caller may
+ * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
+ * themselves. Any null fields will be initialised with default values,
+ * non-null fields are left alone.
+ *
+ * @param jprovider
+ * @return
+ */
+ public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
+ {
+ errorMessage = null;
+ if (uniqueSetSuffix == null)
+ {
+ uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
+ }
+ if (seqRefIds == null)
+ {
+ initSeqRefs();
+ }
+ AlignFrame af = null, _af = null;
+ IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
+ Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
+ final String file = jprovider.getFilename();
+ try
+ {
+ JarInputStream jin = null;
+ JarEntry jarentry = null;
+ int entryCount = 1;
+
+ do
+ {
+ jin = jprovider.getJarInputStream();
+ for (int i = 0; i < entryCount; i++)
+ {
+ jarentry = jin.getNextJarEntry();
+ }
+
+ if (jarentry != null && jarentry.getName().endsWith(".xml"))
+ {
+ InputStreamReader in = new InputStreamReader(jin, UTF_8);
+ // JalviewModel object = new JalviewModel();
+
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(jin);
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ JAXBElement<JalviewModel> jbe = um
+ .unmarshal(streamReader, JalviewModel.class);
+ JalviewModel object = jbe.getValue();
+
+ /*
+ Unmarshaller unmar = new Unmarshaller(object);
+ unmar.setValidation(false);
+ object = (JalviewModel) unmar.unmarshal(in);
+ */
+ if (true) // !skipViewport(object))
+ {
+ _af = loadFromObject(object, file, true, jprovider);
+ if (_af != null && object.getViewport().size() > 0)
+ // getJalviewModelSequence().getViewportCount() > 0)
+ {
+ if (af == null)
+ {
+ // store a reference to the first view
+ af = _af;
+ }
+ if (_af.getViewport().isGatherViewsHere())
+ {
+ // if this is a gathered view, keep its reference since
+ // after gathering views, only this frame will remain
+ af = _af;
+ gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
+ _af);
+ }
+ // Save dataset to register mappings once all resolved
+ importedDatasets.put(
+ af.getViewport().getAlignment().getDataset(),
+ af.getViewport().getAlignment().getDataset());
+ }
+ }
+ entryCount++;
+ }
+ else if (jarentry != null)
+ {
+ // Some other file here.
+ entryCount++;
+ }
+ } while (jarentry != null);
+ resolveFrefedSequences();
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ errorMessage = "Couldn't locate Jalview XML file : " + file;
+ System.err.println(
+ "Exception whilst loading jalview XML file : " + ex + "\n");
+ } catch (Exception ex)
+ {
+ System.err.println("Parsing as Jalview Version 2 file failed.");
+ ex.printStackTrace(System.err);
+ if (attemptversion1parse)
+ {
+ // Is Version 1 Jar file?
+ try
+ {
+ af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
+ } catch (Exception ex2)
+ {
+ System.err.println("Exception whilst loading as jalviewXMLV1:");
+ ex2.printStackTrace();
+ af = null;
+ }
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+ if (af != null)
+ {
+ System.out.println("Successfully loaded archive file");
+ return af;
+ }
+ ex.printStackTrace();
+
+ System.err.println(
+ "Exception whilst loading jalview XML file : " + ex + "\n");
+ } catch (OutOfMemoryError e)
+ {
+ // Don't use the OOM Window here
+ errorMessage = "Out of memory loading jalview XML file";
+ System.err.println("Out of memory whilst loading jalview XML file");
+ e.printStackTrace();
+ }
+
+ /*
+ * Regather multiple views (with the same sequence set id) to the frame (if
+ * any) that is flagged as the one to gather to, i.e. convert them to tabbed
+ * views instead of separate frames. Note this doesn't restore a state where
+ * some expanded views in turn have tabbed views - the last "first tab" read
+ * in will play the role of gatherer for all.
+ */
+ for (AlignFrame fr : gatherToThisFrame.values())
+ {
+ Desktop.instance.gatherViews(fr);
+ }
+
+ restoreSplitFrames();
+ for (AlignmentI ds : importedDatasets.keySet())
+ {
+ if (ds.getCodonFrames() != null)
+ {
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerMappings(ds.getCodonFrames());
+ }
+ }
+ if (errorMessage != null)
+ {
+ reportErrors();
+ }
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+
+ return af;
+ }
+
+ /**
+ * Try to reconstruct and display SplitFrame windows, where each contains
+ * complementary dna and protein alignments. Done by pairing up AlignFrame
+ * objects (created earlier) which have complementary viewport ids associated.
+ */
+ protected void restoreSplitFrames()
+ {
+ List<SplitFrame> gatherTo = new ArrayList<>();
+ List<AlignFrame> addedToSplitFrames = new ArrayList<>();
+ Map<String, AlignFrame> dna = new HashMap<>();
+
+ /*
+ * Identify the DNA alignments
+ */
+ for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (af.getViewport().getAlignment().isNucleotide())
+ {
+ dna.put(candidate.getKey().getId(), af);
+ }
+ }
+
+ /*
+ * Try to match up the protein complements
+ */
+ for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (!af.getViewport().getAlignment().isNucleotide())
+ {
+ String complementId = candidate.getKey().getComplementId();
+ // only non-null complements should be in the Map
+ if (complementId != null && dna.containsKey(complementId))
+ {
+ final AlignFrame dnaFrame = dna.get(complementId);
+ SplitFrame sf = createSplitFrame(dnaFrame, af);
+ addedToSplitFrames.add(dnaFrame);
+ addedToSplitFrames.add(af);
+ dnaFrame.setMenusForViewport();
+ af.setMenusForViewport();
+ if (af.getViewport().isGatherViewsHere())
+ {
+ gatherTo.add(sf);
+ }
+ }
+ }
+ }
+
+ /*
+ * Open any that we failed to pair up (which shouldn't happen!) as
+ * standalone AlignFrame's.
+ */
+ for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (!addedToSplitFrames.contains(af))
+ {
+ Viewport view = candidate.getKey();
+ Desktop.addInternalFrame(af, view.getTitle(),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
+ af.setMenusForViewport();
+ System.err.println("Failed to restore view " + view.getTitle()
+ + " to split frame");
+ }
+ }
+
+ /*
+ * Gather back into tabbed views as flagged.
+ */
+ for (SplitFrame sf : gatherTo)
+ {
+ Desktop.instance.gatherViews(sf);
+ }
+
+ splitFrameCandidates.clear();
+ }
+
+ /**
+ * Construct and display one SplitFrame holding DNA and protein alignments.
+ *
+ * @param dnaFrame
+ * @param proteinFrame
+ * @return
+ */
+ protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
+ AlignFrame proteinFrame)
+ {
+ SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
+ String title = MessageManager.getString("label.linked_view_title");
+ int width = (int) dnaFrame.getBounds().getWidth();
+ int height = (int) (dnaFrame.getBounds().getHeight()
+ + proteinFrame.getBounds().getHeight() + 50);
+
+ /*
+ * SplitFrame location is saved to both enclosed frames
+ */
+ splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
+ Desktop.addInternalFrame(splitFrame, title, width, height);
+
+ /*
+ * And compute cDNA consensus (couldn't do earlier with consensus as
+ * mappings were not yet present)
+ */
+ proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
+
+ return splitFrame;
+ }
+
+ /**
+ * check errorMessage for a valid error message and raise an error box in the
+ * GUI or write the current errorMessage to stderr and then clear the error
+ * state.
+ */
+ protected void reportErrors()
+ {
+ reportErrors(false);
+ }
+
+ protected void reportErrors(final boolean saving)
+ {
+ if (errorMessage != null)
+ {
+ final String finalErrorMessage = errorMessage;
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage,
+ "Error " + (saving ? "saving" : "loading")
+ + " Jalview file",
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ else
+ {
+ System.err.println("Problem loading Jalview file: " + errorMessage);
+ }
+ }
+ errorMessage = null;
+ }
+
+ Map<String, String> alreadyLoadedPDB = new HashMap<>();
+
+ /**
+ * when set, local views will be updated from view stored in JalviewXML
+ * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
+ * sync if this is set to true.
+ */
+ private final boolean updateLocalViews = false;
+
+ /**
+ * Returns the path to a temporary file holding the PDB file for the given PDB
+ * id. The first time of asking, searches for a file of that name in the
+ * Jalview project jar, and copies it to a new temporary file. Any repeat
+ * requests just return the path to the file previously created.
+ *
+ * @param jprovider
+ * @param pdbId
+ * @return
+ */
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
+ String origFile)
+ {
+ if (alreadyLoadedPDB.containsKey(pdbId))
+ {
+ return alreadyLoadedPDB.get(pdbId).toString();
+ }
+
+ String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
+ origFile);
+ if (tempFile != null)
+ {
+ alreadyLoadedPDB.put(pdbId, tempFile);
+ }
+ return tempFile;
+ }
+
+ /**
+ * Copies the jar entry of given name to a new temporary file and returns the
+ * path to the file, or null if the entry is not found.
+ *
+ * @param jprovider
+ * @param jarEntryName
+ * @param prefix
+ * a prefix for the temporary file name, must be at least three
+ * characters long
+ * @param origFile
+ * null or original file - so new file can be given the same suffix
+ * as the old one
+ * @return
+ */
+ protected String copyJarEntry(jarInputStreamProvider jprovider,
+ String jarEntryName, String prefix, String origFile)
+ {
+ BufferedReader in = null;
+ PrintWriter out = null;
+ String suffix = ".tmp";
+ if (origFile == null)
+ {
+ origFile = jarEntryName;
+ }
+ int sfpos = origFile.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (origFile.length() - 3))
+ {
+ suffix = "." + origFile.substring(sfpos + 1);
+ }
+ try
+ {
+ JarInputStream jin = jprovider.getJarInputStream();
+ /*
+ * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
+ * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
+ * FileInputStream(jprovider)); }
+ */
+
+ JarEntry entry = null;
+ do
+ {
+ entry = jin.getNextJarEntry();
+ } while (entry != null && !entry.getName().equals(jarEntryName));
+ if (entry != null)
+ {
+ in = new BufferedReader(new InputStreamReader(jin, UTF_8));
+ File outFile = File.createTempFile(prefix, suffix);
+ outFile.deleteOnExit();
+ out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+
+ while ((data = in.readLine()) != null)
+ {
+ out.println(data);
+ }
+ out.flush();
+ String t = outFile.getAbsolutePath();
+ return t;
+ }
+ else
+ {
+ warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ if (out != null)
+ {
+ out.close();
+ }
+ }
+
+ return null;
+ }
+
+ private class JvAnnotRow
+ {
+ public JvAnnotRow(int i, AlignmentAnnotation jaa)
+ {
+ order = i;
+ template = jaa;
+ }
+
+ /**
+ * persisted version of annotation row from which to take vis properties
+ */
+ public jalview.datamodel.AlignmentAnnotation template;
+
+ /**
+ * original position of the annotation row in the alignment
+ */
+ public int order;
+ }
+
+ /**
+ * Load alignment frame from jalview XML DOM object
+ *
+ * @param jalviewModel
+ * DOM
+ * @param file
+ * filename source string
+ * @param loadTreesAndStructures
+ * when false only create Viewport
+ * @param jprovider
+ * data source provider
+ * @return alignment frame created from view stored in DOM
+ */
+ AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
+ boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
+ {
+ SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+ List<Sequence> vamsasSeqs = vamsasSet.getSequence();
+
+ // JalviewModelSequence jms = object.getJalviewModelSequence();
+
+ // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ // : null;
+ Viewport view = (jalviewModel.getViewport().size() > 0)
+ ? jalviewModel.getViewport().get(0)
+ : null;
+
+ // ////////////////////////////////
+ // LOAD SEQUENCES
+
+ List<SequenceI> hiddenSeqs = null;
+
+ List<SequenceI> tmpseqs = new ArrayList<>();
+
+ boolean multipleView = false;
+ SequenceI referenceseqForView = null;
+ // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
+ List<JSeq> jseqs = jalviewModel.getJSeq();
+ int vi = 0; // counter in vamsasSeq array
+ for (int i = 0; i < jseqs.size(); i++)
+ {
+ JSeq jseq = jseqs.get(i);
+ String seqId = jseq.getId();
+
+ SequenceI tmpSeq = seqRefIds.get(seqId);
+ if (tmpSeq != null)
+ {
+ if (!incompleteSeqs.containsKey(seqId))
+ {
+ // may not need this check, but keep it for at least 2.9,1 release
+ if (tmpSeq.getStart() != jseq.getStart()
+ || tmpSeq.getEnd() != jseq.getEnd())
+ {
+ System.err.println(
+ "Warning JAL-2154 regression: updating start/end for sequence "
+ + tmpSeq.toString() + " to " + jseq);
+ }
+ }
+ else
+ {
+ incompleteSeqs.remove(seqId);
+ }
+ if (vamsasSeqs.size() > vi
+ && vamsasSeqs.get(vi).getId().equals(seqId))
+ {
+ // most likely we are reading a dataset XML document so
+ // update from vamsasSeq section of XML for this sequence
+ tmpSeq.setName(vamsasSeqs.get(vi).getName());
+ tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
+ tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
+ vi++;
+ }
+ else
+ {
+ // reading multiple views, so vamsasSeq set is a subset of JSeq
+ multipleView = true;
+ }
+ tmpSeq.setStart(jseq.getStart());
+ tmpSeq.setEnd(jseq.getEnd());
+ tmpseqs.add(tmpSeq);
+ }
+ else
+ {
+ Sequence vamsasSeq = vamsasSeqs.get(vi);
+ tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
+ vamsasSeq.getSequence());
+ tmpSeq.setDescription(vamsasSeq.getDescription());
+ tmpSeq.setStart(jseq.getStart());
+ tmpSeq.setEnd(jseq.getEnd());
+ tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
+ seqRefIds.put(vamsasSeq.getId(), tmpSeq);
+ tmpseqs.add(tmpSeq);
+ vi++;
+ }
+
+ if (safeBoolean(jseq.isViewreference()))
+ {
+ referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
+ }
+
+ if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
+ {
+ if (hiddenSeqs == null)
+ {
+ hiddenSeqs = new ArrayList<>();
+ }
+
+ hiddenSeqs.add(tmpSeq);
+ }
+ }
+
+ // /
+ // Create the alignment object from the sequence set
+ // ///////////////////////////////
+ SequenceI[] orderedSeqs = tmpseqs
+ .toArray(new SequenceI[tmpseqs.size()]);
+
+ AlignmentI al = null;
+ // so we must create or recover the dataset alignment before going further
+ // ///////////////////////////////
+ if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
+ {
+ // older jalview projects do not have a dataset - so creat alignment and
+ // dataset
+ al = new Alignment(orderedSeqs);
+ al.setDataset(null);
+ }
+ else
+ {
+ boolean isdsal = jalviewModel.getViewport().isEmpty();
+ if (isdsal)
+ {
+ // we are importing a dataset record, so
+ // recover reference to an alignment already materialsed as dataset
+ al = getDatasetFor(vamsasSet.getDatasetId());
+ }
+ if (al == null)
+ {
+ // materialse the alignment
+ al = new Alignment(orderedSeqs);
+ }
+ if (isdsal)
+ {
+ addDatasetRef(vamsasSet.getDatasetId(), al);
+ }
+
+ // finally, verify all data in vamsasSet is actually present in al
+ // passing on flag indicating if it is actually a stored dataset
+ recoverDatasetFor(vamsasSet, al, isdsal);
+ }
+
+ if (referenceseqForView != null)
+ {
+ al.setSeqrep(referenceseqForView);
+ }
+ // / Add the alignment properties
+ for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
+ {
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
+ .get(i);
+ al.setProperty(ssp.getKey(), ssp.getValue());
+ }
+
+ // ///////////////////////////////
+
+ Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
+ if (!multipleView)
+ {
+ // load sequence features, database references and any associated PDB
+ // structures for the alignment
+ //
+ // prior to 2.10, this part would only be executed the first time a
+ // sequence was encountered, but not afterwards.
+ // now, for 2.10 projects, this is also done if the xml doc includes
+ // dataset sequences not actually present in any particular view.
+ //
+ for (int i = 0; i < vamsasSeqs.size(); i++)
+ {
+ JSeq jseq = jseqs.get(i);
+ if (jseq.getFeatures().size() > 0)
+ {
+ List<Feature> features = jseq.getFeatures();
+ for (int f = 0; f < features.size(); f++)
+ {
+ Feature feat = features.get(f);
+ SequenceFeature sf = new SequenceFeature(feat.getType(),
+ feat.getDescription(), feat.getBegin(), feat.getEnd(),
+ safeFloat(feat.getScore()), feat.getFeatureGroup());
+ sf.setStatus(feat.getStatus());
+
+ /*
+ * load any feature attributes - include map-valued attributes
+ */
+ Map<String, Map<String, String>> mapAttributes = new HashMap<>();
+ for (int od = 0; od < feat.getOtherData().size(); od++)
+ {
+ OtherData keyValue = feat.getOtherData().get(od);
+ String attributeName = keyValue.getKey();
+ String attributeValue = keyValue.getValue();
+ if (attributeName.startsWith("LINK"))
+ {
+ sf.addLink(attributeValue);
+ }
+ else
+ {
+ String subAttribute = keyValue.getKey2();
+ if (subAttribute == null)
+ {
+ // simple string-valued attribute
+ sf.setValue(attributeName, attributeValue);
+ }
+ else
+ {
+ // attribute 'key' has sub-attribute 'key2'
+ if (!mapAttributes.containsKey(attributeName))
+ {
+ mapAttributes.put(attributeName, new HashMap<>());
+ }
+ mapAttributes.get(attributeName).put(subAttribute,
+ attributeValue);
+ }
+ }
+ }
+ for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
+ .entrySet())
+ {
+ sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
+ }
+
+ // adds feature to datasequence's feature set (since Jalview 2.10)
+ al.getSequenceAt(i).addSequenceFeature(sf);
+ }
+ }
+ if (vamsasSeqs.get(i).getDBRef().size() > 0)
+ {
+ // adds dbrefs to datasequence's set (since Jalview 2.10)
+ addDBRefs(
+ al.getSequenceAt(i).getDatasetSequence() == null
+ ? al.getSequenceAt(i)
+ : al.getSequenceAt(i).getDatasetSequence(),
+ vamsasSeqs.get(i));
+ }
+ if (jseq.getPdbids().size() > 0)
+ {
+ List<Pdbids> ids = jseq.getPdbids();
+ for (int p = 0; p < ids.size(); p++)
+ {
+ Pdbids pdbid = ids.get(p);
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
+ entry.setId(pdbid.getId());
+ if (pdbid.getType() != null)
+ {
+ if (PDBEntry.Type.getType(pdbid.getType()) != null)
+ {
+ entry.setType(PDBEntry.Type.getType(pdbid.getType()));
+ }
+ else
+ {
+ entry.setType(PDBEntry.Type.FILE);
+ }
+ }
+ // jprovider is null when executing 'New View'
+ if (pdbid.getFile() != null && jprovider != null)
+ {
+ if (!pdbloaded.containsKey(pdbid.getFile()))
+ {
+ entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
+ pdbid.getFile()));
+ }
+ else
+ {
+ entry.setFile(pdbloaded.get(pdbid.getId()).toString());
+ }
+ }
+ /*
+ if (pdbid.getPdbentryItem() != null)
+ {
+ for (PdbentryItem item : pdbid.getPdbentryItem())
+ {
+ for (Property pr : item.getProperty())
+ {
+ entry.setProperty(pr.getName(), pr.getValue());
+ }
+ }
+ }
+ */
+ for (Property prop : pdbid.getProperty())
+ {
+ entry.setProperty(prop.getName(), prop.getValue());
+ }
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerPDBEntry(entry);
+ // adds PDBEntry to datasequence's set (since Jalview 2.10)
+ if (al.getSequenceAt(i).getDatasetSequence() != null)
+ {
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
+ else
+ {
+ al.getSequenceAt(i).addPDBId(entry);
+ }
+ }
+ }
+ }
+ } // end !multipleview
+
+ // ///////////////////////////////
+ // LOAD SEQUENCE MAPPINGS
+
+ if (vamsasSet.getAlcodonFrame().size() > 0)
+ {
+ // TODO Potentially this should only be done once for all views of an
+ // alignment
+ List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
+ for (int i = 0; i < alc.size(); i++)
+ {
+ AlignedCodonFrame cf = new AlignedCodonFrame();
+ if (alc.get(i).getAlcodMap().size() > 0)
+ {
+ List<AlcodMap> maps = alc.get(i).getAlcodMap();
+ for (int m = 0; m < maps.size(); m++)
+ {
+ AlcodMap map = maps.get(m);
+ SequenceI dnaseq = seqRefIds.get(map.getDnasq());
+ // Load Mapping
+ jalview.datamodel.Mapping mapping = null;
+ // attach to dna sequence reference.
+ if (map.getMapping() != null)
+ {
+ mapping = addMapping(map.getMapping());
+ if (dnaseq != null && mapping.getTo() != null)
+ {
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ else
+ {
+ // defer to later
+ frefedSequence.add(
+ newAlcodMapRef(map.getDnasq(), cf, mapping));
+ }
+ }
+ }
+ al.addCodonFrame(cf);
+ }
+ }
+ }
+
+ // ////////////////////////////////
+ // LOAD ANNOTATIONS
+ List<JvAnnotRow> autoAlan = new ArrayList<>();
+
+ /*
+ * store any annotations which forward reference a group's ID
+ */
+ Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
+
+ if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
+ {
+ List<Annotation> an = vamsasSet.getAnnotation();
+
+ for (int i = 0; i < an.size(); i++)
+ {
+ Annotation annotation = an.get(i);
+
+ /**
+ * test if annotation is automatically calculated for this view only
+ */
+ boolean autoForView = false;
+ if (annotation.getLabel().equals("Quality")
+ || annotation.getLabel().equals("Conservation")
+ || annotation.getLabel().equals("Consensus"))
+ {
+ // Kludge for pre 2.5 projects which lacked the autocalculated flag
+ autoForView = true;
+ // JAXB has no has() test; schema defaults value to false
+ // if (!annotation.hasAutoCalculated())
+ // {
+ // annotation.setAutoCalculated(true);
+ // }
+ }
+ if (autoForView || annotation.isAutoCalculated())
+ {
+ // remove ID - we don't recover annotation from other views for
+ // view-specific annotation
+ annotation.setId(null);
+ }
+
+ // set visibility for other annotation in this view
+ String annotationId = annotation.getId();
+ if (annotationId != null && annotationIds.containsKey(annotationId))
+ {
+ AlignmentAnnotation jda = annotationIds.get(annotationId);
+ // in principle Visible should always be true for annotation displayed
+ // in multiple views
+ if (annotation.isVisible() != null)
+ {
+ jda.visible = annotation.isVisible();
+ }
+
+ al.addAnnotation(jda);
+
+ continue;
+ }
+ // Construct new annotation from model.
+ List<AnnotationElement> ae = annotation.getAnnotationElement();
+ jalview.datamodel.Annotation[] anot = null;
+ java.awt.Color firstColour = null;
+ int anpos;
+ if (!annotation.isScoreOnly())
+ {
+ anot = new jalview.datamodel.Annotation[al.getWidth()];
+ for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
+ {
+ AnnotationElement annElement = ae.get(aa);
+ anpos = annElement.getPosition();
+
+ if (anpos >= anot.length)
+ {
+ continue;
+ }
+
+ float value = safeFloat(annElement.getValue());
+ anot[anpos] = new jalview.datamodel.Annotation(
+ annElement.getDisplayCharacter(),
+ annElement.getDescription(),
+ (annElement.getSecondaryStructure() == null
+ || annElement.getSecondaryStructure()
+ .length() == 0)
+ ? ' '
+ : annElement
+ .getSecondaryStructure()
+ .charAt(0),
+ value);
+ anot[anpos].colour = new Color(safeInt(annElement.getColour()));
+ if (firstColour == null)
+ {
+ firstColour = anot[anpos].colour;
+ }
+ }
+ }
+ jalview.datamodel.AlignmentAnnotation jaa = null;
+
+ if (annotation.isGraph())
+ {
+ float llim = 0, hlim = 0;
+ // if (autoForView || an[i].isAutoCalculated()) {
+ // hlim=11f;
+ // }
+ jaa = new jalview.datamodel.AlignmentAnnotation(
+ annotation.getLabel(), annotation.getDescription(), anot,
+ llim, hlim, safeInt(annotation.getGraphType()));
+
+ jaa.graphGroup = safeInt(annotation.getGraphGroup());
+ jaa._linecolour = firstColour;
+ if (annotation.getThresholdLine() != null)
+ {
+ jaa.setThreshold(new jalview.datamodel.GraphLine(
+ safeFloat(annotation.getThresholdLine().getValue()),
+ annotation.getThresholdLine().getLabel(),
+ new java.awt.Color(safeInt(
+ annotation.getThresholdLine().getColour()))));
+ }
+ if (autoForView || annotation.isAutoCalculated())
+ {
+ // Hardwire the symbol display line to ensure that labels for
+ // histograms are displayed
+ jaa.hasText = true;
+ }
+ }
+ else
+ {
+ jaa = new jalview.datamodel.AlignmentAnnotation(
+ annotation.getLabel(), annotation.getDescription(), anot);
+ jaa._linecolour = firstColour;
+ }
+ // register new annotation
+ if (annotation.getId() != null)
+ {
+ annotationIds.put(annotation.getId(), jaa);
+ jaa.annotationId = annotation.getId();
+ }
+ // recover sequence association
+ String sequenceRef = annotation.getSequenceRef();
+ if (sequenceRef != null)
+ {
+ // from 2.9 sequenceRef is to sequence id (JAL-1781)
+ SequenceI sequence = seqRefIds.get(sequenceRef);
+ if (sequence == null)
+ {
+ // in pre-2.9 projects sequence ref is to sequence name
+ sequence = al.findName(sequenceRef);
+ }
+ if (sequence != null)
+ {
+ jaa.createSequenceMapping(sequence, 1, true);
+ sequence.addAlignmentAnnotation(jaa);
+ }
+ }
+ // and make a note of any group association
+ if (annotation.getGroupRef() != null
+ && annotation.getGroupRef().length() > 0)
+ {
+ List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
+ .get(annotation.getGroupRef());
+ if (aal == null)
+ {
+ aal = new ArrayList<>();
+ groupAnnotRefs.put(annotation.getGroupRef(), aal);
+ }
+ aal.add(jaa);
+ }
+
+ if (annotation.getScore() != null)
+ {
+ jaa.setScore(annotation.getScore().doubleValue());
+ }
+ if (annotation.isVisible() != null)
+ {
+ jaa.visible = annotation.isVisible().booleanValue();
+ }
+
+ if (annotation.isCentreColLabels() != null)
+ {
+ jaa.centreColLabels = annotation.isCentreColLabels()
+ .booleanValue();
+ }
+
+ if (annotation.isScaleColLabels() != null)
+ {
+ jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
+ }
+ if (annotation.isAutoCalculated())
+ {
+ // newer files have an 'autoCalculated' flag and store calculation
+ // state in viewport properties
+ jaa.autoCalculated = true; // means annotation will be marked for
+ // update at end of load.
+ }
+ if (annotation.getGraphHeight() != null)
+ {
+ jaa.graphHeight = annotation.getGraphHeight().intValue();
+ }
+ jaa.belowAlignment = annotation.isBelowAlignment();
+ jaa.setCalcId(annotation.getCalcId());
+ if (annotation.getProperty().size() > 0)
+ {
+ for (Annotation.Property prop : annotation
+ .getProperty())
+ {
+ jaa.setProperty(prop.getName(), prop.getValue());
+ }
+ }
+ if (jaa.autoCalculated)
+ {
+ autoAlan.add(new JvAnnotRow(i, jaa));
+ }
+ else
+ // if (!autoForView)
+ {
+ // add autocalculated group annotation and any user created annotation
+ // for the view
+ al.addAnnotation(jaa);
+ }
+ }
+ }
+ // ///////////////////////
+ // LOAD GROUPS
+ // Create alignment markup and styles for this view
+ if (jalviewModel.getJGroup().size() > 0)
+ {
+ List<JGroup> groups = jalviewModel.getJGroup();
+ boolean addAnnotSchemeGroup = false;
+ for (int i = 0; i < groups.size(); i++)
+ {
+ JGroup jGroup = groups.get(i);
+ ColourSchemeI cs = null;
+ if (jGroup.getColour() != null)
+ {
+ if (jGroup.getColour().startsWith("ucs"))
+ {
+ cs = getUserColourScheme(jalviewModel, jGroup.getColour());
+ }
+ else if (jGroup.getColour().equals("AnnotationColourGradient")
+ && jGroup.getAnnotationColours() != null)
+ {
+ addAnnotSchemeGroup = true;
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColourScheme(al,
+ jGroup.getColour());
+ }
+ }
+ int pidThreshold = safeInt(jGroup.getPidThreshold());
+
+ Vector<SequenceI> seqs = new Vector<>();
+
+ for (int s = 0; s < jGroup.getSeq().size(); s++)
+ {
+ String seqId = jGroup.getSeq().get(s);
+ SequenceI ts = seqRefIds.get(seqId);
+
+ if (ts != null)
+ {
+ seqs.addElement(ts);
+ }
+ }
+
+ if (seqs.size() < 1)
+ {
+ continue;
+ }
+
+ SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
+ safeBoolean(jGroup.isDisplayBoxes()),
+ safeBoolean(jGroup.isDisplayText()),
+ safeBoolean(jGroup.isColourText()),
+ safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
+ sg.getGroupColourScheme().setThreshold(pidThreshold, true);
+ sg.getGroupColourScheme()
+ .setConservationInc(safeInt(jGroup.getConsThreshold()));
+ sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
+
+ sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
+ sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
+ sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
+ sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
+ // attributes with a default in the schema are never null
+ sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
+ sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
+ sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
+ sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
+ if (jGroup.getConsThreshold() != null
+ && jGroup.getConsThreshold().intValue() != 0)
+ {
+ Conservation c = new Conservation("All", sg.getSequences(null), 0,
+ sg.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, 25);
+ sg.cs.setConservation(c);
+ }
+
+ if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
+ {
+ // re-instate unique group/annotation row reference
+ List<AlignmentAnnotation> jaal = groupAnnotRefs
+ .get(jGroup.getId());
+ if (jaal != null)
+ {
+ for (AlignmentAnnotation jaa : jaal)
+ {
+ jaa.groupRef = sg;
+ if (jaa.autoCalculated)
+ {
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Consensus for "))
+ {
+ sg.setConsensus(jaa);
+ }
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Conservation for "))
+ {
+ sg.setConservationRow(jaa);
+ }
+ }
+ }
+ }
+ }
+ al.addGroup(sg);
+ if (addAnnotSchemeGroup)
+ {
+ // reconstruct the annotation colourscheme
+ sg.setColourScheme(constructAnnotationColour(
+ jGroup.getAnnotationColours(), null, al, jalviewModel, false));
+ }
+ }
+ }
+ if (view == null)
+ {
+ // only dataset in this model, so just return.
+ return null;
+ }
+ // ///////////////////////////////
+ // LOAD VIEWPORT
+
+ // If we just load in the same jar file again, the sequenceSetId
+ // will be the same, and we end up with multiple references
+ // to the same sequenceSet. We must modify this id on load
+ // so that each load of the file gives a unique id
+ String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
+ String viewId = (view.getId() == null ? null
+ : view.getId() + uniqueSetSuffix);
+ AlignFrame af = null;
+ AlignViewport av = null;
+ // now check to see if we really need to create a new viewport.
+ if (multipleView && viewportsAdded.size() == 0)
+ {
+ // We recovered an alignment for which a viewport already exists.
+ // TODO: fix up any settings necessary for overlaying stored state onto
+ // state recovered from another document. (may not be necessary).
+ // we may need a binding from a viewport in memory to one recovered from
+ // XML.
+ // and then recover its containing af to allow the settings to be applied.
+ // TODO: fix for vamsas demo
+ System.err.println(
+ "About to recover a viewport for existing alignment: Sequence set ID is "
+ + uniqueSeqSetId);
+ Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
+ if (seqsetobj != null)
+ {
+ if (seqsetobj instanceof String)
+ {
+ uniqueSeqSetId = (String) seqsetobj;
+ System.err.println(
+ "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
+ + uniqueSeqSetId);
+ }
+ else
+ {
+ System.err.println(
+ "Warning : Collision between sequence set ID string and existing jalview object mapping.");
+ }
+
+ }
+ }
+ /**
+ * indicate that annotation colours are applied across all groups (pre
+ * Jalview 2.8.1 behaviour)
+ */
+ boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
+ jalviewModel.getVersion());
+
+ AlignmentPanel ap = null;
+ boolean isnewview = true;
+ if (viewId != null)
+ {
+ // Check to see if this alignment already has a view id == viewId
+ jalview.gui.AlignmentPanel views[] = Desktop
+ .getAlignmentPanels(uniqueSeqSetId);
+ if (views != null && views.length > 0)
+ {
+ for (int v = 0; v < views.length; v++)
+ {
+ if (views[v].av.getViewId().equalsIgnoreCase(viewId))
+ {
+ // recover the existing alignpanel, alignframe, viewport
+ af = views[v].alignFrame;
+ av = views[v].av;
+ ap = views[v];
+ // TODO: could even skip resetting view settings if we don't want to
+ // change the local settings from other jalview processes
+ isnewview = false;
+ }
+ }
+ }
+ }
+
+ if (isnewview)
+ {
+ af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
+ uniqueSeqSetId, viewId, autoAlan);
+ av = af.getViewport();
+ ap = af.alignPanel;
+ }
+
+ /*
+ * Load any trees, PDB structures and viewers
+ *
+ * Not done if flag is false (when this method is used for New View)
+ */
+ if (loadTreesAndStructures)
+ {
+ loadTrees(jalviewModel, view, af, av, ap);
+ loadPDBStructures(jprovider, jseqs, af, ap);
+ loadRnaViewers(jprovider, jseqs, ap);
+ }
+ // and finally return.
+ return af;
+ }
+
+ /**
+ * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
+ * panel is restored from separate jar entries, two (gapped and trimmed) per
+ * sequence and secondary structure.
+ *
+ * Currently each viewer shows just one sequence and structure (gapped and
+ * trimmed), however this method is designed to support multiple sequences or
+ * structures in viewers if wanted in future.
+ *
+ * @param jprovider
+ * @param jseqs
+ * @param ap
+ */
+ private void loadRnaViewers(jarInputStreamProvider jprovider,
+ List<JSeq> jseqs, AlignmentPanel ap)
+ {
+ /*
+ * scan the sequences for references to viewers; create each one the first
+ * time it is referenced, add Rna models to existing viewers
+ */
+ for (JSeq jseq : jseqs)
+ {
+ for (int i = 0; i < jseq.getRnaViewer().size(); i++)
+ {
+ RnaViewer viewer = jseq.getRnaViewer().get(i);
+ AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
+ ap);
+
+ for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
+ {
+ SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
+ SequenceI seq = seqRefIds.get(jseq.getId());
+ AlignmentAnnotation ann = this.annotationIds
+ .get(ss.getAnnotationId());
+
+ /*
+ * add the structure to the Varna display (with session state copied
+ * from the jar to a temporary file)
+ */
+ boolean gapped = safeBoolean(ss.isGapped());
+ String rnaTitle = ss.getTitle();
+ String sessionState = ss.getViewerState();
+ String tempStateFile = copyJarEntry(jprovider, sessionState,
+ "varna", null);
+ RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
+ appVarna.addModelSession(rna, rnaTitle, tempStateFile);
+ }
+ appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
+ }
+ }
+ }
+
+ /**
+ * Locate and return an already instantiated matching AppVarna, or create one
+ * if not found
+ *
+ * @param viewer
+ * @param viewIdSuffix
+ * @param ap
+ * @return
+ */
+ protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
+ String viewIdSuffix, AlignmentPanel ap)
+ {
+ /*
+ * on each load a suffix is appended to the saved viewId, to avoid conflicts
+ * if load is repeated
+ */
+ String postLoadId = viewer.getViewId() + viewIdSuffix;
+ for (JInternalFrame frame : getAllFrames())
+ {
+ if (frame instanceof AppVarna)
+ {
+ AppVarna varna = (AppVarna) frame;
+ if (postLoadId.equals(varna.getViewId()))
+ {
+ // this viewer is already instantiated
+ // could in future here add ap as another 'parent' of the
+ // AppVarna window; currently just 1-to-many
+ return varna;
+ }
+ }
+ }
+
+ /*
+ * viewer not found - make it
+ */
+ RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
+ safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
+ safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
+ safeInt(viewer.getDividerLocation()));
+ AppVarna varna = new AppVarna(model, ap);
+
+ return varna;
+ }
+
+ /**
+ * Load any saved trees
+ *
+ * @param jm
+ * @param view
+ * @param af
+ * @param av
+ * @param ap
+ */
+ protected void loadTrees(JalviewModel jm, Viewport view,
+ AlignFrame af, AlignViewport av, AlignmentPanel ap)
+ {
+ // TODO result of automated refactoring - are all these parameters needed?
+ try
+ {
+ for (int t = 0; t < jm.getTree().size(); t++)
+ {
+
+ Tree tree = jm.getTree().get(t);
+
+ TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
+ if (tp == null)
+ {
+ tp = af.showNewickTree(new NewickFile(tree.getNewick()),
+ tree.getTitle(), safeInt(tree.getWidth()),
+ safeInt(tree.getHeight()), safeInt(tree.getXpos()),
+ safeInt(tree.getYpos()));
+ if (tree.getId() != null)
+ {
+ // perhaps bind the tree id to something ?
+ }
+ }
+ else
+ {
+ // update local tree attributes ?
+ // TODO: should check if tp has been manipulated by user - if so its
+ // settings shouldn't be modified
+ tp.setTitle(tree.getTitle());
+ tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
+ safeInt(tree.getYpos()), safeInt(tree.getWidth()),
+ safeInt(tree.getHeight())));
+ tp.setViewport(av); // af.viewport;
+ // TODO: verify 'associate with all views' works still
+ tp.getTreeCanvas().setViewport(av); // af.viewport;
+ tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
+
+ }
+ if (tp == null)
+ {
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
+ continue;
+ }
+
+ tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
+ tp.fitToWindow_actionPerformed(null);
+
+ if (tree.getFontName() != null)
+ {
+ tp.setTreeFont(
+ new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
+ safeInt(tree.getFontSize())));
+ }
+ else
+ {
+ tp.setTreeFont(
+ new Font(view.getFontName(), safeInt(view.getFontStyle()),
+ safeInt(view.getFontSize())));
+ }
+
+ tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
+ tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
+ tp.showDistances(safeBoolean(tree.isShowDistances()));
+
+ tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
+
+ if (safeBoolean(tree.isCurrentTree()))
+ {
+ af.getViewport().setCurrentTree(tp.getTree());
+ }
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * Load and link any saved structure viewers.
+ *
+ * @param jprovider
+ * @param jseqs
+ * @param af
+ * @param ap
+ */
+ protected void loadPDBStructures(jarInputStreamProvider jprovider,
+ List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
+ {
+ /*
+ * Run through all PDB ids on the alignment, and collect mappings between
+ * distinct view ids and all sequences referring to that view.
+ */
+ Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
+
+ for (int i = 0; i < jseqs.size(); i++)
+ {
+ JSeq jseq = jseqs.get(i);
+ if (jseq.getPdbids().size() > 0)
+ {
+ List<Pdbids> ids = jseq.getPdbids();
+ for (int p = 0; p < ids.size(); p++)
+ {
+ Pdbids pdbid = ids.get(p);
+ final int structureStateCount = pdbid.getStructureState().size();
+ for (int s = 0; s < structureStateCount; s++)
+ {
+ // check to see if we haven't already created this structure view
+ final StructureState structureState = pdbid
+ .getStructureState().get(s);
+ String sviewid = (structureState.getViewId() == null) ? null
+ : structureState.getViewId() + uniqueSetSuffix;
+ jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
+ // Originally : pdbid.getFile()
+ // : TODO: verify external PDB file recovery still works in normal
+ // jalview project load
+ jpdb.setFile(
+ loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
+ jpdb.setId(pdbid.getId());
+
+ int x = safeInt(structureState.getXpos());
+ int y = safeInt(structureState.getYpos());
+ int width = safeInt(structureState.getWidth());
+ int height = safeInt(structureState.getHeight());
+
+ // Probably don't need to do this anymore...
+ // Desktop.desktop.getComponentAt(x, y);
+ // TODO: NOW: check that this recovers the PDB file correctly.
+ String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
+ pdbid.getFile());
+ jalview.datamodel.SequenceI seq = seqRefIds
+ .get(jseq.getId() + "");
+ if (sviewid == null)
+ {
+ sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
+ + height;
+ }
+ if (!structureViewers.containsKey(sviewid))
+ {
+ structureViewers.put(sviewid,
+ new StructureViewerModel(x, y, width, height, false,
+ false, true, structureState.getViewId(),
+ structureState.getType()));
+ // Legacy pre-2.7 conversion JAL-823 :
+ // do not assume any view has to be linked for colour by
+ // sequence
+ }
+
+ // assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}, boolean[] {
+ // linkAlignPanel,superposeWithAlignpanel}} from hash
+ StructureViewerModel jmoldat = structureViewers.get(sviewid);
+ jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
+ || structureState.isAlignwithAlignPanel());
+
+ /*
+ * Default colour by linked panel to false if not specified (e.g.
+ * for pre-2.7 projects)
+ */
+ boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
+ colourWithAlignPanel |= structureState.isColourwithAlignPanel();
+ jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
+
+ /*
+ * Default colour by viewer to true if not specified (e.g. for
+ * pre-2.7 projects)
+ */
+ boolean colourByViewer = jmoldat.isColourByViewer();
+ colourByViewer &= structureState.isColourByJmol();
+ jmoldat.setColourByViewer(colourByViewer);
+
+ if (jmoldat.getStateData().length() < structureState
+ .getValue()/*Content()*/.length())
+ {
+ jmoldat.setStateData(structureState.getValue());// Content());
+ }
+ if (pdbid.getFile() != null)
+ {
+ File mapkey = new File(pdbid.getFile());
+ StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
+ if (seqstrmaps == null)
+ {
+ jmoldat.getFileData().put(mapkey,
+ seqstrmaps = jmoldat.new StructureData(pdbFile,
+ pdbid.getId()));
+ }
+ if (!seqstrmaps.getSeqList().contains(seq))
+ {
+ seqstrmaps.getSeqList().add(seq);
+ // TODO and chains?
+ }
+ }
+ else
+ {
+ errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
+ warn(errorMessage);
+ }
+ }
+ }
+ }
+ }
+ // Instantiate the associated structure views
+ for (Entry<String, StructureViewerModel> entry : structureViewers
+ .entrySet())
+ {
+ try
+ {
+ createOrLinkStructureViewer(entry, af, ap, jprovider);
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Error loading structure viewer: " + e.getMessage());
+ // failed - try the next one
+ }
+ }
+ }
+
+ /**
+ *
+ * @param viewerData
+ * @param af
+ * @param ap
+ * @param jprovider
+ */
+ protected void createOrLinkStructureViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af,
+ AlignmentPanel ap, jarInputStreamProvider jprovider)
+ {
+ final StructureViewerModel stateData = viewerData.getValue();
+
+ /*
+ * Search for any viewer windows already open from other alignment views
+ * that exactly match the stored structure state
+ */
+ StructureViewerBase comp = findMatchingViewer(viewerData);
+
+ if (comp != null)
+ {
+ linkStructureViewer(ap, comp, stateData);
+ return;
+ }
+
+ /*
+ * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
+ * "viewer_"+stateData.viewId
+ */
+ if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
+ {
+ createChimeraViewer(viewerData, af, jprovider);
+ }
+ else
+ {
+ /*
+ * else Jmol (if pre-2.9, stateData contains JMOL state string)
+ */
+ createJmolViewer(viewerData, af, jprovider);
+ }
+ }
+
+ /**
+ * Create a new Chimera viewer.
+ *
+ * @param data
+ * @param af
+ * @param jprovider
+ */
+ protected void createChimeraViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af,
+ jarInputStreamProvider jprovider)
+ {
+ StructureViewerModel data = viewerData.getValue();
+ String chimeraSessionFile = data.getStateData();
+
+ /*
+ * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
+ *
+ * NB this is the 'saved' viewId as in the project file XML, _not_ the
+ * 'uniquified' sviewid used to reconstruct the viewer here
+ */
+ String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
+ chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
+ "chimera", null);
+
+ Set<Entry<File, StructureData>> fileData = data.getFileData()
+ .entrySet();
+ List<PDBEntry> pdbs = new ArrayList<>();
+ List<SequenceI[]> allseqs = new ArrayList<>();
+ for (Entry<File, StructureData> pdb : fileData)
+ {
+ String filePath = pdb.getValue().getFilePath();
+ String pdbId = pdb.getValue().getPdbId();
+ // pdbs.add(new PDBEntry(filePath, pdbId));
+ pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
+ final List<SequenceI> seqList = pdb.getValue().getSeqList();
+ SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
+ allseqs.add(seqs);
+ }
+
+ boolean colourByChimera = data.isColourByViewer();
+ boolean colourBySequence = data.isColourWithAlignPanel();
+
+ // TODO use StructureViewer as a factory here, see JAL-1761
+ final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
+ final SequenceI[][] seqsArray = allseqs
+ .toArray(new SequenceI[allseqs.size()][]);
+ String newViewId = viewerData.getKey();
+
+ ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
+ af.alignPanel, pdbArray, seqsArray, colourByChimera,
+ colourBySequence, newViewId);
+ cvf.setSize(data.getWidth(), data.getHeight());
+ cvf.setLocation(data.getX(), data.getY());
+ }
+
+ /**
+ * Create a new Jmol window. First parse the Jmol state to translate filenames
+ * loaded into the view, and record the order in which files are shown in the
+ * Jmol view, so we can add the sequence mappings in same order.
+ *
+ * @param viewerData
+ * @param af
+ * @param jprovider
+ */
+ protected void createJmolViewer(
+ final Entry<String, StructureViewerModel> viewerData,
+ AlignFrame af, jarInputStreamProvider jprovider)
+ {
+ final StructureViewerModel svattrib = viewerData.getValue();
+ String state = svattrib.getStateData();
+
+ /*
+ * Pre-2.9: state element value is the Jmol state string
+ *
+ * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
+ * + viewId
+ */
+ if (ViewerType.JMOL.toString().equals(svattrib.getType()))
+ {
+ state = readJarEntry(jprovider,
+ getViewerJarEntryName(svattrib.getViewId()));
+ }
+
+ List<String> pdbfilenames = new ArrayList<>();
+ List<SequenceI[]> seqmaps = new ArrayList<>();
+ List<String> pdbids = new ArrayList<>();
+ StringBuilder newFileLoc = new StringBuilder(64);
+ int cp = 0, ncp, ecp;
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ do
+ {
+ // look for next filename in load statement
+ newFileLoc.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do
+ // filename
+ // translation differently.
+ StructureData filedat = oldFiles.get(new File(oldfilenam));
+ if (filedat == null)
+ {
+ String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
+ filedat = oldFiles.get(new File(reformatedOldFilename));
+ }
+ newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
+ newFileLoc.append("\"");
+ cp = ecp + 1; // advance beyond last \" and set cursor so we can
+ // look for next file statement.
+ } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
+ }
+ if (cp > 0)
+ {
+ // just append rest of state
+ newFileLoc.append(state.substring(cp));
+ }
+ else
+ {
+ System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
+ newFileLoc = new StringBuilder(state);
+ newFileLoc.append("; load append ");
+ for (File id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in
+ // the viewer
+ StructureData filedat = oldFiles.get(id);
+ newFileLoc.append(filedat.getFilePath());
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
+ newFileLoc.append(" \"");
+ newFileLoc.append(filedat.getFilePath());
+ newFileLoc.append("\"");
+
+ }
+ newFileLoc.append(";");
+ }
+
+ if (newFileLoc.length() == 0)
+ {
+ return;
+ }
+ int histbug = newFileLoc.indexOf("history = ");
+ if (histbug > -1)
+ {
+ /*
+ * change "history = [true|false];" to "history = [1|0];"
+ */
+ histbug += 10;
+ int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
+ String val = (diff == -1) ? null
+ : newFileLoc.substring(histbug, diff);
+ if (val != null && val.length() >= 4)
+ {
+ if (val.contains("e")) // eh? what can it be?
+ {
+ if (val.trim().equals("true"))
+ {
+ val = "1";
+ }
+ else
+ {
+ val = "0";
+ }
+ newFileLoc.replace(histbug, diff, val);
+ }
+ }
+ }
+
+ final String[] pdbf = pdbfilenames
+ .toArray(new String[pdbfilenames.size()]);
+ final String[] id = pdbids.toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = seqmaps
+ .toArray(new SequenceI[seqmaps.size()][]);
+ final String fileloc = newFileLoc.toString();
+ final String sviewid = viewerData.getKey();
+ final AlignFrame alf = af;
+ final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
+ svattrib.getWidth(), svattrib.getHeight());
+ try
+ {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JalviewStructureDisplayI sview = null;
+ try
+ {
+ sview = new StructureViewer(
+ alf.alignPanel.getStructureSelectionManager())
+ .createView(StructureViewer.ViewerType.JMOL,
+ pdbf, id, sq, alf.alignPanel, svattrib,
+ fileloc, rect, sviewid);
+ addNewStructureViewer(sview);
+ } catch (OutOfMemoryError ex)
+ {
+ new OOMWarning("restoring structure view for PDB id " + id,
+ (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
+ {
+ sview.closeViewer(false);
+ sview.setVisible(false);
+ sview.dispose();
+ }
+ }
+ }
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
+
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+
+ }
+
+ /**
+ * Generates a name for the entry in the project jar file to hold state
+ * information for a structure viewer
+ *
+ * @param viewId
+ * @return
+ */
+ protected String getViewerJarEntryName(String viewId)
+ {
+ return VIEWER_PREFIX + viewId;
+ }
+
+ /**
+ * Returns any open frame that matches given structure viewer data. The match
+ * is based on the unique viewId, or (for older project versions) the frame's
+ * geometry.
+ *
+ * @param viewerData
+ * @return
+ */
+ protected StructureViewerBase findMatchingViewer(
+ Entry<String, StructureViewerModel> viewerData)
+ {
+ final String sviewid = viewerData.getKey();
+ final StructureViewerModel svattrib = viewerData.getValue();
+ StructureViewerBase comp = null;
+ JInternalFrame[] frames = getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof StructureViewerBase)
+ {
+ /*
+ * Post jalview 2.4 schema includes structure view id
+ */
+ if (sviewid != null && ((StructureViewerBase) frame).getViewId()
+ .equals(sviewid))
+ {
+ comp = (StructureViewerBase) frame;
+ break; // break added in 2.9
+ }
+ /*
+ * Otherwise test for matching position and size of viewer frame
+ */
+ else if (frame.getX() == svattrib.getX()
+ && frame.getY() == svattrib.getY()
+ && frame.getHeight() == svattrib.getHeight()
+ && frame.getWidth() == svattrib.getWidth())
+ {
+ comp = (StructureViewerBase) frame;
+ // no break in faint hope of an exact match on viewId
+ }
+ }
+ }
+ return comp;
+ }
+
+ /**
+ * Link an AlignmentPanel to an existing structure viewer.
+ *
+ * @param ap
+ * @param viewer
+ * @param oldFiles
+ * @param useinViewerSuperpos
+ * @param usetoColourbyseq
+ * @param viewerColouring
+ */
+ protected void linkStructureViewer(AlignmentPanel ap,
+ StructureViewerBase viewer, StructureViewerModel stateData)
+ {
+ // NOTE: if the jalview project is part of a shared session then
+ // view synchronization should/could be done here.
+
+ final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
+ final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
+ final boolean viewerColouring = stateData.isColourByViewer();
+ Map<File, StructureData> oldFiles = stateData.getFileData();
+
+ /*
+ * Add mapping for sequences in this view to an already open viewer
+ */
+ final AAStructureBindingModel binding = viewer.getBinding();
+ for (File id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in the
+ // viewer
+ StructureData filedat = oldFiles.get(id);
+ String pdbFile = filedat.getFilePath();
+ SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
+ binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
+ null);
+ binding.addSequenceForStructFile(pdbFile, seq);
+ }
+ // and add the AlignmentPanel's reference to the view panel
+ viewer.addAlignmentPanel(ap);
+ if (useinViewerSuperpos)
+ {
+ viewer.useAlignmentPanelForSuperposition(ap);
+ }
+ else
+ {
+ viewer.excludeAlignmentPanelForSuperposition(ap);
+ }
+ if (usetoColourbyseq)
+ {
+ viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
+ }
+ else
+ {
+ viewer.excludeAlignmentPanelForColourbyseq(ap);
+ }
+ }
+
+ /**
+ * Get all frames within the Desktop.
+ *
+ * @return
+ */
+ protected JInternalFrame[] getAllFrames()
+ {
+ JInternalFrame[] frames = null;
+ // TODO is this necessary - is it safe - risk of hanging?
+ do
+ {
+ try
+ {
+ frames = Desktop.desktop.getAllFrames();
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // occasional No such child exceptions are thrown here...
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException f)
+ {
+ }
+ }
+ } while (frames == null);
+ return frames;
+ }
+
+ /**
+ * Answers true if 'version' is equal to or later than 'supported', where each
+ * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
+ * changes. Development and test values for 'version' are leniently treated
+ * i.e. answer true.
+ *
+ * @param supported
+ * - minimum version we are comparing against
+ * @param version
+ * - version of data being processsed
+ * @return
+ */
+ public static boolean isVersionStringLaterThan(String supported,
+ String version)
+ {
+ if (supported == null || version == null
+ || version.equalsIgnoreCase("DEVELOPMENT BUILD")
+ || version.equalsIgnoreCase("Test")
+ || version.equalsIgnoreCase("AUTOMATED BUILD"))
+ {
+ System.err.println("Assuming project file with "
+ + (version == null ? "null" : version)
+ + " is compatible with Jalview version " + supported);
+ return true;
+ }
+ else
+ {
+ return StringUtils.compareVersions(version, supported, "b") >= 0;
+ }
+ }
+
+ Vector<JalviewStructureDisplayI> newStructureViewers = null;
+
+ protected void addNewStructureViewer(JalviewStructureDisplayI sview)
+ {
+ if (newStructureViewers != null)
+ {
+ sview.getBinding().setFinishedLoadingFromArchive(false);
+ newStructureViewers.add(sview);
+ }
+ }
+
+ protected void setLoadingFinishedForNewStructureViewers()
+ {
+ if (newStructureViewers != null)
+ {
+ for (JalviewStructureDisplayI sview : newStructureViewers)
+ {
+ sview.getBinding().setFinishedLoadingFromArchive(true);
+ }
+ newStructureViewers.clear();
+ newStructureViewers = null;
+ }
+ }
+
+ AlignFrame loadViewport(String file, List<JSeq> JSEQ,
+ List<SequenceI> hiddenSeqs, AlignmentI al,
+ JalviewModel jm, Viewport view, String uniqueSeqSetId,
+ String viewId, List<JvAnnotRow> autoAlan)
+ {
+ AlignFrame af = null;
+ af = new AlignFrame(al, safeInt(view.getWidth()),
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId);
+
+ af.setFileName(file, FileFormat.Jalview);
+
+ final AlignViewport viewport = af.getViewport();
+ for (int i = 0; i < JSEQ.size(); i++)
+ {
+ int colour = safeInt(JSEQ.get(i).getColour());
+ viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
+ new Color(colour));
+ }
+
+ if (al.hasSeqrep())
+ {
+ viewport.setColourByReferenceSeq(true);
+ viewport.setDisplayReferenceSeq(true);
+ }
+
+ viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
+
+ if (view.getSequenceSetId() != null)
+ {
+ AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
+
+ viewport.setSequenceSetId(uniqueSeqSetId);
+ if (av != null)
+ {
+ // propagate shared settings to this new view
+ viewport.setHistoryList(av.getHistoryList());
+ viewport.setRedoList(av.getRedoList());
+ }
+ else
+ {
+ viewportsAdded.put(uniqueSeqSetId, viewport);
+ }
+ // TODO: check if this method can be called repeatedly without
+ // side-effects if alignpanel already registered.
+ PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
+ }
+ // apply Hidden regions to view.
+ if (hiddenSeqs != null)
+ {
+ for (int s = 0; s < JSEQ.size(); s++)
+ {
+ SequenceGroup hidden = new SequenceGroup();
+ boolean isRepresentative = false;
+ for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
+ {
+ isRepresentative = true;
+ SequenceI sequenceToHide = al
+ .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
+ hidden.addSequence(sequenceToHide, false);
+ // remove from hiddenSeqs list so we don't try to hide it twice
+ hiddenSeqs.remove(sequenceToHide);
+ }
+ if (isRepresentative)
+ {
+ SequenceI representativeSequence = al.getSequenceAt(s);
+ hidden.addSequence(representativeSequence, false);
+ viewport.hideRepSequences(representativeSequence, hidden);
+ }
+ }
+
+ SequenceI[] hseqs = hiddenSeqs
+ .toArray(new SequenceI[hiddenSeqs.size()]);
+ viewport.hideSequence(hseqs);
+
+ }
+ // recover view properties and display parameters
+
+ viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
+ viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
+ final int pidThreshold = safeInt(view.getPidThreshold());
+ viewport.setThreshold(pidThreshold);
+
+ viewport.setColourText(safeBoolean(view.isShowColourText()));
+
+ viewport
+ .setConservationSelected(
+ safeBoolean(view.isConservationSelected()));
+ viewport.setIncrement(safeInt(view.getConsThreshold()));
+ viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
+ viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
+ viewport.setFont(new Font(view.getFontName(),
+ safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
+ true);
+ ViewStyleI vs = viewport.getViewStyle();
+ vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
+ viewport.setViewStyle(vs);
+ // TODO: allow custom charWidth/Heights to be restored by updating them
+ // after setting font - which means set above to false
+ viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
+ viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
+ viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
+
+ viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
+
+ viewport.setShowText(safeBoolean(view.isShowText()));
+
+ viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
+ viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
+ viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
+ viewport.setShowUnconserved(view.isShowUnconserved());
+ viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
+
+ if (view.getViewName() != null)
+ {
+ viewport.setViewName(view.getViewName());
+ af.setInitialTabVisible();
+ }
+ af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
+ // startSeq set in af.alignPanel.updateLayout below
+ af.alignPanel.updateLayout();
+ ColourSchemeI cs = null;
+ // apply colourschemes
+ if (view.getBgColour() != null)
+ {
+ if (view.getBgColour().startsWith("ucs"))
+ {
+ cs = getUserColourScheme(jm, view.getBgColour());
+ }
+ else if (view.getBgColour().startsWith("Annotation"))
+ {
+ AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
+ cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
+
+ // annpos
+
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+ }
+ }
+
+ viewport.setGlobalColourScheme(cs);
+ viewport.getResidueShading().setThreshold(pidThreshold,
+ view.isIgnoreGapsinConsensus());
+ viewport.getResidueShading()
+ .setConsensus(viewport.getSequenceConsensusHash());
+ viewport.setColourAppliesToAllGroups(false);
+
+ if (safeBoolean(view.isConservationSelected()) && cs != null)
+ {
+ viewport.getResidueShading()
+ .setConservationInc(safeInt(view.getConsThreshold()));
+ }
+
+ af.changeColour(cs);
+
+ viewport.setColourAppliesToAllGroups(true);
+
+ viewport
+ .setShowSequenceFeatures(
+ safeBoolean(view.isShowSequenceFeatures()));
+
+ viewport.setCentreColumnLabels(view.isCentreColumnLabels());
+ viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
+ viewport.setFollowHighlight(view.isFollowHighlight());
+ viewport.followSelection = view.isFollowSelection();
+ viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
+ viewport.setShowSequenceLogo(view.isShowSequenceLogo());
+ viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
+ viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
+ viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
+ viewport.setShowGroupConsensus(view.isShowGroupConsensus());
+ viewport.setShowGroupConservation(view.isShowGroupConservation());
+
+ // recover feature settings
+ if (jm.getFeatureSettings() != null)
+ {
+ FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+ FeaturesDisplayed fdi;
+ viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
+ String[] renderOrder = new String[jm.getFeatureSettings()
+ .getSetting().size()];
+ Map<String, FeatureColourI> featureColours = new Hashtable<>();
+ Map<String, Float> featureOrder = new Hashtable<>();
+
+ for (int fs = 0; fs < jm.getFeatureSettings()
+ .getSetting().size(); fs++)
+ {
+ Setting setting = jm.getFeatureSettings().getSetting().get(fs);
+ String featureType = setting.getType();
+
+ /*
+ * restore feature filters (if any)
+ */
+ jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
+ .getMatcherSet();
+ if (filters != null)
+ {
+ FeatureMatcherSetI filter = Jalview2XML
+ .parseFilter(featureType, filters);
+ if (!filter.isEmpty())
+ {
+ fr.setFeatureFilter(featureType, filter);
+ }
+ }
+
+ /*
+ * restore feature colour scheme
+ */
+ Color maxColour = new Color(setting.getColour());
+ if (setting.getMincolour() != null)
+ {
+ /*
+ * minColour is always set unless a simple colour
+ * (including for colour by label though it doesn't use it)
+ */
+ Color minColour = new Color(setting.getMincolour().intValue());
+ Color noValueColour = minColour;
+ NoValueColour noColour = setting.getNoValueColour();
+ if (noColour == NoValueColour.NONE)
+ {
+ noValueColour = null;
+ }
+ else if (noColour == NoValueColour.MAX)
+ {
+ noValueColour = maxColour;
+ }
+ float min = safeFloat(safeFloat(setting.getMin()));
+ float max = setting.getMax() == null ? 1f
+ : setting.getMax().floatValue();
+ FeatureColourI gc = new FeatureColour(minColour, maxColour,
+ noValueColour, min, max);
+ if (setting.getAttributeName().size() > 0)
+ {
+ gc.setAttributeName(setting.getAttributeName().toArray(
+ new String[setting.getAttributeName().size()]));
+ }
+ if (setting.getThreshold() != null)
+ {
+ gc.setThreshold(setting.getThreshold().floatValue());
+ int threshstate = safeInt(setting.getThreshstate());
+ // -1 = None, 0 = Below, 1 = Above threshold
+ if (threshstate == 0)
+ {
+ gc.setBelowThreshold(true);
+ }
+ else if (threshstate == 1)
+ {
+ gc.setAboveThreshold(true);
+ }
+ }
+ gc.setAutoScaled(true); // default
+ if (setting.isAutoScale() != null)
+ {
+ gc.setAutoScaled(setting.isAutoScale());
+ }
+ if (setting.isColourByLabel() != null)
+ {
+ gc.setColourByLabel(setting.isColourByLabel());
+ }
+ // and put in the feature colour table.
+ featureColours.put(featureType, gc);
+ }
+ else
+ {
+ featureColours.put(featureType,
+ new FeatureColour(maxColour));
+ }
+ renderOrder[fs] = featureType;
+ if (setting.getOrder() != null)
+ {
+ featureOrder.put(featureType, setting.getOrder().floatValue());
+ }
+ else
+ {
+ featureOrder.put(featureType, new Float(
+ fs / jm.getFeatureSettings().getSetting().size()));
+ }
+ if (safeBoolean(setting.isDisplay()))
+ {
+ fdi.setVisible(featureType);
+ }
+ }
+ Map<String, Boolean> fgtable = new Hashtable<>();
+ for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
+ {
+ Group grp = jm.getFeatureSettings().getGroup().get(gs);
+ fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
+ }
+ // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+ // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
+ // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
+ FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+ fgtable, featureColours, 1.0f, featureOrder);
+ fr.transferSettings(frs);
+ }
+
+ if (view.getHiddenColumns().size() > 0)
+ {
+ for (int c = 0; c < view.getHiddenColumns().size(); c++)
+ {
+ final HiddenColumns hc = view.getHiddenColumns().get(c);
+ viewport.hideColumns(safeInt(hc.getStart()),
+ safeInt(hc.getEnd()) /* +1 */);
+ }
+ }
+ if (view.getCalcIdParam() != null)
+ {
+ for (CalcIdParam calcIdParam : view.getCalcIdParam())
+ {
+ if (calcIdParam != null)
+ {
+ if (recoverCalcIdParam(calcIdParam, viewport))
+ {
+ }
+ else
+ {
+ warn("Couldn't recover parameters for "
+ + calcIdParam.getCalcId());
+ }
+ }
+ }
+ }
+ af.setMenusFromViewport(viewport);
+ af.setTitle(view.getTitle());
+ // TODO: we don't need to do this if the viewport is aready visible.
+ /*
+ * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
+ * has a 'cdna/protein complement' view, in which case save it in order to
+ * populate a SplitFrame once all views have been read in.
+ */
+ String complementaryViewId = view.getComplementId();
+ if (complementaryViewId == null)
+ {
+ Desktop.addInternalFrame(af, view.getTitle(),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
+ // recompute any autoannotation
+ af.alignPanel.updateAnnotation(false, true);
+ reorderAutoannotation(af, al, autoAlan);
+ af.alignPanel.alignmentChanged();
+ }
+ else
+ {
+ splitFrameCandidates.put(view, af);
+ }
+ return af;
+ }
+
+ /**
+ * Reads saved data to restore Colour by Annotation settings
+ *
+ * @param viewAnnColour
+ * @param af
+ * @param al
+ * @param model
+ * @param checkGroupAnnColour
+ * @return
+ */
+ private ColourSchemeI constructAnnotationColour(
+ AnnotationColourScheme viewAnnColour, AlignFrame af,
+ AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
+ {
+ boolean propagateAnnColour = false;
+ AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
+ : al;
+ if (checkGroupAnnColour && al.getGroups() != null
+ && al.getGroups().size() > 0)
+ {
+ // pre 2.8.1 behaviour
+ // check to see if we should transfer annotation colours
+ propagateAnnColour = true;
+ for (SequenceGroup sg : al.getGroups())
+ {
+ if (sg.getColourScheme() instanceof AnnotationColourGradient)
+ {
+ propagateAnnColour = false;
+ }
+ }
+ }
+
+ /*
+ * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
+ */
+ String annotationId = viewAnnColour.getAnnotation();
+ AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
+
+ /*
+ * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
+ */
+ if (matchedAnnotation == null
+ && annAlignment.getAlignmentAnnotation() != null)
+ {
+ for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
+ {
+ if (annotationId
+ .equals(annAlignment.getAlignmentAnnotation()[i].label))
+ {
+ matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
+ break;
+ }
+ }
+ }
+ if (matchedAnnotation == null)
+ {
+ System.err.println("Failed to match annotation colour scheme for "
+ + annotationId);
+ return null;
+ }
+ if (matchedAnnotation.getThreshold() == null)
+ {
+ matchedAnnotation.setThreshold(
+ new GraphLine(safeFloat(viewAnnColour.getThreshold()),
+ "Threshold", Color.black));
+ }
+
+ AnnotationColourGradient cs = null;
+ if (viewAnnColour.getColourScheme().equals("None"))
+ {
+ cs = new AnnotationColourGradient(matchedAnnotation,
+ new Color(safeInt(viewAnnColour.getMinColour())),
+ new Color(safeInt(viewAnnColour.getMaxColour())),
+ safeInt(viewAnnColour.getAboveThreshold()));
+ }
+ else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(matchedAnnotation,
+ getUserColourScheme(model, viewAnnColour.getColourScheme()),
+ safeInt(viewAnnColour.getAboveThreshold()));
+ }
+ else
+ {
+ cs = new AnnotationColourGradient(matchedAnnotation,
+ ColourSchemeProperty.getColourScheme(al,
+ viewAnnColour.getColourScheme()),
+ safeInt(viewAnnColour.getAboveThreshold()));
+ }
+
+ boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
+ boolean useOriginalColours = safeBoolean(
+ viewAnnColour.isPredefinedColours());
+ cs.setSeqAssociated(perSequenceOnly);
+ cs.setPredefinedColours(useOriginalColours);
+
+ if (propagateAnnColour && al.getGroups() != null)
+ {
+ // Also use these settings for all the groups
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ SequenceGroup sg = al.getGroups().get(g);
+ if (sg.getGroupColourScheme() == null)
+ {
+ continue;
+ }
+
+ AnnotationColourGradient groupScheme = new AnnotationColourGradient(
+ matchedAnnotation, sg.getColourScheme(),
+ safeInt(viewAnnColour.getAboveThreshold()));
+ sg.setColourScheme(groupScheme);
+ groupScheme.setSeqAssociated(perSequenceOnly);
+ groupScheme.setPredefinedColours(useOriginalColours);
+ }
+ }
+ return cs;
+ }
+
+ private void reorderAutoannotation(AlignFrame af, AlignmentI al,
+ List<JvAnnotRow> autoAlan)
+ {
+ // copy over visualization settings for autocalculated annotation in the
+ // view
+ if (al.getAlignmentAnnotation() != null)
+ {
+ /**
+ * Kludge for magic autoannotation names (see JAL-811)
+ */
+ String[] magicNames = new String[] { "Consensus", "Quality",
+ "Conservation" };
+ JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
+ Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
+ for (String nm : magicNames)
+ {
+ visan.put(nm, nullAnnot);
+ }
+ for (JvAnnotRow auan : autoAlan)
+ {
+ visan.put(auan.template.label
+ + (auan.template.getCalcId() == null ? ""
+ : "\t" + auan.template.getCalcId()),
+ auan);
+ }
+ int hSize = al.getAlignmentAnnotation().length;
+ List<JvAnnotRow> reorder = new ArrayList<>();
+ // work through any autoCalculated annotation already on the view
+ // removing it if it should be placed in a different location on the
+ // annotation panel.
+ List<String> remains = new ArrayList<>(visan.keySet());
+ for (int h = 0; h < hSize; h++)
+ {
+ jalview.datamodel.AlignmentAnnotation jalan = al
+ .getAlignmentAnnotation()[h];
+ if (jalan.autoCalculated)
+ {
+ String k;
+ JvAnnotRow valan = visan.get(k = jalan.label);
+ if (jalan.getCalcId() != null)
+ {
+ valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
+ }
+
+ if (valan != null)
+ {
+ // delete the auto calculated row from the alignment
+ al.deleteAnnotation(jalan, false);
+ remains.remove(k);
+ hSize--;
+ h--;
+ if (valan != nullAnnot)
+ {
+ if (jalan != valan.template)
+ {
+ // newly created autoannotation row instance
+ // so keep a reference to the visible annotation row
+ // and copy over all relevant attributes
+ if (valan.template.graphHeight >= 0)
+
+ {
+ jalan.graphHeight = valan.template.graphHeight;
+ }
+ jalan.visible = valan.template.visible;
+ }
+ reorder.add(new JvAnnotRow(valan.order, jalan));
+ }
+ }
+ }
+ }
+ // Add any (possibly stale) autocalculated rows that were not appended to
+ // the view during construction
+ for (String other : remains)
+ {
+ JvAnnotRow othera = visan.get(other);
+ if (othera != nullAnnot && othera.template.getCalcId() != null
+ && othera.template.getCalcId().length() > 0)
+ {
+ reorder.add(othera);
+ }
+ }
+ // now put the automatic annotation in its correct place
+ int s = 0, srt[] = new int[reorder.size()];
+ JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
+ for (JvAnnotRow jvar : reorder)
+ {
+ rws[s] = jvar;
+ srt[s++] = jvar.order;
+ }
+ reorder.clear();
+ jalview.util.QuickSort.sort(srt, rws);
+ // and re-insert the annotation at its correct position
+ for (JvAnnotRow jvar : rws)
+ {
+ al.addAnnotation(jvar.template, jvar.order);
+ }
+ af.alignPanel.adjustAnnotationHeight();
+ }
+ }
+
+ Hashtable skipList = null;
+
+ /**
+ * TODO remove this method
+ *
+ * @param view
+ * @return AlignFrame bound to sequenceSetId from view, if one exists. private
+ * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
+ * throw new Error("Implementation Error. No skipList defined for this
+ * Jalview2XML instance."); } return (AlignFrame)
+ * skipList.get(view.getSequenceSetId()); }
+ */
+
+ /**
+ * Check if the Jalview view contained in object should be skipped or not.
+ *
+ * @param object
+ * @return true if view's sequenceSetId is a key in skipList
+ */
+ private boolean skipViewport(JalviewModel object)
+ {
+ if (skipList == null)
+ {
+ return false;
+ }
+ String id = object.getViewport().get(0).getSequenceSetId();
+ if (skipList.containsKey(id))
+ {
+ if (Cache.log != null && Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Skipping seuqence set id " + id);
+ }
+ return true;
+ }
+ return false;
+ }
+
+ public void addToSkipList(AlignFrame af)
+ {
+ if (skipList == null)
+ {
+ skipList = new Hashtable();
+ }
+ skipList.put(af.getViewport().getSequenceSetId(), af);
+ }
+
+ public void clearSkipList()
+ {
+ if (skipList != null)
+ {
+ skipList.clear();
+ skipList = null;
+ }
+ }
+
+ private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
+ boolean ignoreUnrefed)
+ {
+ jalview.datamodel.AlignmentI ds = getDatasetFor(
+ vamsasSet.getDatasetId());
+ Vector dseqs = null;
+ if (ds == null)
+ {
+ // create a list of new dataset sequences
+ dseqs = new Vector();
+ }
+ for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
+ {
+ Sequence vamsasSeq = vamsasSet.getSequence().get(i);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
+ }
+ // create a new dataset
+ if (ds == null)
+ {
+ SequenceI[] dsseqs = new SequenceI[dseqs.size()];
+ dseqs.copyInto(dsseqs);
+ ds = new jalview.datamodel.Alignment(dsseqs);
+ debug("Created new dataset " + vamsasSet.getDatasetId()
+ + " for alignment " + System.identityHashCode(al));
+ addDatasetRef(vamsasSet.getDatasetId(), ds);
+ }
+ // set the dataset for the newly imported alignment.
+ if (al.getDataset() == null && !ignoreUnrefed)
+ {
+ al.setDataset(ds);
+ }
+ }
+
+ /**
+ *
+ * @param vamsasSeq
+ * sequence definition to create/merge dataset sequence for
+ * @param ds
+ * dataset alignment
+ * @param dseqs
+ * vector to add new dataset sequence to
+ * @param ignoreUnrefed
+ * - when true, don't create new sequences from vamsasSeq if it's id
+ * doesn't already have an asssociated Jalview sequence.
+ * @param vseqpos
+ * - used to reorder the sequence in the alignment according to the
+ * vamsasSeq array ordering, to preserve ordering of dataset
+ */
+ private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
+ {
+ // JBP TODO: Check this is called for AlCodonFrames to support recovery of
+ // xRef Codon Maps
+ SequenceI sq = seqRefIds.get(vamsasSeq.getId());
+ boolean reorder = false;
+ SequenceI dsq = null;
+ if (sq != null && sq.getDatasetSequence() != null)
+ {
+ dsq = sq.getDatasetSequence();
+ }
+ else
+ {
+ reorder = true;
+ }
+ if (sq == null && ignoreUnrefed)
+ {
+ return;
+ }
+ String sqid = vamsasSeq.getDsseqid();
+ if (dsq == null)
+ {
+ // need to create or add a new dataset sequence reference to this sequence
+ if (sqid != null)
+ {
+ dsq = seqRefIds.get(sqid);
+ }
+ // check again
+ if (dsq == null)
+ {
+ // make a new dataset sequence
+ dsq = sq.createDatasetSequence();
+ if (sqid == null)
+ {
+ // make up a new dataset reference for this sequence
+ sqid = seqHash(dsq);
+ }
+ dsq.setVamsasId(uniqueSetSuffix + sqid);
+ seqRefIds.put(sqid, dsq);
+ if (ds == null)
+ {
+ if (dseqs != null)
+ {
+ dseqs.addElement(dsq);
+ }
+ }
+ else
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ else
+ {
+ if (sq != dsq)
+ { // make this dataset sequence sq's dataset sequence
+ sq.setDatasetSequence(dsq);
+ // and update the current dataset alignment
+ if (ds == null)
+ {
+ if (dseqs != null)
+ {
+ if (!dseqs.contains(dsq))
+ {
+ dseqs.add(dsq);
+ }
+ }
+ else
+ {
+ if (ds.findIndex(dsq) < 0)
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
+ }
+ }
+ }
+ // TODO: refactor this as a merge dataset sequence function
+ // now check that sq (the dataset sequence) sequence really is the union of
+ // all references to it
+ // boolean pre = sq.getStart() < dsq.getStart();
+ // boolean post = sq.getEnd() > dsq.getEnd();
+ // if (pre || post)
+ if (sq != dsq)
+ {
+ // StringBuffer sb = new StringBuffer();
+ String newres = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, sq.getSequenceAsString());
+ if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
+ && newres.length() > dsq.getLength())
+ {
+ // Update with the longer sequence.
+ synchronized (dsq)
+ {
+ /*
+ * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
+ * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
+ * sb.append(newres.substring(newres.length() - sq.getEnd() -
+ * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
+ */
+ dsq.setSequence(newres);
+ }
+ // TODO: merges will never happen if we 'know' we have the real dataset
+ // sequence - this should be detected when id==dssid
+ System.err.println(
+ "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
+ // + (pre ? "prepended" : "") + " "
+ // + (post ? "appended" : ""));
+ }
+ }
+ else
+ {
+ // sequence refs are identical. We may need to update the existing dataset
+ // alignment with this one, though.
+ if (ds != null && dseqs == null)
+ {
+ int opos = ds.findIndex(dsq);
+ SequenceI tseq = null;
+ if (opos != -1 && vseqpos != opos)
+ {
+ // remove from old position
+ ds.deleteSequence(dsq);
+ }
+ if (vseqpos < ds.getHeight())
+ {
+ if (vseqpos != opos)
+ {
+ // save sequence at destination position
+ tseq = ds.getSequenceAt(vseqpos);
+ ds.replaceSequenceAt(vseqpos, dsq);
+ ds.addSequence(tseq);
+ }
+ }
+ else
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
+ }
+
+ /*
+ * TODO use AlignmentI here and in related methods - needs
+ * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
+ */
+ Hashtable<String, AlignmentI> datasetIds = null;
+
+ IdentityHashMap<AlignmentI, String> dataset2Ids = null;
+
+ private AlignmentI getDatasetFor(String datasetId)
+ {
+ if (datasetIds == null)
+ {
+ datasetIds = new Hashtable<>();
+ return null;
+ }
+ if (datasetIds.containsKey(datasetId))
+ {
+ return datasetIds.get(datasetId);
+ }
+ return null;
+ }
+
+ private void addDatasetRef(String datasetId, AlignmentI dataset)
+ {
+ if (datasetIds == null)
+ {
+ datasetIds = new Hashtable<>();
+ }
+ datasetIds.put(datasetId, dataset);
+ }
+
+ /**
+ * make a new dataset ID for this jalview dataset alignment
+ *
+ * @param dataset
+ * @return
+ */
+ private String getDatasetIdRef(AlignmentI dataset)
+ {
+ if (dataset.getDataset() != null)
+ {
+ warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+ }
+ String datasetId = makeHashCode(dataset, null);
+ if (datasetId == null)
+ {
+ // make a new datasetId and record it
+ if (dataset2Ids == null)
+ {
+ dataset2Ids = new IdentityHashMap<>();
+ }
+ else
+ {
+ datasetId = dataset2Ids.get(dataset);
+ }
+ if (datasetId == null)
+ {
+ datasetId = "ds" + dataset2Ids.size() + 1;
+ dataset2Ids.put(dataset, datasetId);
+ }
+ }
+ return datasetId;
+ }
+
+ private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
+ {
+ for (int d = 0; d < sequence.getDBRef().size(); d++)
+ {
+ DBRef dr = sequence.getDBRef().get(d);
+ jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
+ dr.getSource(), dr.getVersion(), dr.getAccessionId());
+ if (dr.getMapping() != null)
+ {
+ entry.setMap(addMapping(dr.getMapping()));
+ }
+ datasetSequence.addDBRef(entry);
+ }
+ }
+
+ private jalview.datamodel.Mapping addMapping(Mapping m)
+ {
+ SequenceI dsto = null;
+ // Mapping m = dr.getMapping();
+ int fr[] = new int[m.getMapListFrom().size() * 2];
+ Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
+ for (int _i = 0; from.hasNext(); _i += 2)
+ {
+ MapListFrom mf = from.next();
+ fr[_i] = mf.getStart();
+ fr[_i + 1] = mf.getEnd();
+ }
+ int fto[] = new int[m.getMapListTo().size() * 2];
+ Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
+ for (int _i = 0; to.hasNext(); _i += 2)
+ {
+ MapListTo mf = to.next();
+ fto[_i] = mf.getStart();
+ fto[_i + 1] = mf.getEnd();
+ }
+ jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
+ fto, m.getMapFromUnit().intValue(),
+ m.getMapToUnit().intValue());
+ // if (m.getMappingChoice() != null)
+ // {
+ // MappingChoice mc = m.getMappingChoice();
+ if (m.getDseqFor() != null)
+ {
+ String dsfor = m.getDseqFor();
+ if (seqRefIds.containsKey(dsfor))
+ {
+ /**
+ * recover from hash
+ */
+ jmap.setTo(seqRefIds.get(dsfor));
+ }
+ else
+ {
+ frefedSequence.add(newMappingRef(dsfor, jmap));
+ }
+ }
+ else
+ {
+ /**
+ * local sequence definition
+ */
+ Sequence ms = m.getSequence();
+ SequenceI djs = null;
+ String sqid = ms.getDsseqid();
+ if (sqid != null && sqid.length() > 0)
+ {
+ /*
+ * recover dataset sequence
+ */
+ djs = seqRefIds.get(sqid);
+ }
+ else
+ {
+ System.err.println(
+ "Warning - making up dataset sequence id for DbRef sequence map reference");
+ sqid = ((Object) ms).toString(); // make up a new hascode for
+ // undefined dataset sequence hash
+ // (unlikely to happen)
+ }
+
+ if (djs == null)
+ {
+ /**
+ * make a new dataset sequence and add it to refIds hash
+ */
+ djs = new jalview.datamodel.Sequence(ms.getName(),
+ ms.getSequence());
+ djs.setStart(jmap.getMap().getToLowest());
+ djs.setEnd(jmap.getMap().getToHighest());
+ djs.setVamsasId(uniqueSetSuffix + sqid);
+ jmap.setTo(djs);
+ incompleteSeqs.put(sqid, djs);
+ seqRefIds.put(sqid, djs);
+
+ }
+ jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ addDBRefs(djs, ms);
+
+ }
+
+ return jmap;
+ }
+
+ /**
+ * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
+ * view as XML (but not to file), and then reloading it
+ *
+ * @param ap
+ * @return
+ */
+ public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
+ {
+ initSeqRefs();
+ JalviewModel jm = saveState(ap, null, null, null);
+
+ uniqueSetSuffix = "";
+ // jm.getJalviewModelSequence().getViewport(0).setId(null);
+ jm.getViewport().get(0).setId(null);
+ // we don't overwrite the view we just copied
+
+ if (this.frefedSequence == null)
+ {
+ frefedSequence = new Vector<>();
+ }
+
+ viewportsAdded.clear();
+
+ AlignFrame af = loadFromObject(jm, null, false, null);
+ af.getAlignPanels().clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ /*
+ * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
+ * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
+ * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
+ * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
+ * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
+ */
+
+ return af.alignPanel;
+ }
+
+ private Hashtable jvids2vobj;
+
+ private void warn(String msg)
+ {
+ warn(msg, null);
+ }
+
+ private void warn(String msg, Exception e)
+ {
+ if (Cache.log != null)
+ {
+ if (e != null)
+ {
+ Cache.log.warn(msg, e);
+ }
+ else
+ {
+ Cache.log.warn(msg);
+ }
+ }
+ else
+ {
+ System.err.println("Warning: " + msg);
+ if (e != null)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ private void debug(String string)
+ {
+ debug(string, null);
+ }
+
+ private void debug(String msg, Exception e)
+ {
+ if (Cache.log != null)
+ {
+ if (e != null)
+ {
+ Cache.log.debug(msg, e);
+ }
+ else
+ {
+ Cache.log.debug(msg);
+ }
+ }
+ else
+ {
+ System.err.println("Warning: " + msg);
+ if (e != null)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * set the object to ID mapping tables used to write/recover objects and XML
+ * ID strings for the jalview project. If external tables are provided then
+ * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
+ * object goes out of scope. - also populates the datasetIds hashtable with
+ * alignment objects containing dataset sequences
+ *
+ * @param vobj2jv
+ * Map from ID strings to jalview datamodel
+ * @param jv2vobj
+ * Map from jalview datamodel to ID strings
+ *
+ *
+ */
+ public void setObjectMappingTables(Hashtable vobj2jv,
+ IdentityHashMap jv2vobj)
+ {
+ this.jv2vobj = jv2vobj;
+ this.vobj2jv = vobj2jv;
+ Iterator ds = jv2vobj.keySet().iterator();
+ String id;
+ while (ds.hasNext())
+ {
+ Object jvobj = ds.next();
+ id = jv2vobj.get(jvobj).toString();
+ if (jvobj instanceof jalview.datamodel.Alignment)
+ {
+ if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
+ {
+ addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
+ }
+ }
+ else if (jvobj instanceof jalview.datamodel.Sequence)
+ {
+ // register sequence object so the XML parser can recover it.
+ if (seqRefIds == null)
+ {
+ seqRefIds = new HashMap<>();
+ }
+ if (seqsToIds == null)
+ {
+ seqsToIds = new IdentityHashMap<>();
+ }
+ seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
+ seqsToIds.put((SequenceI) jvobj, id);
+ }
+ else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
+ {
+ String anid;
+ AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
+ annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
+ if (jvann.annotationId == null)
+ {
+ jvann.annotationId = anid;
+ }
+ if (!jvann.annotationId.equals(anid))
+ {
+ // TODO verify that this is the correct behaviour
+ this.warn("Overriding Annotation ID for " + anid
+ + " from different id : " + jvann.annotationId);
+ jvann.annotationId = anid;
+ }
+ }
+ else if (jvobj instanceof String)
+ {
+ if (jvids2vobj == null)
+ {
+ jvids2vobj = new Hashtable();
+ jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
+ }
+ }
+ else
+ {
+ Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ }
+ }
+ }
+
+ /**
+ * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
+ * objects created from the project archive. If string is null (default for
+ * construction) then suffix will be set automatically.
+ *
+ * @param string
+ */
+ public void setUniqueSetSuffix(String string)
+ {
+ uniqueSetSuffix = string;
+
+ }
+
+ /**
+ * uses skipList2 as the skipList for skipping views on sequence sets
+ * associated with keys in the skipList
+ *
+ * @param skipList2
+ */
+ public void setSkipList(Hashtable skipList2)
+ {
+ skipList = skipList2;
+ }
+
+ /**
+ * Reads the jar entry of given name and returns its contents, or null if the
+ * entry is not found.
+ *
+ * @param jprovider
+ * @param jarEntryName
+ * @return
+ */
+ protected String readJarEntry(jarInputStreamProvider jprovider,
+ String jarEntryName)
+ {
+ String result = null;
+ BufferedReader in = null;
+
+ try
+ {
+ /*
+ * Reopen the jar input stream and traverse its entries to find a matching
+ * name
+ */
+ JarInputStream jin = jprovider.getJarInputStream();
+ JarEntry entry = null;
+ do
+ {
+ entry = jin.getNextJarEntry();
+ } while (entry != null && !entry.getName().equals(jarEntryName));
+
+ if (entry != null)
+ {
+ StringBuilder out = new StringBuilder(256);
+ in = new BufferedReader(new InputStreamReader(jin, UTF_8));
+ String data;
+
+ while ((data = in.readLine()) != null)
+ {
+ out.append(data);
+ }
+ result = out.toString();
+ }
+ else
+ {
+ warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Returns an incrementing counter (0, 1, 2...)
+ *
+ * @return
+ */
+ private synchronized int nextCounter()
+ {
+ return counter++;
+ }
+
+ /**
+ * Populates an XML model of the feature colour scheme for one feature type
+ *
+ * @param featureType
+ * @param fcol
+ * @return
+ */
+ public static Colour marshalColour(
+ String featureType, FeatureColourI fcol)
+ {
+ Colour col = new Colour();
+ if (fcol.isSimpleColour())
+ {
+ col.setRGB(Format.getHexString(fcol.getColour()));
+ }
+ else
+ {
+ col.setRGB(Format.getHexString(fcol.getMaxColour()));
+ col.setMin(fcol.getMin());
+ col.setMax(fcol.getMax());
+ col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
+ col.setAutoScale(fcol.isAutoScaled());
+ col.setThreshold(fcol.getThreshold());
+ col.setColourByLabel(fcol.isColourByLabel());
+ col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
+ : (fcol.isBelowThreshold() ? ThresholdType.BELOW
+ : ThresholdType.NONE));
+ if (fcol.isColourByAttribute())
+ {
+ final String[] attName = fcol.getAttributeName();
+ col.getAttributeName().add(attName[0]);
+ if (attName.length > 1)
+ {
+ col.getAttributeName().add(attName[1]);
+ }
+ }
+ Color noColour = fcol.getNoColour();
+ if (noColour == null)
+ {
+ col.setNoValueColour(NoValueColour.NONE);
+ }
+ else if (noColour == fcol.getMaxColour())
+ {
+ col.setNoValueColour(NoValueColour.MAX);
+ }
+ else
+ {
+ col.setNoValueColour(NoValueColour.MIN);
+ }
+ }
+ col.setName(featureType);
+ return col;
+ }
+
+ /**
+ * Populates an XML model of the feature filter(s) for one feature type
+ *
+ * @param firstMatcher
+ * the first (or only) match condition)
+ * @param filter
+ * remaining match conditions (if any)
+ * @param and
+ * if true, conditions are and-ed, else or-ed
+ */
+ public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
+ FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
+ boolean and)
+ {
+ jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
+
+ if (filters.hasNext())
+ {
+ /*
+ * compound matcher
+ */
+ CompoundMatcher compound = new CompoundMatcher();
+ compound.setAnd(and);
+ jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
+ firstMatcher, Collections.emptyIterator(), and);
+ // compound.addMatcherSet(matcher1);
+ compound.getMatcherSet().add(matcher1);
+ FeatureMatcherI nextMatcher = filters.next();
+ jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
+ nextMatcher, filters, and);
+ // compound.addMatcherSet(matcher2);
+ compound.getMatcherSet().add(matcher2);
+ result.setCompoundMatcher(compound);
+ }
+ else
+ {
+ /*
+ * single condition matcher
+ */
+ // MatchCondition matcherModel = new MatchCondition();
+ jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
+ matcherModel.setCondition(
+ firstMatcher.getMatcher().getCondition().getStableName());
+ matcherModel.setValue(firstMatcher.getMatcher().getPattern());
+ if (firstMatcher.isByAttribute())
+ {
+ matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
+ // matcherModel.setAttributeName(firstMatcher.getAttribute());
+ String[] attName = firstMatcher.getAttribute();
+ matcherModel.getAttributeName().add(attName[0]); // attribute
+ if (attName.length > 1)
+ {
+ matcherModel.getAttributeName().add(attName[1]); // sub-attribute
+ }
+ }
+ else if (firstMatcher.isByLabel())
+ {
+ matcherModel.setBy(FilterBy.BY_LABEL);
+ }
+ else if (firstMatcher.isByScore())
+ {
+ matcherModel.setBy(FilterBy.BY_SCORE);
+ }
+ result.setMatchCondition(matcherModel);
+ }
+
+ return result;
+ }
+
+ /**
+ * Loads one XML model of a feature filter to a Jalview object
+ *
+ * @param featureType
+ * @param matcherSetModel
+ * @return
+ */
+ public static FeatureMatcherSetI parseFilter(
+ String featureType,
+ jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
+ {
+ FeatureMatcherSetI result = new FeatureMatcherSet();
+ try
+ {
+ parseFilterConditions(result, matcherSetModel, true);
+ } catch (IllegalStateException e)
+ {
+ // mixing AND and OR conditions perhaps
+ System.err.println(
+ String.format("Error reading filter conditions for '%s': %s",
+ featureType, e.getMessage()));
+ // return as much as was parsed up to the error
+ }
+
+ return result;
+ }
+
+ /**
+ * Adds feature match conditions to matcherSet as unmarshalled from XML
+ * (possibly recursively for compound conditions)
+ *
+ * @param matcherSet
+ * @param matcherSetModel
+ * @param and
+ * if true, multiple conditions are AND-ed, else they are OR-ed
+ * @throws IllegalStateException
+ * if AND and OR conditions are mixed
+ */
+ protected static void parseFilterConditions(
+ FeatureMatcherSetI matcherSet,
+ jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
+ boolean and)
+ {
+ jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
+ .getMatchCondition();
+ if (mc != null)
+ {
+ /*
+ * single condition
+ */
+ FilterBy filterBy = mc.getBy();
+ Condition cond = Condition.fromString(mc.getCondition());
+ String pattern = mc.getValue();
+ FeatureMatcherI matchCondition = null;
+ if (filterBy == FilterBy.BY_LABEL)
+ {
+ matchCondition = FeatureMatcher.byLabel(cond, pattern);
+ }
+ else if (filterBy == FilterBy.BY_SCORE)
+ {
+ matchCondition = FeatureMatcher.byScore(cond, pattern);
+
+ }
+ else if (filterBy == FilterBy.BY_ATTRIBUTE)
+ {
+ final List<String> attributeName = mc.getAttributeName();
+ String[] attNames = attributeName
+ .toArray(new String[attributeName.size()]);
+ matchCondition = FeatureMatcher.byAttribute(cond, pattern,
+ attNames);
+ }
+
+ /*
+ * note this throws IllegalStateException if AND-ing to a
+ * previously OR-ed compound condition, or vice versa
+ */
+ if (and)
+ {
+ matcherSet.and(matchCondition);
+ }
+ else
+ {
+ matcherSet.or(matchCondition);
+ }
+ }
+ else
+ {
+ /*
+ * compound condition
+ */
+ List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
+ .getCompoundMatcher().getMatcherSet();
+ boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
+ if (matchers.size() == 2)
+ {
+ parseFilterConditions(matcherSet, matchers.get(0), anded);
+ parseFilterConditions(matcherSet, matchers.get(1), anded);
+ }
+ else
+ {
+ System.err.println("Malformed compound filter condition");
+ }
+ }
+ }
+
+ /**
+ * Loads one XML model of a feature colour to a Jalview object
+ *
+ * @param colourModel
+ * @return
+ */
+ public static FeatureColourI parseColour(Colour colourModel)
+ {
+ FeatureColourI colour = null;
+
+ if (colourModel.getMax() != null)
+ {
+ Color mincol = null;
+ Color maxcol = null;
+ Color noValueColour = null;
+
+ try
+ {
+ mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
+ maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
+ } catch (Exception e)
+ {
+ Cache.log.warn("Couldn't parse out graduated feature color.", e);
+ }
+
+ NoValueColour noCol = colourModel.getNoValueColour();
+ if (noCol == NoValueColour.MIN)
+ {
+ noValueColour = mincol;
+ }
+ else if (noCol == NoValueColour.MAX)
+ {
+ noValueColour = maxcol;
+ }
+
+ colour = new FeatureColour(mincol, maxcol, noValueColour,
+ safeFloat(colourModel.getMin()),
+ safeFloat(colourModel.getMax()));
+ final List<String> attributeName = colourModel.getAttributeName();
+ String[] attributes = attributeName
+ .toArray(new String[attributeName.size()]);
+ if (attributes != null && attributes.length > 0)
+ {
+ colour.setAttributeName(attributes);
+ }
+ if (colourModel.isAutoScale() != null)
+ {
+ colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
+ }
+ if (colourModel.isColourByLabel() != null)
+ {
+ colour.setColourByLabel(
+ colourModel.isColourByLabel().booleanValue());
+ }
+ if (colourModel.getThreshold() != null)
+ {
+ colour.setThreshold(colourModel.getThreshold().floatValue());
+ }
+ ThresholdType ttyp = colourModel.getThreshType();
+ if (ttyp == ThresholdType.ABOVE)
+ {
+ colour.setAboveThreshold(true);
+ }
+ else if (ttyp == ThresholdType.BELOW)
+ {
+ colour.setBelowThreshold(true);
+ }
+ }
+ else
+ {
+ Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
+ colour = new FeatureColour(color);
+ }
+
+ return colour;
+ }
+}
*/
package jalview.schemes;
-import jalview.binding.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours;
import java.awt.Color;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStreamReader;
-import org.exolab.castor.xml.Unmarshaller;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
public class ColourSchemeLoader
{
InputStreamReader in = new InputStreamReader(
new FileInputStream(file), "UTF-8");
- jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-
- org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
- jucs);
- jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
- .unmarshal(in);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(in);
+ JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+ JalviewUserColours.class);
+ JalviewUserColours jucs = jbe.getValue();
/*
* non-case-sensitive colours are for 20 amino acid codes,
String name;
int index;
- for (int i = 0; i < jucs.getColourCount(); i++)
+ for (int i = 0; i < jucs.getColour().size(); i++)
{
- name = jucs.getColour(i).getName();
+ name = jucs.getColour().get(i).getName();
if (ResidueProperties.aa3Hash.containsKey(name))
{
index = ResidueProperties.aa3Hash.get(name).intValue();
}
Color color = new Color(
- Integer.parseInt(jucs.getColour(i).getRGB(), 16));
+ Integer.parseInt(jucs.getColour().get(i).getRGB(), 16));
if (name.toLowerCase().equals(name))
{
caseSensitive = true;
jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
- jucs = JalviewUserColours.unmarshal(in);
+ jucs = jalview.binding.JalviewUserColours.unmarshal(in);
newColours = new Color[jucs.getColourCount()];
*/
package jalview.ws.dbsources;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.embl.EmblEntry;
-import jalview.datamodel.xdb.embl.EmblFile;
+import jalview.util.DBRefUtils;
+import jalview.util.DnaUtils;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
+import jalview.xml.binding.embl.EntryType;
+import jalview.xml.binding.embl.EntryType.Feature;
+import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
+import jalview.xml.binding.embl.XrefType;
import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.text.ParseException;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.regex.Pattern;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
*/
private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
+ private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
+
public EmblXmlSource()
{
super();
}
/**
- * retrieve and parse an emblxml file
+ * Retrieves and parses an emblxml file, and returns an alignment containing
+ * the parsed sequences, or null if none were found
*
* @param emprefx
- * either EMBL or EMBLCDS strings are allowed - anything else will
- * not retrieve emblxml
+ * "EMBL" or "EMBLCDS" - anything else will not retrieve emblxml
* @param query
* @return
* @throws Exception
*/
- public AlignmentI getEmblSequenceRecords(String emprefx, String query)
+ protected AlignmentI getEmblSequenceRecords(String emprefx, String query)
throws Exception
{
startQuery();
* @return
* @throws Exception
*/
- public AlignmentI getEmblSequenceRecords(String emprefx, String query,
+ protected AlignmentI getEmblSequenceRecords(String emprefx, String query,
File reply) throws Exception
{
- EmblFile efile = null;
- List<SequenceI> seqs = new ArrayList<>();
-
+ List<EntryType> entries = null;
if (reply != null && reply.exists())
{
file = reply.getAbsolutePath();
if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
{
- efile = EmblFile.getEmblFile(reply);
+ InputStream is = new FileInputStream(reply);
+ entries = getEmblEntries(is);
}
}
* EmbFile reads something like (e.g.) this ungrammatical phrase
* Entry: <acc> display type is either not supported or entry is not found.
*/
+ AlignmentI al = null;
+ List<SequenceI> seqs = new ArrayList<>();
List<SequenceI> peptides = new ArrayList<>();
- if (efile != null && efile.getEntries() != null)
+ if (entries != null)
{
- for (EmblEntry entry : efile.getEntries())
+ for (EntryType entry : entries)
{
- SequenceI seq = entry.getSequence(emprefx, peptides);
+ SequenceI seq = getSequence(emprefx, entry, peptides);
if (seq != null)
{
seqs.add(seq.deriveSequence());
// place DBReferences on dataset and refer
}
}
+ if (!seqs.isEmpty())
+ {
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ else
+ {
+ System.out.println(
+ "No record found for '" + emprefx + ":" + query + "'");
+ }
}
- AlignmentI al = null;
- if (!seqs.isEmpty())
- {
- al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
- }
stopQuery();
return al;
}
+ /**
+ * Reads the XML reply from file and unmarshals it to Java objects. Answers a
+ * (possibly empty) list of <code>EntryType</code> objects.
+ *
+ * is
+ *
+ * @return
+ */
+ List<EntryType> getEmblEntries(InputStream is)
+ {
+ List<EntryType> entries = new ArrayList<>();
+ try
+ {
+ JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.embl");
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(is);
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ jalview.xml.binding.embl.ROOT root = (jalview.xml.binding.embl.ROOT) um
+ .unmarshal(streamReader);
+
+ /*
+ * document root contains either "entry" or "entrySet"
+ */
+ if (root == null)
+ {
+ return entries;
+ }
+ if (root.getEntrySet() != null)
+ {
+ entries = root.getEntrySet().getEntry();
+ }
+ else if (root.getEntry() != null)
+ {
+ entries.add(root.getEntry());
+ }
+ } catch (JAXBException | XMLStreamException
+ | FactoryConfigurationError e)
+ {
+ e.printStackTrace();
+ }
+ return entries;
+ }
+
+ /**
+ * A helper method to parse XML data and construct a sequence, with any
+ * available database references and features
+ *
+ * @param emprefx
+ * @param entry
+ * @param peptides
+ * @return
+ */
+ SequenceI getSequence(String sourceDb, EntryType entry,
+ List<SequenceI> peptides)
+ {
+ String seqString = entry.getSequence();
+ if (seqString == null)
+ {
+ return null;
+ }
+ seqString = seqString.replace(" ", "").replace("\n", "").replace("\t",
+ "");
+ String accession = entry.getAccession();
+ SequenceI dna = new Sequence(sourceDb + "|" + accession, seqString);
+
+ dna.setDescription(entry.getDescription());
+ String sequenceVersion = String.valueOf(entry.getVersion().intValue());
+ DBRefEntry selfRref = new DBRefEntry(sourceDb, sequenceVersion,
+ accession);
+ dna.addDBRef(selfRref);
+ selfRref.setMap(
+ new Mapping(null, new int[]
+ { 1, dna.getLength() }, new int[] { 1, dna.getLength() }, 1,
+ 1));
+
+ /*
+ * add db references
+ */
+ List<XrefType> xrefs = entry.getXref();
+ if (xrefs != null)
+ {
+ for (XrefType xref : xrefs)
+ {
+ String acc = xref.getId();
+ String source = DBRefUtils.getCanonicalName(xref.getDb());
+ String version = xref.getSecondaryId();
+ if (version == null || "".equals(version))
+ {
+ version = "0";
+ }
+ dna.addDBRef(new DBRefEntry(source, version, acc));
+ }
+ }
+
+ SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
+ try
+ {
+ List<Feature> features = entry.getFeature();
+ if (features != null)
+ {
+ for (Feature feature : features)
+ {
+ if (FeatureProperties.isCodingFeature(sourceDb,
+ feature.getName()))
+ {
+ parseCodingFeature(entry, feature, sourceDb, dna, peptides,
+ matcher);
+ }
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err.println("EMBL Record Features parsing error!");
+ System.err
+ .println("Please report the following to help@jalview.org :");
+ System.err.println("EMBL Record " + accession);
+ System.err.println("Resulted in exception: " + e.getMessage());
+ e.printStackTrace(System.err);
+ }
+
+ return dna;
+ }
+
+ /**
+ * Extracts coding region and product from a CDS feature and decorates it with
+ * annotations
+ *
+ * @param entry
+ * @param feature
+ * @param sourceDb
+ * @param dna
+ * @param peptides
+ * @param matcher
+ */
+ void parseCodingFeature(EntryType entry, Feature feature, String sourceDb,
+ SequenceI dna, List<SequenceI> peptides,
+ SequenceIdMatcher matcher)
+ {
+ final boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
+ final String accession = entry.getAccession();
+ final String sequenceVersion = entry.getVersion().toString();
+
+ int[] exons = getCdsRanges(entry.getAccession(), feature);
+
+ String translation = null;
+ String proteinName = "";
+ String proteinId = null;
+ Map<String, String> vals = new Hashtable<>();
+
+ /*
+ * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
+ * (phase is required for CDS features in GFF3 format)
+ */
+ int codonStart = 1;
+
+ /*
+ * parse qualifiers, saving protein translation, protein id,
+ * codon start position, product (name), and 'other values'
+ */
+ if (feature.getQualifier() != null)
+ {
+ for (Qualifier q : feature.getQualifier())
+ {
+ String qname = q.getName();
+ String value = q.getValue();
+ value = value == null ? ""
+ : value.trim().replace(" ", "").replace("\n", "")
+ .replace("\t", "");
+ if (qname.equals("translation"))
+ {
+ translation = value;
+ }
+ else if (qname.equals("protein_id"))
+ {
+ proteinId = value;
+ }
+ else if (qname.equals("codon_start"))
+ {
+ try
+ {
+ codonStart = Integer.parseInt(value.trim());
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Invalid codon_start in XML for "
+ + entry.getAccession() + ": " + e.getMessage());
+ }
+ }
+ else if (qname.equals("product"))
+ {
+ // sometimes name is returned e.g. for V00488
+ proteinName = value;
+ }
+ else
+ {
+ // throw anything else into the additional properties hash
+ if (!"".equals(value))
+ {
+ vals.put(qname, value);
+ }
+ }
+ }
+ }
+
+ DBRefEntry proteinToEmblProteinRef = null;
+ exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
+
+ SequenceI product = null;
+ Mapping dnaToProteinMapping = null;
+ if (translation != null && proteinName != null && proteinId != null)
+ {
+ int translationLength = translation.length();
+
+ /*
+ * look for product in peptides list, if not found, add it
+ */
+ product = matcher.findIdMatch(proteinId);
+ if (product == null)
+ {
+ product = new Sequence(proteinId, translation, 1,
+ translationLength);
+ product.setDescription(((proteinName.length() == 0)
+ ? "Protein Product from " + sourceDb
+ : proteinName));
+ peptides.add(product);
+ matcher.add(product);
+ }
+
+ // we have everything - create the mapping and perhaps the protein
+ // sequence
+ if (exons == null || exons.length == 0)
+ {
+ /*
+ * workaround until we handle dna location for CDS sequence
+ * e.g. location="X53828.1:60..1058" correctly
+ */
+ System.err.println(
+ "Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ + sourceDb + ":" + entry.getAccession() + ")");
+ int dnaLength = dna.getLength();
+ if (translationLength * 3 == (1 - codonStart + dnaLength))
+ {
+ System.err.println(
+ "Not allowing for additional stop codon at end of cDNA fragment... !");
+ // this might occur for CDS sequences where no features are marked
+ exons = new int[] { dna.getStart() + (codonStart - 1),
+ dna.getEnd() };
+ dnaToProteinMapping = new Mapping(product, exons,
+ new int[]
+ { 1, translationLength }, 3, 1);
+ }
+ if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
+ {
+ System.err.println(
+ "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
+ exons = new int[] { dna.getStart() + (codonStart - 1),
+ dna.getEnd() - 3 };
+ dnaToProteinMapping = new Mapping(product, exons,
+ new int[]
+ { 1, translationLength }, 3, 1);
+ }
+ }
+ else
+ {
+ // Trim the exon mapping if necessary - the given product may only be a
+ // fragment of a larger protein. (EMBL:AY043181 is an example)
+
+ if (isEmblCdna)
+ {
+ // TODO: Add a DbRef back to the parent EMBL sequence with the exon
+ // map
+ // if given a dataset reference, search dataset for parent EMBL
+ // sequence if it exists and set its map
+ // make a new feature annotating the coding contig
+ }
+ else
+ {
+ // final product length truncation check
+ int[] cdsRanges = adjustForProteinLength(translationLength,
+ exons);
+ dnaToProteinMapping = new Mapping(product, cdsRanges,
+ new int[]
+ { 1, translationLength }, 3, 1);
+ if (product != null)
+ {
+ /*
+ * make xref with mapping from protein to EMBL dna
+ */
+ DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
+ sequenceVersion, proteinId,
+ new Mapping(dnaToProteinMapping.getMap().getInverse()));
+ product.addDBRef(proteinToEmblRef);
+
+ /*
+ * make xref from protein to EMBLCDS; we assume here that the
+ * CDS sequence version is same as dna sequence (?!)
+ */
+ MapList proteinToCdsMapList = new MapList(
+ new int[]
+ { 1, translationLength },
+ new int[]
+ { 1 + (codonStart - 1),
+ (codonStart - 1) + 3 * translationLength },
+ 1, 3);
+ DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
+ DBRefSource.EMBLCDS, sequenceVersion, proteinId,
+ new Mapping(proteinToCdsMapList));
+ product.addDBRef(proteinToEmblCdsRef);
+
+ /*
+ * make 'direct' xref from protein to EMBLCDSPROTEIN
+ */
+ proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
+ proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
+ proteinToEmblProteinRef.setMap(null);
+ product.addDBRef(proteinToEmblProteinRef);
+ }
+ }
+ }
+
+ /*
+ * add cds features to dna sequence
+ */
+ String cds = feature.getName(); // "CDS"
+ for (int xint = 0; exons != null
+ && xint < exons.length - 1; xint += 2)
+ {
+ int exonStart = exons[xint];
+ int exonEnd = exons[xint + 1];
+ int begin = Math.min(exonStart, exonEnd);
+ int end = Math.max(exonStart, exonEnd);
+ int exonNumber = xint / 2 + 1;
+ String desc = String.format("Exon %d for protein '%s' EMBLCDS:%s",
+ exonNumber, proteinName, proteinId);
+
+ SequenceFeature sf = makeCdsFeature(cds, desc, begin, end, sourceDb,
+ vals);
+
+ sf.setEnaLocation(feature.getLocation());
+ boolean forwardStrand = exonStart <= exonEnd;
+ sf.setStrand(forwardStrand ? "+" : "-");
+ sf.setPhase(String.valueOf(codonStart - 1));
+ sf.setValue(FeatureProperties.EXONPOS, exonNumber);
+ sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
+
+ dna.addSequenceFeature(sf);
+ }
+ }
+
+ /*
+ * add feature dbRefs to sequence, and mappings for Uniprot xrefs
+ */
+ boolean hasUniprotDbref = false;
+ List<XrefType> xrefs = feature.getXref();
+ if (xrefs != null)
+ {
+ boolean mappingUsed = false;
+ for (XrefType xref : xrefs)
+ {
+ /*
+ * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+ */
+ String source = DBRefUtils.getCanonicalName(xref.getDb());
+ String version = xref.getSecondaryId();
+ if (version == null || "".equals(version))
+ {
+ version = "0";
+ }
+ DBRefEntry dbref = new DBRefEntry(source, version, xref.getId());
+ DBRefEntry proteinDbRef = new DBRefEntry(source, version,
+ dbref.getAccessionId());
+ if (source.equals(DBRefSource.UNIPROT))
+ {
+ String proteinSeqName = DBRefSource.UNIPROT + "|"
+ + dbref.getAccessionId();
+ if (dnaToProteinMapping != null
+ && dnaToProteinMapping.getTo() != null)
+ {
+ if (mappingUsed)
+ {
+ /*
+ * two or more Uniprot xrefs for the same CDS -
+ * each needs a distinct Mapping (as to a different sequence)
+ */
+ dnaToProteinMapping = new Mapping(dnaToProteinMapping);
+ }
+ mappingUsed = true;
+
+ /*
+ * try to locate the protein mapped to (possibly by a
+ * previous CDS feature); if not found, construct it from
+ * the EMBL translation
+ */
+ SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
+ if (proteinSeq == null)
+ {
+ proteinSeq = new Sequence(proteinSeqName,
+ product.getSequenceAsString());
+ matcher.add(proteinSeq);
+ peptides.add(proteinSeq);
+ }
+ dnaToProteinMapping.setTo(proteinSeq);
+ dnaToProteinMapping.setMappedFromId(proteinId);
+ proteinSeq.addDBRef(proteinDbRef);
+ dbref.setMap(dnaToProteinMapping);
+ }
+ hasUniprotDbref = true;
+ }
+ if (product != null)
+ {
+ /*
+ * copy feature dbref to our protein product
+ */
+ DBRefEntry pref = proteinDbRef;
+ pref.setMap(null); // reference is direct
+ product.addDBRef(pref);
+ // Add converse mapping reference
+ if (dnaToProteinMapping != null)
+ {
+ Mapping pmap = new Mapping(dna,
+ dnaToProteinMapping.getMap().getInverse());
+ pref = new DBRefEntry(sourceDb, sequenceVersion, accession);
+ pref.setMap(pmap);
+ if (dnaToProteinMapping.getTo() != null)
+ {
+ dnaToProteinMapping.getTo().addDBRef(pref);
+ }
+ }
+ }
+ dna.addDBRef(dbref);
+ }
+ }
+
+ /*
+ * if we have a product (translation) but no explicit Uniprot dbref
+ * (example: EMBL AAFI02000057 protein_id EAL65544.1)
+ * then construct mappings to an assumed EMBLCDSPROTEIN accession
+ */
+ if (!hasUniprotDbref && product != null)
+ {
+ if (proteinToEmblProteinRef == null)
+ {
+ // assuming CDSPROTEIN sequence version = dna version (?!)
+ proteinToEmblProteinRef = new DBRefEntry(DBRefSource.EMBLCDSProduct,
+ sequenceVersion, proteinId);
+ }
+ product.addDBRef(proteinToEmblProteinRef);
+
+ if (dnaToProteinMapping != null
+ && dnaToProteinMapping.getTo() != null)
+ {
+ DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
+ DBRefSource.EMBLCDSProduct, sequenceVersion,
+ proteinId);
+ dnaToEmblProteinRef.setMap(dnaToProteinMapping);
+ dnaToProteinMapping.setMappedFromId(proteinId);
+ dna.addDBRef(dnaToEmblProteinRef);
+ }
+ }
+ }
+
@Override
public boolean isDnaCoding()
{
return true;
}
+ /**
+ * Returns the CDS positions as a single array of [start, end, start, end...]
+ * positions. If on the reverse strand, these will be in descending order.
+ *
+ * @param accession
+ * @param feature
+ * @return
+ */
+ protected int[] getCdsRanges(String accession, Feature feature)
+ {
+ String location = feature.getLocation();
+ if (location == null)
+ {
+ return new int[] {};
+ }
+
+ try
+ {
+ List<int[]> ranges = DnaUtils.parseLocation(location);
+ return listToArray(ranges);
+ } catch (ParseException e)
+ {
+ Cache.log.warn(
+ String.format("Not parsing inexact CDS location %s in ENA %s",
+ location, accession));
+ return new int[] {};
+ }
+ }
+
+ /**
+ * Converts a list of [start, end] ranges to a single array of [start, end,
+ * start, end ...]
+ *
+ * @param ranges
+ * @return
+ */
+ int[] listToArray(List<int[]> ranges)
+ {
+ int[] result = new int[ranges.size() * 2];
+ int i = 0;
+ for (int[] range : ranges)
+ {
+ result[i++] = range[0];
+ result[i++] = range[1];
+ }
+ return result;
+ }
+
+ /**
+ * Helper method to construct a SequenceFeature for one cds range
+ *
+ * @param type
+ * feature type ("CDS")
+ * @param desc
+ * description
+ * @param begin
+ * start position
+ * @param end
+ * end position
+ * @param group
+ * feature group
+ * @param vals
+ * map of 'miscellaneous values' for feature
+ * @return
+ */
+ protected SequenceFeature makeCdsFeature(String type, String desc,
+ int begin, int end, String group, Map<String, String> vals)
+ {
+ SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
+ if (!vals.isEmpty())
+ {
+ StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for (Entry<String, String> val : vals.entrySet())
+ {
+ if (!first)
+ {
+ sb.append(";");
+ }
+ sb.append(val.getKey()).append("=").append(val.getValue());
+ first = false;
+ sf.setValue(val.getKey(), val.getValue());
+ }
+ sf.setAttributes(sb.toString());
+ }
+ return sf;
+ }
+
+ /**
+ * Truncates (if necessary) the exon intervals to match 3 times the length of
+ * the protein; also accepts 3 bases longer (for stop codon not included in
+ * protein)
+ *
+ * @param proteinLength
+ * @param exon
+ * an array of [start, end, start, end...] intervals
+ * @return the same array (if unchanged) or a truncated copy
+ */
+ static int[] adjustForProteinLength(int proteinLength, int[] exon)
+ {
+ if (proteinLength <= 0 || exon == null)
+ {
+ return exon;
+ }
+ int expectedCdsLength = proteinLength * 3;
+ int exonLength = MappingUtils.getLength(Arrays.asList(exon));
+
+ /*
+ * if exon length matches protein, or is shorter, or longer by the
+ * length of a stop codon (3 bases), then leave it unchanged
+ */
+ if (expectedCdsLength >= exonLength
+ || expectedCdsLength == exonLength - 3)
+ {
+ return exon;
+ }
+
+ int origxon[];
+ int sxpos = -1;
+ int endxon = 0;
+ origxon = new int[exon.length];
+ System.arraycopy(exon, 0, origxon, 0, exon.length);
+ int cdspos = 0;
+ for (int x = 0; x < exon.length; x += 2)
+ {
+ cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
+ if (expectedCdsLength <= cdspos)
+ {
+ // advanced beyond last codon.
+ sxpos = x;
+ if (expectedCdsLength != cdspos)
+ {
+ // System.err
+ // .println("Truncating final exon interval on region by "
+ // + (cdspos - cdslength));
+ }
+
+ /*
+ * shrink the final exon - reduce end position if forward
+ * strand, increase it if reverse
+ */
+ if (exon[x + 1] >= exon[x])
+ {
+ endxon = exon[x + 1] - cdspos + expectedCdsLength;
+ }
+ else
+ {
+ endxon = exon[x + 1] + cdspos - expectedCdsLength;
+ }
+ break;
+ }
+ }
+
+ if (sxpos != -1)
+ {
+ // and trim the exon interval set if necessary
+ int[] nxon = new int[sxpos + 2];
+ System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
+ nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
+ // set
+ exon = nxon;
+ }
+ return exon;
+ }
+
}
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.uniprot.UniprotEntry;
-import jalview.datamodel.xdb.uniprot.UniprotFeature;
-import jalview.datamodel.xdb.uniprot.UniprotFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.StringUtils;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
+import jalview.xml.binding.uniprot.DbReferenceType;
+import jalview.xml.binding.uniprot.Entry;
+import jalview.xml.binding.uniprot.FeatureType;
+import jalview.xml.binding.uniprot.LocationType;
+import jalview.xml.binding.uniprot.PositionType;
+import jalview.xml.binding.uniprot.PropertyType;
import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
+import java.util.List;
import java.util.Vector;
-import org.exolab.castor.mapping.Mapping;
-import org.exolab.castor.xml.Unmarshaller;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
import com.stevesoft.pat.Regex;
/**
+ * This class queries the Uniprot database for sequence data, unmarshals the
+ * returned XML, and converts it to Jalview Sequence records (including attached
+ * database references and sequence features)
+ *
* @author JimP
*
*/
private static final String BAR_DELIMITER = "|";
- /*
- * Castor mapping loaded from uniprot_mapping.xml
- */
- private static Mapping map;
-
/**
* Constructor
*/
return "0"; // we really don't know what version we're on.
}
- /**
- * Reads a file containing the reply to the EBI Fetch Uniprot data query,
- * unmarshals it to a UniprotFile object, and returns the list of UniprotEntry
- * data models (mapped from <entry> elements)
- *
- * @param fileReader
- * @return
- */
- public Vector<UniprotEntry> getUniprotEntries(Reader fileReader)
- {
- UniprotFile uni = new UniprotFile();
- try
- {
- if (map == null)
- {
- // 1. Load the mapping information from the file
- map = new Mapping(uni.getClass().getClassLoader());
- URL url = getClass().getResource("/uniprot_mapping.xml");
- map.loadMapping(url);
- }
-
- // 2. Unmarshal the data
- Unmarshaller unmar = new Unmarshaller(uni);
- unmar.setIgnoreExtraElements(true);
- unmar.setMapping(map);
- if (fileReader != null)
- {
- uni = (UniprotFile) unmar.unmarshal(fileReader);
- }
- } catch (Exception e)
- {
- System.out.println("Error getUniprotEntries() " + e);
- }
-
- return uni.getUniprotEntries();
- }
-
/*
* (non-Javadoc)
*
String downloadstring = getDomain() + "/uniprot/" + queries
+ ".xml";
- URL url = null;
- URLConnection urlconn = null;
- url = new URL(downloadstring);
- urlconn = url.openConnection();
+ URL url = new URL(downloadstring);
+ URLConnection urlconn = url.openConnection();
InputStream istr = urlconn.getInputStream();
- Vector<UniprotEntry> entries = getUniprotEntries(
- new InputStreamReader(istr, "UTF-8"));
-
+ List<Entry> entries = getUniprotEntries(istr);
if (entries != null)
{
- ArrayList<SequenceI> seqs = new ArrayList<>();
- for (UniprotEntry entry : entries)
+ List<SequenceI> seqs = new ArrayList<>();
+ for (Entry entry : entries)
{
- seqs.add(uniprotEntryToSequenceI(entry));
+ seqs.add(uniprotEntryToSequence(entry));
}
- al = new Alignment(seqs.toArray(new SequenceI[0]));
-
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
}
+
stopQuery();
return al;
} catch (Exception e)
}
/**
+ * Converts an Entry object (bound from Uniprot XML) to a Jalview Sequence
*
* @param entry
- * UniprotEntry
- * @return SequenceI instance created from the UniprotEntry instance
+ * @return
*/
- public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
+ SequenceI uniprotEntryToSequence(Entry entry)
{
String id = getUniprotEntryId(entry);
+ String seqString = entry.getSequence().getValue();
+
+ /*
+ * for backwards compatibility with Castor processing,
+ * remove any internal spaces
+ */
+ if (seqString.indexOf(' ') > -1)
+ {
+ seqString = seqString.replace(" ", "");
+ }
SequenceI sequence = new Sequence(id,
- entry.getUniprotSequence().getContent());
+ seqString);
sequence.setDescription(getUniprotEntryDescription(entry));
+ /*
+ * add a 'self' DBRefEntry for each accession
+ */
final String dbVersion = getDbVersion();
- ArrayList<DBRefEntry> dbRefs = new ArrayList<>();
+ List<DBRefEntry> dbRefs = new ArrayList<>();
for (String accessionId : entry.getAccession())
{
DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
accessionId);
-
- // mark dbRef as a primary reference for this sequence
dbRefs.add(dbRef);
}
- Vector<PDBEntry> onlyPdbEntries = new Vector<>();
- for (PDBEntry pdb : entry.getDbReference())
+ /*
+ * add a DBRefEntry for each dbReference element in the XML;
+ * also add a PDBEntry if type="PDB";
+ * also add an EMBLCDS dbref if protein sequence id is given
+ * also add an Ensembl dbref " " " " " "
+ */
+ Vector<PDBEntry> pdbRefs = new Vector<>();
+ for (DbReferenceType dbref : entry.getDbReference())
{
- DBRefEntry dbr = new DBRefEntry();
- dbr.setSource(pdb.getType());
- dbr.setAccessionId(pdb.getId());
- dbr.setVersion(DBRefSource.UNIPROT + ":" + dbVersion);
+ String type = dbref.getType();
+ DBRefEntry dbr = new DBRefEntry(type,
+ DBRefSource.UNIPROT + ":" + dbVersion, dbref.getId());
dbRefs.add(dbr);
- if ("PDB".equals(pdb.getType()))
+ if ("PDB".equals(type))
{
- onlyPdbEntries.addElement(pdb);
+ pdbRefs.add(new PDBEntry(dbr));
}
- if ("EMBL".equals(pdb.getType()))
+ if ("EMBL".equals(type))
{
- // look for a CDS reference and add it, too.
- String cdsId = (String) pdb.getProperty("protein sequence ID");
+ /*
+ * e.g. Uniprot accession Q9BXM7 has
+ * <dbReference type="EMBL" id="M19359">
+ * <property type="protein sequence ID" value="AAA40981.1"/>
+ * <property type="molecule type" value="Genomic_DNA"/>
+ * </dbReference>
+ */
+ String cdsId = getProperty(dbref.getProperty(),
+ "protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
// remove version
String[] vrs = cdsId.split("\\.");
- dbr = new DBRefEntry(DBRefSource.EMBLCDS, vrs.length > 1 ? vrs[1]
- : DBRefSource.UNIPROT + ":" + dbVersion, vrs[0]);
+ String version = vrs.length > 1 ? vrs[1]
+ : DBRefSource.UNIPROT + ":" + dbVersion;
+ dbr = new DBRefEntry(DBRefSource.EMBLCDS, version, vrs[0]);
dbRefs.add(dbr);
}
}
- if ("Ensembl".equals(pdb.getType()))
+ if ("Ensembl".equals(type))
{
- /*UniprotXML
+ /*
+ * e.g. Uniprot accession Q9BXM7 has
* <dbReference type="Ensembl" id="ENST00000321556">
- * <molecule id="Q9BXM7-1"/>
- * <property type="protein sequence ID" value="ENSP00000364204"/>
- * <property type="gene ID" value="ENSG00000158828"/>
- * </dbReference>
+ * <molecule id="Q9BXM7-1"/>
+ * <property type="protein sequence ID" value="ENSP00000364204"/>
+ * <property type="gene ID" value="ENSG00000158828"/>
+ * </dbReference>
*/
- String cdsId = (String) pdb.getProperty("protein sequence ID");
+ String cdsId = getProperty(dbref.getProperty(),
+ "protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
dbr = new DBRefEntry(DBRefSource.ENSEMBL,
DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim());
dbRefs.add(dbr);
-
}
}
}
- sequence.setPDBId(onlyPdbEntries);
+ /*
+ * create features; they have either begin and end, or position, in XML
+ */
+ sequence.setPDBId(pdbRefs);
if (entry.getFeature() != null)
{
- for (UniprotFeature uf : entry.getFeature())
+ for (FeatureType uf : entry.getFeature())
{
- SequenceFeature copy = new SequenceFeature(uf.getType(),
- uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
- copy.setStatus(uf.getStatus());
- sequence.addSequenceFeature(copy);
+ LocationType location = uf.getLocation();
+ int start = 0;
+ int end = 0;
+ if (location.getPosition() != null)
+ {
+ start = location.getPosition().getPosition().intValue();
+ end = start;
+ }
+ else
+ {
+ start = location.getBegin().getPosition().intValue();
+ end = location.getEnd().getPosition().intValue();
+ }
+ SequenceFeature sf = new SequenceFeature(uf.getType(),
+ getDescription(uf), start, end, "Uniprot");
+ sf.setStatus(uf.getStatus());
+ sequence.addSequenceFeature(sf);
}
}
for (DBRefEntry dbr : dbRefs)
}
/**
+ * A helper method that builds a sequence feature description
*
- * @param entry
- * UniportEntry
- * @return protein name(s) delimited by a white space character
+ * @param feature
+ * @return
*/
- public static String getUniprotEntryDescription(UniprotEntry entry)
+ static String getDescription(FeatureType feature)
{
- StringBuilder desc = new StringBuilder(32);
- if (entry.getProtein() != null && entry.getProtein().getName() != null)
+ String orig = feature.getOriginal();
+ List<String> variants = feature.getVariation();
+ StringBuilder sb = new StringBuilder();
+
+ /*
+ * append variant in standard format if present
+ * e.g. p.Arg59Lys
+ * multiple variants are split over lines using <br>
+ */
+ boolean asHtml = false;
+ if (orig != null && !orig.isEmpty() && variants != null
+ && !variants.isEmpty())
{
- boolean first = true;
- for (String nm : entry.getProtein().getName())
+ int p = 0;
+ for (String var : variants)
{
- if (!first)
+ // TODO proper HGVS nomenclature for delins structural variations
+ // http://varnomen.hgvs.org/recommendations/protein/variant/delins/
+ // for now we are pragmatic - any orig/variant sequence longer than
+ // three characters is shown with single-character notation rather than
+ // three-letter notation
+ sb.append("p.");
+ if (orig.length() < 4)
+ {
+ for (int c = 0, clen = orig.length(); c < clen; c++)
+ {
+ char origchar = orig.charAt(c);
+ String orig3 = ResidueProperties.aa2Triplet.get("" + origchar);
+ sb.append(orig3 == null ? origchar
+ : StringUtils.toSentenceCase(orig3));
+ }
+ }
+ else
{
- desc.append(" ");
+ sb.append(orig);
+ }
+
+ LocationType location = feature.getLocation();
+ PositionType start = location.getPosition() == null
+ ? location.getBegin()
+ : location.getPosition();
+ sb.append(Integer.toString(start.getPosition().intValue()));
+
+ if (var.length() < 4)
+ {
+ for (int c = 0, clen = var.length(); c < clen; c++)
+ {
+ char varchar = var.charAt(c);
+ String var3 = ResidueProperties.aa2Triplet.get("" + varchar);
+
+ sb.append(var3 != null ? StringUtils.toSentenceCase(var3)
+ : "" + varchar);
+ }
+ }
+ else
+ {
+ sb.append(var);
+ }
+ if (++p != variants.size())
+ {
+ sb.append("<br/> ");
+ asHtml = true;
+ }
+ else
+ {
+ sb.append(" ");
}
- first = false;
- desc.append(nm);
}
}
- return desc.toString();
+ String description = feature.getDescription();
+ if (description != null)
+ {
+ sb.append(description);
+ }
+ if (asHtml)
+ {
+ sb.insert(0, "<html>");
+ sb.append("</html>");
+ }
+
+ return sb.toString();
+ }
+
+ /**
+ * A helper method that searches the list of properties for one with the given
+ * key, and if found returns the property value, else returns null
+ *
+ * @param properties
+ * @param key
+ * @return
+ */
+ static String getProperty(List<PropertyType> properties, String key)
+ {
+ String value = null;
+ if (properties != null)
+ {
+ for (PropertyType prop : properties)
+ {
+ if (key.equals(prop.getType()))
+ {
+ value = prop.getValue();
+ break;
+ }
+ }
+ }
+ return value;
+ }
+
+ /**
+ * Extracts xml element entry/protein/recommendedName/fullName
+ *
+ * @param entry
+ * @return
+ */
+ static String getUniprotEntryDescription(Entry entry)
+ {
+ String desc = "";
+ if (entry.getProtein() != null
+ && entry.getProtein().getRecommendedName() != null)
+ {
+ // fullName is mandatory if recommendedName is present
+ desc = entry.getProtein().getRecommendedName().getFullName()
+ .getValue();
+ }
+ return desc;
}
/**
- *
+ * Constructs a sequence id by concatenating all entry/name elements with '|'
+ * separator
+ *
* @param entry
- * UniprotEntry
- * @return The accession id(s) and name(s) delimited by '|'.
+ * @return
*/
- public static String getUniprotEntryId(UniprotEntry entry)
+ static String getUniprotEntryId(Entry entry)
{
StringBuilder name = new StringBuilder(32);
for (String n : entry.getName())
{
return 0;
}
+
+ /**
+ * Reads the reply to the EBI Fetch Uniprot data query, unmarshals it to an
+ * Uniprot object, and returns the enclosed Entry objects, or null on any
+ * failure
+ *
+ * @param is
+ * @return
+ */
+ public List<Entry> getUniprotEntries(InputStream is)
+ {
+ List<Entry> entries = null;
+ try
+ {
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.uniprot");
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(is);
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ jalview.xml.binding.uniprot.Uniprot uniprot = (jalview.xml.binding.uniprot.Uniprot) um.unmarshal(streamReader);
+ if (uniprot != null && !uniprot.getEntry().isEmpty())
+ {
+ entries = uniprot.getEntry();
+ }
+ } catch (JAXBException | XMLStreamException
+ | FactoryConfigurationError e)
+ {
+ e.printStackTrace();
+ }
+ return entries;
+ }
}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for EntrySetType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="EntrySetType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence maxOccurs="unbounded">
+ * <element name="entry" type="{}EntryType"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "EntrySetType", propOrder = {
+ "entry"
+})
+public class EntrySetType {
+
+ @XmlElement(required = true)
+ protected List<EntryType> entry;
+
+ /**
+ * Gets the value of the entry property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the entry property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEntry().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType }
+ *
+ *
+ */
+ public List<EntryType> getEntry() {
+ if (entry == null) {
+ entry = new ArrayList<EntryType>();
+ }
+ return this.entry;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElements;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+
+/**
+ * <p>Java class for EntryType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="EntryType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="projectAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="keyword" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="reference" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+ * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="submission"/>
+ * <enumeration value="book"/>
+ * <enumeration value="article"/>
+ * <enumeration value="patent"/>
+ * <enumeration value="thesis"/>
+ * <enumeration value="unpublished"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="feature" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="assembly" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="range" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="contig" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <choice maxOccurs="unbounded" minOccurs="0">
+ * <element name="range">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="gap">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="entryVersion" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="dataClass" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxonomicDivision" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="moleculeType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceLength" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="topology" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="circular"/>
+ * <enumeration value="linear"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="firstPublic" type="{http://www.w3.org/2001/XMLSchema}date" />
+ * <attribute name="firstPublicRelease" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="lastUpdated" type="{http://www.w3.org/2001/XMLSchema}date" />
+ * <attribute name="lastUpdatedRelease" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "EntryType", propOrder = {
+ "secondaryAccession",
+ "projectAccession",
+ "description",
+ "comment",
+ "keyword",
+ "reference",
+ "xref",
+ "feature",
+ "assembly",
+ "contig",
+ "sequence"
+})
+public class EntryType {
+
+ protected List<String> secondaryAccession;
+ protected List<String> projectAccession;
+ @XmlElement(required = true)
+ protected String description;
+ protected String comment;
+ protected List<String> keyword;
+ protected List<EntryType.Reference> reference;
+ protected List<XrefType> xref;
+ protected List<EntryType.Feature> feature;
+ protected EntryType.Assembly assembly;
+ protected EntryType.Contig contig;
+ protected String sequence;
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+ @XmlAttribute(name = "entryVersion")
+ protected BigInteger entryVersion;
+ @XmlAttribute(name = "dataClass", required = true)
+ protected String dataClass;
+ @XmlAttribute(name = "taxonomicDivision", required = true)
+ protected String taxonomicDivision;
+ @XmlAttribute(name = "moleculeType", required = true)
+ protected String moleculeType;
+ @XmlAttribute(name = "sequenceLength", required = true)
+ protected BigInteger sequenceLength;
+ @XmlAttribute(name = "topology", required = true)
+ protected String topology;
+ @XmlAttribute(name = "firstPublic")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar firstPublic;
+ @XmlAttribute(name = "firstPublicRelease")
+ protected BigInteger firstPublicRelease;
+ @XmlAttribute(name = "lastUpdated")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar lastUpdated;
+ @XmlAttribute(name = "lastUpdatedRelease")
+ protected BigInteger lastUpdatedRelease;
+
+ /**
+ * Gets the value of the secondaryAccession property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryAccession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSecondaryAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getSecondaryAccession() {
+ if (secondaryAccession == null) {
+ secondaryAccession = new ArrayList<String>();
+ }
+ return this.secondaryAccession;
+ }
+
+ /**
+ * Gets the value of the projectAccession property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the projectAccession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProjectAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getProjectAccession() {
+ if (projectAccession == null) {
+ projectAccession = new ArrayList<String>();
+ }
+ return this.projectAccession;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the comment property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComment() {
+ return comment;
+ }
+
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComment(String value) {
+ this.comment = value;
+ }
+
+ /**
+ * Gets the value of the keyword property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the keyword property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getKeyword().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getKeyword() {
+ if (keyword == null) {
+ keyword = new ArrayList<String>();
+ }
+ return this.keyword;
+ }
+
+ /**
+ * Gets the value of the reference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the reference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Reference }
+ *
+ *
+ */
+ public List<EntryType.Reference> getReference() {
+ if (reference == null) {
+ reference = new ArrayList<EntryType.Reference>();
+ }
+ return this.reference;
+ }
+
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref() {
+ if (xref == null) {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
+
+ /**
+ * Gets the value of the feature property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the feature property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFeature().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature }
+ *
+ *
+ */
+ public List<EntryType.Feature> getFeature() {
+ if (feature == null) {
+ feature = new ArrayList<EntryType.Feature>();
+ }
+ return this.feature;
+ }
+
+ /**
+ * Gets the value of the assembly property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly getAssembly() {
+ return assembly;
+ }
+
+ /**
+ * Sets the value of the assembly property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Assembly }
+ *
+ */
+ public void setAssembly(EntryType.Assembly value) {
+ this.assembly = value;
+ }
+
+ /**
+ * Gets the value of the contig property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig getContig() {
+ return contig;
+ }
+
+ /**
+ * Sets the value of the contig property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Contig }
+ *
+ */
+ public void setContig(EntryType.Contig value) {
+ this.contig = value;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequence(String value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccession() {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccession(String value) {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the entryVersion property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEntryVersion() {
+ return entryVersion;
+ }
+
+ /**
+ * Sets the value of the entryVersion property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEntryVersion(BigInteger value) {
+ this.entryVersion = value;
+ }
+
+ /**
+ * Gets the value of the dataClass property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDataClass() {
+ return dataClass;
+ }
+
+ /**
+ * Sets the value of the dataClass property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDataClass(String value) {
+ this.dataClass = value;
+ }
+
+ /**
+ * Gets the value of the taxonomicDivision property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTaxonomicDivision() {
+ return taxonomicDivision;
+ }
+
+ /**
+ * Sets the value of the taxonomicDivision property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTaxonomicDivision(String value) {
+ this.taxonomicDivision = value;
+ }
+
+ /**
+ * Gets the value of the moleculeType property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMoleculeType() {
+ return moleculeType;
+ }
+
+ /**
+ * Sets the value of the moleculeType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMoleculeType(String value) {
+ this.moleculeType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceLength property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getSequenceLength() {
+ return sequenceLength;
+ }
+
+ /**
+ * Sets the value of the sequenceLength property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setSequenceLength(BigInteger value) {
+ this.sequenceLength = value;
+ }
+
+ /**
+ * Gets the value of the topology property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTopology() {
+ return topology;
+ }
+
+ /**
+ * Sets the value of the topology property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTopology(String value) {
+ this.topology = value;
+ }
+
+ /**
+ * Gets the value of the firstPublic property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getFirstPublic() {
+ return firstPublic;
+ }
+
+ /**
+ * Sets the value of the firstPublic property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setFirstPublic(XMLGregorianCalendar value) {
+ this.firstPublic = value;
+ }
+
+ /**
+ * Gets the value of the firstPublicRelease property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getFirstPublicRelease() {
+ return firstPublicRelease;
+ }
+
+ /**
+ * Sets the value of the firstPublicRelease property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setFirstPublicRelease(BigInteger value) {
+ this.firstPublicRelease = value;
+ }
+
+ /**
+ * Gets the value of the lastUpdated property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getLastUpdated() {
+ return lastUpdated;
+ }
+
+ /**
+ * Sets the value of the lastUpdated property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setLastUpdated(XMLGregorianCalendar value) {
+ this.lastUpdated = value;
+ }
+
+ /**
+ * Gets the value of the lastUpdatedRelease property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getLastUpdatedRelease() {
+ return lastUpdatedRelease;
+ }
+
+ /**
+ * Sets the value of the lastUpdatedRelease property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setLastUpdatedRelease(BigInteger value) {
+ this.lastUpdatedRelease = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="range" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "range"
+ })
+ public static class Assembly {
+
+ @XmlElement(required = true)
+ protected List<EntryType.Assembly.Range> range;
+
+ /**
+ * Gets the value of the range property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the range property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRange().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Assembly.Range }
+ *
+ *
+ */
+ public List<EntryType.Assembly.Range> getRange() {
+ if (range == null) {
+ range = new ArrayList<EntryType.Assembly.Range>();
+ }
+ return this.range;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin() {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value) {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd() {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value) {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccession() {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccession(String value) {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isComplement() {
+ if (complement == null) {
+ return false;
+ } else {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value) {
+ this.complement = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <choice maxOccurs="unbounded" minOccurs="0">
+ * <element name="range">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="gap">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "rangeOrGap"
+ })
+ public static class Contig {
+
+ @XmlElements({
+ @XmlElement(name = "range", type = EntryType.Contig.Range.class),
+ @XmlElement(name = "gap", type = EntryType.Contig.Gap.class)
+ })
+ protected List<Object> rangeOrGap;
+
+ /**
+ * Gets the value of the rangeOrGap property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the rangeOrGap property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRangeOrGap().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Contig.Range }
+ * {@link EntryType.Contig.Gap }
+ *
+ *
+ */
+ public List<Object> getRangeOrGap() {
+ if (rangeOrGap == null) {
+ rangeOrGap = new ArrayList<Object>();
+ }
+ return this.rangeOrGap;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Gap {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+ @XmlAttribute(name = "length", required = true)
+ protected BigInteger length;
+ @XmlAttribute(name = "unknownLength")
+ protected Boolean unknownLength;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the length property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getLength() {
+ return length;
+ }
+
+ /**
+ * Sets the value of the length property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setLength(BigInteger value) {
+ this.length = value;
+ }
+
+ /**
+ * Gets the value of the unknownLength property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isUnknownLength() {
+ if (unknownLength == null) {
+ return false;
+ } else {
+ return unknownLength;
+ }
+ }
+
+ /**
+ * Sets the value of the unknownLength property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setUnknownLength(Boolean value) {
+ this.unknownLength = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin() {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value) {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd() {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value) {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccession() {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccession(String value) {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isComplement() {
+ if (complement == null) {
+ return false;
+ } else {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value) {
+ this.complement = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "taxon",
+ "xref",
+ "qualifier"
+ })
+ public static class Feature {
+
+ protected EntryType.Feature.FeatureTaxon taxon;
+ protected List<XrefType> xref;
+ protected List<EntryType.Feature.Qualifier> qualifier;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "location", required = true)
+ protected String location;
+
+ /**
+ * Gets the value of the taxon property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon getTaxon() {
+ return taxon;
+ }
+
+ /**
+ * Sets the value of the taxon property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public void setTaxon(EntryType.Feature.FeatureTaxon value) {
+ this.taxon = value;
+ }
+
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref() {
+ if (xref == null) {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
+
+ /**
+ * Gets the value of the qualifier property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the qualifier property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getQualifier().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature.Qualifier }
+ *
+ *
+ */
+ public List<EntryType.Feature.Qualifier> getQualifier() {
+ if (qualifier == null) {
+ qualifier = new ArrayList<EntryType.Feature.Qualifier>();
+ }
+ return this.qualifier;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the location property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLocation() {
+ return location;
+ }
+
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocation(String value) {
+ this.location = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "lineage"
+ })
+ public static class FeatureTaxon {
+
+ protected EntryType.Feature.FeatureTaxon.Lineage lineage;
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+ @XmlAttribute(name = "commonName")
+ protected String commonName;
+ @XmlAttribute(name = "taxId")
+ protected BigInteger taxId;
+
+ /**
+ * Gets the value of the lineage property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage getLineage() {
+ return lineage;
+ }
+
+ /**
+ * Sets the value of the lineage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value) {
+ this.lineage = value;
+ }
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getScientificName() {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setScientificName(String value) {
+ this.scientificName = value;
+ }
+
+ /**
+ * Gets the value of the commonName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * Sets the value of the commonName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCommonName(String value) {
+ this.commonName = value;
+ }
+
+ /**
+ * Gets the value of the taxId property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getTaxId() {
+ return taxId;
+ }
+
+ /**
+ * Sets the value of the taxId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setTaxId(BigInteger value) {
+ this.taxId = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "taxon"
+ })
+ public static class Lineage {
+
+ @XmlElement(required = true)
+ protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
+
+ /**
+ * Gets the value of the taxon property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the taxon property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTaxon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+ *
+ *
+ */
+ public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon() {
+ if (taxon == null) {
+ taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
+ }
+ return this.taxon;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Taxon {
+
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getScientificName() {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setScientificName(String value) {
+ this.scientificName = value;
+ }
+
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Qualifier {
+
+ protected String value;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+ * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="submission"/>
+ * <enumeration value="book"/>
+ * <enumeration value="article"/>
+ * <enumeration value="patent"/>
+ * <enumeration value="thesis"/>
+ * <enumeration value="unpublished"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "title",
+ "author",
+ "applicant",
+ "consortium",
+ "submissionDate",
+ "journal",
+ "year",
+ "volume",
+ "issue",
+ "firstPage",
+ "lastPage",
+ "comment",
+ "referenceLocation",
+ "xref"
+ })
+ public static class Reference {
+
+ protected String title;
+ protected List<String> author;
+ protected List<String> applicant;
+ protected String consortium;
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar submissionDate;
+ protected String journal;
+ protected String year;
+ protected String volume;
+ protected String issue;
+ protected String firstPage;
+ protected String lastPage;
+ protected String comment;
+ protected String referenceLocation;
+ protected List<XrefType> xref;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "number", required = true)
+ protected BigInteger number;
+ @XmlAttribute(name = "location")
+ protected String location;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the author property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the author property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAuthor().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAuthor() {
+ if (author == null) {
+ author = new ArrayList<String>();
+ }
+ return this.author;
+ }
+
+ /**
+ * Gets the value of the applicant property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the applicant property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getApplicant().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getApplicant() {
+ if (applicant == null) {
+ applicant = new ArrayList<String>();
+ }
+ return this.applicant;
+ }
+
+ /**
+ * Gets the value of the consortium property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getConsortium() {
+ return consortium;
+ }
+
+ /**
+ * Sets the value of the consortium property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setConsortium(String value) {
+ this.consortium = value;
+ }
+
+ /**
+ * Gets the value of the submissionDate property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getSubmissionDate() {
+ return submissionDate;
+ }
+
+ /**
+ * Sets the value of the submissionDate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setSubmissionDate(XMLGregorianCalendar value) {
+ this.submissionDate = value;
+ }
+
+ /**
+ * Gets the value of the journal property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getJournal() {
+ return journal;
+ }
+
+ /**
+ * Sets the value of the journal property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setJournal(String value) {
+ this.journal = value;
+ }
+
+ /**
+ * Gets the value of the year property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getYear() {
+ return year;
+ }
+
+ /**
+ * Sets the value of the year property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setYear(String value) {
+ this.year = value;
+ }
+
+ /**
+ * Gets the value of the volume property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVolume() {
+ return volume;
+ }
+
+ /**
+ * Sets the value of the volume property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVolume(String value) {
+ this.volume = value;
+ }
+
+ /**
+ * Gets the value of the issue property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getIssue() {
+ return issue;
+ }
+
+ /**
+ * Sets the value of the issue property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setIssue(String value) {
+ this.issue = value;
+ }
+
+ /**
+ * Gets the value of the firstPage property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFirstPage() {
+ return firstPage;
+ }
+
+ /**
+ * Sets the value of the firstPage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFirstPage(String value) {
+ this.firstPage = value;
+ }
+
+ /**
+ * Gets the value of the lastPage property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLastPage() {
+ return lastPage;
+ }
+
+ /**
+ * Sets the value of the lastPage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLastPage(String value) {
+ this.lastPage = value;
+ }
+
+ /**
+ * Gets the value of the comment property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComment() {
+ return comment;
+ }
+
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComment(String value) {
+ this.comment = value;
+ }
+
+ /**
+ * Gets the value of the referenceLocation property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getReferenceLocation() {
+ return referenceLocation;
+ }
+
+ /**
+ * Sets the value of the referenceLocation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setReferenceLocation(String value) {
+ this.referenceLocation = value;
+ }
+
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref() {
+ if (xref == null) {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the number property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getNumber() {
+ return number;
+ }
+
+ /**
+ * Sets the value of the number property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setNumber(BigInteger value) {
+ this.number = value;
+ }
+
+ /**
+ * Gets the value of the location property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLocation() {
+ return location;
+ }
+
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocation(String value) {
+ this.location = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import javax.xml.bind.annotation.XmlRegistry;
+
+
+/**
+ * This object contains factory methods for each
+ * Java content interface and Java element interface
+ * generated in the jalview.xml.binding.embl package.
+ * <p>An ObjectFactory allows you to programatically
+ * construct new instances of the Java representation
+ * for XML content. The Java representation of XML
+ * content can consist of schema derived interfaces
+ * and classes representing the binding of schema
+ * type definitions, element declarations and model
+ * groups. Factory methods for each of these are
+ * provided in this class.
+ *
+ */
+@XmlRegistry
+public class ObjectFactory {
+
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.embl
+ *
+ */
+ public ObjectFactory() {
+ }
+
+ /**
+ * Create an instance of {@link EntryType }
+ *
+ */
+ public EntryType createEntryType() {
+ return new EntryType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig createEntryTypeContig() {
+ return new EntryType.Contig();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly createEntryTypeAssembly() {
+ return new EntryType.Assembly();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature }
+ *
+ */
+ public EntryType.Feature createEntryTypeFeature() {
+ return new EntryType.Feature();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() {
+ return new EntryType.Feature.FeatureTaxon();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() {
+ return new EntryType.Feature.FeatureTaxon.Lineage();
+ }
+
+ /**
+ * Create an instance of {@link ROOT }
+ *
+ */
+ public ROOT createROOT() {
+ return new ROOT();
+ }
+
+ /**
+ * Create an instance of {@link EntrySetType }
+ *
+ */
+ public EntrySetType createEntrySetType() {
+ return new EntrySetType();
+ }
+
+ /**
+ * Create an instance of {@link XrefType }
+ *
+ */
+ public XrefType createXrefType() {
+ return new XrefType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Reference }
+ *
+ */
+ public EntryType.Reference createEntryTypeReference() {
+ return new EntryType.Reference();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Range }
+ *
+ */
+ public EntryType.Contig.Range createEntryTypeContigRange() {
+ return new EntryType.Contig.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Gap }
+ *
+ */
+ public EntryType.Contig.Gap createEntryTypeContigGap() {
+ return new EntryType.Contig.Gap();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly.Range }
+ *
+ */
+ public EntryType.Assembly.Range createEntryTypeAssemblyRange() {
+ return new EntryType.Assembly.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.Qualifier }
+ *
+ */
+ public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() {
+ return new EntryType.Feature.Qualifier();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() {
+ return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <choice>
+ * <element name="entrySet" type="{}EntrySetType"/>
+ * <element name="entry" type="{}EntryType"/>
+ * </choice>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "entrySet",
+ "entry"
+})
+@XmlRootElement(name = "ROOT")
+public class ROOT {
+
+ protected EntrySetType entrySet;
+ protected EntryType entry;
+
+ /**
+ * Gets the value of the entrySet property.
+ *
+ * @return
+ * possible object is
+ * {@link EntrySetType }
+ *
+ */
+ public EntrySetType getEntrySet() {
+ return entrySet;
+ }
+
+ /**
+ * Sets the value of the entrySet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntrySetType }
+ *
+ */
+ public void setEntrySet(EntrySetType value) {
+ this.entrySet = value;
+ }
+
+ /**
+ * Gets the value of the entry property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType }
+ *
+ */
+ public EntryType getEntry() {
+ return entry;
+ }
+
+ /**
+ * Sets the value of the entry property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType }
+ *
+ */
+ public void setEntry(EntryType value) {
+ this.entry = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Database cross-reference.
+ *
+ * <p>Java class for XrefType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="XrefType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="db" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="secondaryId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "XrefType")
+public class XrefType {
+
+ @XmlAttribute(name = "db", required = true)
+ protected String db;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "secondaryId")
+ protected String secondaryId;
+
+ /**
+ * Gets the value of the db property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDb() {
+ return db;
+ }
+
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDb(String value) {
+ this.db = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the secondaryId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSecondaryId() {
+ return secondaryId;
+ }
+
+ /**
+ * Sets the value of the secondaryId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSecondaryId(String value) {
+ this.secondaryId = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ * </sequence>
+ * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "alcodon",
+ "alcodMap"
+})
+@XmlRootElement(name = "AlcodonFrame")
+public class AlcodonFrame {
+
+ protected List<AlcodonFrame.Alcodon> alcodon;
+ protected List<AlcodonFrame.AlcodMap> alcodMap;
+
+ /**
+ * Gets the value of the alcodon property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alcodon property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlcodon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.Alcodon }
+ *
+ *
+ */
+ public List<AlcodonFrame.Alcodon> getAlcodon() {
+ if (alcodon == null) {
+ alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+ }
+ return this.alcodon;
+ }
+
+ /**
+ * Gets the value of the alcodMap property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlcodMap().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.AlcodMap }
+ *
+ *
+ */
+ public List<AlcodonFrame.AlcodMap> getAlcodMap() {
+ if (alcodMap == null) {
+ alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+ }
+ return this.alcodMap;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ * </sequence>
+ * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "mapping"
+ })
+ public static class AlcodMap {
+
+ @XmlElement(name = "Mapping", required = true)
+ protected Mapping mapping;
+ @XmlAttribute(name = "dnasq", required = true)
+ protected String dnasq;
+
+ /**
+ *
+ * a Mapping entry and an associated protein sequence
+ *
+ *
+ * @return
+ * possible object is
+ * {@link Mapping }
+ *
+ */
+ public Mapping getMapping() {
+ return mapping;
+ }
+
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Mapping }
+ *
+ */
+ public void setMapping(Mapping value) {
+ this.mapping = value;
+ }
+
+ /**
+ * Gets the value of the dnasq property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDnasq() {
+ return dnasq;
+ }
+
+ /**
+ * Sets the value of the dnasq property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDnasq(String value) {
+ this.dnasq = value;
+ }
+
+ }
+
+
+ /**
+ *
+ * specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
+ * Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
+ *
+ *
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Alcodon {
+
+ @XmlAttribute(name = "pos1")
+ protected BigInteger pos1;
+ @XmlAttribute(name = "pos2")
+ protected BigInteger pos2;
+ @XmlAttribute(name = "pos3")
+ protected BigInteger pos3;
+
+ /**
+ * Gets the value of the pos1 property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPos1() {
+ return pos1;
+ }
+
+ /**
+ * Sets the value of the pos1 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPos1(BigInteger value) {
+ this.pos1 = value;
+ }
+
+ /**
+ * Gets the value of the pos2 property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPos2() {
+ return pos2;
+ }
+
+ /**
+ * Sets the value of the pos2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPos2(BigInteger value) {
+ this.pos2 = value;
+ }
+
+ /**
+ * Gets the value of the pos3 property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPos3() {
+ return pos3;
+ }
+
+ /**
+ * Sets the value of the pos3 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPos3(BigInteger value) {
+ this.pos3 = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="thresholdLine" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="property" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "annotationElement",
+ "label",
+ "description",
+ "thresholdLine",
+ "property"
+})
+@XmlRootElement(name = "Annotation")
+public class Annotation {
+
+ protected List<AnnotationElement> annotationElement;
+ @XmlElement(required = true)
+ protected String label;
+ protected String description;
+ protected Annotation.ThresholdLine thresholdLine;
+ protected List<Annotation.Property> property;
+ @XmlAttribute(name = "graph", required = true)
+ protected boolean graph;
+ @XmlAttribute(name = "graphType")
+ protected Integer graphType;
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+ @XmlAttribute(name = "groupRef")
+ protected String groupRef;
+ @XmlAttribute(name = "graphColour")
+ protected Integer graphColour;
+ @XmlAttribute(name = "graphGroup")
+ protected Integer graphGroup;
+ @XmlAttribute(name = "graphHeight")
+ protected Integer graphHeight;
+ @XmlAttribute(name = "id")
+ protected String id;
+ @XmlAttribute(name = "scoreOnly")
+ protected Boolean scoreOnly;
+ @XmlAttribute(name = "score")
+ protected Double score;
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+ @XmlAttribute(name = "centreColLabels")
+ protected Boolean centreColLabels;
+ @XmlAttribute(name = "scaleColLabels")
+ protected Boolean scaleColLabels;
+ @XmlAttribute(name = "showAllColLabels")
+ protected Boolean showAllColLabels;
+ @XmlAttribute(name = "autoCalculated")
+ protected Boolean autoCalculated;
+ @XmlAttribute(name = "belowAlignment")
+ protected Boolean belowAlignment;
+ @XmlAttribute(name = "calcId")
+ protected String calcId;
+
+ /**
+ * Gets the value of the annotationElement property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAnnotationElement().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AnnotationElement }
+ *
+ *
+ */
+ public List<AnnotationElement> getAnnotationElement() {
+ if (annotationElement == null) {
+ annotationElement = new ArrayList<AnnotationElement>();
+ }
+ return this.annotationElement;
+ }
+
+ /**
+ * Gets the value of the label property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLabel() {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLabel(String value) {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the thresholdLine property.
+ *
+ * @return
+ * possible object is
+ * {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine getThresholdLine() {
+ return thresholdLine;
+ }
+
+ /**
+ * Sets the value of the thresholdLine property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Annotation.ThresholdLine }
+ *
+ */
+ public void setThresholdLine(Annotation.ThresholdLine value) {
+ this.thresholdLine = value;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Annotation.Property }
+ *
+ *
+ */
+ public List<Annotation.Property> getProperty() {
+ if (property == null) {
+ property = new ArrayList<Annotation.Property>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the graph property.
+ *
+ */
+ public boolean isGraph() {
+ return graph;
+ }
+
+ /**
+ * Sets the value of the graph property.
+ *
+ */
+ public void setGraph(boolean value) {
+ this.graph = value;
+ }
+
+ /**
+ * Gets the value of the graphType property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGraphType() {
+ return graphType;
+ }
+
+ /**
+ * Sets the value of the graphType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphType(Integer value) {
+ this.graphType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceRef() {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceRef(String value) {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the groupRef property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getGroupRef() {
+ return groupRef;
+ }
+
+ /**
+ * Sets the value of the groupRef property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setGroupRef(String value) {
+ this.groupRef = value;
+ }
+
+ /**
+ * Gets the value of the graphColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGraphColour() {
+ return graphColour;
+ }
+
+ /**
+ * Sets the value of the graphColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphColour(Integer value) {
+ this.graphColour = value;
+ }
+
+ /**
+ * Gets the value of the graphGroup property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGraphGroup() {
+ return graphGroup;
+ }
+
+ /**
+ * Sets the value of the graphGroup property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphGroup(Integer value) {
+ this.graphGroup = value;
+ }
+
+ /**
+ * Gets the value of the graphHeight property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGraphHeight() {
+ return graphHeight;
+ }
+
+ /**
+ * Sets the value of the graphHeight property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphHeight(Integer value) {
+ this.graphHeight = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the scoreOnly property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isScoreOnly() {
+ if (scoreOnly == null) {
+ return false;
+ } else {
+ return scoreOnly;
+ }
+ }
+
+ /**
+ * Sets the value of the scoreOnly property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScoreOnly(Boolean value) {
+ this.scoreOnly = value;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * @return
+ * possible object is
+ * {@link Double }
+ *
+ */
+ public Double getScore() {
+ return score;
+ }
+
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Double }
+ *
+ */
+ public void setScore(Double value) {
+ this.score = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value) {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the centreColLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isCentreColLabels() {
+ return centreColLabels;
+ }
+
+ /**
+ * Sets the value of the centreColLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCentreColLabels(Boolean value) {
+ this.centreColLabels = value;
+ }
+
+ /**
+ * Gets the value of the scaleColLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isScaleColLabels() {
+ return scaleColLabels;
+ }
+
+ /**
+ * Sets the value of the scaleColLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScaleColLabels(Boolean value) {
+ this.scaleColLabels = value;
+ }
+
+ /**
+ * Gets the value of the showAllColLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowAllColLabels() {
+ return showAllColLabels;
+ }
+
+ /**
+ * Sets the value of the showAllColLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowAllColLabels(Boolean value) {
+ this.showAllColLabels = value;
+ }
+
+ /**
+ * Gets the value of the autoCalculated property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isAutoCalculated() {
+ if (autoCalculated == null) {
+ return false;
+ } else {
+ return autoCalculated;
+ }
+ }
+
+ /**
+ * Sets the value of the autoCalculated property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoCalculated(Boolean value) {
+ this.autoCalculated = value;
+ }
+
+ /**
+ * Gets the value of the belowAlignment property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isBelowAlignment() {
+ if (belowAlignment == null) {
+ return true;
+ } else {
+ return belowAlignment;
+ }
+ }
+
+ /**
+ * Sets the value of the belowAlignment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setBelowAlignment(Boolean value) {
+ this.belowAlignment = value;
+ }
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCalcId() {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCalcId(String value) {
+ this.calcId = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Property {
+
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "value")
+ protected String value;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class ThresholdLine {
+
+ @XmlAttribute(name = "label")
+ protected String label;
+ @XmlAttribute(name = "value")
+ protected Float value;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ /**
+ * Gets the value of the label property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLabel() {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLabel(String value) {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setValue(Float value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for AnnotationColourScheme complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="AnnotationColourScheme">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
+public class AnnotationColourScheme {
+
+ @XmlAttribute(name = "aboveThreshold")
+ protected Integer aboveThreshold;
+ @XmlAttribute(name = "annotation")
+ protected String annotation;
+ @XmlAttribute(name = "minColour")
+ protected Integer minColour;
+ @XmlAttribute(name = "maxColour")
+ protected Integer maxColour;
+ @XmlAttribute(name = "colourScheme")
+ protected String colourScheme;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "perSequence")
+ protected Boolean perSequence;
+ @XmlAttribute(name = "predefinedColours")
+ protected Boolean predefinedColours;
+
+ /**
+ * Gets the value of the aboveThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getAboveThreshold() {
+ return aboveThreshold;
+ }
+
+ /**
+ * Sets the value of the aboveThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setAboveThreshold(Integer value) {
+ this.aboveThreshold = value;
+ }
+
+ /**
+ * Gets the value of the annotation property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAnnotation() {
+ return annotation;
+ }
+
+ /**
+ * Sets the value of the annotation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAnnotation(String value) {
+ this.annotation = value;
+ }
+
+ /**
+ * Gets the value of the minColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMinColour() {
+ return minColour;
+ }
+
+ /**
+ * Sets the value of the minColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMinColour(Integer value) {
+ this.minColour = value;
+ }
+
+ /**
+ * Gets the value of the maxColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMaxColour() {
+ return maxColour;
+ }
+
+ /**
+ * Sets the value of the maxColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMaxColour(Integer value) {
+ this.maxColour = value;
+ }
+
+ /**
+ * Gets the value of the colourScheme property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getColourScheme() {
+ return colourScheme;
+ }
+
+ /**
+ * Sets the value of the colourScheme property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setColourScheme(String value) {
+ this.colourScheme = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the perSequence property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPerSequence() {
+ return perSequence;
+ }
+
+ /**
+ * Sets the value of the perSequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPerSequence(Boolean value) {
+ this.perSequence = value;
+ }
+
+ /**
+ * Gets the value of the predefinedColours property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPredefinedColours() {
+ return predefinedColours;
+ }
+
+ /**
+ * Sets the value of the predefinedColours property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPredefinedColours(Boolean value) {
+ this.predefinedColours = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="secondaryStructure" minOccurs="0">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <length value="1"/>
+ * </restriction>
+ * </simpleType>
+ * </element>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "displayCharacter",
+ "description",
+ "secondaryStructure",
+ "value"
+})
+@XmlRootElement(name = "annotationElement")
+public class AnnotationElement {
+
+ protected String displayCharacter;
+ protected String description;
+ protected String secondaryStructure;
+ protected Float value;
+ @XmlAttribute(name = "position", required = true)
+ protected int position;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ /**
+ * Gets the value of the displayCharacter property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDisplayCharacter() {
+ return displayCharacter;
+ }
+
+ /**
+ * Sets the value of the displayCharacter property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDisplayCharacter(String value) {
+ this.displayCharacter = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSecondaryStructure() {
+ return secondaryStructure;
+ }
+
+ /**
+ * Sets the value of the secondaryStructure property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSecondaryStructure(String value) {
+ this.secondaryStructure = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setValue(Float value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ */
+ public int getPosition() {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ */
+ public void setPosition(int value) {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for feature complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="feature">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="otherData" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
+ "otherData"
+})
+public class Feature {
+
+ protected List<Feature.OtherData> otherData;
+ @XmlAttribute(name = "begin", required = true)
+ protected int begin;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "description")
+ protected String description;
+ @XmlAttribute(name = "status")
+ protected String status;
+ @XmlAttribute(name = "featureGroup")
+ protected String featureGroup;
+ @XmlAttribute(name = "score")
+ protected Float score;
+
+ /**
+ * Gets the value of the otherData property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the otherData property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getOtherData().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Feature.OtherData }
+ *
+ *
+ */
+ public List<Feature.OtherData> getOtherData() {
+ if (otherData == null) {
+ otherData = new ArrayList<Feature.OtherData>();
+ }
+ return this.otherData;
+ }
+
+ /**
+ * Gets the value of the begin property.
+ *
+ */
+ public int getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ */
+ public void setBegin(int value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getStatus() {
+ return status;
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
+
+ /**
+ * Gets the value of the featureGroup property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFeatureGroup() {
+ return featureGroup;
+ }
+
+ /**
+ * Sets the value of the featureGroup property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFeatureGroup(String value) {
+ this.featureGroup = value;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getScore() {
+ return score;
+ }
+
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setScore(Float value) {
+ this.score = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class OtherData {
+
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
+ @XmlAttribute(name = "key2")
+ protected String key2;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey() {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey(String value) {
+ this.key = value;
+ }
+
+ /**
+ * Gets the value of the key2 property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey2() {
+ return key2;
+ }
+
+ /**
+ * Sets the value of the key2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey2(String value) {
+ this.key2 = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for FeatureMatcher complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="FeatureMatcher">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attribute name="by" type="{www.jalview.org/colours}FilterBy" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
+ "attributeName",
+ "condition",
+ "value"
+})
+public class FeatureMatcher {
+
+ @XmlElement(namespace = "")
+ protected List<String> attributeName;
+ @XmlElement(namespace = "", required = true)
+ protected String condition;
+ @XmlElement(namespace = "", required = true)
+ protected String value;
+ @XmlAttribute(name = "by")
+ protected FilterBy by;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the condition property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCondition() {
+ return condition;
+ }
+
+ /**
+ * Sets the value of the condition property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCondition(String value) {
+ this.condition = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the by property.
+ *
+ * @return
+ * possible object is
+ * {@link FilterBy }
+ *
+ */
+ public FilterBy getBy() {
+ return by;
+ }
+
+ /**
+ * Sets the value of the by property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FilterBy }
+ *
+ */
+ public void setBy(FilterBy value) {
+ this.by = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * A feature match condition, which may be simple or compound
+ *
+ * <p>Java class for FeatureMatcherSet complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="FeatureMatcherSet">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <choice>
+ * <element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
+ * <element name="compoundMatcher">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+ * </sequence>
+ * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
+ "matchCondition",
+ "compoundMatcher"
+})
+public class FeatureMatcherSet {
+
+ @XmlElement(namespace = "")
+ protected FeatureMatcher matchCondition;
+ @XmlElement(namespace = "")
+ protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+
+ /**
+ * Gets the value of the matchCondition property.
+ *
+ * @return
+ * possible object is
+ * {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher getMatchCondition() {
+ return matchCondition;
+ }
+
+ /**
+ * Sets the value of the matchCondition property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcher }
+ *
+ */
+ public void setMatchCondition(FeatureMatcher value) {
+ this.matchCondition = value;
+ }
+
+ /**
+ * Gets the value of the compoundMatcher property.
+ *
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() {
+ return compoundMatcher;
+ }
+
+ /**
+ * Sets the value of the compoundMatcher property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
+ this.compoundMatcher = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+ * </sequence>
+ * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "matcherSet"
+ })
+ public static class CompoundMatcher {
+
+ @XmlElement(namespace = "", required = true)
+ protected List<FeatureMatcherSet> matcherSet;
+ @XmlAttribute(name = "and", required = true)
+ protected boolean and;
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMatcherSet().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link FeatureMatcherSet }
+ *
+ *
+ */
+ public List<FeatureMatcherSet> getMatcherSet() {
+ if (matcherSet == null) {
+ matcherSet = new ArrayList<FeatureMatcherSet>();
+ }
+ return this.matcherSet;
+ }
+
+ /**
+ * Gets the value of the and property.
+ *
+ */
+ public boolean isAnd() {
+ return and;
+ }
+
+ /**
+ * Sets the value of the and property.
+ *
+ */
+ public void setAnd(boolean value) {
+ this.and = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlEnum;
+import javax.xml.bind.annotation.XmlEnumValue;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for FilterBy.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * <simpleType name="FilterBy">
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="byLabel"/>
+ * <enumeration value="byScore"/>
+ * <enumeration value="byAttribute"/>
+ * </restriction>
+ * </simpleType>
+ * </pre>
+ *
+ */
+@XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
+@XmlEnum
+public enum FilterBy {
+
+ @XmlEnumValue("byLabel")
+ BY_LABEL("byLabel"),
+ @XmlEnumValue("byScore")
+ BY_SCORE("byScore"),
+ @XmlEnumValue("byAttribute")
+ BY_ATTRIBUTE("byAttribute");
+ private final String value;
+
+ FilterBy(String v) {
+ value = v;
+ }
+
+ public String value() {
+ return value;
+ }
+
+ public static FilterBy fromValue(String v) {
+ for (FilterBy c: FilterBy.values()) {
+ if (c.value.equals(v)) {
+ return c;
+ }
+ }
+ throw new IllegalArgumentException(v);
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlID;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+
+/**
+ * <p>Java class for JalviewModel complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="JalviewModel">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ * <sequence>
+ * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="tree" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="FeatureSettings" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
+ "creationDate",
+ "version",
+ "vamsasModel",
+ "jSeq",
+ "jGroup",
+ "viewport",
+ "userColours",
+ "tree",
+ "featureSettings"
+})
+public class JalviewModel {
+
+ @XmlElement(required = true)
+ @XmlSchemaType(name = "dateTime")
+ protected XMLGregorianCalendar creationDate;
+ @XmlElement(required = true)
+ protected String version;
+ @XmlElement(required = true)
+ protected VAMSAS vamsasModel;
+ @XmlElement(name = "JSeq")
+ protected List<JalviewModel.JSeq> jSeq;
+ @XmlElement(name = "JGroup")
+ protected List<JalviewModel.JGroup> jGroup;
+ @XmlElement(name = "Viewport")
+ protected List<JalviewModel.Viewport> viewport;
+ @XmlElement(name = "UserColours")
+ protected List<JalviewModel.UserColours> userColours;
+ protected List<JalviewModel.Tree> tree;
+ @XmlElement(name = "FeatureSettings")
+ protected JalviewModel.FeatureSettings featureSettings;
+
+ /**
+ * Gets the value of the creationDate property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreationDate() {
+ return creationDate;
+ }
+
+ /**
+ * Sets the value of the creationDate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreationDate(XMLGregorianCalendar value) {
+ this.creationDate = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVersion(String value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the vamsasModel property.
+ *
+ * @return
+ * possible object is
+ * {@link VAMSAS }
+ *
+ */
+ public VAMSAS getVamsasModel() {
+ return vamsasModel;
+ }
+
+ /**
+ * Sets the value of the vamsasModel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link VAMSAS }
+ *
+ */
+ public void setVamsasModel(VAMSAS value) {
+ this.vamsasModel = value;
+ }
+
+ /**
+ * Gets the value of the jSeq property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getJSeq().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq> getJSeq() {
+ if (jSeq == null) {
+ jSeq = new ArrayList<JalviewModel.JSeq>();
+ }
+ return this.jSeq;
+ }
+
+ /**
+ * Gets the value of the jGroup property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getJGroup().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JGroup }
+ *
+ *
+ */
+ public List<JalviewModel.JGroup> getJGroup() {
+ if (jGroup == null) {
+ jGroup = new ArrayList<JalviewModel.JGroup>();
+ }
+ return this.jGroup;
+ }
+
+ /**
+ * Gets the value of the viewport property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the viewport property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getViewport().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport> getViewport() {
+ if (viewport == null) {
+ viewport = new ArrayList<JalviewModel.Viewport>();
+ }
+ return this.viewport;
+ }
+
+ /**
+ * Gets the value of the userColours property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the userColours property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getUserColours().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.UserColours }
+ *
+ *
+ */
+ public List<JalviewModel.UserColours> getUserColours() {
+ if (userColours == null) {
+ userColours = new ArrayList<JalviewModel.UserColours>();
+ }
+ return this.userColours;
+ }
+
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Tree }
+ *
+ *
+ */
+ public List<JalviewModel.Tree> getTree() {
+ if (tree == null) {
+ tree = new ArrayList<JalviewModel.Tree>();
+ }
+ return this.tree;
+ }
+
+ /**
+ * Gets the value of the featureSettings property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings getFeatureSettings() {
+ return featureSettings;
+ }
+
+ /**
+ * Sets the value of the featureSettings property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public void setFeatureSettings(JalviewModel.FeatureSettings value) {
+ this.featureSettings = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "setting",
+ "group"
+ })
+ public static class FeatureSettings {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Setting> setting;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Group> group;
+
+ /**
+ * Gets the value of the setting property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the setting property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSetting().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Setting }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Setting> getSetting() {
+ if (setting == null) {
+ setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+ }
+ return this.setting;
+ }
+
+ /**
+ * Gets the value of the group property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the group property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGroup().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Group }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Group> getGroup() {
+ if (group == null) {
+ group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+ }
+ return this.group;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay() {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value) {
+ this.display = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "attributeName",
+ "matcherSet"
+ })
+ public static class Setting {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<String> attributeName;
+ @XmlElement(namespace = "www.jalview.org")
+ protected FeatureMatcherSet matcherSet;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "colour", required = true)
+ protected int colour;
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+ @XmlAttribute(name = "order")
+ protected Float order;
+ @XmlAttribute(name = "mincolour")
+ protected Integer mincolour;
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "threshstate")
+ protected Integer threshstate;
+ @XmlAttribute(name = "max")
+ protected Float max;
+ @XmlAttribute(name = "min")
+ protected Float min;
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet() {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value) {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ */
+ public int getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ */
+ public void setColour(int value) {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay() {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value) {
+ this.display = value;
+ }
+
+ /**
+ * Gets the value of the order property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getOrder() {
+ return order;
+ }
+
+ /**
+ * Sets the value of the order property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setOrder(Float value) {
+ this.order = value;
+ }
+
+ /**
+ * Gets the value of the mincolour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMincolour() {
+ return mincolour;
+ }
+
+ /**
+ * Sets the value of the mincolour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMincolour(Integer value) {
+ this.mincolour = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour() {
+ if (noValueColour == null) {
+ return NoValueColour.MIN;
+ } else {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value) {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the threshstate property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getThreshstate() {
+ return threshstate;
+ }
+
+ /**
+ * Sets the value of the threshstate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setThreshstate(Integer value) {
+ this.threshstate = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMax() {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMax(Float value) {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMin() {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMin(Float value) {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel() {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value) {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale() {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value) {
+ this.autoScale = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "seq",
+ "annotationColours"
+ })
+ public static class JGroup {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<String> seq;
+ @XmlElement(namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+ @XmlAttribute(name = "start")
+ protected Integer start;
+ @XmlAttribute(name = "end")
+ protected Integer end;
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "colour")
+ protected String colour;
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+ @XmlAttribute(name = "outlineColour")
+ protected Integer outlineColour;
+ @XmlAttribute(name = "displayBoxes")
+ protected Boolean displayBoxes;
+ @XmlAttribute(name = "displayText")
+ protected Boolean displayText;
+ @XmlAttribute(name = "colourText")
+ protected Boolean colourText;
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the seq property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the seq property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSeq().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getSeq() {
+ if (seq == null) {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
+ }
+
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return
+ * possible object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours() {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value) {
+ this.annotationColours = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStart(Integer value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setEnd(Integer value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setColour(String value) {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getConsThreshold() {
+ return consThreshold;
+ }
+
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value) {
+ this.consThreshold = value;
+ }
+
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getPidThreshold() {
+ return pidThreshold;
+ }
+
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value) {
+ this.pidThreshold = value;
+ }
+
+ /**
+ * Gets the value of the outlineColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getOutlineColour() {
+ return outlineColour;
+ }
+
+ /**
+ * Sets the value of the outlineColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setOutlineColour(Integer value) {
+ this.outlineColour = value;
+ }
+
+ /**
+ * Gets the value of the displayBoxes property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isDisplayBoxes() {
+ return displayBoxes;
+ }
+
+ /**
+ * Sets the value of the displayBoxes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setDisplayBoxes(Boolean value) {
+ this.displayBoxes = value;
+ }
+
+ /**
+ * Gets the value of the displayText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isDisplayText() {
+ return displayText;
+ }
+
+ /**
+ * Sets the value of the displayText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setDisplayText(Boolean value) {
+ this.displayText = value;
+ }
+
+ /**
+ * Gets the value of the colourText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isColourText() {
+ return colourText;
+ }
+
+ /**
+ * Sets the value of the colourText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourText(Boolean value) {
+ this.colourText = value;
+ }
+
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol1() {
+ return textCol1;
+ }
+
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value) {
+ this.textCol1 = value;
+ }
+
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol2() {
+ return textCol2;
+ }
+
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value) {
+ this.textCol2 = value;
+ }
+
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold() {
+ return textColThreshold;
+ }
+
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value) {
+ this.textColThreshold = value;
+ }
+
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowUnconserved() {
+ return showUnconserved;
+ }
+
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value) {
+ this.showUnconserved = value;
+ }
+
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus() {
+ if (ignoreGapsinConsensus == null) {
+ return true;
+ } else {
+ return ignoreGapsinConsensus;
+ }
+ }
+
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value) {
+ this.ignoreGapsinConsensus = value;
+ }
+
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram() {
+ if (showConsensusHistogram == null) {
+ return true;
+ } else {
+ return showConsensusHistogram;
+ }
+ }
+
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value) {
+ this.showConsensusHistogram = value;
+ }
+
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo() {
+ if (showSequenceLogo == null) {
+ return false;
+ } else {
+ return showSequenceLogo;
+ }
+ }
+
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value) {
+ this.showSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo() {
+ if (normaliseSequenceLogo == null) {
+ return false;
+ } else {
+ return normaliseSequenceLogo;
+ }
+ }
+
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value) {
+ this.normaliseSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "features",
+ "pdbids",
+ "hiddenSequences",
+ "rnaViewer"
+ })
+ public static class JSeq {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<Feature> features;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids> pdbids;
+ @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+ protected List<Integer> hiddenSequences;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "hidden")
+ protected Boolean hidden;
+ @XmlAttribute(name = "viewreference")
+ protected Boolean viewreference;
+
+ /**
+ * Gets the value of the features property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the features property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFeatures().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Feature }
+ *
+ *
+ */
+ public List<Feature> getFeatures() {
+ if (features == null) {
+ features = new ArrayList<Feature>();
+ }
+ return this.features;
+ }
+
+ /**
+ * Gets the value of the pdbids property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getPdbids().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.Pdbids> getPdbids() {
+ if (pdbids == null) {
+ pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
+ }
+ return this.pdbids;
+ }
+
+ /**
+ * Gets the value of the hiddenSequences property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getHiddenSequences().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getHiddenSequences() {
+ if (hiddenSequences == null) {
+ hiddenSequences = new ArrayList<Integer>();
+ }
+ return this.hiddenSequences;
+ }
+
+ /**
+ * Gets the value of the rnaViewer property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRnaViewer().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
+ if (rnaViewer == null) {
+ rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
+ }
+ return this.rnaViewer;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the hidden property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isHidden() {
+ return hidden;
+ }
+
+ /**
+ * Sets the value of the hidden property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setHidden(Boolean value) {
+ this.hidden = value;
+ }
+
+ /**
+ * Gets the value of the viewreference property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isViewreference() {
+ return viewreference;
+ }
+
+ /**
+ * Sets the value of the viewreference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setViewreference(Boolean value) {
+ this.viewreference = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "structureState"
+ })
+ public static class Pdbids
+ extends Pdbentry
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
+
+ /**
+ * Gets the value of the structureState property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the structureState property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getStructureState().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
+ if (structureState == null) {
+ structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
+ }
+ return this.structureState;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class StructureState {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+ @XmlAttribute(name = "type")
+ protected String type;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value) {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewId() {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewId(String value) {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the alignwithAlignPanel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isAlignwithAlignPanel() {
+ if (alignwithAlignPanel == null) {
+ return true;
+ } else {
+ return alignwithAlignPanel;
+ }
+ }
+
+ /**
+ * Sets the value of the alignwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAlignwithAlignPanel(Boolean value) {
+ this.alignwithAlignPanel = value;
+ }
+
+ /**
+ * Gets the value of the colourwithAlignPanel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColourwithAlignPanel() {
+ if (colourwithAlignPanel == null) {
+ return false;
+ } else {
+ return colourwithAlignPanel;
+ }
+ }
+
+ /**
+ * Sets the value of the colourwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourwithAlignPanel(Boolean value) {
+ this.colourwithAlignPanel = value;
+ }
+
+ /**
+ * Gets the value of the colourByJmol property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColourByJmol() {
+ if (colourByJmol == null) {
+ return true;
+ } else {
+ return colourByJmol;
+ }
+ }
+
+ /**
+ * Sets the value of the colourByJmol property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByJmol(Boolean value) {
+ this.colourByJmol = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "secondaryStructure"
+ })
+ public static class RnaViewer {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+ @XmlAttribute(name = "dividerLocation")
+ protected Integer dividerLocation;
+ @XmlAttribute(name = "selectedRna")
+ protected Integer selectedRna;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSecondaryStructure().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
+ if (secondaryStructure == null) {
+ secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
+ }
+ return this.secondaryStructure;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewId() {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewId(String value) {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the dividerLocation property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getDividerLocation() {
+ return dividerLocation;
+ }
+
+ /**
+ * Sets the value of the dividerLocation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setDividerLocation(Integer value) {
+ this.dividerLocation = value;
+ }
+
+ /**
+ * Gets the value of the selectedRna property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getSelectedRna() {
+ return selectedRna;
+ }
+
+ /**
+ * Sets the value of the selectedRna property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setSelectedRna(Integer value) {
+ this.selectedRna = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure {
+
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the annotationId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAnnotationId() {
+ return annotationId;
+ }
+
+ /**
+ * Sets the value of the annotationId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAnnotationId(String value) {
+ this.annotationId = value;
+ }
+
+ /**
+ * Gets the value of the gapped property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isGapped() {
+ return gapped;
+ }
+
+ /**
+ * Sets the value of the gapped property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setGapped(Boolean value) {
+ this.gapped = value;
+ }
+
+ /**
+ * Gets the value of the viewerState property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewerState() {
+ return viewerState;
+ }
+
+ /**
+ * Sets the value of the viewerState property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewerState(String value) {
+ this.viewerState = value;
+ }
+
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "title",
+ "newick"
+ })
+ public static class Tree {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getNewick() {
+ return newick;
+ }
+
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setNewick(String value) {
+ this.newick = value;
+ }
+
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
+
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
+
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
+
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
+
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
+
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap() {
+ return showBootstrap;
+ }
+
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value) {
+ this.showBootstrap = value;
+ }
+
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances() {
+ return showDistances;
+ }
+
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value) {
+ this.showDistances = value;
+ }
+
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked() {
+ return markUnlinked;
+ }
+
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value) {
+ this.markUnlinked = value;
+ }
+
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow() {
+ return fitToWindow;
+ }
+
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value) {
+ this.fitToWindow = value;
+ }
+
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree() {
+ return currentTree;
+ }
+
+ /**
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCurrentTree(Boolean value) {
+ this.currentTree = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "userColourScheme"
+ })
+ public static class UserColours {
+
+ @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
+ protected JalviewUserColours userColourScheme;
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme() {
+ return userColourScheme;
+ }
+
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value) {
+ this.userColourScheme = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "annotationColours",
+ "hiddenColumns",
+ "calcIdParam"
+ })
+ public static class Viewport {
+
+ @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+ @XmlAttribute(name = "conservationSelected")
+ protected Boolean conservationSelected;
+ @XmlAttribute(name = "pidSelected")
+ protected Boolean pidSelected;
+ @XmlAttribute(name = "bgColour")
+ protected String bgColour;
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "showFullId")
+ protected Boolean showFullId;
+ @XmlAttribute(name = "rightAlignIds")
+ protected Boolean rightAlignIds;
+ @XmlAttribute(name = "showText")
+ protected Boolean showText;
+ @XmlAttribute(name = "showColourText")
+ protected Boolean showColourText;
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+ @XmlAttribute(name = "showBoxes")
+ protected Boolean showBoxes;
+ @XmlAttribute(name = "wrapAlignment")
+ protected Boolean wrapAlignment;
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
+ @XmlAttribute(name = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
+ @XmlAttribute(name = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
+ @XmlAttribute(name = "viewName")
+ protected String viewName;
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return
+ * possible object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours() {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value) {
+ this.annotationColours = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColumns property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getHiddenColumns().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
+ if (hiddenColumns == null) {
+ hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
+ }
+ return this.hiddenColumns;
+ }
+
+ /**
+ * Gets the value of the calcIdParam property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCalcIdParam().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
+ if (calcIdParam == null) {
+ calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
+ }
+ return this.calcIdParam;
+ }
+
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected() {
+ return conservationSelected;
+ }
+
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value) {
+ this.conservationSelected = value;
+ }
+
+ /**
+ * Gets the value of the pidSelected property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected() {
+ return pidSelected;
+ }
+
+ /**
+ * Sets the value of the pidSelected property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPidSelected(Boolean value) {
+ this.pidSelected = value;
+ }
+
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getBgColour() {
+ return bgColour;
+ }
+
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setBgColour(String value) {
+ this.bgColour = value;
+ }
+
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getConsThreshold() {
+ return consThreshold;
+ }
+
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value) {
+ this.consThreshold = value;
+ }
+
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getPidThreshold() {
+ return pidThreshold;
+ }
+
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value) {
+ this.pidThreshold = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the showFullId property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowFullId() {
+ return showFullId;
+ }
+
+ /**
+ * Sets the value of the showFullId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowFullId(Boolean value) {
+ this.showFullId = value;
+ }
+
+ /**
+ * Gets the value of the rightAlignIds property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isRightAlignIds() {
+ return rightAlignIds;
+ }
+
+ /**
+ * Sets the value of the rightAlignIds property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setRightAlignIds(Boolean value) {
+ this.rightAlignIds = value;
+ }
+
+ /**
+ * Gets the value of the showText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowText() {
+ return showText;
+ }
+
+ /**
+ * Sets the value of the showText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowText(Boolean value) {
+ this.showText = value;
+ }
+
+ /**
+ * Gets the value of the showColourText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowColourText() {
+ return showColourText;
+ }
+
+ /**
+ * Sets the value of the showColourText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowColourText(Boolean value) {
+ this.showColourText = value;
+ }
+
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowUnconserved() {
+ if (showUnconserved == null) {
+ return false;
+ } else {
+ return showUnconserved;
+ }
+ }
+
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value) {
+ this.showUnconserved = value;
+ }
+
+ /**
+ * Gets the value of the showBoxes property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBoxes() {
+ return showBoxes;
+ }
+
+ /**
+ * Sets the value of the showBoxes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBoxes(Boolean value) {
+ this.showBoxes = value;
+ }
+
+ /**
+ * Gets the value of the wrapAlignment property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isWrapAlignment() {
+ return wrapAlignment;
+ }
+
+ /**
+ * Sets the value of the wrapAlignment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setWrapAlignment(Boolean value) {
+ this.wrapAlignment = value;
+ }
+
+ /**
+ * Gets the value of the renderGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isRenderGaps() {
+ return renderGaps;
+ }
+
+ /**
+ * Sets the value of the renderGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setRenderGaps(Boolean value) {
+ this.renderGaps = value;
+ }
+
+ /**
+ * Gets the value of the showSequenceFeatures property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures() {
+ return showSequenceFeatures;
+ }
+
+ /**
+ * Sets the value of the showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value) {
+ this.showSequenceFeatures = value;
+ }
+
+ /**
+ * Gets the value of the showNPfeatureTooltip property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip() {
+ return showNPfeatureTooltip;
+ }
+
+ /**
+ * Sets the value of the showNPfeatureTooltip property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowNPfeatureTooltip(Boolean value) {
+ this.showNPfeatureTooltip = value;
+ }
+
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip() {
+ return showDbRefTooltip;
+ }
+
+ /**
+ * Sets the value of the showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value) {
+ this.showDbRefTooltip = value;
+ }
+
+ /**
+ * Gets the value of the followHighlight property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight() {
+ if (followHighlight == null) {
+ return true;
+ } else {
+ return followHighlight;
+ }
+ }
+
+ /**
+ * Sets the value of the followHighlight property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value) {
+ this.followHighlight = value;
+ }
+
+ /**
+ * Gets the value of the followSelection property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection() {
+ if (followSelection == null) {
+ return true;
+ } else {
+ return followSelection;
+ }
+ }
+
+ /**
+ * Sets the value of the followSelection property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value) {
+ this.followSelection = value;
+ }
+
+ /**
+ * Gets the value of the showAnnotation property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation() {
+ return showAnnotation;
+ }
+
+ /**
+ * Sets the value of the showAnnotation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value) {
+ this.showAnnotation = value;
+ }
+
+ /**
+ * Gets the value of the centreColumnLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels() {
+ if (centreColumnLabels == null) {
+ return false;
+ } else {
+ return centreColumnLabels;
+ }
+ }
+
+ /**
+ * Sets the value of the centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value) {
+ this.centreColumnLabels = value;
+ }
+
+ /**
+ * Gets the value of the showGroupConservation property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation() {
+ if (showGroupConservation == null) {
+ return false;
+ } else {
+ return showGroupConservation;
+ }
+ }
+
+ /**
+ * Sets the value of the showGroupConservation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowGroupConservation(Boolean value) {
+ this.showGroupConservation = value;
+ }
+
+ /**
+ * Gets the value of the showGroupConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus() {
+ if (showGroupConsensus == null) {
+ return false;
+ } else {
+ return showGroupConsensus;
+ }
+ }
+
+ /**
+ * Sets the value of the showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowGroupConsensus(Boolean value) {
+ this.showGroupConsensus = value;
+ }
+
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram() {
+ if (showConsensusHistogram == null) {
+ return true;
+ } else {
+ return showConsensusHistogram;
+ }
+ }
+
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value) {
+ this.showConsensusHistogram = value;
+ }
+
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo() {
+ if (showSequenceLogo == null) {
+ return false;
+ } else {
+ return showSequenceLogo;
+ }
+ }
+
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value) {
+ this.showSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo() {
+ if (normaliseSequenceLogo == null) {
+ return false;
+ } else {
+ return normaliseSequenceLogo;
+ }
+ }
+
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value) {
+ this.normaliseSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus() {
+ if (ignoreGapsinConsensus == null) {
+ return true;
+ } else {
+ return ignoreGapsinConsensus;
+ }
+ }
+
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value) {
+ this.ignoreGapsinConsensus = value;
+ }
+
+ /**
+ * Gets the value of the startRes property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStartRes() {
+ return startRes;
+ }
+
+ /**
+ * Sets the value of the startRes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStartRes(Integer value) {
+ this.startRes = value;
+ }
+
+ /**
+ * Gets the value of the startSeq property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStartSeq() {
+ return startSeq;
+ }
+
+ /**
+ * Sets the value of the startSeq property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStartSeq(Integer value) {
+ this.startSeq = value;
+ }
+
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
+
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
+
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
+
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
+
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
+
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
+
+ /**
+ * Gets the value of the scaleProteinAsCdna property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isScaleProteinAsCdna() {
+ if (scaleProteinAsCdna == null) {
+ return true;
+ } else {
+ return scaleProteinAsCdna;
+ }
+ }
+
+ /**
+ * Sets the value of the scaleProteinAsCdna property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScaleProteinAsCdna(Boolean value) {
+ this.scaleProteinAsCdna = value;
+ }
+
+ /**
+ * Gets the value of the viewName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewName() {
+ return viewName;
+ }
+
+ /**
+ * Sets the value of the viewName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewName(String value) {
+ this.viewName = value;
+ }
+
+ /**
+ * Gets the value of the sequenceSetId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceSetId() {
+ return sequenceSetId;
+ }
+
+ /**
+ * Sets the value of the sequenceSetId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceSetId(String value) {
+ this.sequenceSetId = value;
+ }
+
+ /**
+ * Gets the value of the gatheredViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isGatheredViews() {
+ return gatheredViews;
+ }
+
+ /**
+ * Sets the value of the gatheredViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setGatheredViews(Boolean value) {
+ this.gatheredViews = value;
+ }
+
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol1() {
+ return textCol1;
+ }
+
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value) {
+ this.textCol1 = value;
+ }
+
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol2() {
+ return textCol2;
+ }
+
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value) {
+ this.textCol2 = value;
+ }
+
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold() {
+ return textColThreshold;
+ }
+
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value) {
+ this.textColThreshold = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the complementId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComplementId() {
+ return complementId;
+ }
+
+ /**
+ * Sets the value of the complementId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComplementId(String value) {
+ this.complementId = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam
+ extends WebServiceParameterSet
+ {
+
+ @XmlAttribute(name = "calcId", required = true)
+ protected String calcId;
+ @XmlAttribute(name = "needsUpdate")
+ protected Boolean needsUpdate;
+ @XmlAttribute(name = "autoUpdate", required = true)
+ protected boolean autoUpdate;
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCalcId() {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCalcId(String value) {
+ this.calcId = value;
+ }
+
+ /**
+ * Gets the value of the needsUpdate property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNeedsUpdate() {
+ if (needsUpdate == null) {
+ return false;
+ } else {
+ return needsUpdate;
+ }
+ }
+
+ /**
+ * Sets the value of the needsUpdate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNeedsUpdate(Boolean value) {
+ this.needsUpdate = value;
+ }
+
+ /**
+ * Gets the value of the autoUpdate property.
+ *
+ */
+ public boolean isAutoUpdate() {
+ return autoUpdate;
+ }
+
+ /**
+ * Sets the value of the autoUpdate property.
+ *
+ */
+ public void setAutoUpdate(boolean value) {
+ this.autoUpdate = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStart(Integer value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setEnd(Integer value) {
+ this.end = value;
+ }
+
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.18 at 01:33:02 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlID;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+
+/**
+ * <p>Java class for JalviewModelType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="JalviewModelType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ * <sequence>
+ * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="tree" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="FeatureSettings" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "JalviewModelType", namespace = "www.jalview.org", propOrder = {
+ "creationDate",
+ "version",
+ "vamsasModel",
+ "jSeq",
+ "jGroup",
+ "viewport",
+ "userColours",
+ "tree",
+ "featureSettings"
+})
+public class JalviewModelType {
+
+ @XmlElement(required = true)
+ @XmlSchemaType(name = "dateTime")
+ protected XMLGregorianCalendar creationDate;
+ @XmlElement(required = true)
+ protected String version;
+ @XmlElement(required = true)
+ protected VAMSAS vamsasModel;
+ @XmlElement(name = "JSeq")
+ protected List<JalviewModelType.JSeq> jSeq;
+ @XmlElement(name = "JGroup")
+ protected List<JalviewModelType.JGroup> jGroup;
+ @XmlElement(name = "Viewport")
+ protected List<JalviewModelType.Viewport> viewport;
+ @XmlElement(name = "UserColours")
+ protected List<JalviewModelType.UserColours> userColours;
+ protected List<JalviewModelType.Tree> tree;
+ @XmlElement(name = "FeatureSettings")
+ protected JalviewModelType.FeatureSettings featureSettings;
+
+ /**
+ * Gets the value of the creationDate property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreationDate() {
+ return creationDate;
+ }
+
+ /**
+ * Sets the value of the creationDate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreationDate(XMLGregorianCalendar value) {
+ this.creationDate = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVersion(String value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the vamsasModel property.
+ *
+ * @return
+ * possible object is
+ * {@link VAMSAS }
+ *
+ */
+ public VAMSAS getVamsasModel() {
+ return vamsasModel;
+ }
+
+ /**
+ * Sets the value of the vamsasModel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link VAMSAS }
+ *
+ */
+ public void setVamsasModel(VAMSAS value) {
+ this.vamsasModel = value;
+ }
+
+ /**
+ * Gets the value of the jSeq property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getJSeq().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq> getJSeq() {
+ if (jSeq == null) {
+ jSeq = new ArrayList<JalviewModelType.JSeq>();
+ }
+ return this.jSeq;
+ }
+
+ /**
+ * Gets the value of the jGroup property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getJGroup().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JGroup }
+ *
+ *
+ */
+ public List<JalviewModelType.JGroup> getJGroup() {
+ if (jGroup == null) {
+ jGroup = new ArrayList<JalviewModelType.JGroup>();
+ }
+ return this.jGroup;
+ }
+
+ /**
+ * Gets the value of the viewport property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the viewport property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getViewport().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.Viewport }
+ *
+ *
+ */
+ public List<JalviewModelType.Viewport> getViewport() {
+ if (viewport == null) {
+ viewport = new ArrayList<JalviewModelType.Viewport>();
+ }
+ return this.viewport;
+ }
+
+ /**
+ * Gets the value of the userColours property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the userColours property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getUserColours().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.UserColours }
+ *
+ *
+ */
+ public List<JalviewModelType.UserColours> getUserColours() {
+ if (userColours == null) {
+ userColours = new ArrayList<JalviewModelType.UserColours>();
+ }
+ return this.userColours;
+ }
+
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.Tree }
+ *
+ *
+ */
+ public List<JalviewModelType.Tree> getTree() {
+ if (tree == null) {
+ tree = new ArrayList<JalviewModelType.Tree>();
+ }
+ return this.tree;
+ }
+
+ /**
+ * Gets the value of the featureSettings property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModelType.FeatureSettings }
+ *
+ */
+ public JalviewModelType.FeatureSettings getFeatureSettings() {
+ return featureSettings;
+ }
+
+ /**
+ * Sets the value of the featureSettings property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModelType.FeatureSettings }
+ *
+ */
+ public void setFeatureSettings(JalviewModelType.FeatureSettings value) {
+ this.featureSettings = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "setting",
+ "group"
+ })
+ public static class FeatureSettings {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.FeatureSettings.Setting> setting;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.FeatureSettings.Group> group;
+
+ /**
+ * Gets the value of the setting property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the setting property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSetting().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.FeatureSettings.Setting }
+ *
+ *
+ */
+ public List<JalviewModelType.FeatureSettings.Setting> getSetting() {
+ if (setting == null) {
+ setting = new ArrayList<JalviewModelType.FeatureSettings.Setting>();
+ }
+ return this.setting;
+ }
+
+ /**
+ * Gets the value of the group property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the group property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGroup().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.FeatureSettings.Group }
+ *
+ *
+ */
+ public List<JalviewModelType.FeatureSettings.Group> getGroup() {
+ if (group == null) {
+ group = new ArrayList<JalviewModelType.FeatureSettings.Group>();
+ }
+ return this.group;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay() {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value) {
+ this.display = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "attributeName",
+ "matcherSet"
+ })
+ public static class Setting {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<String> attributeName;
+ @XmlElement(namespace = "www.jalview.org")
+ protected FeatureMatcherSet matcherSet;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "colour", required = true)
+ protected int colour;
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+ @XmlAttribute(name = "order")
+ protected Float order;
+ @XmlAttribute(name = "mincolour")
+ protected Integer mincolour;
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "threshstate")
+ protected Integer threshstate;
+ @XmlAttribute(name = "max")
+ protected Float max;
+ @XmlAttribute(name = "min")
+ protected Float min;
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet() {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value) {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ */
+ public int getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ */
+ public void setColour(int value) {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay() {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value) {
+ this.display = value;
+ }
+
+ /**
+ * Gets the value of the order property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getOrder() {
+ return order;
+ }
+
+ /**
+ * Sets the value of the order property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setOrder(Float value) {
+ this.order = value;
+ }
+
+ /**
+ * Gets the value of the mincolour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMincolour() {
+ return mincolour;
+ }
+
+ /**
+ * Sets the value of the mincolour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMincolour(Integer value) {
+ this.mincolour = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour() {
+ if (noValueColour == null) {
+ return NoValueColour.MIN;
+ } else {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value) {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the threshstate property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getThreshstate() {
+ return threshstate;
+ }
+
+ /**
+ * Sets the value of the threshstate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setThreshstate(Integer value) {
+ this.threshstate = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMax() {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMax(Float value) {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMin() {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMin(Float value) {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel() {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value) {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale() {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value) {
+ this.autoScale = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "seq",
+ "annotationColours"
+ })
+ public static class JGroup {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<String> seq;
+ @XmlElement(namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+ @XmlAttribute(name = "start")
+ protected Integer start;
+ @XmlAttribute(name = "end")
+ protected Integer end;
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "colour")
+ protected String colour;
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+ @XmlAttribute(name = "outlineColour")
+ protected Integer outlineColour;
+ @XmlAttribute(name = "displayBoxes")
+ protected Boolean displayBoxes;
+ @XmlAttribute(name = "displayText")
+ protected Boolean displayText;
+ @XmlAttribute(name = "colourText")
+ protected Boolean colourText;
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the seq property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the seq property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSeq().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getSeq() {
+ if (seq == null) {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
+ }
+
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return
+ * possible object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours() {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value) {
+ this.annotationColours = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStart(Integer value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setEnd(Integer value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setColour(String value) {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getConsThreshold() {
+ return consThreshold;
+ }
+
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value) {
+ this.consThreshold = value;
+ }
+
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getPidThreshold() {
+ return pidThreshold;
+ }
+
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value) {
+ this.pidThreshold = value;
+ }
+
+ /**
+ * Gets the value of the outlineColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getOutlineColour() {
+ return outlineColour;
+ }
+
+ /**
+ * Sets the value of the outlineColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setOutlineColour(Integer value) {
+ this.outlineColour = value;
+ }
+
+ /**
+ * Gets the value of the displayBoxes property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isDisplayBoxes() {
+ return displayBoxes;
+ }
+
+ /**
+ * Sets the value of the displayBoxes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setDisplayBoxes(Boolean value) {
+ this.displayBoxes = value;
+ }
+
+ /**
+ * Gets the value of the displayText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isDisplayText() {
+ return displayText;
+ }
+
+ /**
+ * Sets the value of the displayText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setDisplayText(Boolean value) {
+ this.displayText = value;
+ }
+
+ /**
+ * Gets the value of the colourText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isColourText() {
+ return colourText;
+ }
+
+ /**
+ * Sets the value of the colourText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourText(Boolean value) {
+ this.colourText = value;
+ }
+
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol1() {
+ return textCol1;
+ }
+
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value) {
+ this.textCol1 = value;
+ }
+
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol2() {
+ return textCol2;
+ }
+
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value) {
+ this.textCol2 = value;
+ }
+
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold() {
+ return textColThreshold;
+ }
+
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value) {
+ this.textColThreshold = value;
+ }
+
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowUnconserved() {
+ return showUnconserved;
+ }
+
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value) {
+ this.showUnconserved = value;
+ }
+
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus() {
+ if (ignoreGapsinConsensus == null) {
+ return true;
+ } else {
+ return ignoreGapsinConsensus;
+ }
+ }
+
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value) {
+ this.ignoreGapsinConsensus = value;
+ }
+
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram() {
+ if (showConsensusHistogram == null) {
+ return true;
+ } else {
+ return showConsensusHistogram;
+ }
+ }
+
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value) {
+ this.showConsensusHistogram = value;
+ }
+
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo() {
+ if (showSequenceLogo == null) {
+ return false;
+ } else {
+ return showSequenceLogo;
+ }
+ }
+
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value) {
+ this.showSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo() {
+ if (normaliseSequenceLogo == null) {
+ return false;
+ } else {
+ return normaliseSequenceLogo;
+ }
+ }
+
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value) {
+ this.normaliseSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "features",
+ "pdbids",
+ "hiddenSequences",
+ "rnaViewer"
+ })
+ public static class JSeq {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<Feature> features;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.JSeq.Pdbids> pdbids;
+ @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+ protected List<Integer> hiddenSequences;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.JSeq.RnaViewer> rnaViewer;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "hidden")
+ protected Boolean hidden;
+ @XmlAttribute(name = "viewreference")
+ protected Boolean viewreference;
+
+ /**
+ * Gets the value of the features property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the features property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFeatures().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Feature }
+ *
+ *
+ */
+ public List<Feature> getFeatures() {
+ if (features == null) {
+ features = new ArrayList<Feature>();
+ }
+ return this.features;
+ }
+
+ /**
+ * Gets the value of the pdbids property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getPdbids().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq.Pdbids }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq.Pdbids> getPdbids() {
+ if (pdbids == null) {
+ pdbids = new ArrayList<JalviewModelType.JSeq.Pdbids>();
+ }
+ return this.pdbids;
+ }
+
+ /**
+ * Gets the value of the hiddenSequences property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getHiddenSequences().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getHiddenSequences() {
+ if (hiddenSequences == null) {
+ hiddenSequences = new ArrayList<Integer>();
+ }
+ return this.hiddenSequences;
+ }
+
+ /**
+ * Gets the value of the rnaViewer property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRnaViewer().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq.RnaViewer }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq.RnaViewer> getRnaViewer() {
+ if (rnaViewer == null) {
+ rnaViewer = new ArrayList<JalviewModelType.JSeq.RnaViewer>();
+ }
+ return this.rnaViewer;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the hidden property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isHidden() {
+ return hidden;
+ }
+
+ /**
+ * Sets the value of the hidden property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setHidden(Boolean value) {
+ this.hidden = value;
+ }
+
+ /**
+ * Gets the value of the viewreference property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isViewreference() {
+ return viewreference;
+ }
+
+ /**
+ * Sets the value of the viewreference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setViewreference(Boolean value) {
+ this.viewreference = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "structureState"
+ })
+ public static class Pdbids
+ extends Pdbentry
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.JSeq.Pdbids.StructureState> structureState;
+
+ /**
+ * Gets the value of the structureState property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the structureState property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getStructureState().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq.Pdbids.StructureState }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq.Pdbids.StructureState> getStructureState() {
+ if (structureState == null) {
+ structureState = new ArrayList<JalviewModelType.JSeq.Pdbids.StructureState>();
+ }
+ return this.structureState;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class StructureState {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+ @XmlAttribute(name = "type")
+ protected String type;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value) {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewId() {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewId(String value) {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the alignwithAlignPanel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isAlignwithAlignPanel() {
+ if (alignwithAlignPanel == null) {
+ return true;
+ } else {
+ return alignwithAlignPanel;
+ }
+ }
+
+ /**
+ * Sets the value of the alignwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAlignwithAlignPanel(Boolean value) {
+ this.alignwithAlignPanel = value;
+ }
+
+ /**
+ * Gets the value of the colourwithAlignPanel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColourwithAlignPanel() {
+ if (colourwithAlignPanel == null) {
+ return false;
+ } else {
+ return colourwithAlignPanel;
+ }
+ }
+
+ /**
+ * Sets the value of the colourwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourwithAlignPanel(Boolean value) {
+ this.colourwithAlignPanel = value;
+ }
+
+ /**
+ * Gets the value of the colourByJmol property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColourByJmol() {
+ if (colourByJmol == null) {
+ return true;
+ } else {
+ return colourByJmol;
+ }
+ }
+
+ /**
+ * Sets the value of the colourByJmol property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByJmol(Boolean value) {
+ this.colourByJmol = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "secondaryStructure"
+ })
+ public static class RnaViewer {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+ @XmlAttribute(name = "dividerLocation")
+ protected Integer dividerLocation;
+ @XmlAttribute(name = "selectedRna")
+ protected Integer selectedRna;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSecondaryStructure().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
+ if (secondaryStructure == null) {
+ secondaryStructure = new ArrayList<JalviewModelType.JSeq.RnaViewer.SecondaryStructure>();
+ }
+ return this.secondaryStructure;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewId() {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewId(String value) {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the dividerLocation property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getDividerLocation() {
+ return dividerLocation;
+ }
+
+ /**
+ * Sets the value of the dividerLocation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setDividerLocation(Integer value) {
+ this.dividerLocation = value;
+ }
+
+ /**
+ * Gets the value of the selectedRna property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getSelectedRna() {
+ return selectedRna;
+ }
+
+ /**
+ * Sets the value of the selectedRna property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setSelectedRna(Integer value) {
+ this.selectedRna = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure {
+
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the annotationId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAnnotationId() {
+ return annotationId;
+ }
+
+ /**
+ * Sets the value of the annotationId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAnnotationId(String value) {
+ this.annotationId = value;
+ }
+
+ /**
+ * Gets the value of the gapped property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isGapped() {
+ return gapped;
+ }
+
+ /**
+ * Sets the value of the gapped property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setGapped(Boolean value) {
+ this.gapped = value;
+ }
+
+ /**
+ * Gets the value of the viewerState property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewerState() {
+ return viewerState;
+ }
+
+ /**
+ * Sets the value of the viewerState property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewerState(String value) {
+ this.viewerState = value;
+ }
+
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "title",
+ "newick"
+ })
+ public static class Tree {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getNewick() {
+ return newick;
+ }
+
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setNewick(String value) {
+ this.newick = value;
+ }
+
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
+
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
+
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
+
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
+
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
+
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap() {
+ return showBootstrap;
+ }
+
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value) {
+ this.showBootstrap = value;
+ }
+
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances() {
+ return showDistances;
+ }
+
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value) {
+ this.showDistances = value;
+ }
+
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked() {
+ return markUnlinked;
+ }
+
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value) {
+ this.markUnlinked = value;
+ }
+
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow() {
+ return fitToWindow;
+ }
+
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value) {
+ this.fitToWindow = value;
+ }
+
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree() {
+ return currentTree;
+ }
+
+ /**
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCurrentTree(Boolean value) {
+ this.currentTree = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "userColourScheme"
+ })
+ public static class UserColours {
+
+ @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
+ protected JalviewUserColours userColourScheme;
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme() {
+ return userColourScheme;
+ }
+
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value) {
+ this.userColourScheme = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "annotationColours",
+ "hiddenColumns",
+ "calcIdParam"
+ })
+ public static class Viewport {
+
+ @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.Viewport.HiddenColumns> hiddenColumns;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.Viewport.CalcIdParam> calcIdParam;
+ @XmlAttribute(name = "conservationSelected")
+ protected Boolean conservationSelected;
+ @XmlAttribute(name = "pidSelected")
+ protected Boolean pidSelected;
+ @XmlAttribute(name = "bgColour")
+ protected String bgColour;
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "showFullId")
+ protected Boolean showFullId;
+ @XmlAttribute(name = "rightAlignIds")
+ protected Boolean rightAlignIds;
+ @XmlAttribute(name = "showText")
+ protected Boolean showText;
+ @XmlAttribute(name = "showColourText")
+ protected Boolean showColourText;
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+ @XmlAttribute(name = "showBoxes")
+ protected Boolean showBoxes;
+ @XmlAttribute(name = "wrapAlignment")
+ protected Boolean wrapAlignment;
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
+ @XmlAttribute(name = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
+ @XmlAttribute(name = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
+ @XmlAttribute(name = "viewName")
+ protected String viewName;
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return
+ * possible object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours() {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value) {
+ this.annotationColours = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColumns property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getHiddenColumns().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.Viewport.HiddenColumns }
+ *
+ *
+ */
+ public List<JalviewModelType.Viewport.HiddenColumns> getHiddenColumns() {
+ if (hiddenColumns == null) {
+ hiddenColumns = new ArrayList<JalviewModelType.Viewport.HiddenColumns>();
+ }
+ return this.hiddenColumns;
+ }
+
+ /**
+ * Gets the value of the calcIdParam property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCalcIdParam().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.Viewport.CalcIdParam }
+ *
+ *
+ */
+ public List<JalviewModelType.Viewport.CalcIdParam> getCalcIdParam() {
+ if (calcIdParam == null) {
+ calcIdParam = new ArrayList<JalviewModelType.Viewport.CalcIdParam>();
+ }
+ return this.calcIdParam;
+ }
+
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected() {
+ return conservationSelected;
+ }
+
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value) {
+ this.conservationSelected = value;
+ }
+
+ /**
+ * Gets the value of the pidSelected property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected() {
+ return pidSelected;
+ }
+
+ /**
+ * Sets the value of the pidSelected property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPidSelected(Boolean value) {
+ this.pidSelected = value;
+ }
+
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getBgColour() {
+ return bgColour;
+ }
+
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setBgColour(String value) {
+ this.bgColour = value;
+ }
+
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getConsThreshold() {
+ return consThreshold;
+ }
+
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value) {
+ this.consThreshold = value;
+ }
+
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getPidThreshold() {
+ return pidThreshold;
+ }
+
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value) {
+ this.pidThreshold = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the showFullId property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowFullId() {
+ return showFullId;
+ }
+
+ /**
+ * Sets the value of the showFullId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowFullId(Boolean value) {
+ this.showFullId = value;
+ }
+
+ /**
+ * Gets the value of the rightAlignIds property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isRightAlignIds() {
+ return rightAlignIds;
+ }
+
+ /**
+ * Sets the value of the rightAlignIds property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setRightAlignIds(Boolean value) {
+ this.rightAlignIds = value;
+ }
+
+ /**
+ * Gets the value of the showText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowText() {
+ return showText;
+ }
+
+ /**
+ * Sets the value of the showText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowText(Boolean value) {
+ this.showText = value;
+ }
+
+ /**
+ * Gets the value of the showColourText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowColourText() {
+ return showColourText;
+ }
+
+ /**
+ * Sets the value of the showColourText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowColourText(Boolean value) {
+ this.showColourText = value;
+ }
+
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowUnconserved() {
+ if (showUnconserved == null) {
+ return false;
+ } else {
+ return showUnconserved;
+ }
+ }
+
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value) {
+ this.showUnconserved = value;
+ }
+
+ /**
+ * Gets the value of the showBoxes property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBoxes() {
+ return showBoxes;
+ }
+
+ /**
+ * Sets the value of the showBoxes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBoxes(Boolean value) {
+ this.showBoxes = value;
+ }
+
+ /**
+ * Gets the value of the wrapAlignment property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isWrapAlignment() {
+ return wrapAlignment;
+ }
+
+ /**
+ * Sets the value of the wrapAlignment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setWrapAlignment(Boolean value) {
+ this.wrapAlignment = value;
+ }
+
+ /**
+ * Gets the value of the renderGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isRenderGaps() {
+ return renderGaps;
+ }
+
+ /**
+ * Sets the value of the renderGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setRenderGaps(Boolean value) {
+ this.renderGaps = value;
+ }
+
+ /**
+ * Gets the value of the showSequenceFeatures property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures() {
+ return showSequenceFeatures;
+ }
+
+ /**
+ * Sets the value of the showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value) {
+ this.showSequenceFeatures = value;
+ }
+
+ /**
+ * Gets the value of the showNPfeatureTooltip property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip() {
+ return showNPfeatureTooltip;
+ }
+
+ /**
+ * Sets the value of the showNPfeatureTooltip property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowNPfeatureTooltip(Boolean value) {
+ this.showNPfeatureTooltip = value;
+ }
+
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip() {
+ return showDbRefTooltip;
+ }
+
+ /**
+ * Sets the value of the showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value) {
+ this.showDbRefTooltip = value;
+ }
+
+ /**
+ * Gets the value of the followHighlight property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight() {
+ if (followHighlight == null) {
+ return true;
+ } else {
+ return followHighlight;
+ }
+ }
+
+ /**
+ * Sets the value of the followHighlight property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value) {
+ this.followHighlight = value;
+ }
+
+ /**
+ * Gets the value of the followSelection property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection() {
+ if (followSelection == null) {
+ return true;
+ } else {
+ return followSelection;
+ }
+ }
+
+ /**
+ * Sets the value of the followSelection property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value) {
+ this.followSelection = value;
+ }
+
+ /**
+ * Gets the value of the showAnnotation property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation() {
+ return showAnnotation;
+ }
+
+ /**
+ * Sets the value of the showAnnotation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value) {
+ this.showAnnotation = value;
+ }
+
+ /**
+ * Gets the value of the centreColumnLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels() {
+ if (centreColumnLabels == null) {
+ return false;
+ } else {
+ return centreColumnLabels;
+ }
+ }
+
+ /**
+ * Sets the value of the centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value) {
+ this.centreColumnLabels = value;
+ }
+
+ /**
+ * Gets the value of the showGroupConservation property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation() {
+ if (showGroupConservation == null) {
+ return false;
+ } else {
+ return showGroupConservation;
+ }
+ }
+
+ /**
+ * Sets the value of the showGroupConservation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowGroupConservation(Boolean value) {
+ this.showGroupConservation = value;
+ }
+
+ /**
+ * Gets the value of the showGroupConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus() {
+ if (showGroupConsensus == null) {
+ return false;
+ } else {
+ return showGroupConsensus;
+ }
+ }
+
+ /**
+ * Sets the value of the showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowGroupConsensus(Boolean value) {
+ this.showGroupConsensus = value;
+ }
+
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram() {
+ if (showConsensusHistogram == null) {
+ return true;
+ } else {
+ return showConsensusHistogram;
+ }
+ }
+
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value) {
+ this.showConsensusHistogram = value;
+ }
+
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo() {
+ if (showSequenceLogo == null) {
+ return false;
+ } else {
+ return showSequenceLogo;
+ }
+ }
+
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value) {
+ this.showSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo() {
+ if (normaliseSequenceLogo == null) {
+ return false;
+ } else {
+ return normaliseSequenceLogo;
+ }
+ }
+
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value) {
+ this.normaliseSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus() {
+ if (ignoreGapsinConsensus == null) {
+ return true;
+ } else {
+ return ignoreGapsinConsensus;
+ }
+ }
+
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value) {
+ this.ignoreGapsinConsensus = value;
+ }
+
+ /**
+ * Gets the value of the startRes property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStartRes() {
+ return startRes;
+ }
+
+ /**
+ * Sets the value of the startRes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStartRes(Integer value) {
+ this.startRes = value;
+ }
+
+ /**
+ * Gets the value of the startSeq property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStartSeq() {
+ return startSeq;
+ }
+
+ /**
+ * Sets the value of the startSeq property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStartSeq(Integer value) {
+ this.startSeq = value;
+ }
+
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
+
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
+
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
+
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
+
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
+
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
+
+ /**
+ * Gets the value of the scaleProteinAsCdna property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isScaleProteinAsCdna() {
+ if (scaleProteinAsCdna == null) {
+ return true;
+ } else {
+ return scaleProteinAsCdna;
+ }
+ }
+
+ /**
+ * Sets the value of the scaleProteinAsCdna property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScaleProteinAsCdna(Boolean value) {
+ this.scaleProteinAsCdna = value;
+ }
+
+ /**
+ * Gets the value of the viewName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewName() {
+ return viewName;
+ }
+
+ /**
+ * Sets the value of the viewName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewName(String value) {
+ this.viewName = value;
+ }
+
+ /**
+ * Gets the value of the sequenceSetId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceSetId() {
+ return sequenceSetId;
+ }
+
+ /**
+ * Sets the value of the sequenceSetId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceSetId(String value) {
+ this.sequenceSetId = value;
+ }
+
+ /**
+ * Gets the value of the gatheredViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isGatheredViews() {
+ return gatheredViews;
+ }
+
+ /**
+ * Sets the value of the gatheredViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setGatheredViews(Boolean value) {
+ this.gatheredViews = value;
+ }
+
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol1() {
+ return textCol1;
+ }
+
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value) {
+ this.textCol1 = value;
+ }
+
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol2() {
+ return textCol2;
+ }
+
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value) {
+ this.textCol2 = value;
+ }
+
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold() {
+ return textColThreshold;
+ }
+
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value) {
+ this.textColThreshold = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the complementId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComplementId() {
+ return complementId;
+ }
+
+ /**
+ * Sets the value of the complementId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComplementId(String value) {
+ this.complementId = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam
+ extends WebServiceParameterSet
+ {
+
+ @XmlAttribute(name = "calcId", required = true)
+ protected String calcId;
+ @XmlAttribute(name = "needsUpdate")
+ protected Boolean needsUpdate;
+ @XmlAttribute(name = "autoUpdate", required = true)
+ protected boolean autoUpdate;
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCalcId() {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCalcId(String value) {
+ this.calcId = value;
+ }
+
+ /**
+ * Gets the value of the needsUpdate property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNeedsUpdate() {
+ if (needsUpdate == null) {
+ return false;
+ } else {
+ return needsUpdate;
+ }
+ }
+
+ /**
+ * Sets the value of the needsUpdate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNeedsUpdate(Boolean value) {
+ this.needsUpdate = value;
+ }
+
+ /**
+ * Gets the value of the autoUpdate property.
+ *
+ */
+ public boolean isAutoUpdate() {
+ return autoUpdate;
+ }
+
+ /**
+ * Sets the value of the autoUpdate property.
+ *
+ */
+ public void setAutoUpdate(boolean value) {
+ this.autoUpdate = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStart(Integer value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setEnd(Integer value) {
+ this.end = value;
+ }
+
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for JalviewUserColours complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="JalviewUserColours">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="colour" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="filter" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+ * </sequence>
+ * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
+ "version",
+ "colour",
+ "filter"
+})
+public class JalviewUserColours {
+
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
+ @XmlElement(namespace = "")
+ protected List<JalviewUserColours.Colour> colour;
+ @XmlElement(namespace = "")
+ protected List<JalviewUserColours.Filter> filter;
+ @XmlAttribute(name = "schemeName")
+ protected String schemeName;
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVersion(String value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the colour property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getColour().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Colour }
+ *
+ *
+ */
+ public List<JalviewUserColours.Colour> getColour() {
+ if (colour == null) {
+ colour = new ArrayList<JalviewUserColours.Colour>();
+ }
+ return this.colour;
+ }
+
+ /**
+ * Gets the value of the filter property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the filter property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFilter().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Filter }
+ *
+ *
+ */
+ public List<JalviewUserColours.Filter> getFilter() {
+ if (filter == null) {
+ filter = new ArrayList<JalviewUserColours.Filter>();
+ }
+ return this.filter;
+ }
+
+ /**
+ * Gets the value of the schemeName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSchemeName() {
+ return schemeName;
+ }
+
+ /**
+ * Sets the value of the schemeName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSchemeName(String value) {
+ this.schemeName = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "attributeName"
+ })
+ public static class Colour {
+
+ @XmlElement(namespace = "")
+ protected List<String> attributeName;
+ @XmlAttribute(name = "Name")
+ protected String name;
+ @XmlAttribute(name = "RGB", required = true)
+ protected String rgb;
+ @XmlAttribute(name = "minRGB")
+ protected String minRGB;
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+ @XmlAttribute(name = "threshType")
+ protected ThresholdType threshType;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "max")
+ protected Float max;
+ @XmlAttribute(name = "min")
+ protected Float min;
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the rgb property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getRGB() {
+ return rgb;
+ }
+
+ /**
+ * Sets the value of the rgb property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setRGB(String value) {
+ this.rgb = value;
+ }
+
+ /**
+ * Gets the value of the minRGB property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMinRGB() {
+ return minRGB;
+ }
+
+ /**
+ * Sets the value of the minRGB property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMinRGB(String value) {
+ this.minRGB = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour() {
+ if (noValueColour == null) {
+ return NoValueColour.MIN;
+ } else {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value) {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshType property.
+ *
+ * @return
+ * possible object is
+ * {@link ThresholdType }
+ *
+ */
+ public ThresholdType getThreshType() {
+ return threshType;
+ }
+
+ /**
+ * Sets the value of the threshType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ThresholdType }
+ *
+ */
+ public void setThreshType(ThresholdType value) {
+ this.threshType = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMax() {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMax(Float value) {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMin() {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMin(Float value) {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel() {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value) {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale() {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value) {
+ this.autoScale = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+ * </sequence>
+ * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "matcherSet"
+ })
+ public static class Filter {
+
+ @XmlElement(namespace = "", required = true)
+ protected FeatureMatcherSet matcherSet;
+ @XmlAttribute(name = "featureType", required = true)
+ protected String featureType;
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet() {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value) {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the featureType property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFeatureType() {
+ return featureType;
+ }
+
+ /**
+ * Sets the value of the featureType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFeatureType(String value) {
+ this.featureType = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ *
+ * This effectively represents a java.util.MapList object
+ *
+ *
+ * <p>Java class for mapListType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="mapListType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ * <attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "mapListType", propOrder = {
+ "mapListFrom",
+ "mapListTo"
+})
+@XmlSeeAlso({
+ Mapping.class
+})
+public class MapListType {
+
+ protected List<MapListType.MapListFrom> mapListFrom;
+ protected List<MapListType.MapListTo> mapListTo;
+ @XmlAttribute(name = "mapFromUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapFromUnit;
+ @XmlAttribute(name = "mapToUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapToUnit;
+
+ /**
+ * Gets the value of the mapListFrom property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMapListFrom().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListFrom }
+ *
+ *
+ */
+ public List<MapListType.MapListFrom> getMapListFrom() {
+ if (mapListFrom == null) {
+ mapListFrom = new ArrayList<MapListType.MapListFrom>();
+ }
+ return this.mapListFrom;
+ }
+
+ /**
+ * Gets the value of the mapListTo property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMapListTo().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListTo }
+ *
+ *
+ */
+ public List<MapListType.MapListTo> getMapListTo() {
+ if (mapListTo == null) {
+ mapListTo = new ArrayList<MapListType.MapListTo>();
+ }
+ return this.mapListTo;
+ }
+
+ /**
+ * Gets the value of the mapFromUnit property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getMapFromUnit() {
+ return mapFromUnit;
+ }
+
+ /**
+ * Sets the value of the mapFromUnit property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setMapFromUnit(BigInteger value) {
+ this.mapFromUnit = value;
+ }
+
+ /**
+ * Gets the value of the mapToUnit property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getMapToUnit() {
+ return mapToUnit;
+ }
+
+ /**
+ * Sets the value of the mapToUnit property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setMapToUnit(BigInteger value) {
+ this.mapToUnit = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListFrom {
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListTo {
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ *
+ * Represent the jalview.datamodel.Mapping object - it also provides
+ * a way of storing sequences that are mapped 'to' without adding them
+ * to the sequence set (which will mean they are then added to the alignment too).
+ *
+ *
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
+ * <sequence>
+ * <choice minOccurs="0">
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
+ * <element name="dseqFor">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * </restriction>
+ * </simpleType>
+ * </element>
+ * </choice>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "sequence",
+ "dseqFor"
+})
+@XmlRootElement(name = "Mapping")
+public class Mapping
+ extends MapListType
+{
+
+ @XmlElement(name = "Sequence")
+ protected Sequence sequence;
+ protected String dseqFor;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link Sequence }
+ *
+ */
+ public Sequence getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Sequence }
+ *
+ */
+ public void setSequence(Sequence value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the dseqFor property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDseqFor() {
+ return dseqFor;
+ }
+
+ /**
+ * Sets the value of the dseqFor property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDseqFor(String value) {
+ this.dseqFor = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlEnum;
+import javax.xml.bind.annotation.XmlEnumValue;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for NoValueColour.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * <simpleType name="NoValueColour">
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="None"/>
+ * <enumeration value="Min"/>
+ * <enumeration value="Max"/>
+ * </restriction>
+ * </simpleType>
+ * </pre>
+ *
+ */
+@XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
+@XmlEnum
+public enum NoValueColour {
+
+ @XmlEnumValue("None")
+ NONE("None"),
+ @XmlEnumValue("Min")
+ MIN("Min"),
+ @XmlEnumValue("Max")
+ MAX("Max");
+ private final String value;
+
+ NoValueColour(String v) {
+ value = v;
+ }
+
+ public String value() {
+ return value;
+ }
+
+ public static NoValueColour fromValue(String v) {
+ for (NoValueColour c: NoValueColour.values()) {
+ if (c.value.equals(v)) {
+ return c;
+ }
+ }
+ throw new IllegalArgumentException(v);
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.annotation.XmlElementDecl;
+import javax.xml.bind.annotation.XmlRegistry;
+import javax.xml.namespace.QName;
+
+
+/**
+ * This object contains factory methods for each
+ * Java content interface and Java element interface
+ * generated in the jalview.xml.binding.jalview package.
+ * <p>An ObjectFactory allows you to programatically
+ * construct new instances of the Java representation
+ * for XML content. The Java representation of XML
+ * content can consist of schema derived interfaces
+ * and classes representing the binding of schema
+ * type definitions, element declarations and model
+ * groups. Factory methods for each of these are
+ * provided in this class.
+ *
+ */
+@XmlRegistry
+public class ObjectFactory {
+
+ private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+ private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
+ private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
+ *
+ */
+ public ObjectFactory() {
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame }
+ *
+ */
+ public AlcodonFrame createAlcodonFrame() {
+ return new AlcodonFrame();
+ }
+
+ /**
+ * Create an instance of {@link MapListType }
+ *
+ */
+ public MapListType createMapListType() {
+ return new MapListType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence }
+ *
+ */
+ public Sequence createSequence() {
+ return new Sequence();
+ }
+
+ /**
+ * Create an instance of {@link Annotation }
+ *
+ */
+ public Annotation createAnnotation() {
+ return new Annotation();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet }
+ *
+ */
+ public SequenceSet createSequenceSet() {
+ return new SequenceSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet createFeatureMatcherSet() {
+ return new FeatureMatcherSet();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours createJalviewUserColours() {
+ return new JalviewUserColours();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry }
+ *
+ */
+ public Pdbentry createPdbentry() {
+ return new Pdbentry();
+ }
+
+ /**
+ * Create an instance of {@link Feature }
+ *
+ */
+ public Feature createFeature() {
+ return new Feature();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel }
+ *
+ */
+ public JalviewModel createJalviewModel() {
+ return new JalviewModel();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
+ return new JalviewModel.FeatureSettings();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport }
+ *
+ */
+ public JalviewModel.Viewport createJalviewModelViewport() {
+ return new JalviewModel.Viewport();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq }
+ *
+ */
+ public JalviewModel.JSeq createJalviewModelJSeq() {
+ return new JalviewModel.JSeq();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
+ return new JalviewModel.JSeq.RnaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
+ return new JalviewModel.JSeq.Pdbids();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme createAnnotationColourScheme() {
+ return new AnnotationColourScheme();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.Alcodon }
+ *
+ */
+ public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
+ return new AlcodonFrame.Alcodon();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.AlcodMap }
+ *
+ */
+ public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
+ return new AlcodonFrame.AlcodMap();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationElement }
+ *
+ */
+ public AnnotationElement createAnnotationElement() {
+ return new AnnotationElement();
+ }
+
+ /**
+ * Create an instance of {@link Mapping }
+ *
+ */
+ public Mapping createMapping() {
+ return new Mapping();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListFrom }
+ *
+ */
+ public MapListType.MapListFrom createMapListTypeMapListFrom() {
+ return new MapListType.MapListFrom();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListTo }
+ *
+ */
+ public MapListType.MapListTo createMapListTypeMapListTo() {
+ return new MapListType.MapListTo();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType() {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence.DBRef }
+ *
+ */
+ public Sequence.DBRef createSequenceDBRef() {
+ return new Sequence.DBRef();
+ }
+
+ /**
+ * Create an instance of {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine createAnnotationThresholdLine() {
+ return new Annotation.ThresholdLine();
+ }
+
+ /**
+ * Create an instance of {@link Annotation.Property }
+ *
+ */
+ public Annotation.Property createAnnotationProperty() {
+ return new Annotation.Property();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet.SequenceSetProperties }
+ *
+ */
+ public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
+ return new SequenceSet.SequenceSetProperties();
+ }
+
+ /**
+ * Create an instance of {@link VAMSAS }
+ *
+ */
+ public VAMSAS createVAMSAS() {
+ return new VAMSAS();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher createFeatureMatcher() {
+ return new FeatureMatcher();
+ }
+
+ /**
+ * Create an instance of {@link WebServiceParameterSet }
+ *
+ */
+ public WebServiceParameterSet createWebServiceParameterSet() {
+ return new WebServiceParameterSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
+ return new FeatureMatcherSet.CompoundMatcher();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Colour }
+ *
+ */
+ public JalviewUserColours.Colour createJalviewUserColoursColour() {
+ return new JalviewUserColours.Colour();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Filter }
+ *
+ */
+ public JalviewUserColours.Filter createJalviewUserColoursFilter() {
+ return new JalviewUserColours.Filter();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry.Property }
+ *
+ */
+ public Pdbentry.Property createPdbentryProperty() {
+ return new Pdbentry.Property();
+ }
+
+ /**
+ * Create an instance of {@link Feature.OtherData }
+ *
+ */
+ public Feature.OtherData createFeatureOtherData() {
+ return new Feature.OtherData();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JGroup }
+ *
+ */
+ public JalviewModel.JGroup createJalviewModelJGroup() {
+ return new JalviewModel.JGroup();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.UserColours }
+ *
+ */
+ public JalviewModel.UserColours createJalviewModelUserColours() {
+ return new JalviewModel.UserColours();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Tree }
+ *
+ */
+ public JalviewModel.Tree createJalviewModelTree() {
+ return new JalviewModel.Tree();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+ *
+ */
+ public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
+ return new JalviewModel.FeatureSettings.Setting();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+ *
+ */
+ public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
+ return new JalviewModel.FeatureSettings.Group();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ */
+ public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
+ return new JalviewModel.Viewport.HiddenColumns();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ */
+ public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
+ return new JalviewModel.Viewport.CalcIdParam();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
+ return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
+ return new JalviewModel.JSeq.Pdbids.StructureState();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}}
+ *
+ */
+ @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
+ public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
+ return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}}
+ *
+ */
+ @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+ public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
+ return new JAXBElement<JalviewModel>(_JalviewModel_QNAME, JalviewModel.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}}
+ *
+ */
+ @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
+ public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
+ return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for pdbentry complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="pdbentry">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence maxOccurs="unbounded" minOccurs="0">
+ * <element name="property" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
+ "property"
+})
+@XmlSeeAlso({
+ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
+})
+public class Pdbentry {
+
+ protected List<Pdbentry.Property> property;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "type")
+ protected String type;
+ @XmlAttribute(name = "file")
+ protected String file;
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Pdbentry.Property }
+ *
+ *
+ */
+ public List<Pdbentry.Property> getProperty() {
+ if (property == null) {
+ property = new ArrayList<Pdbentry.Property>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the file property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFile() {
+ return file;
+ }
+
+ /**
+ * Sets the value of the file property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFile(String value) {
+ this.file = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Property {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
+ * <sequence>
+ * <element name="DBRef" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "dbRef"
+})
+@XmlRootElement(name = "Sequence")
+public class Sequence
+ extends SequenceType
+{
+
+ @XmlElement(name = "DBRef")
+ protected List<Sequence.DBRef> dbRef;
+ @XmlAttribute(name = "dsseqid")
+ protected String dsseqid;
+
+ /**
+ * Gets the value of the dbRef property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbRef property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDBRef().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Sequence.DBRef }
+ *
+ *
+ */
+ public List<Sequence.DBRef> getDBRef() {
+ if (dbRef == null) {
+ dbRef = new ArrayList<Sequence.DBRef>();
+ }
+ return this.dbRef;
+ }
+
+ /**
+ * Gets the value of the dsseqid property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDsseqid() {
+ return dsseqid;
+ }
+
+ /**
+ * Sets the value of the dsseqid property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDsseqid(String value) {
+ this.dsseqid = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "mapping"
+ })
+ public static class DBRef {
+
+ @XmlElement(name = "Mapping")
+ protected Mapping mapping;
+ @XmlAttribute(name = "source")
+ protected String source;
+ @XmlAttribute(name = "version")
+ protected String version;
+ @XmlAttribute(name = "accessionId")
+ protected String accessionId;
+
+ /**
+ * Gets the value of the mapping property.
+ *
+ * @return
+ * possible object is
+ * {@link Mapping }
+ *
+ */
+ public Mapping getMapping() {
+ return mapping;
+ }
+
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Mapping }
+ *
+ */
+ public void setMapping(Mapping value) {
+ this.mapping = value;
+ }
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSource() {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSource(String value) {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVersion(String value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the accessionId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccessionId() {
+ return accessionId;
+ }
+
+ /**
+ * Sets the value of the accessionId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccessionId(String value) {
+ this.accessionId = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "sequence",
+ "annotation",
+ "sequenceSetProperties",
+ "alcodonFrame"
+})
+@XmlRootElement(name = "SequenceSet")
+public class SequenceSet {
+
+ @XmlElement(name = "Sequence")
+ protected List<Sequence> sequence;
+ @XmlElement(name = "Annotation")
+ protected List<Annotation> annotation;
+ protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+ @XmlElement(name = "AlcodonFrame")
+ protected List<AlcodonFrame> alcodonFrame;
+ @XmlAttribute(name = "gapChar", required = true)
+ protected String gapChar;
+ @XmlAttribute(name = "datasetId")
+ protected String datasetId;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Sequence }
+ *
+ *
+ */
+ public List<Sequence> getSequence() {
+ if (sequence == null) {
+ sequence = new ArrayList<Sequence>();
+ }
+ return this.sequence;
+ }
+
+ /**
+ * Gets the value of the annotation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the annotation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAnnotation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Annotation }
+ *
+ *
+ */
+ public List<Annotation> getAnnotation() {
+ if (annotation == null) {
+ annotation = new ArrayList<Annotation>();
+ }
+ return this.annotation;
+ }
+
+ /**
+ * Gets the value of the sequenceSetProperties property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequenceSetProperties().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SequenceSet.SequenceSetProperties }
+ *
+ *
+ */
+ public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
+ if (sequenceSetProperties == null) {
+ sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+ }
+ return this.sequenceSetProperties;
+ }
+
+ /**
+ * Gets the value of the alcodonFrame property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlcodonFrame().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame }
+ *
+ *
+ */
+ public List<AlcodonFrame> getAlcodonFrame() {
+ if (alcodonFrame == null) {
+ alcodonFrame = new ArrayList<AlcodonFrame>();
+ }
+ return this.alcodonFrame;
+ }
+
+ /**
+ * Gets the value of the gapChar property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getGapChar() {
+ return gapChar;
+ }
+
+ /**
+ * Sets the value of the gapChar property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setGapChar(String value) {
+ this.gapChar = value;
+ }
+
+ /**
+ * Gets the value of the datasetId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDatasetId() {
+ return datasetId;
+ }
+
+ /**
+ * Sets the value of the datasetId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDatasetId(String value) {
+ this.datasetId = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequenceSetProperties {
+
+ @XmlAttribute(name = "key")
+ protected String key;
+ @XmlAttribute(name = "value")
+ protected String value;
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey() {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey(String value) {
+ this.key = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for SequenceType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="SequenceType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "SequenceType", propOrder = {
+ "sequence",
+ "name"
+})
+@XmlSeeAlso({
+ Sequence.class
+})
+public class SequenceType {
+
+ protected String sequence;
+ protected String name;
+ @XmlAttribute(name = "id")
+ protected String id;
+ @XmlAttribute(name = "description")
+ protected String description;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequence(String value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlEnum;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for ThresholdType.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * <simpleType name="ThresholdType">
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="NONE"/>
+ * <enumeration value="ABOVE"/>
+ * <enumeration value="BELOW"/>
+ * </restriction>
+ * </simpleType>
+ * </pre>
+ *
+ */
+@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
+@XmlEnum
+public enum ThresholdType {
+
+ NONE,
+ ABOVE,
+ BELOW;
+
+ public String value() {
+ return name();
+ }
+
+ public static ThresholdType fromValue(String v) {
+ return valueOf(v);
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for VAMSAS complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="VAMSAS">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "VAMSAS", propOrder = {
+ "tree",
+ "sequenceSet"
+})
+public class VAMSAS {
+
+ @XmlElement(name = "Tree")
+ protected List<String> tree;
+ @XmlElement(name = "SequenceSet")
+ protected List<SequenceSet> sequenceSet;
+
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getTree() {
+ if (tree == null) {
+ tree = new ArrayList<String>();
+ }
+ return this.tree;
+ }
+
+ /**
+ * Gets the value of the sequenceSet property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequenceSet().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SequenceSet }
+ *
+ *
+ */
+ public List<SequenceSet> getSequenceSet() {
+ if (sequenceSet == null) {
+ sequenceSet = new ArrayList<SequenceSet>();
+ }
+ return this.sequenceSet;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for WebServiceParameterSet complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="WebServiceParameterSet">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
+ * <element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
+ "version",
+ "description",
+ "serviceURL",
+ "parameters"
+})
+@XmlSeeAlso({
+ jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
+})
+public class WebServiceParameterSet {
+
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
+ @XmlElement(namespace = "")
+ protected String description;
+ @XmlElement(namespace = "", required = true)
+ @XmlSchemaType(name = "anyURI")
+ protected List<String> serviceURL;
+ @XmlElement(namespace = "", required = true)
+ protected String parameters;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVersion(String value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the serviceURL property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getServiceURL().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getServiceURL() {
+ if (serviceURL == null) {
+ serviceURL = new ArrayList<String>();
+ }
+ return this.serviceURL;
+ }
+
+ /**
+ * Gets the value of the parameters property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getParameters() {
+ return parameters;
+ }
+
+ /**
+ * Sets the value of the parameters property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setParameters(String value) {
+ this.parameters = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.28 at 12:18:54 PM BST
+//
+
+@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+package jalview.xml.binding.jalview;
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes different types of citations.
+ * Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.
+ *
+ * <p>Java class for citationType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="citationType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="editorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/>
+ * <element name="authorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/>
+ * <element name="locator" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="book"/>
+ * <enumeration value="journal article"/>
+ * <enumeration value="online journal article"/>
+ * <enumeration value="patent"/>
+ * <enumeration value="submission"/>
+ * <enumeration value="thesis"/>
+ * <enumeration value="unpublished observations"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="date">
+ * <simpleType>
+ * <union memberTypes=" {http://www.w3.org/2001/XMLSchema}date {http://www.w3.org/2001/XMLSchema}gYearMonth {http://www.w3.org/2001/XMLSchema}gYear">
+ * </union>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="volume" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="first" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="last" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="publisher" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="city" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="db" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="number" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="institute" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="country" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "citationType", propOrder = {
+ "title",
+ "editorList",
+ "authorList",
+ "locator",
+ "dbReference"
+})
+public class CitationType {
+
+ protected String title;
+ protected NameListType editorList;
+ protected NameListType authorList;
+ protected String locator;
+ protected List<DbReferenceType> dbReference;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "date")
+ protected String date;
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "volume")
+ protected String volume;
+ @XmlAttribute(name = "first")
+ protected String first;
+ @XmlAttribute(name = "last")
+ protected String last;
+ @XmlAttribute(name = "publisher")
+ protected String publisher;
+ @XmlAttribute(name = "city")
+ protected String city;
+ @XmlAttribute(name = "db")
+ protected String db;
+ @XmlAttribute(name = "number")
+ protected String number;
+ @XmlAttribute(name = "institute")
+ protected String institute;
+ @XmlAttribute(name = "country")
+ protected String country;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the editorList property.
+ *
+ * @return
+ * possible object is
+ * {@link NameListType }
+ *
+ */
+ public NameListType getEditorList() {
+ return editorList;
+ }
+
+ /**
+ * Sets the value of the editorList property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NameListType }
+ *
+ */
+ public void setEditorList(NameListType value) {
+ this.editorList = value;
+ }
+
+ /**
+ * Gets the value of the authorList property.
+ *
+ * @return
+ * possible object is
+ * {@link NameListType }
+ *
+ */
+ public NameListType getAuthorList() {
+ return authorList;
+ }
+
+ /**
+ * Sets the value of the authorList property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NameListType }
+ *
+ */
+ public void setAuthorList(NameListType value) {
+ this.authorList = value;
+ }
+
+ /**
+ * Gets the value of the locator property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLocator() {
+ return locator;
+ }
+
+ /**
+ * Sets the value of the locator property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocator(String value) {
+ this.locator = value;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference() {
+ if (dbReference == null) {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the date property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDate() {
+ return date;
+ }
+
+ /**
+ * Sets the value of the date property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDate(String value) {
+ this.date = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the volume property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVolume() {
+ return volume;
+ }
+
+ /**
+ * Sets the value of the volume property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVolume(String value) {
+ this.volume = value;
+ }
+
+ /**
+ * Gets the value of the first property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFirst() {
+ return first;
+ }
+
+ /**
+ * Sets the value of the first property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFirst(String value) {
+ this.first = value;
+ }
+
+ /**
+ * Gets the value of the last property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLast() {
+ return last;
+ }
+
+ /**
+ * Sets the value of the last property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLast(String value) {
+ this.last = value;
+ }
+
+ /**
+ * Gets the value of the publisher property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getPublisher() {
+ return publisher;
+ }
+
+ /**
+ * Sets the value of the publisher property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setPublisher(String value) {
+ this.publisher = value;
+ }
+
+ /**
+ * Gets the value of the city property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCity() {
+ return city;
+ }
+
+ /**
+ * Sets the value of the city property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCity(String value) {
+ this.city = value;
+ }
+
+ /**
+ * Gets the value of the db property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDb() {
+ return db;
+ }
+
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDb(String value) {
+ this.db = value;
+ }
+
+ /**
+ * Gets the value of the number property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getNumber() {
+ return number;
+ }
+
+ /**
+ * Sets the value of the number property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setNumber(String value) {
+ this.number = value;
+ }
+
+ /**
+ * Gets the value of the institute property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getInstitute() {
+ return institute;
+ }
+
+ /**
+ * Sets the value of the institute property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setInstitute(String value) {
+ this.institute = value;
+ }
+
+ /**
+ * Gets the value of the country property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCountry() {
+ return country;
+ }
+
+ /**
+ * Sets the value of the country property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCountry(String value) {
+ this.country = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes a cofactor.
+ *
+ * <p>Java class for cofactorType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="cofactorType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+ * </sequence>
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "cofactorType", propOrder = {
+ "name",
+ "dbReference"
+})
+public class CofactorType {
+
+ @XmlElement(required = true)
+ protected String name;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return
+ * possible object is
+ * {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference() {
+ return dbReference;
+ }
+
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value) {
+ this.dbReference = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes different types of general annotations.
+ * Equivalent to the flat file CC-line.
+ *
+ * <p>Java class for commentType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="commentType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/>
+ * <choice minOccurs="0">
+ * <group ref="{http://uniprot.org/uniprot}bpcCommentGroup"/>
+ * <sequence>
+ * <element name="cofactor" type="{http://uniprot.org/uniprot}cofactorType" maxOccurs="unbounded"/>
+ * </sequence>
+ * <sequence>
+ * <element name="subcellularLocation" type="{http://uniprot.org/uniprot}subcellularLocationType" maxOccurs="unbounded"/>
+ * </sequence>
+ * <element name="conflict">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequence" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="resource" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="EMBL-CDS"/>
+ * <enumeration value="EMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="frameshift"/>
+ * <enumeration value="erroneous initiation"/>
+ * <enumeration value="erroneous termination"/>
+ * <enumeration value="erroneous gene model prediction"/>
+ * <enumeration value="erroneous translation"/>
+ * <enumeration value="miscellaneous discrepancy"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <sequence>
+ * <element name="link" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <sequence>
+ * <element name="event" type="{http://uniprot.org/uniprot}eventType" maxOccurs="4"/>
+ * <element name="isoform" type="{http://uniprot.org/uniprot}isoformType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <sequence>
+ * <element name="interactant" type="{http://uniprot.org/uniprot}interactantType" maxOccurs="2" minOccurs="2"/>
+ * <element name="organismsDiffer" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
+ * <element name="experiments" type="{http://www.w3.org/2001/XMLSchema}int"/>
+ * </sequence>
+ * <element name="disease">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+ * </sequence>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * <element name="location" type="{http://uniprot.org/uniprot}locationType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="allergen"/>
+ * <enumeration value="alternative products"/>
+ * <enumeration value="biotechnology"/>
+ * <enumeration value="biophysicochemical properties"/>
+ * <enumeration value="catalytic activity"/>
+ * <enumeration value="caution"/>
+ * <enumeration value="cofactor"/>
+ * <enumeration value="developmental stage"/>
+ * <enumeration value="disease"/>
+ * <enumeration value="domain"/>
+ * <enumeration value="disruption phenotype"/>
+ * <enumeration value="activity regulation"/>
+ * <enumeration value="function"/>
+ * <enumeration value="induction"/>
+ * <enumeration value="miscellaneous"/>
+ * <enumeration value="pathway"/>
+ * <enumeration value="pharmaceutical"/>
+ * <enumeration value="polymorphism"/>
+ * <enumeration value="PTM"/>
+ * <enumeration value="RNA editing"/>
+ * <enumeration value="similarity"/>
+ * <enumeration value="subcellular location"/>
+ * <enumeration value="sequence caution"/>
+ * <enumeration value="subunit"/>
+ * <enumeration value="tissue specificity"/>
+ * <enumeration value="toxic dose"/>
+ * <enumeration value="online information"/>
+ * <enumeration value="mass spectrometry"/>
+ * <enumeration value="interaction"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="locationType" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="mass" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="error" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="method" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "commentType", propOrder = {
+ "molecule",
+ "absorption",
+ "kinetics",
+ "phDependence",
+ "redoxPotential",
+ "temperatureDependence",
+ "cofactor",
+ "subcellularLocation",
+ "conflict",
+ "link",
+ "event",
+ "isoform",
+ "interactant",
+ "organismsDiffer",
+ "experiments",
+ "disease",
+ "location",
+ "text"
+})
+public class CommentType {
+
+ protected MoleculeType molecule;
+ protected CommentType.Absorption absorption;
+ protected CommentType.Kinetics kinetics;
+ protected CommentType.PhDependence phDependence;
+ protected CommentType.RedoxPotential redoxPotential;
+ protected CommentType.TemperatureDependence temperatureDependence;
+ protected List<CofactorType> cofactor;
+ protected List<SubcellularLocationType> subcellularLocation;
+ protected CommentType.Conflict conflict;
+ protected List<CommentType.Link> link;
+ protected List<EventType> event;
+ protected List<IsoformType> isoform;
+ protected List<InteractantType> interactant;
+ @XmlElement(defaultValue = "false")
+ protected Boolean organismsDiffer;
+ protected Integer experiments;
+ protected CommentType.Disease disease;
+ protected List<LocationType> location;
+ protected List<EvidencedStringType> text;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "locationType")
+ protected String locationType;
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "mass")
+ protected Float mass;
+ @XmlAttribute(name = "error")
+ protected String error;
+ @XmlAttribute(name = "method")
+ protected String method;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the molecule property.
+ *
+ * @return
+ * possible object is
+ * {@link MoleculeType }
+ *
+ */
+ public MoleculeType getMolecule() {
+ return molecule;
+ }
+
+ /**
+ * Sets the value of the molecule property.
+ *
+ * @param value
+ * allowed object is
+ * {@link MoleculeType }
+ *
+ */
+ public void setMolecule(MoleculeType value) {
+ this.molecule = value;
+ }
+
+ /**
+ * Gets the value of the absorption property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.Absorption }
+ *
+ */
+ public CommentType.Absorption getAbsorption() {
+ return absorption;
+ }
+
+ /**
+ * Sets the value of the absorption property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.Absorption }
+ *
+ */
+ public void setAbsorption(CommentType.Absorption value) {
+ this.absorption = value;
+ }
+
+ /**
+ * Gets the value of the kinetics property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.Kinetics }
+ *
+ */
+ public CommentType.Kinetics getKinetics() {
+ return kinetics;
+ }
+
+ /**
+ * Sets the value of the kinetics property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.Kinetics }
+ *
+ */
+ public void setKinetics(CommentType.Kinetics value) {
+ this.kinetics = value;
+ }
+
+ /**
+ * Gets the value of the phDependence property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.PhDependence }
+ *
+ */
+ public CommentType.PhDependence getPhDependence() {
+ return phDependence;
+ }
+
+ /**
+ * Sets the value of the phDependence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.PhDependence }
+ *
+ */
+ public void setPhDependence(CommentType.PhDependence value) {
+ this.phDependence = value;
+ }
+
+ /**
+ * Gets the value of the redoxPotential property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.RedoxPotential }
+ *
+ */
+ public CommentType.RedoxPotential getRedoxPotential() {
+ return redoxPotential;
+ }
+
+ /**
+ * Sets the value of the redoxPotential property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.RedoxPotential }
+ *
+ */
+ public void setRedoxPotential(CommentType.RedoxPotential value) {
+ this.redoxPotential = value;
+ }
+
+ /**
+ * Gets the value of the temperatureDependence property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.TemperatureDependence }
+ *
+ */
+ public CommentType.TemperatureDependence getTemperatureDependence() {
+ return temperatureDependence;
+ }
+
+ /**
+ * Sets the value of the temperatureDependence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.TemperatureDependence }
+ *
+ */
+ public void setTemperatureDependence(CommentType.TemperatureDependence value) {
+ this.temperatureDependence = value;
+ }
+
+ /**
+ * Gets the value of the cofactor property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the cofactor property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCofactor().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CofactorType }
+ *
+ *
+ */
+ public List<CofactorType> getCofactor() {
+ if (cofactor == null) {
+ cofactor = new ArrayList<CofactorType>();
+ }
+ return this.cofactor;
+ }
+
+ /**
+ * Gets the value of the subcellularLocation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the subcellularLocation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSubcellularLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SubcellularLocationType }
+ *
+ *
+ */
+ public List<SubcellularLocationType> getSubcellularLocation() {
+ if (subcellularLocation == null) {
+ subcellularLocation = new ArrayList<SubcellularLocationType>();
+ }
+ return this.subcellularLocation;
+ }
+
+ /**
+ * Gets the value of the conflict property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.Conflict }
+ *
+ */
+ public CommentType.Conflict getConflict() {
+ return conflict;
+ }
+
+ /**
+ * Sets the value of the conflict property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.Conflict }
+ *
+ */
+ public void setConflict(CommentType.Conflict value) {
+ this.conflict = value;
+ }
+
+ /**
+ * Gets the value of the link property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the link property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getLink().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CommentType.Link }
+ *
+ *
+ */
+ public List<CommentType.Link> getLink() {
+ if (link == null) {
+ link = new ArrayList<CommentType.Link>();
+ }
+ return this.link;
+ }
+
+ /**
+ * Gets the value of the event property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the event property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvent().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EventType }
+ *
+ *
+ */
+ public List<EventType> getEvent() {
+ if (event == null) {
+ event = new ArrayList<EventType>();
+ }
+ return this.event;
+ }
+
+ /**
+ * Gets the value of the isoform property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the isoform property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getIsoform().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link IsoformType }
+ *
+ *
+ */
+ public List<IsoformType> getIsoform() {
+ if (isoform == null) {
+ isoform = new ArrayList<IsoformType>();
+ }
+ return this.isoform;
+ }
+
+ /**
+ * Gets the value of the interactant property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the interactant property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getInteractant().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link InteractantType }
+ *
+ *
+ */
+ public List<InteractantType> getInteractant() {
+ if (interactant == null) {
+ interactant = new ArrayList<InteractantType>();
+ }
+ return this.interactant;
+ }
+
+ /**
+ * Gets the value of the organismsDiffer property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isOrganismsDiffer() {
+ return organismsDiffer;
+ }
+
+ /**
+ * Sets the value of the organismsDiffer property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setOrganismsDiffer(Boolean value) {
+ this.organismsDiffer = value;
+ }
+
+ /**
+ * Gets the value of the experiments property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getExperiments() {
+ return experiments;
+ }
+
+ /**
+ * Sets the value of the experiments property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setExperiments(Integer value) {
+ this.experiments = value;
+ }
+
+ /**
+ * Gets the value of the disease property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.Disease }
+ *
+ */
+ public CommentType.Disease getDisease() {
+ return disease;
+ }
+
+ /**
+ * Sets the value of the disease property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.Disease }
+ *
+ */
+ public void setDisease(CommentType.Disease value) {
+ this.disease = value;
+ }
+
+ /**
+ * Gets the value of the location property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the location property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link LocationType }
+ *
+ *
+ */
+ public List<LocationType> getLocation() {
+ if (location == null) {
+ location = new ArrayList<LocationType>();
+ }
+ return this.location;
+ }
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the locationType property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLocationType() {
+ return locationType;
+ }
+
+ /**
+ * Sets the value of the locationType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocationType(String value) {
+ this.locationType = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the mass property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMass() {
+ return mass;
+ }
+
+ /**
+ * Sets the value of the mass property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMass(Float value) {
+ this.mass = value;
+ }
+
+ /**
+ * Gets the value of the error property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getError() {
+ return error;
+ }
+
+ /**
+ * Sets the value of the error property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setError(String value) {
+ this.error = value;
+ }
+
+ /**
+ * Gets the value of the method property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMethod() {
+ return method;
+ }
+
+ /**
+ * Sets the value of the method property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMethod(String value) {
+ this.method = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "max",
+ "text"
+ })
+ public static class Absorption {
+
+ protected EvidencedStringType max;
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getMax() {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setMax(EvidencedStringType value) {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequence" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="resource" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="EMBL-CDS"/>
+ * <enumeration value="EMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="frameshift"/>
+ * <enumeration value="erroneous initiation"/>
+ * <enumeration value="erroneous termination"/>
+ * <enumeration value="erroneous gene model prediction"/>
+ * <enumeration value="erroneous translation"/>
+ * <enumeration value="miscellaneous discrepancy"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "sequence"
+ })
+ public static class Conflict {
+
+ protected CommentType.Conflict.Sequence sequence;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "ref")
+ protected String ref;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.Conflict.Sequence }
+ *
+ */
+ public CommentType.Conflict.Sequence getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.Conflict.Sequence }
+ *
+ */
+ public void setSequence(CommentType.Conflict.Sequence value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getRef() {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setRef(String value) {
+ this.ref = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="resource" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="EMBL-CDS"/>
+ * <enumeration value="EMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Sequence {
+
+ @XmlAttribute(name = "resource", required = true)
+ protected String resource;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "version")
+ protected Integer version;
+
+ /**
+ * Gets the value of the resource property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getResource() {
+ return resource;
+ }
+
+ /**
+ * Sets the value of the resource property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setResource(String value) {
+ this.resource = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setVersion(Integer value) {
+ this.version = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+ * </sequence>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "name",
+ "acronym",
+ "description",
+ "dbReference"
+ })
+ public static class Disease {
+
+ @XmlElement(required = true)
+ protected String name;
+ @XmlElement(required = true)
+ protected String acronym;
+ @XmlElement(required = true)
+ protected String description;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the acronym property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAcronym() {
+ return acronym;
+ }
+
+ /**
+ * Sets the value of the acronym property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAcronym(String value) {
+ this.acronym = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return
+ * possible object is
+ * {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference() {
+ return dbReference;
+ }
+
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value) {
+ this.dbReference = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "km",
+ "vmax",
+ "text"
+ })
+ public static class Kinetics {
+
+ @XmlElement(name = "KM")
+ protected List<EvidencedStringType> km;
+ @XmlElement(name = "Vmax")
+ protected List<EvidencedStringType> vmax;
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the km property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the km property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getKM().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getKM() {
+ if (km == null) {
+ km = new ArrayList<EvidencedStringType>();
+ }
+ return this.km;
+ }
+
+ /**
+ * Gets the value of the vmax property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the vmax property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getVmax().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getVmax() {
+ if (vmax == null) {
+ vmax = new ArrayList<EvidencedStringType>();
+ }
+ return this.vmax;
+ }
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Link {
+
+ @XmlAttribute(name = "uri", required = true)
+ @XmlSchemaType(name = "anyURI")
+ protected String uri;
+
+ /**
+ * Gets the value of the uri property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getUri() {
+ return uri;
+ }
+
+ /**
+ * Sets the value of the uri property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setUri(String value) {
+ this.uri = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "text"
+ })
+ public static class PhDependence {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "text"
+ })
+ public static class RedoxPotential {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "text"
+ })
+ public static class TemperatureDependence {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes the authors of a citation when these are represented by a consortium.
+ * Equivalent to the flat file RG-line.
+ *
+ * <p>Java class for consortiumType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="consortiumType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "consortiumType")
+public class ConsortiumType {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes a database cross-reference.
+ * Equivalent to the flat file DR-line.
+ *
+ *
+ * <p>Java class for dbReferenceType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="dbReferenceType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/>
+ * <element name="property" type="{http://uniprot.org/uniprot}propertyType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "dbReferenceType", propOrder = {
+ "molecule",
+ "property"
+})
+public class DbReferenceType {
+
+ protected MoleculeType molecule;
+ protected List<PropertyType> property;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the molecule property.
+ *
+ * @return
+ * possible object is
+ * {@link MoleculeType }
+ *
+ */
+ public MoleculeType getMolecule() {
+ return molecule;
+ }
+
+ /**
+ * Sets the value of the molecule property.
+ *
+ * @param value
+ * allowed object is
+ * {@link MoleculeType }
+ *
+ */
+ public void setMolecule(MoleculeType value) {
+ this.molecule = value;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link PropertyType }
+ *
+ *
+ */
+ public List<PropertyType> getProperty() {
+ if (property == null) {
+ property = new ArrayList<PropertyType>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="accession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="protein" type="{http://uniprot.org/uniprot}proteinType"/>
+ * <element name="gene" type="{http://uniprot.org/uniprot}geneType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="organism" type="{http://uniprot.org/uniprot}organismType"/>
+ * <element name="organismHost" type="{http://uniprot.org/uniprot}organismType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="geneLocation" type="{http://uniprot.org/uniprot}geneLocationType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="reference" type="{http://uniprot.org/uniprot}referenceType" maxOccurs="unbounded"/>
+ * <element name="comment" type="{http://uniprot.org/uniprot}commentType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="proteinExistence" type="{http://uniprot.org/uniprot}proteinExistenceType"/>
+ * <element name="keyword" type="{http://uniprot.org/uniprot}keywordType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="feature" type="{http://uniprot.org/uniprot}featureType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="evidence" type="{http://uniprot.org/uniprot}evidenceType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="sequence" type="{http://uniprot.org/uniprot}sequenceType"/>
+ * </sequence>
+ * <attribute name="dataset" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="Swiss-Prot"/>
+ * <enumeration value="TrEMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="created" use="required" type="{http://www.w3.org/2001/XMLSchema}date" />
+ * <attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "accession",
+ "name",
+ "protein",
+ "gene",
+ "organism",
+ "organismHost",
+ "geneLocation",
+ "reference",
+ "comment",
+ "dbReference",
+ "proteinExistence",
+ "keyword",
+ "feature",
+ "evidence",
+ "sequence"
+})
+@XmlRootElement(name = "entry")
+public class Entry {
+
+ @XmlElement(required = true)
+ protected List<String> accession;
+ @XmlElement(required = true)
+ protected List<String> name;
+ @XmlElement(required = true)
+ protected ProteinType protein;
+ protected List<GeneType> gene;
+ @XmlElement(required = true)
+ protected OrganismType organism;
+ protected List<OrganismType> organismHost;
+ protected List<GeneLocationType> geneLocation;
+ @XmlElement(required = true)
+ protected List<ReferenceType> reference;
+ @XmlElement(nillable = true)
+ protected List<CommentType> comment;
+ protected List<DbReferenceType> dbReference;
+ @XmlElement(required = true)
+ protected ProteinExistenceType proteinExistence;
+ protected List<KeywordType> keyword;
+ protected List<FeatureType> feature;
+ protected List<EvidenceType> evidence;
+ @XmlElement(required = true)
+ protected SequenceType sequence;
+ @XmlAttribute(name = "dataset", required = true)
+ protected String dataset;
+ @XmlAttribute(name = "created", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar created;
+ @XmlAttribute(name = "modified", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar modified;
+ @XmlAttribute(name = "version", required = true)
+ protected int version;
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the accession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAccession() {
+ if (accession == null) {
+ accession = new ArrayList<String>();
+ }
+ return this.accession;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getName() {
+ if (name == null) {
+ name = new ArrayList<String>();
+ }
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the protein property.
+ *
+ * @return
+ * possible object is
+ * {@link ProteinType }
+ *
+ */
+ public ProteinType getProtein() {
+ return protein;
+ }
+
+ /**
+ * Sets the value of the protein property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ProteinType }
+ *
+ */
+ public void setProtein(ProteinType value) {
+ this.protein = value;
+ }
+
+ /**
+ * Gets the value of the gene property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the gene property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGene().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneType }
+ *
+ *
+ */
+ public List<GeneType> getGene() {
+ if (gene == null) {
+ gene = new ArrayList<GeneType>();
+ }
+ return this.gene;
+ }
+
+ /**
+ * Gets the value of the organism property.
+ *
+ * @return
+ * possible object is
+ * {@link OrganismType }
+ *
+ */
+ public OrganismType getOrganism() {
+ return organism;
+ }
+
+ /**
+ * Sets the value of the organism property.
+ *
+ * @param value
+ * allowed object is
+ * {@link OrganismType }
+ *
+ */
+ public void setOrganism(OrganismType value) {
+ this.organism = value;
+ }
+
+ /**
+ * Gets the value of the organismHost property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the organismHost property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getOrganismHost().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link OrganismType }
+ *
+ *
+ */
+ public List<OrganismType> getOrganismHost() {
+ if (organismHost == null) {
+ organismHost = new ArrayList<OrganismType>();
+ }
+ return this.organismHost;
+ }
+
+ /**
+ * Gets the value of the geneLocation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the geneLocation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGeneLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneLocationType }
+ *
+ *
+ */
+ public List<GeneLocationType> getGeneLocation() {
+ if (geneLocation == null) {
+ geneLocation = new ArrayList<GeneLocationType>();
+ }
+ return this.geneLocation;
+ }
+
+ /**
+ * Gets the value of the reference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the reference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ReferenceType }
+ *
+ *
+ */
+ public List<ReferenceType> getReference() {
+ if (reference == null) {
+ reference = new ArrayList<ReferenceType>();
+ }
+ return this.reference;
+ }
+
+ /**
+ * Gets the value of the comment property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the comment property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getComment().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CommentType }
+ *
+ *
+ */
+ public List<CommentType> getComment() {
+ if (comment == null) {
+ comment = new ArrayList<CommentType>();
+ }
+ return this.comment;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference() {
+ if (dbReference == null) {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
+ }
+
+ /**
+ * Gets the value of the proteinExistence property.
+ *
+ * @return
+ * possible object is
+ * {@link ProteinExistenceType }
+ *
+ */
+ public ProteinExistenceType getProteinExistence() {
+ return proteinExistence;
+ }
+
+ /**
+ * Sets the value of the proteinExistence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ProteinExistenceType }
+ *
+ */
+ public void setProteinExistence(ProteinExistenceType value) {
+ this.proteinExistence = value;
+ }
+
+ /**
+ * Gets the value of the keyword property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the keyword property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getKeyword().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link KeywordType }
+ *
+ *
+ */
+ public List<KeywordType> getKeyword() {
+ if (keyword == null) {
+ keyword = new ArrayList<KeywordType>();
+ }
+ return this.keyword;
+ }
+
+ /**
+ * Gets the value of the feature property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the feature property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFeature().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link FeatureType }
+ *
+ *
+ */
+ public List<FeatureType> getFeature() {
+ if (feature == null) {
+ feature = new ArrayList<FeatureType>();
+ }
+ return this.feature;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidenceType }
+ *
+ *
+ */
+ public List<EvidenceType> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<EvidenceType>();
+ }
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link SequenceType }
+ *
+ */
+ public SequenceType getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link SequenceType }
+ *
+ */
+ public void setSequence(SequenceType value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the dataset property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDataset() {
+ return dataset;
+ }
+
+ /**
+ * Sets the value of the dataset property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDataset(String value) {
+ this.dataset = value;
+ }
+
+ /**
+ * Gets the value of the created property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreated() {
+ return created;
+ }
+
+ /**
+ * Sets the value of the created property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreated(XMLGregorianCalendar value) {
+ this.created = value;
+ }
+
+ /**
+ * Gets the value of the modified property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getModified() {
+ return modified;
+ }
+
+ /**
+ * Sets the value of the modified property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setModified(XMLGregorianCalendar value) {
+ this.modified = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ */
+ public int getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ */
+ public void setVersion(int value) {
+ this.version = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes the type of events that cause alternative products.
+ *
+ * <p>Java class for eventType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="eventType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="alternative splicing"/>
+ * <enumeration value="alternative initiation"/>
+ * <enumeration value="alternative promoter"/>
+ * <enumeration value="ribosomal frameshifting"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "eventType")
+public class EventType {
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.math.BigInteger;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes the evidence for an annotation.
+ * No flat file equivalent.
+ *
+ * <p>Java class for evidenceType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="evidenceType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="source" type="{http://uniprot.org/uniprot}sourceType" minOccurs="0"/>
+ * <element name="importedFrom" type="{http://uniprot.org/uniprot}importedFromType" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "evidenceType", propOrder = {
+ "source",
+ "importedFrom"
+})
+public class EvidenceType {
+
+ protected SourceType source;
+ protected ImportedFromType importedFrom;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "key", required = true)
+ protected BigInteger key;
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return
+ * possible object is
+ * {@link SourceType }
+ *
+ */
+ public SourceType getSource() {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is
+ * {@link SourceType }
+ *
+ */
+ public void setSource(SourceType value) {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the importedFrom property.
+ *
+ * @return
+ * possible object is
+ * {@link ImportedFromType }
+ *
+ */
+ public ImportedFromType getImportedFrom() {
+ return importedFrom;
+ }
+
+ /**
+ * Sets the value of the importedFrom property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ImportedFromType }
+ *
+ */
+ public void setImportedFrom(ImportedFromType value) {
+ this.importedFrom = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getKey() {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setKey(BigInteger value) {
+ this.key = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+
+
+/**
+ * <p>Java class for evidencedStringType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="evidencedStringType">
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * <attribute name="status">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="by similarity"/>
+ * <enumeration value="probable"/>
+ * <enumeration value="potential"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "evidencedStringType", propOrder = {
+ "value"
+})
+public class EvidencedStringType {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "status")
+ protected String status;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getStatus() {
+ return status;
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes different types of sequence annotations.
+ * Equivalent to the flat file FT-line.
+ *
+ * <p>Java class for featureType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="featureType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="original" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="variation" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="location" type="{http://uniprot.org/uniprot}locationType"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="active site"/>
+ * <enumeration value="binding site"/>
+ * <enumeration value="calcium-binding region"/>
+ * <enumeration value="chain"/>
+ * <enumeration value="coiled-coil region"/>
+ * <enumeration value="compositionally biased region"/>
+ * <enumeration value="cross-link"/>
+ * <enumeration value="disulfide bond"/>
+ * <enumeration value="DNA-binding region"/>
+ * <enumeration value="domain"/>
+ * <enumeration value="glycosylation site"/>
+ * <enumeration value="helix"/>
+ * <enumeration value="initiator methionine"/>
+ * <enumeration value="lipid moiety-binding region"/>
+ * <enumeration value="metal ion-binding site"/>
+ * <enumeration value="modified residue"/>
+ * <enumeration value="mutagenesis site"/>
+ * <enumeration value="non-consecutive residues"/>
+ * <enumeration value="non-terminal residue"/>
+ * <enumeration value="nucleotide phosphate-binding region"/>
+ * <enumeration value="peptide"/>
+ * <enumeration value="propeptide"/>
+ * <enumeration value="region of interest"/>
+ * <enumeration value="repeat"/>
+ * <enumeration value="non-standard amino acid"/>
+ * <enumeration value="sequence conflict"/>
+ * <enumeration value="sequence variant"/>
+ * <enumeration value="short sequence motif"/>
+ * <enumeration value="signal peptide"/>
+ * <enumeration value="site"/>
+ * <enumeration value="splice variant"/>
+ * <enumeration value="strand"/>
+ * <enumeration value="topological domain"/>
+ * <enumeration value="transit peptide"/>
+ * <enumeration value="transmembrane region"/>
+ * <enumeration value="turn"/>
+ * <enumeration value="unsure residue"/>
+ * <enumeration value="zinc finger region"/>
+ * <enumeration value="intramembrane region"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="status">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="by similarity"/>
+ * <enumeration value="probable"/>
+ * <enumeration value="potential"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "featureType", propOrder = {
+ "original",
+ "variation",
+ "location"
+})
+public class FeatureType {
+
+ protected String original;
+ protected List<String> variation;
+ @XmlElement(required = true)
+ protected LocationType location;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "status")
+ protected String status;
+ @XmlAttribute(name = "id")
+ protected String id;
+ @XmlAttribute(name = "description")
+ protected String description;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "ref")
+ protected String ref;
+
+ /**
+ * Gets the value of the original property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getOriginal() {
+ return original;
+ }
+
+ /**
+ * Sets the value of the original property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setOriginal(String value) {
+ this.original = value;
+ }
+
+ /**
+ * Gets the value of the variation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the variation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getVariation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getVariation() {
+ if (variation == null) {
+ variation = new ArrayList<String>();
+ }
+ return this.variation;
+ }
+
+ /**
+ * Gets the value of the location property.
+ *
+ * @return
+ * possible object is
+ * {@link LocationType }
+ *
+ */
+ public LocationType getLocation() {
+ return location;
+ }
+
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is
+ * {@link LocationType }
+ *
+ */
+ public void setLocation(LocationType value) {
+ this.location = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getStatus() {
+ return status;
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getRef() {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setRef(String value) {
+ this.ref = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes non-nuclear gene locations (organelles and plasmids).
+ * Equivalent to the flat file OG-line.
+ *
+ * <p>Java class for geneLocationType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="geneLocationType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="name" type="{http://uniprot.org/uniprot}statusType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="apicoplast"/>
+ * <enumeration value="chloroplast"/>
+ * <enumeration value="organellar chromatophore"/>
+ * <enumeration value="cyanelle"/>
+ * <enumeration value="hydrogenosome"/>
+ * <enumeration value="mitochondrion"/>
+ * <enumeration value="non-photosynthetic plastid"/>
+ * <enumeration value="nucleomorph"/>
+ * <enumeration value="plasmid"/>
+ * <enumeration value="plastid"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "geneLocationType", propOrder = {
+ "name"
+})
+public class GeneLocationType {
+
+ protected List<StatusType> name;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link StatusType }
+ *
+ *
+ */
+ public List<StatusType> getName() {
+ if (name == null) {
+ name = new ArrayList<StatusType>();
+ }
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+
+
+/**
+ * Describes different types of gene designations.
+ * Equivalent to the flat file GN-line.
+ *
+ * <p>Java class for geneNameType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="geneNameType">
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="primary"/>
+ * <enumeration value="synonym"/>
+ * <enumeration value="ordered locus"/>
+ * <enumeration value="ORF"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "geneNameType", propOrder = {
+ "value"
+})
+public class GeneNameType {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes a gene.
+ * Equivalent to the flat file GN-line.
+ *
+ * <p>Java class for geneType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="geneType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="name" type="{http://uniprot.org/uniprot}geneNameType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "geneType", propOrder = {
+ "name"
+})
+public class GeneType {
+
+ @XmlElement(required = true)
+ protected List<GeneNameType> name;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneNameType }
+ *
+ *
+ */
+ public List<GeneNameType> getName() {
+ if (name == null) {
+ name = new ArrayList<GeneNameType>();
+ }
+ return this.name;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.
+ *
+ * <p>Java class for importedFromType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="importedFromType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "importedFromType", propOrder = {
+ "dbReference"
+})
+public class ImportedFromType {
+
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return
+ * possible object is
+ * {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference() {
+ return dbReference;
+ }
+
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value) {
+ this.dbReference = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for interactantType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="interactantType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <group ref="{http://uniprot.org/uniprot}interactantGroup" minOccurs="0"/>
+ * <attribute name="intactId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "interactantType", propOrder = {
+ "id",
+ "label"
+})
+public class InteractantType {
+
+ protected String id;
+ protected String label;
+ @XmlAttribute(name = "intactId", required = true)
+ protected String intactId;
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the label property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLabel() {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLabel(String value) {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the intactId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getIntactId() {
+ return intactId;
+ }
+
+ /**
+ * Sets the value of the intactId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setIntactId(String value) {
+ this.intactId = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+
+
+/**
+ * Describes isoforms in 'alternative products' annotations.
+ *
+ * <p>Java class for isoformType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="isoformType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="id" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="name" maxOccurs="unbounded">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * <element name="sequence">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="not described"/>
+ * <enumeration value="described"/>
+ * <enumeration value="displayed"/>
+ * <enumeration value="external"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "isoformType", propOrder = {
+ "id",
+ "name",
+ "sequence",
+ "text"
+})
+public class IsoformType {
+
+ @XmlElement(required = true)
+ protected List<String> id;
+ @XmlElement(required = true)
+ protected List<IsoformType.Name> name;
+ @XmlElement(required = true)
+ protected IsoformType.Sequence sequence;
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the id property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the id property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getId().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getId() {
+ if (id == null) {
+ id = new ArrayList<String>();
+ }
+ return this.id;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link IsoformType.Name }
+ *
+ *
+ */
+ public List<IsoformType.Name> getName() {
+ if (name == null) {
+ name = new ArrayList<IsoformType.Name>();
+ }
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link IsoformType.Sequence }
+ *
+ */
+ public IsoformType.Sequence getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link IsoformType.Sequence }
+ *
+ */
+ public void setSequence(IsoformType.Sequence value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Name {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="not described"/>
+ * <enumeration value="described"/>
+ * <enumeration value="displayed"/>
+ * <enumeration value="external"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Sequence {
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "ref")
+ protected String ref;
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getRef() {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setRef(String value) {
+ this.ref = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+
+
+/**
+ * <p>Java class for keywordType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="keywordType">
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "keywordType", propOrder = {
+ "value"
+})
+public class KeywordType {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry.
+ *
+ * <p>Java class for locationType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="locationType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <choice>
+ * <sequence>
+ * <element name="begin" type="{http://uniprot.org/uniprot}positionType"/>
+ * <element name="end" type="{http://uniprot.org/uniprot}positionType"/>
+ * </sequence>
+ * <element name="position" type="{http://uniprot.org/uniprot}positionType"/>
+ * </choice>
+ * <attribute name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "locationType", propOrder = {
+ "begin",
+ "end",
+ "position"
+})
+public class LocationType {
+
+ protected PositionType begin;
+ protected PositionType end;
+ protected PositionType position;
+ @XmlAttribute(name = "sequence")
+ protected String sequence;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link PositionType }
+ *
+ */
+ public PositionType getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link PositionType }
+ *
+ */
+ public void setBegin(PositionType value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link PositionType }
+ *
+ */
+ public PositionType getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link PositionType }
+ *
+ */
+ public void setEnd(PositionType value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ * @return
+ * possible object is
+ * {@link PositionType }
+ *
+ */
+ public PositionType getPosition() {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ * @param value
+ * allowed object is
+ * {@link PositionType }
+ *
+ */
+ public void setPosition(PositionType value) {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequence(String value) {
+ this.sequence = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+
+
+/**
+ * Describes a molecule by name or unique identifier.
+ *
+ * <p>Java class for moleculeType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="moleculeType">
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "moleculeType", propOrder = {
+ "value"
+})
+public class MoleculeType {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElements;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for nameListType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="nameListType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <choice maxOccurs="unbounded">
+ * <element name="consortium" type="{http://uniprot.org/uniprot}consortiumType"/>
+ * <element name="person" type="{http://uniprot.org/uniprot}personType"/>
+ * </choice>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "nameListType", propOrder = {
+ "consortiumOrPerson"
+})
+public class NameListType {
+
+ @XmlElements({
+ @XmlElement(name = "consortium", type = ConsortiumType.class),
+ @XmlElement(name = "person", type = PersonType.class)
+ })
+ protected List<Object> consortiumOrPerson;
+
+ /**
+ * Gets the value of the consortiumOrPerson property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the consortiumOrPerson property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getConsortiumOrPerson().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ConsortiumType }
+ * {@link PersonType }
+ *
+ *
+ */
+ public List<Object> getConsortiumOrPerson() {
+ if (consortiumOrPerson == null) {
+ consortiumOrPerson = new ArrayList<Object>();
+ }
+ return this.consortiumOrPerson;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.annotation.XmlElementDecl;
+import javax.xml.bind.annotation.XmlRegistry;
+import javax.xml.namespace.QName;
+
+
+/**
+ * This object contains factory methods for each
+ * Java content interface and Java element interface
+ * generated in the jalview.xml.binding.uniprot package.
+ * <p>An ObjectFactory allows you to programatically
+ * construct new instances of the Java representation
+ * for XML content. The Java representation of XML
+ * content can consist of schema derived interfaces
+ * and classes representing the binding of schema
+ * type definitions, element declarations and model
+ * groups. Factory methods for each of these are
+ * provided in this class.
+ *
+ */
+@XmlRegistry
+public class ObjectFactory {
+
+ private final static QName _Copyright_QNAME = new QName("http://uniprot.org/uniprot", "copyright");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.uniprot
+ *
+ */
+ public ObjectFactory() {
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType }
+ *
+ */
+ public SourceDataType createSourceDataType() {
+ return new SourceDataType();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType }
+ *
+ */
+ public IsoformType createIsoformType() {
+ return new IsoformType();
+ }
+
+ /**
+ * Create an instance of {@link CommentType }
+ *
+ */
+ public CommentType createCommentType() {
+ return new CommentType();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Conflict }
+ *
+ */
+ public CommentType.Conflict createCommentTypeConflict() {
+ return new CommentType.Conflict();
+ }
+
+ /**
+ * Create an instance of {@link OrganismType }
+ *
+ */
+ public OrganismType createOrganismType() {
+ return new OrganismType();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType }
+ *
+ */
+ public ProteinType createProteinType() {
+ return new ProteinType();
+ }
+
+ /**
+ * Create an instance of {@link Entry }
+ *
+ */
+ public Entry createEntry() {
+ return new Entry();
+ }
+
+ /**
+ * Create an instance of {@link GeneType }
+ *
+ */
+ public GeneType createGeneType() {
+ return new GeneType();
+ }
+
+ /**
+ * Create an instance of {@link GeneLocationType }
+ *
+ */
+ public GeneLocationType createGeneLocationType() {
+ return new GeneLocationType();
+ }
+
+ /**
+ * Create an instance of {@link ReferenceType }
+ *
+ */
+ public ReferenceType createReferenceType() {
+ return new ReferenceType();
+ }
+
+ /**
+ * Create an instance of {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType createDbReferenceType() {
+ return new DbReferenceType();
+ }
+
+ /**
+ * Create an instance of {@link ProteinExistenceType }
+ *
+ */
+ public ProteinExistenceType createProteinExistenceType() {
+ return new ProteinExistenceType();
+ }
+
+ /**
+ * Create an instance of {@link KeywordType }
+ *
+ */
+ public KeywordType createKeywordType() {
+ return new KeywordType();
+ }
+
+ /**
+ * Create an instance of {@link FeatureType }
+ *
+ */
+ public FeatureType createFeatureType() {
+ return new FeatureType();
+ }
+
+ /**
+ * Create an instance of {@link EvidenceType }
+ *
+ */
+ public EvidenceType createEvidenceType() {
+ return new EvidenceType();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType() {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Uniprot }
+ *
+ */
+ public Uniprot createUniprot() {
+ return new Uniprot();
+ }
+
+ /**
+ * Create an instance of {@link StatusType }
+ *
+ */
+ public StatusType createStatusType() {
+ return new StatusType();
+ }
+
+ /**
+ * Create an instance of {@link PositionType }
+ *
+ */
+ public PositionType createPositionType() {
+ return new PositionType();
+ }
+
+ /**
+ * Create an instance of {@link ConsortiumType }
+ *
+ */
+ public ConsortiumType createConsortiumType() {
+ return new ConsortiumType();
+ }
+
+ /**
+ * Create an instance of {@link GeneNameType }
+ *
+ */
+ public GeneNameType createGeneNameType() {
+ return new GeneNameType();
+ }
+
+ /**
+ * Create an instance of {@link LocationType }
+ *
+ */
+ public LocationType createLocationType() {
+ return new LocationType();
+ }
+
+ /**
+ * Create an instance of {@link CitationType }
+ *
+ */
+ public CitationType createCitationType() {
+ return new CitationType();
+ }
+
+ /**
+ * Create an instance of {@link PropertyType }
+ *
+ */
+ public PropertyType createPropertyType() {
+ return new PropertyType();
+ }
+
+ /**
+ * Create an instance of {@link CofactorType }
+ *
+ */
+ public CofactorType createCofactorType() {
+ return new CofactorType();
+ }
+
+ /**
+ * Create an instance of {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType createEvidencedStringType() {
+ return new EvidencedStringType();
+ }
+
+ /**
+ * Create an instance of {@link PersonType }
+ *
+ */
+ public PersonType createPersonType() {
+ return new PersonType();
+ }
+
+ /**
+ * Create an instance of {@link ImportedFromType }
+ *
+ */
+ public ImportedFromType createImportedFromType() {
+ return new ImportedFromType();
+ }
+
+ /**
+ * Create an instance of {@link EventType }
+ *
+ */
+ public EventType createEventType() {
+ return new EventType();
+ }
+
+ /**
+ * Create an instance of {@link InteractantType }
+ *
+ */
+ public InteractantType createInteractantType() {
+ return new InteractantType();
+ }
+
+ /**
+ * Create an instance of {@link NameListType }
+ *
+ */
+ public NameListType createNameListType() {
+ return new NameListType();
+ }
+
+ /**
+ * Create an instance of {@link SourceType }
+ *
+ */
+ public SourceType createSourceType() {
+ return new SourceType();
+ }
+
+ /**
+ * Create an instance of {@link MoleculeType }
+ *
+ */
+ public MoleculeType createMoleculeType() {
+ return new MoleculeType();
+ }
+
+ /**
+ * Create an instance of {@link OrganismNameType }
+ *
+ */
+ public OrganismNameType createOrganismNameType() {
+ return new OrganismNameType();
+ }
+
+ /**
+ * Create an instance of {@link SubcellularLocationType }
+ *
+ */
+ public SubcellularLocationType createSubcellularLocationType() {
+ return new SubcellularLocationType();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Strain }
+ *
+ */
+ public SourceDataType.Strain createSourceDataTypeStrain() {
+ return new SourceDataType.Strain();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Plasmid }
+ *
+ */
+ public SourceDataType.Plasmid createSourceDataTypePlasmid() {
+ return new SourceDataType.Plasmid();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Transposon }
+ *
+ */
+ public SourceDataType.Transposon createSourceDataTypeTransposon() {
+ return new SourceDataType.Transposon();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Tissue }
+ *
+ */
+ public SourceDataType.Tissue createSourceDataTypeTissue() {
+ return new SourceDataType.Tissue();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType.Name }
+ *
+ */
+ public IsoformType.Name createIsoformTypeName() {
+ return new IsoformType.Name();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType.Sequence }
+ *
+ */
+ public IsoformType.Sequence createIsoformTypeSequence() {
+ return new IsoformType.Sequence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Absorption }
+ *
+ */
+ public CommentType.Absorption createCommentTypeAbsorption() {
+ return new CommentType.Absorption();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Kinetics }
+ *
+ */
+ public CommentType.Kinetics createCommentTypeKinetics() {
+ return new CommentType.Kinetics();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.PhDependence }
+ *
+ */
+ public CommentType.PhDependence createCommentTypePhDependence() {
+ return new CommentType.PhDependence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.RedoxPotential }
+ *
+ */
+ public CommentType.RedoxPotential createCommentTypeRedoxPotential() {
+ return new CommentType.RedoxPotential();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.TemperatureDependence }
+ *
+ */
+ public CommentType.TemperatureDependence createCommentTypeTemperatureDependence() {
+ return new CommentType.TemperatureDependence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Link }
+ *
+ */
+ public CommentType.Link createCommentTypeLink() {
+ return new CommentType.Link();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Disease }
+ *
+ */
+ public CommentType.Disease createCommentTypeDisease() {
+ return new CommentType.Disease();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Conflict.Sequence }
+ *
+ */
+ public CommentType.Conflict.Sequence createCommentTypeConflictSequence() {
+ return new CommentType.Conflict.Sequence();
+ }
+
+ /**
+ * Create an instance of {@link OrganismType.Lineage }
+ *
+ */
+ public OrganismType.Lineage createOrganismTypeLineage() {
+ return new OrganismType.Lineage();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName createProteinTypeRecommendedName() {
+ return new ProteinType.RecommendedName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.AlternativeName }
+ *
+ */
+ public ProteinType.AlternativeName createProteinTypeAlternativeName() {
+ return new ProteinType.AlternativeName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.SubmittedName }
+ *
+ */
+ public ProteinType.SubmittedName createProteinTypeSubmittedName() {
+ return new ProteinType.SubmittedName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.Domain }
+ *
+ */
+ public ProteinType.Domain createProteinTypeDomain() {
+ return new ProteinType.Domain();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.Component }
+ *
+ */
+ public ProteinType.Component createProteinTypeComponent() {
+ return new ProteinType.Component();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
+ *
+ */
+ @XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright")
+ public JAXBElement<String> createCopyright(String value) {
+ return new JAXBElement<String>(_Copyright_QNAME, String.class, null, value);
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+
+
+/**
+ * Describes different types of source organism names.
+ *
+ * <p>Java class for organismNameType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="organismNameType">
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="common"/>
+ * <enumeration value="full"/>
+ * <enumeration value="scientific"/>
+ * <enumeration value="synonym"/>
+ * <enumeration value="abbreviation"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "organismNameType", propOrder = {
+ "value"
+})
+public class OrganismNameType {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes the source organism.
+ *
+ * <p>Java class for organismType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="organismType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="name" type="{http://uniprot.org/uniprot}organismNameType" maxOccurs="unbounded"/>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "organismType", propOrder = {
+ "name",
+ "dbReference",
+ "lineage"
+})
+public class OrganismType {
+
+ @XmlElement(required = true)
+ protected List<OrganismNameType> name;
+ @XmlElement(required = true)
+ protected List<DbReferenceType> dbReference;
+ protected OrganismType.Lineage lineage;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link OrganismNameType }
+ *
+ *
+ */
+ public List<OrganismNameType> getName() {
+ if (name == null) {
+ name = new ArrayList<OrganismNameType>();
+ }
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference() {
+ if (dbReference == null) {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
+ }
+
+ /**
+ * Gets the value of the lineage property.
+ *
+ * @return
+ * possible object is
+ * {@link OrganismType.Lineage }
+ *
+ */
+ public OrganismType.Lineage getLineage() {
+ return lineage;
+ }
+
+ /**
+ * Sets the value of the lineage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link OrganismType.Lineage }
+ *
+ */
+ public void setLineage(OrganismType.Lineage value) {
+ this.lineage = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "taxon"
+ })
+ public static class Lineage {
+
+ @XmlElement(required = true)
+ protected List<String> taxon;
+
+ /**
+ * Gets the value of the taxon property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the taxon property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTaxon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getTaxon() {
+ if (taxon == null) {
+ taxon = new ArrayList<String>();
+ }
+ return this.taxon;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for personType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="personType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "personType")
+public class PersonType {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for positionType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="positionType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="position" type="{http://www.w3.org/2001/XMLSchema}unsignedLong" />
+ * <attribute name="status" default="certain">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="certain"/>
+ * <enumeration value="uncertain"/>
+ * <enumeration value="less than"/>
+ * <enumeration value="greater than"/>
+ * <enumeration value="unknown"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "positionType")
+public class PositionType {
+
+ @XmlAttribute(name = "position")
+ @XmlSchemaType(name = "unsignedLong")
+ protected BigInteger position;
+ @XmlAttribute(name = "status")
+ protected String status;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the position property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPosition() {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPosition(BigInteger value) {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getStatus() {
+ if (status == null) {
+ return "certain";
+ } else {
+ return status;
+ }
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for propertyType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="propertyType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "propertyType")
+public class PropertyType {
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes the evidence for the protein's existence.
+ * Equivalent to the flat file PE-line.
+ *
+ * <p>Java class for proteinExistenceType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="proteinExistenceType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="evidence at protein level"/>
+ * <enumeration value="evidence at transcript level"/>
+ * <enumeration value="inferred from homology"/>
+ * <enumeration value="predicted"/>
+ * <enumeration value="uncertain"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "proteinExistenceType")
+public class ProteinExistenceType {
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes the names for the protein and parts thereof.
+ * Equivalent to the flat file DE-line.
+ *
+ * <p>Java class for proteinType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="proteinType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * <element name="domain" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="component" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "proteinType", propOrder = {
+ "recommendedName",
+ "alternativeName",
+ "submittedName",
+ "allergenName",
+ "biotechName",
+ "cdAntigenName",
+ "innName",
+ "domain",
+ "component"
+})
+public class ProteinType {
+
+ protected ProteinType.RecommendedName recommendedName;
+ protected List<ProteinType.AlternativeName> alternativeName;
+ protected List<ProteinType.SubmittedName> submittedName;
+ protected EvidencedStringType allergenName;
+ protected EvidencedStringType biotechName;
+ protected List<EvidencedStringType> cdAntigenName;
+ protected List<EvidencedStringType> innName;
+ protected List<ProteinType.Domain> domain;
+ protected List<ProteinType.Component> component;
+
+ /**
+ * Gets the value of the recommendedName property.
+ *
+ * @return
+ * possible object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName getRecommendedName() {
+ return recommendedName;
+ }
+
+ /**
+ * Sets the value of the recommendedName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public void setRecommendedName(ProteinType.RecommendedName value) {
+ this.recommendedName = value;
+ }
+
+ /**
+ * Gets the value of the alternativeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlternativeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.AlternativeName }
+ *
+ *
+ */
+ public List<ProteinType.AlternativeName> getAlternativeName() {
+ if (alternativeName == null) {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
+ }
+
+ /**
+ * Gets the value of the submittedName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the submittedName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSubmittedName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.SubmittedName }
+ *
+ *
+ */
+ public List<ProteinType.SubmittedName> getSubmittedName() {
+ if (submittedName == null) {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
+ }
+
+ /**
+ * Gets the value of the allergenName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getAllergenName() {
+ return allergenName;
+ }
+
+ /**
+ * Sets the value of the allergenName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setAllergenName(EvidencedStringType value) {
+ this.allergenName = value;
+ }
+
+ /**
+ * Gets the value of the biotechName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getBiotechName() {
+ return biotechName;
+ }
+
+ /**
+ * Sets the value of the biotechName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setBiotechName(EvidencedStringType value) {
+ this.biotechName = value;
+ }
+
+ /**
+ * Gets the value of the cdAntigenName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCdAntigenName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getCdAntigenName() {
+ if (cdAntigenName == null) {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
+ }
+
+ /**
+ * Gets the value of the innName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the innName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getInnName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getInnName() {
+ if (innName == null) {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+
+ /**
+ * Gets the value of the domain property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the domain property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDomain().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.Domain }
+ *
+ *
+ */
+ public List<ProteinType.Domain> getDomain() {
+ if (domain == null) {
+ domain = new ArrayList<ProteinType.Domain>();
+ }
+ return this.domain;
+ }
+
+ /**
+ * Gets the value of the component property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the component property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getComponent().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.Component }
+ *
+ *
+ */
+ public List<ProteinType.Component> getComponent() {
+ if (component == null) {
+ component = new ArrayList<ProteinType.Component>();
+ }
+ return this.component;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+ * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "fullName",
+ "shortName",
+ "ecNumber"
+ })
+ public static class AlternativeName {
+
+ protected EvidencedStringType fullName;
+ protected List<EvidencedStringType> shortName;
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName() {
+ return fullName;
+ }
+
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value) {
+ this.fullName = value;
+ }
+
+ /**
+ * Gets the value of the shortName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the shortName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getShortName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getShortName() {
+ if (shortName == null) {
+ shortName = new ArrayList<EvidencedStringType>();
+ }
+ return this.shortName;
+ }
+
+ /**
+ * Gets the value of the ecNumber property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEcNumber().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getEcNumber() {
+ if (ecNumber == null) {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "recommendedName",
+ "alternativeName",
+ "submittedName",
+ "allergenName",
+ "biotechName",
+ "cdAntigenName",
+ "innName"
+ })
+ public static class Component {
+
+ protected ProteinType.RecommendedName recommendedName;
+ protected List<ProteinType.AlternativeName> alternativeName;
+ protected List<ProteinType.SubmittedName> submittedName;
+ protected EvidencedStringType allergenName;
+ protected EvidencedStringType biotechName;
+ protected List<EvidencedStringType> cdAntigenName;
+ protected List<EvidencedStringType> innName;
+
+ /**
+ * Gets the value of the recommendedName property.
+ *
+ * @return
+ * possible object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName getRecommendedName() {
+ return recommendedName;
+ }
+
+ /**
+ * Sets the value of the recommendedName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public void setRecommendedName(ProteinType.RecommendedName value) {
+ this.recommendedName = value;
+ }
+
+ /**
+ * Gets the value of the alternativeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlternativeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.AlternativeName }
+ *
+ *
+ */
+ public List<ProteinType.AlternativeName> getAlternativeName() {
+ if (alternativeName == null) {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
+ }
+
+ /**
+ * Gets the value of the submittedName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the submittedName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSubmittedName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.SubmittedName }
+ *
+ *
+ */
+ public List<ProteinType.SubmittedName> getSubmittedName() {
+ if (submittedName == null) {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
+ }
+
+ /**
+ * Gets the value of the allergenName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getAllergenName() {
+ return allergenName;
+ }
+
+ /**
+ * Sets the value of the allergenName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setAllergenName(EvidencedStringType value) {
+ this.allergenName = value;
+ }
+
+ /**
+ * Gets the value of the biotechName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getBiotechName() {
+ return biotechName;
+ }
+
+ /**
+ * Sets the value of the biotechName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setBiotechName(EvidencedStringType value) {
+ this.biotechName = value;
+ }
+
+ /**
+ * Gets the value of the cdAntigenName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCdAntigenName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getCdAntigenName() {
+ if (cdAntigenName == null) {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
+ }
+
+ /**
+ * Gets the value of the innName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the innName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getInnName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getInnName() {
+ if (innName == null) {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "recommendedName",
+ "alternativeName",
+ "submittedName",
+ "allergenName",
+ "biotechName",
+ "cdAntigenName",
+ "innName"
+ })
+ public static class Domain {
+
+ protected ProteinType.RecommendedName recommendedName;
+ protected List<ProteinType.AlternativeName> alternativeName;
+ protected List<ProteinType.SubmittedName> submittedName;
+ protected EvidencedStringType allergenName;
+ protected EvidencedStringType biotechName;
+ protected List<EvidencedStringType> cdAntigenName;
+ protected List<EvidencedStringType> innName;
+
+ /**
+ * Gets the value of the recommendedName property.
+ *
+ * @return
+ * possible object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName getRecommendedName() {
+ return recommendedName;
+ }
+
+ /**
+ * Sets the value of the recommendedName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public void setRecommendedName(ProteinType.RecommendedName value) {
+ this.recommendedName = value;
+ }
+
+ /**
+ * Gets the value of the alternativeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlternativeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.AlternativeName }
+ *
+ *
+ */
+ public List<ProteinType.AlternativeName> getAlternativeName() {
+ if (alternativeName == null) {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
+ }
+
+ /**
+ * Gets the value of the submittedName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the submittedName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSubmittedName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.SubmittedName }
+ *
+ *
+ */
+ public List<ProteinType.SubmittedName> getSubmittedName() {
+ if (submittedName == null) {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
+ }
+
+ /**
+ * Gets the value of the allergenName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getAllergenName() {
+ return allergenName;
+ }
+
+ /**
+ * Sets the value of the allergenName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setAllergenName(EvidencedStringType value) {
+ this.allergenName = value;
+ }
+
+ /**
+ * Gets the value of the biotechName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getBiotechName() {
+ return biotechName;
+ }
+
+ /**
+ * Sets the value of the biotechName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setBiotechName(EvidencedStringType value) {
+ this.biotechName = value;
+ }
+
+ /**
+ * Gets the value of the cdAntigenName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCdAntigenName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getCdAntigenName() {
+ if (cdAntigenName == null) {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
+ }
+
+ /**
+ * Gets the value of the innName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the innName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getInnName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getInnName() {
+ if (innName == null) {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+ * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "fullName",
+ "shortName",
+ "ecNumber"
+ })
+ public static class RecommendedName {
+
+ @XmlElement(required = true)
+ protected EvidencedStringType fullName;
+ protected List<EvidencedStringType> shortName;
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName() {
+ return fullName;
+ }
+
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value) {
+ this.fullName = value;
+ }
+
+ /**
+ * Gets the value of the shortName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the shortName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getShortName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getShortName() {
+ if (shortName == null) {
+ shortName = new ArrayList<EvidencedStringType>();
+ }
+ return this.shortName;
+ }
+
+ /**
+ * Gets the value of the ecNumber property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEcNumber().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getEcNumber() {
+ if (ecNumber == null) {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "fullName",
+ "ecNumber"
+ })
+ public static class SubmittedName {
+
+ @XmlElement(required = true)
+ protected EvidencedStringType fullName;
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName() {
+ return fullName;
+ }
+
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value) {
+ this.fullName = value;
+ }
+
+ /**
+ * Gets the value of the ecNumber property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEcNumber().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getEcNumber() {
+ if (ecNumber == null) {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes a citation and a summary of its content.
+ * Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
+ *
+ * <p>Java class for referenceType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="referenceType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="citation" type="{http://uniprot.org/uniprot}citationType"/>
+ * <group ref="{http://uniprot.org/uniprot}sptrCitationGroup"/>
+ * </sequence>
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "referenceType", propOrder = {
+ "citation",
+ "scope",
+ "source"
+})
+public class ReferenceType {
+
+ @XmlElement(required = true)
+ protected CitationType citation;
+ @XmlElement(required = true)
+ protected List<String> scope;
+ protected SourceDataType source;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
+
+ /**
+ * Gets the value of the citation property.
+ *
+ * @return
+ * possible object is
+ * {@link CitationType }
+ *
+ */
+ public CitationType getCitation() {
+ return citation;
+ }
+
+ /**
+ * Sets the value of the citation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CitationType }
+ *
+ */
+ public void setCitation(CitationType value) {
+ this.citation = value;
+ }
+
+ /**
+ * Gets the value of the scope property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the scope property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getScope().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getScope() {
+ if (scope == null) {
+ scope = new ArrayList<String>();
+ }
+ return this.scope;
+ }
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return
+ * possible object is
+ * {@link SourceDataType }
+ *
+ */
+ public SourceDataType getSource() {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is
+ * {@link SourceDataType }
+ *
+ */
+ public void setSource(SourceDataType value) {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey() {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey(String value) {
+ this.key = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+
+/**
+ * <p>Java class for sequenceType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="sequenceType">
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="checksum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="precursor" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fragment">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="single"/>
+ * <enumeration value="multiple"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "sequenceType", propOrder = {
+ "value"
+})
+public class SequenceType {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "length", required = true)
+ protected int length;
+ @XmlAttribute(name = "mass", required = true)
+ protected int mass;
+ @XmlAttribute(name = "checksum", required = true)
+ protected String checksum;
+ @XmlAttribute(name = "modified", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar modified;
+ @XmlAttribute(name = "version", required = true)
+ protected int version;
+ @XmlAttribute(name = "precursor")
+ protected Boolean precursor;
+ @XmlAttribute(name = "fragment")
+ protected String fragment;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the length property.
+ *
+ */
+ public int getLength() {
+ return length;
+ }
+
+ /**
+ * Sets the value of the length property.
+ *
+ */
+ public void setLength(int value) {
+ this.length = value;
+ }
+
+ /**
+ * Gets the value of the mass property.
+ *
+ */
+ public int getMass() {
+ return mass;
+ }
+
+ /**
+ * Sets the value of the mass property.
+ *
+ */
+ public void setMass(int value) {
+ this.mass = value;
+ }
+
+ /**
+ * Gets the value of the checksum property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getChecksum() {
+ return checksum;
+ }
+
+ /**
+ * Sets the value of the checksum property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setChecksum(String value) {
+ this.checksum = value;
+ }
+
+ /**
+ * Gets the value of the modified property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getModified() {
+ return modified;
+ }
+
+ /**
+ * Sets the value of the modified property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setModified(XMLGregorianCalendar value) {
+ this.modified = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ */
+ public int getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ */
+ public void setVersion(int value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the precursor property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPrecursor() {
+ return precursor;
+ }
+
+ /**
+ * Sets the value of the precursor property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPrecursor(Boolean value) {
+ this.precursor = value;
+ }
+
+ /**
+ * Gets the value of the fragment property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFragment() {
+ return fragment;
+ }
+
+ /**
+ * Sets the value of the fragment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFragment(String value) {
+ this.fragment = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElements;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+
+
+/**
+ * Describes the source of the sequence according to the citation.
+ * Equivalent to the flat file RC-line.
+ *
+ * <p>Java class for sourceDataType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="sourceDataType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <choice maxOccurs="unbounded">
+ * <element name="strain">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * <element name="plasmid">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * <element name="transposon">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * <element name="tissue">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "sourceDataType", propOrder = {
+ "strainOrPlasmidOrTransposon"
+})
+public class SourceDataType {
+
+ @XmlElements({
+ @XmlElement(name = "strain", type = SourceDataType.Strain.class),
+ @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
+ @XmlElement(name = "transposon", type = SourceDataType.Transposon.class),
+ @XmlElement(name = "tissue", type = SourceDataType.Tissue.class)
+ })
+ protected List<Object> strainOrPlasmidOrTransposon;
+
+ /**
+ * Gets the value of the strainOrPlasmidOrTransposon property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the strainOrPlasmidOrTransposon property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getStrainOrPlasmidOrTransposon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SourceDataType.Strain }
+ * {@link SourceDataType.Plasmid }
+ * {@link SourceDataType.Transposon }
+ * {@link SourceDataType.Tissue }
+ *
+ *
+ */
+ public List<Object> getStrainOrPlasmidOrTransposon() {
+ if (strainOrPlasmidOrTransposon == null) {
+ strainOrPlasmidOrTransposon = new ArrayList<Object>();
+ }
+ return this.strainOrPlasmidOrTransposon;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Plasmid {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Strain {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Tissue {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Transposon {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.math.BigInteger;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).
+ *
+ * <p>Java class for sourceType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="sourceType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "sourceType", propOrder = {
+ "dbReference"
+})
+public class SourceType {
+
+ protected DbReferenceType dbReference;
+ @XmlAttribute(name = "ref")
+ protected BigInteger ref;
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return
+ * possible object is
+ * {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference() {
+ return dbReference;
+ }
+
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value) {
+ this.dbReference = value;
+ }
+
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getRef() {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setRef(BigInteger value) {
+ this.ref = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+
+
+/**
+ * Indicates whether the name of a plasmid is known or unknown.
+ *
+ * <p>Java class for statusType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="statusType">
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="status" default="known">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="known"/>
+ * <enumeration value="unknown"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "statusType", propOrder = {
+ "value"
+})
+public class StatusType {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "status")
+ protected String status;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getStatus() {
+ if (status == null) {
+ return "known";
+ } else {
+ return status;
+ }
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Describes the subcellular location and optionally the topology and orientation of a molecule.
+ *
+ * <p>Java class for subcellularLocationType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="subcellularLocationType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="location" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * <element name="topology" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="orientation" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "subcellularLocationType", propOrder = {
+ "location",
+ "topology",
+ "orientation"
+})
+public class SubcellularLocationType {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> location;
+ protected List<EvidencedStringType> topology;
+ protected List<EvidencedStringType> orientation;
+
+ /**
+ * Gets the value of the location property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the location property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getLocation() {
+ if (location == null) {
+ location = new ArrayList<EvidencedStringType>();
+ }
+ return this.location;
+ }
+
+ /**
+ * Gets the value of the topology property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the topology property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTopology().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getTopology() {
+ if (topology == null) {
+ topology = new ArrayList<EvidencedStringType>();
+ }
+ return this.topology;
+ }
+
+ /**
+ * Gets the value of the orientation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the orientation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getOrientation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getOrientation() {
+ if (orientation == null) {
+ orientation = new ArrayList<EvidencedStringType>();
+ }
+ return this.orientation;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+
+package jalview.xml.binding.uniprot;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{http://uniprot.org/uniprot}entry" maxOccurs="unbounded"/>
+ * <element ref="{http://uniprot.org/uniprot}copyright" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "entry",
+ "copyright"
+})
+@XmlRootElement(name = "uniprot")
+public class Uniprot {
+
+ @XmlElement(required = true)
+ protected List<Entry> entry;
+ protected String copyright;
+
+ /**
+ * Gets the value of the entry property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the entry property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEntry().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry }
+ *
+ *
+ */
+ public List<Entry> getEntry() {
+ if (entry == null) {
+ entry = new ArrayList<Entry>();
+ }
+ return this.entry;
+ }
+
+ /**
+ * Gets the value of the copyright property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCopyright() {
+ return copyright;
+ }
+
+ /**
+ * Sets the value of the copyright property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCopyright(String value) {
+ this.copyright = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.13 at 10:18:53 AM BST
+//
+
+@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+package jalview.xml.binding.uniprot;
-20181030183630
\ No newline at end of file
+20181030183630
\ No newline at end of file
-20180917232142
+20180923174836
--- /dev/null
+20180927214151
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ScanResult;
+
public class CommandLineOperations
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private static final int TEST_TIMEOUT = 4500; // Note longer timeout needed on
+ private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed on
// full test run than on
// individual tests
private static final int MINFILESIZE_BIG = 4096;
- private ArrayList<String> successfulCMDs = new ArrayList<String>();
+ private ArrayList<String> successfulCMDs = new ArrayList<>();
/***
* from
}
}
+ private static ClassGraph scanner = null;
+
+ private static String classpath = null;
+
+ public synchronized static String getClassPath()
+ {
+ if (scanner == null)
+ {
+ scanner = new ClassGraph();
+ ScanResult scan = scanner.scan();
+ classpath = scan.getClasspath();
+ }
+ while (classpath == null)
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException x)
+ {
+
+ }
+ }
+ return classpath;
+ }
private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
int timeout)
{
+ // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
+ // not expanded by the shell
+ String classpath = getClassPath();
String _cmd = "java "
+ (withAwt ? "-Djava.awt.headless=true" : "")
- + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
- System.out.println("CMD [" + cmd + "]");
+ + " -classpath " + classpath + " jalview.bin.Jalview ";
Process ls2_proc = null;
Worker worker = null;
try
import java.util.Map;
import java.util.Set;
-import junit.extensions.PA;
-
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SequenceFeaturesTest
{
@Test(groups = "Functional")
assertTrue(store.getFeaturesByOntology(new String[] {}).isEmpty());
assertTrue(store.getFeaturesByOntology((String[]) null).isEmpty());
- SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20,
+ SequenceFeature transcriptFeature = new SequenceFeature("transcript", "desc", 10, 20,
Float.NaN, null);
- store.add(sf1);
+ store.add(transcriptFeature);
- // mRNA isA transcript; added here 'as if' non-positional
- // just to show that non-positional features are included in results
- SequenceFeature sf2 = new SequenceFeature("mRNA", "desc", 0, 0,
+ /*
+ * mRNA is a sub-type of transcript; added here 'as if' non-positional
+ * just to show that non-positional features are included in results
+ */
+ SequenceFeature mrnaFeature = new SequenceFeature("mRNA", "desc", 0, 0,
Float.NaN, null);
- store.add(sf2);
+ store.add(mrnaFeature);
- SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 30, 40,
+ SequenceFeature pfamFeature = new SequenceFeature("Pfam", "desc", 30, 40,
Float.NaN, null);
- store.add(sf3);
+ store.add(pfamFeature);
+ /*
+ * "transcript" matches both itself and the sub-term "mRNA"
+ */
features = store.getFeaturesByOntology("transcript");
assertEquals(features.size(), 2);
- assertTrue(features.contains(sf1));
- assertTrue(features.contains(sf2));
+ assertTrue(features.contains(transcriptFeature));
+ assertTrue(features.contains(mrnaFeature));
+ /*
+ * "mRNA" matches itself but not parent term "transcript"
+ */
features = store.getFeaturesByOntology("mRNA");
assertEquals(features.size(), 1);
- assertTrue(features.contains(sf2));
+ assertTrue(features.contains(mrnaFeature));
+ /*
+ * "pfam" is not an SO term but is included as an exact match
+ */
features = store.getFeaturesByOntology("mRNA", "Pfam");
assertEquals(features.size(), 2);
- assertTrue(features.contains(sf2));
- assertTrue(features.contains(sf3));
+ assertTrue(features.contains(mrnaFeature));
+ assertTrue(features.contains(pfamFeature));
features = store.getFeaturesByOntology("sequence_variant");
assertTrue(features.isEmpty());
@Test(groups = "Functional")
public void testSortFeatures()
{
- List<SequenceFeature> sfs = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> sfs = new ArrayList<>();
SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 80,
Float.NaN, null);
sfs.add(sf1);
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertSame;
-
-import jalview.analysis.SequenceIdMatcher;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class EmblEntryTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = "Functional")
- public void testGetCdsRanges()
- {
- EmblEntry testee = new EmblEntry();
-
- /*
- * Make a (CDS) Feature with 5 locations
- */
- EmblFeature cds = new EmblFeature();
- cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
-
- int[] exons = testee.getCdsRanges(cds);
- assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
- Arrays.toString(exons));
- }
-
- @Test(groups = "Functional")
- public void testParseCodingFeature()
- {
- // not the whole sequence but enough for this test...
- List<SequenceI> peptides = new ArrayList<SequenceI>();
- SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
- EmblFile ef = EmblTestHelper.getEmblFile();
- assertEquals(1, ef.getEntries().size());
- EmblEntry testee = ef.getEntries().get(0);
- String sourceDb = "EMBL";
- SequenceI dna = testee.makeSequence(sourceDb);
-
- /*
- * parse three CDS features, with two/one/no Uniprot cross-refs
- */
- for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
- {
- if ("CDS".equals(feature.getName()))
- {
- testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
- }
- }
-
- /*
- * peptides should now have five entries:
- * EMBL product and two Uniprot accessions for the first CDS / translation
- * EMBL product and one Uniprot accession for the second CDS / "
- * EMBL product only for the third
- */
- assertEquals(6, peptides.size());
- assertEquals("CAA30420.1", peptides.get(0).getName());
- assertEquals("MLCF", peptides.get(0).getSequenceAsString());
- assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
- assertEquals("MLCF", peptides.get(1).getSequenceAsString());
- assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
- assertEquals("MLCF", peptides.get(2).getSequenceAsString());
- assertEquals("CAA30421.1", peptides.get(3).getName());
- assertEquals("MSSS", peptides.get(3).getSequenceAsString());
- assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
- assertEquals("MSSS", peptides.get(4).getSequenceAsString());
- assertEquals("CAA12345.6", peptides.get(5).getName());
- assertEquals("MSS", peptides.get(5).getSequenceAsString());
-
- /*
- * verify dna sequence has dbrefs with CDS mappings to the peptide 'products'
- */
- MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
- 3, 1);
- MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
- 3, 1);
- MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
- 1, 3 }, 3, 1);
- DBRefEntry[] dbrefs = dna.getDBRefs();
- assertEquals(4, dbrefs.length);
- DBRefEntry dbRefEntry = dbrefs[0];
- assertEquals("UNIPROT", dbRefEntry.getSource());
- assertEquals("B0BCM4", dbRefEntry.getAccessionId());
- assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
- assertEquals(cds1Map, dbRefEntry.getMap().getMap());
-
- dbRefEntry = dbrefs[1];
- assertEquals("UNIPROT", dbRefEntry.getSource());
- assertEquals("P0CE20", dbRefEntry.getAccessionId());
- assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
- assertEquals(cds1Map, dbRefEntry.getMap().getMap());
-
- dbRefEntry = dbrefs[2];
- assertEquals("UNIPROT", dbRefEntry.getSource());
- assertEquals("B0BCM3", dbRefEntry.getAccessionId());
- assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
- assertEquals(cds2Map, dbRefEntry.getMap().getMap());
-
- dbRefEntry = dbrefs[3];
- assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
- assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
- assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
- assertEquals(cds3Map, dbRefEntry.getMap().getMap());
-
- /*
- * verify peptides have dbrefs
- * - to EMBL sequence (with inverse 1:3 cds mapping)
- * - to EMBLCDS (with 1:3 mapping)
- * - direct (no mapping) to other protein accessions
- */
- MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
- 1, 12 }, 1, 3);
- MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
- 1, 9 }, 1, 3);
-
- // dbrefs for first CDS EMBL product CAA30420.1
- dbrefs = peptides.get(0).getDBRefs();
- assertEquals(5, dbrefs.length);
- assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
- assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
- // TODO: verify getPrimaryDBRefs() for peptide products
- assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
- assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
- assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
- assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
- assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
- assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
- assertNull(dbrefs[2].getMap());
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
- dbrefs[3]);
- assertNull(dbrefs[3].getMap());
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
- dbrefs[4]);
- assertNull(dbrefs[4].getMap());
-
- // dbrefs for first CDS first Uniprot xref
- dbrefs = peptides.get(1).getDBRefs();
- assertEquals(2, dbrefs.length);
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
- dbrefs[0]);
- assertNull(dbrefs[0].getMap());
- assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
- assertEquals("X07547", dbrefs[1].getAccessionId());
- assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
-
- // dbrefs for first CDS second Uniprot xref
- dbrefs = peptides.get(2).getDBRefs();
- assertEquals(2, dbrefs.length);
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
- dbrefs[0]);
- assertNull(dbrefs[0].getMap());
- assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
- assertEquals("X07547", dbrefs[1].getAccessionId());
- assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
-
- // dbrefs for second CDS EMBL product CAA30421.1
- dbrefs = peptides.get(3).getDBRefs();
- assertEquals(4, dbrefs.length);
- assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
- assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
- assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
- assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
- assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
- assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
- assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
- assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
- assertNull(dbrefs[2].getMap());
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
- dbrefs[3]);
- assertNull(dbrefs[3].getMap());
-
- // dbrefs for second CDS second Uniprot xref
- dbrefs = peptides.get(4).getDBRefs();
- assertEquals(2, dbrefs.length);
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
- dbrefs[0]);
- assertNull(dbrefs[0].getMap());
- assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
- assertEquals("X07547", dbrefs[1].getAccessionId());
- assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());
-
- // dbrefs for third CDS inferred EMBL product CAA12345.6
- dbrefs = peptides.get(5).getDBRefs();
- assertEquals(3, dbrefs.length);
- assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
- assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
- assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
- assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
- assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
- assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
- assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
- assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
- assertNull(dbrefs[2].getMap());
- }
-
- @Test(groups = "Functional")
- public void testAdjustForProteinLength()
- {
- int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
-
- // exact length match:
- assertSame(exons, EmblEntry.adjustForProteinLength(6, exons));
-
- // match if we assume exons include stop codon not in protein:
- assertSame(exons, EmblEntry.adjustForProteinLength(5, exons));
-
- // truncate last exon by 6bp
- int[] truncated = EmblEntry.adjustForProteinLength(4, exons);
- assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
-
- // remove last exon and truncate preceding by 1bp
- truncated = EmblEntry.adjustForProteinLength(3, exons);
- assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
-
- // exact removal of exon case:
- exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
- truncated = EmblEntry.adjustForProteinLength(4, exons);
- assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
-
- // what if exons are too short for protein?
- truncated = EmblEntry.adjustForProteinLength(7, exons);
- assertSame(exons, truncated);
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNull;
-
-import jalview.datamodel.DBRefEntry;
-import jalview.gui.JvOptionPane;
-
-import java.util.Vector;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class EmblFileTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void testGetEmblFile()
- {
- Vector<EmblEntry> entries = EmblTestHelper.getEmblFile().getEntries();
- assertEquals(1, entries.size());
- EmblEntry entry = entries.get(0);
-
- assertEquals("X07547", entry.getAccession());
- assertEquals("C. trachomatis plasmid", entry.getDescription());
- assertEquals("STD", entry.getDataClass());
- assertEquals("PRO", entry.getTaxonomicDivision());
- assertEquals("1999-02-10", entry.getLastUpdatedDate());
- assertEquals("58", entry.getLastUpdatedRelease());
- assertEquals("1988-11-10", entry.getFirstPublicDate());
- assertEquals("18", entry.getFirstPublicRelease());
- assertEquals("genomic DNA", entry.getMoleculeType());
- assertEquals("1", entry.getSequenceVersion());
- assertEquals("8", entry.getEntryVersion());
- assertEquals("linear", entry.getTopology());
- assertEquals("7499", entry.getSequenceLength());
-
- /*
- * FIXME these assertions fail - values are null - why?? Adding or removing
- * attributes in the test XML modifies behaviour. eg. inserting an attribute
- * _before_ lastUpdated results in a null value in this field.
- */
- assertEquals("1988-11-10", entry.getFirstPublicDate());
- assertEquals("18", entry.getFirstPublicRelease());
-
- assertEquals(2, entry.getKeywords().size());
- assertEquals("plasmid", entry.getKeywords().get(0));
- assertEquals("unidentified reading frame", entry.getKeywords().get(1));
-
- /*
- * dbrefs
- */
- assertEquals(2, entry.getDbRefs().size());
- DBRefEntry dbref = entry.getDbRefs().get(0);
- assertEquals("EuropePMC", dbref.getSource());
- assertEquals("PMC107176", dbref.getAccessionId());
- assertEquals("9573186", dbref.getVersion());
- dbref = entry.getDbRefs().get(1);
- assertEquals("MD5", dbref.getSource());
- assertEquals("ac73317", dbref.getAccessionId());
- // blank version has been converted to "0"
- assertEquals("0", dbref.getVersion());
-
- /*
- * three sequence features for CDS
- */
- assertEquals(3, entry.getFeatures().size());
- /*
- * first CDS
- */
- EmblFeature ef = entry.getFeatures().get(0);
- assertEquals("CDS", ef.getName());
- assertEquals("complement(46..57)", ef.getLocation());
- assertEquals(2, ef.getDbRefs().size());
- dbref = ef.getDbRefs().get(0);
- assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
- assertEquals("B0BCM4", dbref.getAccessionId());
- assertEquals("2.1", dbref.getVersion());
- dbref = ef.getDbRefs().get(1);
- assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
- assertEquals("P0CE20", dbref.getAccessionId());
- // blank version gets converted to "0":
- assertEquals("0", dbref.getVersion());
- // CDS feature qualifiers
- assertEquals(3, ef.getQualifiers().size());
- Qualifier q = ef.getQualifiers().get(0);
- assertEquals("note", q.getName());
- assertEquals(2, q.getValues().length);
- assertEquals("ORF 8 (AA 1-330)", q.getValues()[0]);
- assertEquals("pickle", q.getValues()[1]);
- assertNull(q.getEvidence());
- q = ef.getQualifiers().get(1);
- assertEquals("protein_id", q.getName());
- assertEquals(1, q.getValues().length);
- assertEquals("CAA30420.1", q.getValues()[0]);
- q = ef.getQualifiers().get(2);
- assertEquals("translation", q.getName());
- assertEquals(1, q.getValues().length);
- assertEquals("MLCF", q.getValues()[0]);
- assertEquals(1, q.getEvidence().length);
- assertEquals("Keith", q.getEvidence()[0]);
-
- /*
- * second CDS
- */
- ef = entry.getFeatures().get(1);
- assertEquals("CDS", ef.getName());
- assertEquals("4..15", ef.getLocation());
- assertEquals(1, ef.getDbRefs().size());
- dbref = ef.getDbRefs().get(0);
- assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
- assertEquals("B0BCM3", dbref.getAccessionId());
- assertEquals("0", dbref.getVersion());
- assertEquals(2, ef.getQualifiers().size());
- q = ef.getQualifiers().get(0);
- assertEquals("protein_id", q.getName());
- assertEquals(1, q.getValues().length);
- assertEquals("CAA30421.1", q.getValues()[0]);
- q = ef.getQualifiers().get(1);
- assertEquals("translation", q.getName());
- assertEquals(1, q.getValues().length);
- assertEquals("MSSS", q.getValues()[0]);
-
- /*
- * third CDS
- */
- ef = entry.getFeatures().get(2);
- assertEquals("CDS", ef.getName());
- assertEquals("join(4..6,10..15)", ef.getLocation());
- assertNull(ef.getDbRefs());
- assertEquals(2, ef.getQualifiers().size());
- q = ef.getQualifiers().get(0);
- assertEquals("protein_id", q.getName());
- assertEquals(1, q.getValues().length);
- assertEquals("CAA12345.6", q.getValues()[0]);
- q = ef.getQualifiers().get(1);
- assertEquals("translation", q.getName());
- assertEquals(1, q.getValues().length);
- assertEquals("MSS", q.getValues()[0]);
-
- /*
- * Sequence - verify newline not converted to space (JAL-2029)
- */
- EmblSequence seq = entry.getSequence();
- assertEquals(
- "GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
- seq.getSequence());
-
- /*
- * getSequence() converts empty DBRefEntry.version to "0"
- */
- assertEquals("0", entry.getDbRefs().get(1).getVersion());
- assertEquals("0", entry.getFeatures().get(0).getDbRefs().get(1)
- .getVersion());
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import java.io.StringReader;
-
-public class EmblTestHelper
-{
- // adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
- // dna and translations truncated for convenience
- private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
- + "<ROOT>"
- + "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
- + " dataClass=\"STD\" taxonomicDivision=\"PRO\""
- + " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
- + " firstPublic=\"1988-11-10\" firstPublicRelease=\"18\""
- + " lastUpdated=\"1999-02-10\" lastUpdatedRelease=\"58\">"
- + "<secondaryAccession>X07574</secondaryAccession>"
- + "<description>C. trachomatis plasmid</description>"
- + "<keyword>plasmid</keyword><keyword>unidentified reading frame</keyword>"
- + "<xref db=\"EuropePMC\" id=\"PMC107176\" secondaryId=\"9573186\" />"
- + "<xref db=\"MD5\" id=\"ac73317\" />"
- /*
- * first CDS (range and translation changed to keep test data manageable)
- */
- + "<feature name=\"CDS\" location=\"complement(46..57)\">"
- // test the case of >1 cross-ref to the same database (JAL-2029)
- + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM4\" secondaryId=\"2.1\" />"
- + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"P0CE20\" />"
- + "<qualifier name=\"note\"><value>ORF 8 (AA 1-330)</value><value>pickle</value></qualifier>"
- + "<qualifier name=\"protein_id\"><value>CAA30420.1</value></qualifier>"
- + "<qualifier name=\"translation\"><value>MLCF</value><evidence>Keith</evidence></qualifier>"
- + "</feature>"
- /*
- * second CDS (range and translation changed to keep test data manageable)
- */
- + "<feature name=\"CDS\" location=\"4..15\">"
- + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM3\" />"
- + "<qualifier name=\"protein_id\"><value>CAA30421.1</value></qualifier>"
- + "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
- + "</feature>"
- /*
- * third CDS is made up - has no xref - code should synthesize
- * one to an assumed EMBLCDSPROTEIN accession
- */
- + "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
- + "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
- + "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
- + "</feature>"
- /*
- * sequence (modified for test purposes)
- * emulates EMBL XML 1.2 which splits sequence data every 60 characters
- * see EmblSequence.setSequence
- */
- + "<sequence>GGTATGTCCTCTAGTACAAAC\n"
- + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
- + "</sequence></entry></ROOT>";
-
- static EmblFile getEmblFile()
- {
- return EmblFile.getEmblFile(new StringReader(TESTDATA));
- }
-}
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
* accession id as parent
*/
@Test(groups = "Functional")
- public void testIdentifiesSequence()
+ public void testGetIdentifyingFeatures()
{
String accId = "ABC123";
- EnsemblCdna testee = new EnsemblCdna();
+ SequenceI seq = new Sequence(accId, "MKLNFRQIE");
- // exon with no parent not valid
- SequenceFeature sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
- assertFalse(testee.identifiesSequence(sf, accId));
+ // exon with no parent: not valid
+ SequenceFeature sf1 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ seq.addSequenceFeature(sf1);
- // exon with wrong parent not valid
- sf.setValue("Parent", "transcript:XYZ");
- assertFalse(testee.identifiesSequence(sf, accId));
+ // exon with wrong parent: not valid
+ SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ sf2.setValue("Parent", "transcript:XYZ");
+ seq.addSequenceFeature(sf2);
// exon with right parent is valid
- sf.setValue("Parent", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ sf3.setValue("Parent", "transcript:" + accId);
+ seq.addSequenceFeature(sf3);
// exon sub-type with right parent is valid
- sf = new SequenceFeature("coding_exon", "", 1, 2, 0f, null);
- sf.setValue("Parent", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
+ null);
+ sf4.setValue("Parent", "transcript:" + accId);
+ seq.addSequenceFeature(sf4);
// transcript not valid:
- sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
- sf.setValue("Parent", "transcript:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ null);
+ sf5.setValue("Parent", "transcript:" + accId);
+ seq.addSequenceFeature(sf5);
// CDS not valid:
- sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
- sf.setValue("Parent", "transcript:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ null);
+ sf6.setValue("Parent", "transcript:" + accId);
+ seq.addSequenceFeature(sf6);
+
+ List<SequenceFeature> sfs = new EnsemblCdna()
+ .getIdentifyingFeatures(seq, accId);
+ assertFalse(sfs.contains(sf1));
+ assertFalse(sfs.contains(sf2));
+ assertTrue(sfs.contains(sf3));
+ assertTrue(sfs.contains(sf4));
+ assertFalse(sfs.contains(sf5));
+ assertFalse(sfs.contains(sf6));
}
@Test(groups = "Functional")
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
* accession id as parent
*/
@Test(groups = "Functional")
- public void testIdentifiesSequence()
+ public void testGetIdentifyingFeatures()
{
String accId = "ABC123";
- EnsemblCds testee = new EnsemblCds();
+ SequenceI seq = new Sequence(accId, "MKDONS");
// cds with no parent not valid
- SequenceFeature sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf1 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
+ seq.addSequenceFeature(sf1);
// cds with wrong parent not valid
- sf.setValue("Parent", "transcript:XYZ");
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
+ sf2.setValue("Parent", "transcript:XYZ");
+ seq.addSequenceFeature(sf2);
// cds with right parent is valid
- sf.setValue("Parent", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
+ sf3.setValue("Parent", "transcript:" + accId);
+ seq.addSequenceFeature(sf3);
// cds sub-type with right parent is valid
- sf = new SequenceFeature("CDS_predicted", "", 1, 2, 0f, null);
- sf.setValue("Parent", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 1, 2, 0f,
+ null);
+ sf4.setValue("Parent", "transcript:" + accId);
+ seq.addSequenceFeature(sf4);
// transcript not valid:
- sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
- sf.setValue("Parent", "transcript:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ null);
+ sf5.setValue("Parent", "transcript:" + accId);
+ seq.addSequenceFeature(sf5);
// exon not valid:
- sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf.setValue("Parent", "transcript:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ sf6.setValue("Parent", "transcript:" + accId);
+ seq.addSequenceFeature(sf6);
+
+ List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,
+ accId);
+ assertFalse(sfs.contains(sf1));
+ assertFalse(sfs.contains(sf2));
+ assertTrue(sfs.contains(sf3));
+ assertTrue(sfs.contains(sf4));
+ assertFalse(sfs.contains(sf5));
+ assertFalse(sfs.contains(sf6));
}
@Test(groups = "Functional")
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
genomic.setEnd(50000);
String geneId = "ABC123";
- // gene at (start+20000) length 501
- // should be ignored - the first 'gene' found defines the whole range
- // (note features are found in position order, not addition order)
- SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
- null);
- sf.setValue("ID", "gene:" + geneId);
- sf.setStrand("+");
- genomic.addSequenceFeature(sf);
-
// gene at (start + 10500) length 101
- sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
+ SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
+ null);
sf.setValue("ID", "gene:" + geneId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
genomic.setEnd(50000);
String geneId = "ABC123";
- // gene at (start+20000) length 501
- // should be ignored - the first 'gene' found defines the whole range
- // (real data would only have one such feature)
- SequenceFeature sf = new SequenceFeature("ncRNA_gene", "", 20000,
- 20500, 0f, null);
- sf.setValue("ID", "gene:" + geneId);
- sf.setStrand("-");
- genomic.addSequenceFeature(sf);
-
// gene at (start + 10500) length 101
- sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
+ SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
+ null);
sf.setValue("ID", "gene:" + geneId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
* accession id as ID
*/
@Test(groups = "Functional")
- public void testIdentifiesSequence()
+ public void testGetIdentifyingFeatures()
{
String accId = "ABC123";
- EnsemblGene testee = new EnsemblGene();
+ SequenceI seq = new Sequence(accId, "HIBEES");
// gene with no ID not valid
- SequenceFeature sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf1 = new SequenceFeature("gene", "", 1, 2, 0f, null);
+ seq.addSequenceFeature(sf1);
// gene with wrong ID not valid
- sf.setValue("ID", "gene:XYZ");
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf2 = new SequenceFeature("gene", "", 1, 2, 0f, null);
+ sf2.setValue("ID", "gene:XYZ");
+ seq.addSequenceFeature(sf2);
// gene with right ID is valid
- sf.setValue("ID", "gene:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf3 = new SequenceFeature("gene", "", 1, 2, 0f, null);
+ sf3.setValue("ID", "gene:" + accId);
+ seq.addSequenceFeature(sf3);
// gene sub-type with right ID is valid
- sf = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
- sf.setValue("ID", "gene:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
-
- // test is not case-sensitive
- assertTrue(testee.identifiesSequence(sf, accId.toLowerCase()));
+ SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
+ sf4.setValue("ID", "gene:" + accId);
+ seq.addSequenceFeature(sf4);
// transcript not valid:
- sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
- sf.setValue("ID", "gene:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+ sf5.setValue("ID", "gene:" + accId);
+ seq.addSequenceFeature(sf5);
// exon not valid:
- sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf.setValue("ID", "gene:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ sf6.setValue("ID", "gene:" + accId);
+ seq.addSequenceFeature(sf6);
+
+ List<SequenceFeature> sfs = new EnsemblGene()
+ .getIdentifyingFeatures(seq, accId);
+ assertFalse(sfs.contains(sf1));
+ assertFalse(sfs.contains(sf2));
+ assertTrue(sfs.contains(sf3));
+ assertTrue(sfs.contains(sf4));
+ assertFalse(sfs.contains(sf5));
+ assertFalse(sfs.contains(sf6));
}
/**
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
* accession id as ID
*/
@Test(groups = "Functional")
- public void testIdentifiesSequence()
+ public void testGetIdentifyingFeatures()
{
String accId = "ABC123";
- EnsemblGenome testee = new EnsemblGenome();
+ SequenceI seq = new Sequence(accId, "HEARTS");
// transcript with no ID not valid
- SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
+ SequenceFeature sf1 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
- assertFalse(testee.identifiesSequence(sf, accId));
+ seq.addSequenceFeature(sf1);
// transcript with wrong ID not valid
- sf.setValue("ID", "transcript");
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf2 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ null);
+ sf2.setValue("ID", "transcript");
+ seq.addSequenceFeature(sf2);
// transcript with right ID is valid
- sf.setValue("ID", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf3 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ null);
+ sf3.setValue("ID", "transcript:" + accId);
+ seq.addSequenceFeature(sf3);
// transcript sub-type with right ID is valid
- sf = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
- sf.setValue("ID", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
+ sf4.setValue("ID", "transcript:" + accId);
+ seq.addSequenceFeature(sf4);
// Ensembl treats NMD_transcript_variant as if a transcript
- sf = new SequenceFeature("NMD_transcript_variant", "", 1, 2, 0f, null);
- sf.setValue("ID", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
+ 1, 2, 0f, null);
+ sf5.setValue("ID", "transcript:" + accId);
+ seq.addSequenceFeature(sf5);
// gene not valid:
- sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
- sf.setValue("ID", "transcript:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
+ sf6.setValue("ID", "transcript:" + accId);
+ seq.addSequenceFeature(sf6);
// exon not valid:
- sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf.setValue("ID", "transcript:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ sf7.setValue("ID", "transcript:" + accId);
+ seq.addSequenceFeature(sf7);
+
+ List<SequenceFeature> sfs = new EnsemblGenome()
+ .getIdentifyingFeatures(seq, accId);
+ assertFalse(sfs.contains(sf1));
+ assertFalse(sfs.contains(sf2));
+ assertTrue(sfs.contains(sf3));
+ assertTrue(sfs.contains(sf4));
+ assertTrue(sfs.contains(sf5));
+ assertFalse(sfs.contains(sf6));
+ assertFalse(sfs.contains(sf7));
}
}
{
return false;
}
-
- @Override
- protected String getRequestMimeType(boolean b)
- {
- return null;
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return null;
- }
-
};
}
package jalview.ext.ensembl;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.List;
/**
* A convenience class to simplify writing unit tests (pending Mockito or
}
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- return false;
+ return new ArrayList<>();
}
}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FastaFile;
-import jalview.io.FileParse;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
+ "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
+ "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
+ "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
- + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
+ + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
+ // ? insertion added in ENSP00000288602.11, not in P15056
+ + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
+ // end insertion
+ + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
+ "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
+ "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
+ "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
}
@Test(dataProvider = "ens_seqs", suiteName = "live")
- public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
+ public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
String fastasq) throws Exception
{
- FileParse fp = proxy.getSequenceReader(Arrays
- .asList(new String[] { sq }));
- SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
- SequenceI[] trueSqs = trueRes.getSeqsAsArray();
- Assert.assertEquals(sqs.length, trueSqs.length,
+ SequenceI[] expected = trueRes.getSeqsAsArray();
+ AlignmentI retrieved = proxy.getSequenceRecords(sq);
+
+ Assert.assertEquals(retrieved.getHeight(), expected.length,
"Different number of sequences retrieved for query " + sq);
- Alignment ral = new Alignment(sqs);
- for (SequenceI tr : trueSqs)
+
+ for (SequenceI tr : expected)
{
SequenceI[] rseq;
Assert.assertNotNull(
- rseq = ral.findSequenceMatch(tr.getName()),
+ rseq = retrieved.findSequenceMatch(tr.getName()),
"Couldn't find sequences matching expected sequence "
+ tr.getName());
Assert.assertEquals(rseq.length, 1,
"Sequences differ for " + tr.getName() + "\n" + "Exp:"
+ tr.getSequenceAsString() + "\n" + "Got:"
+ rseq[0].getSequenceAsString());
-
}
}
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
}
static String PfamFile = "examples/PF00111_seed.stk",
- RfamFile = "examples/RF00031_folded.stk";
+ RfamFile = "examples/RF00031_folded.stk",
+ RnaSSTestFile = "examples/rna_ss_test.stk";
@Test(groups = { "Functional" })
public void pfamFileIO() throws Exception
// we might want to revise this in future
int aa_new_size = (aa_new == null ? 0 : aa_new.length);
int aa_original_size = (aa_original == null ? 0 : aa_original.length);
- Map<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
- Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();
+ Map<Integer, BitSet> orig_groups = new HashMap<>();
+ Map<Integer, BitSet> new_groups = new HashMap<>();
if (aa_new != null && aa_original != null)
{
{
for (char ch : new char[] { '{', '}', '[', ']', '(', ')', '<', '>' })
{
- Assert.assertTrue(StockholmFile.DETECT_BRACKETS.matchAt("" + ch, 0),
- "Didn't recognise " + ch + " as a WUSS bracket");
+ Assert.assertTrue(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
+ "Didn't recognise '" + ch + "' as a WUSS bracket");
}
- for (char ch : new char[] { '@', '!', 'V', 'Q', '*', ' ', '-', '.' })
+ for (char ch : new char[] { '@', '!', '*', ' ', '-', '.' })
{
- Assert.assertFalse(StockholmFile.DETECT_BRACKETS.matchAt("" + ch, 0),
- "Shouldn't recognise " + ch + " as a WUSS bracket");
+ Assert.assertFalse(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
+ "Shouldn't recognise '" + ch + "' as a WUSS bracket");
}
}
private static void roundTripSSForRNA(String aliFile, String annFile)
testAlignmentEquivalence(al, newAl, true, true, true);
}
+
+ // this is the single sequence alignment and the SS annotations equivalent to
+ // the ones in file RnaSSTestFile
+ String aliFileRnaSS = ">Test.sequence/1-14\n"
+ + "GUACAAAAAAAAAA";
+ String annFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|E,E|H,H|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+ String wrongAnnFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|H,H|E,E|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+ @Test(groups = { "Functional" })
+ public void stockholmFileRnaSSAlphaChars() throws Exception
+ {
+ AppletFormatAdapter af = new AppletFormatAdapter();
+ AlignmentI al = af.readFile(RnaSSTestFile, DataSourceType.FILE,
+ jalview.io.FileFormat.Stockholm);
+ Iterable<AlignmentAnnotation> aai = al.findAnnotations(null, null,
+ "Secondary Structure");
+ AlignmentAnnotation aa = aai.iterator().next();
+ Assert.assertTrue(aa.isRNA(),
+ "'" + RnaSSTestFile + "' not recognised as RNA SS");
+ Assert.assertTrue(aa.isValidStruc(),
+ "'" + RnaSSTestFile + "' not recognised as valid structure");
+ Annotation[] as = aa.annotations;
+ char[] As = new char[as.length];
+ for (int i = 0; i < as.length; i++)
+ {
+ As[i] = as[i].secondaryStructure;
+ }
+ char[] shouldBe = { '<', '(', 'E', 'H', 'B', 'h', 'e', 'b', '(', 'E',
+ ')', 'e', ')', '>' };
+ Assert.assertTrue(
+ Arrays.equals(As, shouldBe),
+ "Annotation is " + new String(As) + " but should be "
+ + new String(shouldBe));
+
+ // this should result in the same RNA SS Annotations
+ AlignmentI newAl = new AppletFormatAdapter().readFile(
+ aliFileRnaSS,
+ DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
+ AnnotationFile aaf = new AnnotationFile();
+ aaf.readAnnotationFile(newAl, annFileRnaSSAlphaChars,
+ DataSourceType.PASTE);
+
+ Assert.assertTrue(
+ testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0],
+ newAl.getAlignmentAnnotation()[0]),
+ "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n"
+ + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n"
+ + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]);
+
+ // this should NOT result in the same RNA SS Annotations
+ newAl = new AppletFormatAdapter().readFile(
+ aliFileRnaSS, DataSourceType.PASTE,
+ jalview.io.FileFormat.Fasta);
+ aaf = new AnnotationFile();
+ aaf.readAnnotationFile(newAl, wrongAnnFileRnaSSAlphaChars,
+ DataSourceType.PASTE);
+
+ boolean mismatch = testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0],
+ newAl.getAlignmentAnnotation()[0]);
+ Assert.assertFalse(mismatch,
+ "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n"
+ + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n"
+ + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]);
+ }
+
+ private static boolean testRnaSSAnnotationsEquivalent(
+ AlignmentAnnotation a1,
+ AlignmentAnnotation a2)
+ {
+ return a1.rnaSecondaryStructureEquivalent(a2);
+ }
+
+ String annFileRnaSSWithSpaceChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H| , |B,B|h,h| , |b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+ String annFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|.,.|B,B|h,h|.,.|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
+ String wrongAnnFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|Z,Z|B,B|h,h|z,z|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
+ @Test(groups = { "Functional" })
+ public void stockholmFileRnaSSSpaceChars() throws Exception
+ {
+ AlignmentI alWithSpaces = new AppletFormatAdapter().readFile(
+ aliFileRnaSS, DataSourceType.PASTE,
+ jalview.io.FileFormat.Fasta);
+ AnnotationFile afWithSpaces = new AnnotationFile();
+ afWithSpaces.readAnnotationFile(alWithSpaces,
+ annFileRnaSSWithSpaceChars, DataSourceType.PASTE);
+
+ Iterable<AlignmentAnnotation> aaiWithSpaces = alWithSpaces
+ .findAnnotations(null, null, "Secondary Structure");
+ AlignmentAnnotation aaWithSpaces = aaiWithSpaces.iterator().next();
+ Assert.assertTrue(aaWithSpaces.isRNA(),
+ "'" + aaWithSpaces + "' not recognised as RNA SS");
+ Assert.assertTrue(aaWithSpaces.isValidStruc(),
+ "'" + aaWithSpaces + "' not recognised as valid structure");
+ Annotation[] annWithSpaces = aaWithSpaces.annotations;
+ char[] As = new char[annWithSpaces.length];
+ for (int i = 0; i < annWithSpaces.length; i++)
+ {
+ As[i] = annWithSpaces[i].secondaryStructure;
+ }
+ // check all spaces and dots are spaces in the internal representation
+ char[] shouldBe = { '<', ' ', 'H', ' ', 'B', 'h', ' ', 'b', '(', 'E',
+ ' ', 'e', ')', '>' };
+ Assert.assertTrue(Arrays.equals(As, shouldBe), "Annotation is "
+ + new String(As) + " but should be " + new String(shouldBe));
+
+ // this should result in the same RNA SS Annotations
+ AlignmentI alWithoutSpaces = new AppletFormatAdapter().readFile(
+ aliFileRnaSS, DataSourceType.PASTE,
+ jalview.io.FileFormat.Fasta);
+ AnnotationFile afWithoutSpaces = new AnnotationFile();
+ afWithoutSpaces.readAnnotationFile(alWithoutSpaces,
+ annFileRnaSSWithoutSpaceChars,
+ DataSourceType.PASTE);
+
+ Assert.assertTrue(
+ testRnaSSAnnotationsEquivalent(
+ alWithSpaces.getAlignmentAnnotation()[0],
+ alWithoutSpaces.getAlignmentAnnotation()[0]),
+ "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n"
+ + "RNA SS A 1:"
+ + alWithSpaces.getAlignmentAnnotation()[0]
+ .getRnaSecondaryStructure()
+ + "\n" + "RNA SS A 2:"
+ + alWithoutSpaces.getAlignmentAnnotation()[0]
+ .getRnaSecondaryStructure());
+
+ // this should NOT result in the same RNA SS Annotations
+ AlignmentI wrongAlWithoutSpaces = new AppletFormatAdapter().readFile(
+ aliFileRnaSS, DataSourceType.PASTE,
+ jalview.io.FileFormat.Fasta);
+ AnnotationFile wrongAfWithoutSpaces = new AnnotationFile();
+ wrongAfWithoutSpaces.readAnnotationFile(wrongAlWithoutSpaces,
+ wrongAnnFileRnaSSWithoutSpaceChars,
+ DataSourceType.PASTE);
+
+ Assert.assertFalse(
+ testRnaSSAnnotationsEquivalent(
+ alWithSpaces.getAlignmentAnnotation()[0],
+ wrongAlWithoutSpaces.getAlignmentAnnotation()[0]),
+ "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n"
+ + "RNA SS A 1:"
+ + alWithSpaces.getAlignmentAnnotation()[0]
+ .getRnaSecondaryStructure()
+ + "\n" + "RNA SS A 2:"
+ + wrongAlWithoutSpaces.getAlignmentAnnotation()[0]
+ .getRnaSecondaryStructure());
+
+ // check no spaces in the output
+ // TODO: create a better 'save as <format>' pattern
+ alWithSpaces.getAlignmentAnnotation()[0].visible = true;
+ StockholmFile sf = new StockholmFile(alWithSpaces);
+
+ String stockholmFile = sf.print(alWithSpaces.getSequencesArray(), true);
+ Pattern noSpacesInRnaSSAnnotation = Pattern
+ .compile("\\n#=GC SS_cons\\s+\\S{14}\\n");
+ Matcher m = noSpacesInRnaSSAnnotation.matcher(stockholmFile);
+ boolean matches = m.find();
+ Assert.assertTrue(matches,
+ "StockholmFile output does not contain expected output (may contain spaces):\n"
+ + stockholmFile);
+
+ }
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.project;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
+import jalview.api.ViewStyleI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.JvOptionPane;
+import jalview.gui.PopupMenu;
+import jalview.gui.SliderPanel;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileLoader;
+import jalview.io.Jalview2xmlBase;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.RNAHelicesColour;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.util.matcher.Condition;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+@Test(singleThreaded = true)
+public class Jalview2xmlTests extends Jalview2xmlBase
+{
+
+ @Override
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testRNAStructureRecovery() throws Exception
+ {
+ String inFile = "examples/RF00031_folded.stk";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+ int olddsann = countDsAnn(af.getViewport());
+ assertTrue(olddsann > 0, "Didn't find any dataset annotations");
+ af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
+ .toString());
+ assertTrue(
+ af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
+ "Couldn't apply RNA helices colourscheme");
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
+ "Failed to store as a project.");
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new FileLoader()
+ .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+ assertNotNull(af, "Failed to import new project");
+ int newdsann = countDsAnn(af.getViewport());
+ assertEquals(olddsann, newdsann,
+ "Differing numbers of dataset sequence annotation\nOriginally "
+ + olddsann + " and now " + newdsann);
+ System.out
+ .println("Read in same number of annotations as originally present ("
+ + olddsann + ")");
+ assertTrue(
+
+ af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
+ "RNA helices colourscheme was not applied on import.");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testTCoffeeScores() throws Exception
+ {
+ String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+ af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
+ assertSame(af.getViewport().getGlobalColourScheme().getClass(),
+ TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
+ assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport()
+ .getAlignment(), af.getViewport().getGlobalColourScheme()
+ .getSchemeName()), "Recognise T-Coffee score from string");
+
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
+ "Failed to store as a project.");
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new FileLoader()
+ .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+ assertNotNull(af, "Failed to import new project");
+ assertSame(af.getViewport().getGlobalColourScheme().getClass(),
+ TCoffeeColourScheme.class,
+ "Didn't set T-coffee colourscheme for imported project.");
+ System.out
+ .println("T-Coffee score shading successfully recovered from project.");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testColourByAnnotScores() throws Exception
+ {
+ String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+ af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
+ AlignmentAnnotation[] aa = af.getViewport().getAlignment()
+ .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
+ assertTrue(
+
+ aa != null && aa.length > 0,
+ "Didn't find any IUPred annotation to use to shade alignment.");
+ AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
+ AnnotationColourGradient.ABOVE_THRESHOLD);
+ AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0],
+ null, AnnotationColourGradient.BELOW_THRESHOLD);
+ cs.setSeqAssociated(true);
+ gcs.setSeqAssociated(true);
+ af.changeColour(cs);
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(57);
+ sg.setEndRes(92);
+ sg.cs.setColourScheme(gcs);
+ af.getViewport().getAlignment().addGroup(sg);
+ sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
+ sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
+ af.alignPanel.alignmentChanged();
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
+ "Failed to store as a project.");
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new FileLoader()
+ .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+ assertNotNull(af, "Failed to import new project");
+
+ // check for group and alignment colourschemes
+
+ ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
+ ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
+ .get(0).getColourScheme();
+ assertNotNull(_rcs, "Didn't recover global colourscheme");
+ assertTrue(_rcs instanceof AnnotationColourGradient,
+ "Didn't recover annotation colour global scheme");
+ AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
+ assertTrue(__rcs.isSeqAssociated(),
+ "Annotation colourscheme wasn't sequence associated");
+
+ boolean diffseqcols = false, diffgseqcols = false;
+ SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
+ for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+ && (!diffseqcols || !diffgseqcols); p++)
+ {
+ if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
+ .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
+ {
+ diffseqcols = true;
+ }
+ }
+ assertTrue(diffseqcols, "Got Different sequence colours");
+ System.out
+ .println("Per sequence colourscheme (Background) successfully applied and recovered.");
+
+ assertNotNull(_rgcs, "Didn't recover group colourscheme");
+ assertTrue(_rgcs instanceof AnnotationColourGradient,
+ "Didn't recover annotation colour group colourscheme");
+ __rcs = (AnnotationColourGradient) _rgcs;
+ assertTrue(__rcs.isSeqAssociated(),
+ "Group Annotation colourscheme wasn't sequence associated");
+
+ for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+ && (!diffseqcols || !diffgseqcols); p++)
+ {
+ if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
+ .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
+ {
+ diffgseqcols = true;
+ }
+ }
+ assertTrue(diffgseqcols, "Got Different group sequence colours");
+ System.out
+ .println("Per sequence (Group) colourscheme successfully applied and recovered.");
+ }
+
+ @Test(groups = { "Functional" })
+ public void gatherViewsHere() throws Exception
+ {
+ int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
+ .getAlignFrames().length;
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
+ "Didn't gather the views in the example file.");
+
+ }
+
+ /**
+ * Test for JAL-2223 - multiple mappings in View Mapping report
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void noDuplicatePdbMappingsMade() throws Exception
+ {
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+
+ // locate Jmol viewer
+ // count number of PDB mappings the structure selection manager holds -
+ String pdbFile = af.getCurrentView().getStructureSelectionManager()
+ .findFileForPDBId("1A70");
+ assertEquals(
+ af.getCurrentView().getStructureSelectionManager()
+ .getMapping(pdbFile).length,
+ 2, "Expected only two mappings for 1A70");
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void viewRefPdbAnnotation() throws Exception
+ {
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ AlignmentViewPanel sps = null;
+ for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
+ {
+ if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
+ {
+ sps = ap;
+ break;
+ }
+ }
+ assertNotNull(sps, "Couldn't find the structure view");
+ AlignmentAnnotation refan = null;
+ for (AlignmentAnnotation ra : sps.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (ra.graph != 0)
+ {
+ refan = ra;
+ break;
+ }
+ }
+ assertNotNull(refan, "Annotation secondary structure not found.");
+ SequenceI sq = sps.getAlignment().findName("1A70|");
+ assertNotNull(sq, "Couldn't find 1a70 null chain");
+ // compare the manually added temperature factor annotation
+ // to the track automatically transferred from the pdb structure on load
+ assertNotNull(sq.getDatasetSequence().getAnnotation(),
+ "1a70 has no annotation");
+ for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
+ {
+ AlignmentAnnotation alaa;
+ sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
+ alaa.adjustForAlignment();
+ if (ala.graph == refan.graph)
+ {
+ for (int p = 0; p < ala.annotations.length; p++)
+ {
+ sq.findPosition(p);
+ try
+ {
+ assertTrue(
+ (alaa.annotations[p] == null && refan.annotations[p] == null)
+ || alaa.annotations[p].value == refan.annotations[p].value,
+ "Mismatch at alignment position " + p);
+ } catch (NullPointerException q)
+ {
+ Assert.fail("Mismatch of alignment annotations at position "
+ + p + " Ref seq ann: " + refan.annotations[p]
+ + " alignment " + alaa.annotations[p]);
+ }
+ }
+ }
+ }
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testCopyViewSettings() throws Exception
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ AlignmentViewPanel sps = null, groups = null;
+ for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
+ {
+ if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
+ {
+ sps = ap;
+ }
+ if (ap.getViewName().contains("MAFFT"))
+ {
+ groups = ap;
+ }
+ }
+ assertNotNull(sps, "Couldn't find the structure view");
+ assertNotNull(groups, "Couldn't find the MAFFT view");
+
+ ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
+ ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
+ AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
+
+ groups.getAlignViewport().setViewStyle(structureStyle);
+ AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
+ .getViewStyle()));
+ Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
+ .getViewStyle()));
+
+ }
+
+ /**
+ * test store and recovery of expanded views
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" }, enabled = true)
+ public void testStoreAndRecoverExpandedviews() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
+ Assert.assertEquals(Desktop.getAlignFrames().length, 1);
+ String afid = af.getViewport().getSequenceSetId();
+
+ // check FileLoader returned a reference to the one alignFrame that is
+ // actually on the Desktop
+ assertSame(
+ af,
+ Desktop.getAlignFrameFor(af.getViewport()),
+ "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
+
+ Desktop.explodeViews(af);
+
+ int oldviews = Desktop.getAlignFrames().length;
+ Assert.assertEquals(Desktop.getAlignFrames().length,
+ Desktop.getAlignmentPanels(afid).length);
+ File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Error e)
+ {
+ Assert.fail("Didn't save the expanded view state", e);
+ } catch (Exception e)
+ {
+ Assert.fail("Didn't save the expanded view state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ Assert.assertNotNull(af);
+ Assert.assertEquals(
+ Desktop.getAlignFrames().length,
+ Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+ Assert.assertEquals(
+ Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
+ oldviews);
+ }
+
+ /**
+ * Test save and reload of a project with a different representative sequence
+ * in each view.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverReferenceSeqSettings() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ String afid = af.getViewport().getSequenceSetId();
+
+ // remember reference sequence for each panel
+ Map<String, SequenceI> refseqs = new HashMap<>();
+
+ /*
+ * mark sequence 2, 3, 4.. in panels 1, 2, 3...
+ * as reference sequence for itself and the preceding sequence
+ */
+ int n = 1;
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ AlignViewportI av = ap.getAlignViewport();
+ AlignmentI alignment = ap.getAlignment();
+ int repIndex = n % alignment.getHeight();
+ SequenceI rep = alignment.getSequenceAt(repIndex);
+ refseqs.put(ap.getViewName(), rep);
+
+ // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
+ // todo refactor this to an alignment view controller
+ av.setDisplayReferenceSeq(true);
+ av.setColourByReferenceSeq(true);
+ av.getAlignment().setSeqrep(rep);
+
+ n++;
+ }
+ File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
+ ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the expanded view state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ afid = af.getViewport().getSequenceSetId();
+
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ // check representative
+ AlignmentI alignment = ap.getAlignment();
+ SequenceI rep = alignment.getSeqrep();
+ Assert.assertNotNull(rep,
+ "Couldn't restore sequence representative from project");
+ // can't use a strong equals here, because by definition, the sequence IDs
+ // will be different.
+ // could set vamsas session save/restore flag to preserve IDs across
+ // load/saves.
+ Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
+ rep.toString(),
+ "Representative wasn't the same when recovered.");
+ Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
+ "Display reference sequence view setting not set.");
+ Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
+ "Colour By Reference Seq view setting not set.");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsVersionStringLaterThan()
+ {
+ /*
+ * No version / development / test / autobuild is leniently assumed to be
+ * compatible
+ */
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null,
+ "Development Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null,
+ "DEVELOPMENT BUILD"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+ "Development Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
+ assertTrue(Jalview2XML
+ .isVersionStringLaterThan(null, "Automated Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+ "Automated Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+ "AUTOMATED BUILD"));
+
+ /*
+ * same version returns true i.e. compatible
+ */
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
+
+ /*
+ * later version returns true
+ */
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
+
+ /*
+ * earlier version returns false
+ */
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
+ }
+
+ /**
+ * Test save and reload of a project with a different sequence group (and
+ * representative sequence) in each view.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverGroupRepSeqs() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ String afid = af.getViewport().getSequenceSetId();
+ // make a second view of the alignment
+ af.newView_actionPerformed(null);
+
+ /*
+ * remember representative and hidden sequences marked
+ * on each panel
+ */
+ Map<String, SequenceI> repSeqs = new HashMap<>();
+ Map<String, List<String>> hiddenSeqNames = new HashMap<>();
+
+ /*
+ * mark sequence 2, 3, 4.. in panels 1, 2, 3...
+ * as reference sequence for itself and the preceding sequence
+ */
+ int n = 1;
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ AlignViewportI av = ap.getAlignViewport();
+ AlignmentI alignment = ap.getAlignment();
+ int repIndex = n % alignment.getHeight();
+ // ensure at least one preceding sequence i.e. index >= 1
+ repIndex = Math.max(repIndex, 1);
+ SequenceI repSeq = alignment.getSequenceAt(repIndex);
+ repSeqs.put(ap.getViewName(), repSeq);
+ List<String> hiddenNames = new ArrayList<>();
+ hiddenSeqNames.put(ap.getViewName(), hiddenNames);
+
+ /*
+ * have rep sequence represent itself and the one before it
+ * this hides the group (except for the rep seq)
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(repSeq, false);
+ SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
+ sg.addSequence(precedingSeq, false);
+ sg.setSeqrep(repSeq);
+ assertTrue(sg.getSequences().contains(repSeq));
+ assertTrue(sg.getSequences().contains(precedingSeq));
+ av.setSelectionGroup(sg);
+ assertSame(repSeq, sg.getSeqrep());
+
+ /*
+ * represent group with sequence adds to a map of hidden rep sequences
+ * (it does not create a group on the alignment)
+ */
+ ((AlignmentViewport) av).hideSequences(repSeq, true);
+ assertSame(repSeq, sg.getSeqrep());
+ assertTrue(sg.getSequences().contains(repSeq));
+ assertTrue(sg.getSequences().contains(precedingSeq));
+ assertTrue(alignment.getGroups().isEmpty(), "alignment has groups");
+ Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
+ .getHiddenRepSequences();
+ assertNotNull(hiddenRepSeqsMap);
+ assertEquals(1, hiddenRepSeqsMap.size());
+ assertSame(sg, hiddenRepSeqsMap.get(repSeq));
+ assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
+ assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
+ hiddenNames.add(precedingSeq.getName());
+
+ n++;
+ }
+ File tfile = File
+ .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the expanded view state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ afid = af.getViewport().getSequenceSetId();
+
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ String viewName = ap.getViewName();
+ AlignViewportI av = ap.getAlignViewport();
+ AlignmentI alignment = ap.getAlignment();
+ List<SequenceGroup> groups = alignment.getGroups();
+ assertNotNull(groups);
+ assertTrue(groups.isEmpty(), "Alignment has groups");
+ Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
+ .getHiddenRepSequences();
+ assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
+ assertEquals(1, hiddenRepSeqsMap.size());
+ assertEquals(repSeqs.get(viewName).getDisplayId(true),
+ hiddenRepSeqsMap.keySet().iterator().next()
+ .getDisplayId(true));
+
+ /*
+ * verify hidden sequences in restored panel
+ */
+ List<String> hidden = hiddenSeqNames.get(ap.getViewName());
+ HiddenSequences hs = alignment.getHiddenSequences();
+ assertEquals(
+ hidden.size(),
+ hs.getSize(),
+ "wrong number of restored hidden sequences in "
+ + ap.getViewName());
+ }
+ }
+
+ /**
+ * Test save and reload of PDBEntry in Jalview project
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverPDBEntry() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ String exampleFile = "examples/3W5V.pdb";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ String afid = af.getViewport().getSequenceSetId();
+
+ AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
+ System.out.println();
+ AlignmentViewPanel ap = alignPanels[0];
+ String tfileBase = new File(".").getAbsolutePath().replace(".", "");
+ String testFile = tfileBase + exampleFile;
+ AlignmentI alignment = ap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] seqs = alignment.getSequencesArray();
+ Assert.assertNotNull(seqs[0]);
+ Assert.assertNotNull(seqs[1]);
+ Assert.assertNotNull(seqs[2]);
+ Assert.assertNotNull(seqs[3]);
+ Assert.assertNotNull(seqs[0].getDatasetSequence());
+ Assert.assertNotNull(seqs[1].getDatasetSequence());
+ Assert.assertNotNull(seqs[2].getDatasetSequence());
+ Assert.assertNotNull(seqs[3].getDatasetSequence());
+ PDBEntry[] pdbEntries = new PDBEntry[4];
+ pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
+ pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
+ pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
+ pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
+ Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
+ .get(0), pdbEntries[0]);
+ Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
+ .get(0), pdbEntries[1]);
+ Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
+ .get(0), pdbEntries[2]);
+ Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
+ .get(0), pdbEntries[3]);
+
+ File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), DataSourceType.FILE);
+ String rfid = restoredFrame.getViewport().getSequenceSetId();
+ AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
+ AlignmentViewPanel rap = rAlignPanels[0];
+ AlignmentI rAlignment = rap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] rseqs = rAlignment.getSequencesArray();
+ Assert.assertNotNull(rseqs[0]);
+ Assert.assertNotNull(rseqs[1]);
+ Assert.assertNotNull(rseqs[2]);
+ Assert.assertNotNull(rseqs[3]);
+ Assert.assertNotNull(rseqs[0].getDatasetSequence());
+ Assert.assertNotNull(rseqs[1].getDatasetSequence());
+ Assert.assertNotNull(rseqs[2].getDatasetSequence());
+ Assert.assertNotNull(rseqs[3].getDatasetSequence());
+
+ // The Asserts below are expected to fail until the PDB chainCode is
+ // recoverable from a Jalview projects
+ for (int chain = 0; chain < 4; chain++)
+ {
+ PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
+ .get(0);
+ PDBEntry expected = pdbEntries[chain];
+ Assert.assertEquals(recov.getId(), expected.getId(),
+ "Mismatch PDB ID");
+ Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
+ "Mismatch PDB ID");
+ Assert.assertEquals(recov.getType(), expected.getType(),
+ "Mismatch PDBEntry 'Type'");
+ Assert.assertNotNull(recov.getFile(),
+ "Recovered PDBEntry should have a non-null file entry");
+ }
+ }
+
+ /**
+ * Configure an alignment and a sub-group each with distinct colour schemes,
+ * Conservation and PID thresholds, and confirm these are restored from the
+ * saved project.
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverColourThresholds() throws IOException
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+
+ AlignViewport av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+
+ /*
+ * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
+ assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
+ af.abovePIDThreshold_actionPerformed(true);
+ SliderPanel sp = SliderPanel.getSliderPanel();
+ assertFalse(sp.isForConservation());
+ sp.valueChanged(10);
+ af.conservationMenuItem_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertTrue(sp.isForConservation());
+ sp.valueChanged(20);
+ ResidueShaderI rs = av.getResidueShading();
+ assertEquals(rs.getThreshold(), 10);
+ assertTrue(rs.conservationApplied());
+ assertEquals(rs.getConservationInc(), 20);
+
+ /*
+ * create a group with Strand colouring, 30% Conservation
+ * and 40% PID threshold
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(al.getSequenceAt(0), false);
+ sg.setStartRes(15);
+ sg.setEndRes(25);
+ av.setSelectionGroup(sg);
+ PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+ popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
+ .toString());
+ assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
+ assertEquals(al.getGroups().size(), 1);
+ assertSame(al.getGroups().get(0), sg);
+ popupMenu.conservationMenuItem_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertTrue(sp.isForConservation());
+ sp.valueChanged(30);
+ popupMenu.abovePIDColour_actionPerformed(true);
+ sp = SliderPanel.getSliderPanel();
+ assertFalse(sp.isForConservation());
+ sp.valueChanged(40);
+ assertTrue(sg.getGroupColourScheme().conservationApplied());
+ assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
+ assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
+
+ /*
+ * save project, close windows, reload project, verify
+ */
+ File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
+ ".jvp");
+ tfile.deleteOnExit();
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.instance.closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ Assert.assertNotNull(af, "Failed to reload project");
+
+ /*
+ * verify alignment (background) colouring
+ */
+ rs = af.getViewport().getResidueShading();
+ assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
+ assertEquals(rs.getThreshold(), 10);
+ assertTrue(rs.conservationApplied());
+ assertEquals(rs.getConservationInc(), 20);
+
+ /*
+ * verify group colouring
+ */
+ assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
+ rs = af.getViewport().getAlignment().getGroups().get(0)
+ .getGroupColourScheme();
+ assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
+ assertEquals(rs.getThreshold(), 40);
+ assertTrue(rs.conservationApplied());
+ assertEquals(rs.getConservationInc(), 30);
+ }
+
+ /**
+ * Test save and reload of feature colour schemes and filter settings
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testSaveLoadFeatureColoursAndFilters() throws IOException
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
+ SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
+
+ /*
+ * add some features to the sequence
+ */
+ int score = 1;
+ addFeatures(seq1, "type1", score++);
+ addFeatures(seq1, "type2", score++);
+ addFeatures(seq1, "type3", score++);
+ addFeatures(seq1, "type4", score++);
+ addFeatures(seq1, "type5", score++);
+
+ /*
+ * set colour schemes for features
+ */
+ FeatureRenderer fr = af.getFeatureRenderer();
+ fr.findAllFeatures(true);
+
+ // type1: red
+ fr.setColour("type1", new FeatureColour(Color.red));
+
+ // type2: by label
+ FeatureColourI byLabel = new FeatureColour();
+ byLabel.setColourByLabel(true);
+ fr.setColour("type2", byLabel);
+
+ // type3: by score above threshold
+ FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
+ 10);
+ byScore.setAboveThreshold(true);
+ byScore.setThreshold(2f);
+ fr.setColour("type3", byScore);
+
+ // type4: by attribute AF
+ FeatureColourI byAF = new FeatureColour();
+ byAF.setColourByLabel(true);
+ byAF.setAttributeName("AF");
+ fr.setColour("type4", byAF);
+
+ // type5: by attribute CSQ:PolyPhen below threshold
+ FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
+ 1, 10);
+ byPolyPhen.setBelowThreshold(true);
+ byPolyPhen.setThreshold(3f);
+ byPolyPhen.setAttributeName("CSQ", "PolyPhen");
+ fr.setColour("type5", byPolyPhen);
+
+ /*
+ * set filters for feature types
+ */
+
+ // filter type1 features by (label contains "x")
+ FeatureMatcherSetI filterByX = new FeatureMatcherSet();
+ filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
+ fr.setFeatureFilter("type1", filterByX);
+
+ // filter type2 features by (score <= 2.4 and score > 1.1)
+ FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
+ filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
+ filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
+ fr.setFeatureFilter("type2", filterByScore);
+
+ // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
+ FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
+ filterByXY
+ .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
+ filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
+ "PolyPhen"));
+ fr.setFeatureFilter("type3", filterByXY);
+
+ /*
+ * save as Jalview project
+ */
+ File tfile = File.createTempFile("JalviewTest", ".jvp");
+ tfile.deleteOnExit();
+ String filePath = tfile.getAbsolutePath();
+ af.saveAlignment(filePath, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
+ "Failed to store as a project.");
+
+ /*
+ * close current alignment and load the saved project
+ */
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new FileLoader()
+ .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
+ assertNotNull(af, "Failed to import new project");
+
+ /*
+ * verify restored feature colour schemes and filters
+ */
+ fr = af.getFeatureRenderer();
+ FeatureColourI fc = fr.getFeatureStyle("type1");
+ assertTrue(fc.isSimpleColour());
+ assertEquals(fc.getColour(), Color.red);
+ fc = fr.getFeatureStyle("type2");
+ assertTrue(fc.isColourByLabel());
+ fc = fr.getFeatureStyle("type3");
+ assertTrue(fc.isGraduatedColour());
+ assertNull(fc.getAttributeName());
+ assertTrue(fc.isAboveThreshold());
+ assertEquals(fc.getThreshold(), 2f);
+ fc = fr.getFeatureStyle("type4");
+ assertTrue(fc.isColourByLabel());
+ assertTrue(fc.isColourByAttribute());
+ assertEquals(fc.getAttributeName(), new String[] { "AF" });
+ fc = fr.getFeatureStyle("type5");
+ assertTrue(fc.isGraduatedColour());
+ assertTrue(fc.isColourByAttribute());
+ assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
+ assertTrue(fc.isBelowThreshold());
+ assertEquals(fc.getThreshold(), 3f);
+
+ assertEquals(fr.getFeatureFilter("type1").toStableString(),
+ "Label Contains x");
+ assertEquals(fr.getFeatureFilter("type2").toStableString(),
+ "(Score LE 2.4) AND (Score GT 1.1)");
+ assertEquals(fr.getFeatureFilter("type3").toStableString(),
+ "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
+ }
+
+ private void addFeature(SequenceI seq, String featureType, int score)
+ {
+ SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
+ score, "grp");
+ sf.setValue("AF", score);
+ sf.setValue("CSQ", new HashMap<String, String>()
+ {
+ {
+ put("PolyPhen", Integer.toString(score));
+ }
+ });
+ seq.addSequenceFeature(sf);
+ }
+
+ /**
+ * Adds two features of the given type to the given sequence, also setting the
+ * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
+ *
+ * @param seq
+ * @param featureType
+ * @param score
+ */
+ private void addFeatures(SequenceI seq, String featureType, int score)
+ {
+ addFeature(seq, featureType, score++);
+ addFeature(seq, featureType, score);
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.util.MapList;
+import jalview.xml.binding.embl.EntryType;
+import jalview.xml.binding.embl.EntryType.Feature;
+import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
+import jalview.xml.binding.embl.XrefType;
+
+import java.io.ByteArrayInputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class EmblSourceTest
+{
+
+ // adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
+ // dna and translations truncated for convenience
+ static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
+ + "<ROOT>"
+ + "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
+ + " dataClass=\"STD\" taxonomicDivision=\"PRO\""
+ + " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
+ + " firstPublic=\"1988-11-10\" firstPublicRelease=\"18\""
+ + " lastUpdated=\"1999-02-10\" lastUpdatedRelease=\"58\">"
+ + "<secondaryAccession>X07574</secondaryAccession>"
+ + "<description>C. trachomatis plasmid</description>"
+ + "<keyword>plasmid</keyword><keyword>unidentified reading frame</keyword>"
+ + "<xref db=\"EuropePMC\" id=\"PMC107176\" secondaryId=\"9573186\" />"
+ + "<xref db=\"MD5\" id=\"ac73317\" />"
+ /*
+ * first CDS (range and translation changed to keep test data manageable)
+ */
+ + "<feature name=\"CDS\" location=\"complement(46..57)\">"
+ // test the case of >1 cross-ref to the same database (JAL-2029)
+ + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM4\" secondaryId=\"2.1\" />"
+ + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"P0CE20\" />"
+ + "<qualifier name=\"note\"><value>ORF 8 (AA 1-330)</value></qualifier>"
+ + "<qualifier name=\"protein_id\"><value>CAA30420.1</value></qualifier>"
+ + "<qualifier name=\"translation\"><value>MLCF</value></qualifier>"
+ + "</feature>"
+ /*
+ * second CDS (range and translation changed to keep test data manageable)
+ */
+ + "<feature name=\"CDS\" location=\"4..15\">"
+ + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM3\" />"
+ + "<qualifier name=\"protein_id\"><value>CAA30421.1</value></qualifier>"
+ + "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
+ + "</feature>"
+ /*
+ * third CDS is made up - has no xref - code should synthesize
+ * one to an assumed EMBLCDSPROTEIN accession
+ */
+ + "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
+ + "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
+ + "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
+ + "</feature>"
+ /*
+ * sequence (modified for test purposes)
+ * emulates EMBL XML 1.2 which splits sequence data every 60 characters
+ * see EmblSequence.setSequence
+ */
+ + "<sequence>GGTATGTCCTCTAGTACAAAC\n"
+ + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
+ + "</sequence></entry></ROOT>";
+
+ @Test(groups = "Functional")
+ public void testGetCdsRanges()
+ {
+ EmblSource testee = new EmblSource();
+
+ /*
+ * Make a (CDS) Feature with 5 locations
+ */
+ Feature cds = new Feature();
+ cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
+
+ int[] exons = testee.getCdsRanges("EMBL", cds);
+ assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
+ Arrays.toString(exons));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSequence()
+ {
+ // not the whole sequence but enough for this test...
+ List<SequenceI> peptides = new ArrayList<>();
+ List<EntryType> entries = EmblSourceTest.getEmblEntries();
+ assertEquals(1, entries.size());
+ EntryType entry = entries.get(0);
+ EmblSource testee = new EmblSource();
+ String sourceDb = "EMBL";
+ SequenceI dna = testee.getSequence(sourceDb, entry, peptides);
+
+ /*
+ * newline has been removed from sequence
+ */
+ String seq = dna.getSequenceAsString();
+ assertEquals(
+ "GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
+ seq);
+
+ /*
+ * peptides should now have five entries:
+ * EMBL product and two Uniprot accessions for the first CDS / translation
+ * EMBL product and one Uniprot accession for the second CDS / "
+ * EMBL product only for the third
+ */
+ assertEquals(6, peptides.size());
+ assertEquals("CAA30420.1", peptides.get(0).getName());
+ assertEquals("MLCF", peptides.get(0).getSequenceAsString());
+ assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
+ assertEquals("MLCF", peptides.get(1).getSequenceAsString());
+ assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
+ assertEquals("MLCF", peptides.get(2).getSequenceAsString());
+ assertEquals("CAA30421.1", peptides.get(3).getName());
+ assertEquals("MSSS", peptides.get(3).getSequenceAsString());
+ assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
+ assertEquals("MSSS", peptides.get(4).getSequenceAsString());
+ assertEquals("CAA12345.6", peptides.get(5).getName());
+ assertEquals("MSS", peptides.get(5).getSequenceAsString());
+
+ /*
+ * verify dna sequence has dbrefs
+ * - to 'self' (synthesized dbref)
+ * - to EuropePMC
+ * - to MD5 (with null version as "0")
+ * - with CDS mappings to the peptide 'products'
+ */
+ MapList mapToSelf = new MapList(new int[] { 1, 57 },
+ new int[]
+ { 1, 57 }, 1, 1);
+ MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
+ 3, 1);
+ MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
+ 3, 1);
+ MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
+ 1, 3 }, 3, 1);
+
+ DBRefEntry[] dbrefs = dna.getDBRefs();
+ assertEquals(7, dbrefs.length);
+
+ DBRefEntry dbRefEntry = dbrefs[0];
+ assertEquals("EMBL", dbRefEntry.getSource());
+ assertEquals("X07547", dbRefEntry.getAccessionId());
+ assertEquals("1", dbRefEntry.getVersion());
+ assertNotNull(dbRefEntry.getMap());
+ assertNull(dbRefEntry.getMap().getTo());
+ assertEquals(mapToSelf, dbRefEntry.getMap().getMap());
+
+ dbRefEntry = dbrefs[1];
+ // DBRefEntry constructor puts dbSource in upper case
+ assertEquals("EUROPEPMC", dbRefEntry.getSource());
+ assertEquals("PMC107176", dbRefEntry.getAccessionId());
+ assertEquals("9573186", dbRefEntry.getVersion());
+ assertNull(dbRefEntry.getMap());
+
+ dbRefEntry = dbrefs[2];
+ assertEquals("MD5", dbRefEntry.getSource());
+ assertEquals("ac73317", dbRefEntry.getAccessionId());
+ assertEquals("0", dbRefEntry.getVersion());
+ assertNull(dbRefEntry.getMap());
+
+ dbRefEntry = dbrefs[3];
+ assertEquals("UNIPROT", dbRefEntry.getSource());
+ assertEquals("B0BCM4", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
+ assertEquals(cds1Map, dbRefEntry.getMap().getMap());
+
+ dbRefEntry = dbrefs[4];
+ assertEquals("UNIPROT", dbRefEntry.getSource());
+ assertEquals("P0CE20", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
+ assertEquals(cds1Map, dbRefEntry.getMap().getMap());
+
+ dbRefEntry = dbrefs[5];
+ assertEquals("UNIPROT", dbRefEntry.getSource());
+ assertEquals("B0BCM3", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
+ assertEquals(cds2Map, dbRefEntry.getMap().getMap());
+
+ dbRefEntry = dbrefs[6];
+ assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
+ assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
+ assertEquals(cds3Map, dbRefEntry.getMap().getMap());
+
+ /*
+ * verify peptides have dbrefs
+ * - to EMBL sequence (with inverse 1:3 cds mapping)
+ * - to EMBLCDS (with 1:3 mapping)
+ * - direct (no mapping) to other protein accessions
+ */
+ MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
+ 1, 12 }, 1, 3);
+ MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
+ 1, 9 }, 1, 3);
+
+ // dbrefs for first CDS EMBL product CAA30420.1
+ dbrefs = peptides.get(0).getDBRefs();
+ assertEquals(5, dbrefs.length);
+ assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+ assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
+ // TODO: verify getPrimaryDBRefs() for peptide products
+ assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+ assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
+ assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+ assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
+ assertNull(dbrefs[2].getMap());
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+ dbrefs[3]);
+ assertNull(dbrefs[3].getMap());
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+ dbrefs[4]);
+ assertNull(dbrefs[4].getMap());
+
+ // dbrefs for first CDS first Uniprot xref
+ dbrefs = peptides.get(1).getDBRefs();
+ assertEquals(2, dbrefs.length);
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+ dbrefs[0]);
+ assertNull(dbrefs[0].getMap());
+ assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+ assertEquals("X07547", dbrefs[1].getAccessionId());
+ assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+ // dbrefs for first CDS second Uniprot xref
+ dbrefs = peptides.get(2).getDBRefs();
+ assertEquals(2, dbrefs.length);
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+ dbrefs[0]);
+ assertNull(dbrefs[0].getMap());
+ assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+ assertEquals("X07547", dbrefs[1].getAccessionId());
+ assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+ // dbrefs for second CDS EMBL product CAA30421.1
+ dbrefs = peptides.get(3).getDBRefs();
+ assertEquals(4, dbrefs.length);
+ assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+ assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
+ assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+ assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
+ assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+ assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
+ assertNull(dbrefs[2].getMap());
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+ dbrefs[3]);
+ assertNull(dbrefs[3].getMap());
+
+ // dbrefs for second CDS second Uniprot xref
+ dbrefs = peptides.get(4).getDBRefs();
+ assertEquals(2, dbrefs.length);
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+ dbrefs[0]);
+ assertNull(dbrefs[0].getMap());
+ assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+ assertEquals("X07547", dbrefs[1].getAccessionId());
+ assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());
+
+ // dbrefs for third CDS inferred EMBL product CAA12345.6
+ dbrefs = peptides.get(5).getDBRefs();
+ assertEquals(3, dbrefs.length);
+ assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+ assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
+ assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+ assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
+ assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+ assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
+ assertNull(dbrefs[2].getMap());
+ }
+
+ @Test(groups = "Functional")
+ public void testAdjustForProteinLength()
+ {
+ int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
+
+ // exact length match:
+ assertSame(exons, EmblXmlSource.adjustForProteinLength(6, exons));
+
+ // match if we assume exons include stop codon not in protein:
+ assertSame(exons, EmblXmlSource.adjustForProteinLength(5, exons));
+
+ // truncate last exon by 6bp
+ int[] truncated = EmblXmlSource.adjustForProteinLength(4, exons);
+ assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
+
+ // remove last exon and truncate preceding by 1bp
+ truncated = EmblXmlSource.adjustForProteinLength(3, exons);
+ assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
+
+ // exact removal of exon case:
+ exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
+ truncated = EmblXmlSource.adjustForProteinLength(4, exons);
+ assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
+
+ // what if exons are too short for protein?
+ truncated = EmblXmlSource.adjustForProteinLength(7, exons);
+ assertSame(exons, truncated);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetEmblEntries()
+ {
+ List<EntryType> entries = EmblSourceTest.getEmblEntries();
+ assertEquals(1, entries.size());
+ EntryType entry = entries.get(0);
+
+ assertEquals("X07547", entry.getAccession());
+ assertEquals("C. trachomatis plasmid", entry.getDescription());
+ assertEquals("STD", entry.getDataClass());
+ assertEquals("PRO", entry.getTaxonomicDivision());
+ assertEquals("1999-02-10", entry.getLastUpdated().toString());
+ assertEquals(58, entry.getLastUpdatedRelease().intValue());
+ assertEquals("1988-11-10", entry.getFirstPublic().toString());
+ assertEquals(18, entry.getFirstPublicRelease().intValue());
+ assertEquals("genomic DNA", entry.getMoleculeType());
+ assertEquals(1, entry.getVersion().intValue());
+ assertEquals(8, entry.getEntryVersion().intValue());
+ assertEquals("linear", entry.getTopology());
+ assertEquals(7499, entry.getSequenceLength().intValue());
+ assertEquals(2, entry.getKeyword().size());
+ assertEquals("plasmid", entry.getKeyword().get(0));
+ assertEquals("unidentified reading frame", entry.getKeyword().get(1));
+
+ /*
+ * dbrefs
+ */
+ assertEquals(2, entry.getXref().size());
+ XrefType dbref = entry.getXref().get(0);
+ assertEquals("EuropePMC", dbref.getDb());
+ assertEquals("PMC107176", dbref.getId());
+ assertEquals("9573186", dbref.getSecondaryId());
+ dbref = entry.getXref().get(1);
+ assertEquals("MD5", dbref.getDb());
+ assertEquals("ac73317", dbref.getId());
+ assertNull(dbref.getSecondaryId());
+
+ /*
+ * three sequence features for CDS
+ */
+ assertEquals(3, entry.getFeature().size());
+ /*
+ * first CDS
+ */
+ Feature ef = entry.getFeature().get(0);
+ assertEquals("CDS", ef.getName());
+ assertEquals("complement(46..57)", ef.getLocation());
+ assertEquals(2, ef.getXref().size());
+ dbref = ef.getXref().get(0);
+ assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
+ assertEquals("B0BCM4", dbref.getId());
+ assertEquals("2.1", dbref.getSecondaryId());
+ dbref = ef.getXref().get(1);
+ assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
+ assertEquals("P0CE20", dbref.getId());
+ assertNull(dbref.getSecondaryId());
+ // CDS feature qualifiers
+ assertEquals(3, ef.getQualifier().size());
+ Qualifier q = ef.getQualifier().get(0);
+ assertEquals("note", q.getName());
+ assertEquals("ORF 8 (AA 1-330)", q.getValue());
+ q = ef.getQualifier().get(1);
+ assertEquals("protein_id", q.getName());
+ assertEquals("CAA30420.1", q.getValue());
+ q = ef.getQualifier().get(2);
+ assertEquals("translation", q.getName());
+ assertEquals("MLCF", q.getValue());
+
+ /*
+ * second CDS
+ */
+ ef = entry.getFeature().get(1);
+ assertEquals("CDS", ef.getName());
+ assertEquals("4..15", ef.getLocation());
+ assertEquals(1, ef.getXref().size());
+ dbref = ef.getXref().get(0);
+ assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
+ assertEquals("B0BCM3", dbref.getId());
+ assertNull(dbref.getSecondaryId());
+ assertEquals(2, ef.getQualifier().size());
+ q = ef.getQualifier().get(0);
+ assertEquals("protein_id", q.getName());
+ assertEquals("CAA30421.1", q.getValue());
+ q = ef.getQualifier().get(1);
+ assertEquals("translation", q.getName());
+ assertEquals("MSSS", q.getValue());
+
+ /*
+ * third CDS
+ */
+ ef = entry.getFeature().get(2);
+ assertEquals("CDS", ef.getName());
+ assertEquals("join(4..6,10..15)", ef.getLocation());
+ assertNotNull(ef.getXref());
+ assertTrue(ef.getXref().isEmpty());
+ assertEquals(2, ef.getQualifier().size());
+ q = ef.getQualifier().get(0);
+ assertEquals("protein_id", q.getName());
+ assertEquals("CAA12345.6", q.getValue());
+ q = ef.getQualifier().get(1);
+ assertEquals("translation", q.getName());
+ assertEquals("MSS", q.getValue());
+
+ /*
+ * Sequence - raw data before removal of newlines
+ */
+ String seq = entry.getSequence();
+ assertEquals(
+ "GGTATGTCCTCTAGTACAAAC\n"
+ + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
+ seq);
+
+ /*
+ * getSequence() converts empty DBRefEntry.version to "0"
+ */
+ assertNull(entry.getXref().get(1).getSecondaryId());
+ assertNull(entry.getFeature().get(0).getXref().get(1).getSecondaryId());
+ }
+
+ static List<EntryType> getEmblEntries()
+ {
+ return new EmblSource()
+ .getEmblEntries(new ByteArrayInputStream(TESTDATA.getBytes()));
+ }
+}
package jalview.ws.dbsources;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.uniprot.UniprotEntry;
-import jalview.datamodel.xdb.uniprot.UniprotFeature;
import jalview.gui.JvOptionPane;
+import jalview.xml.binding.uniprot.DbReferenceType;
+import jalview.xml.binding.uniprot.Entry;
+import jalview.xml.binding.uniprot.FeatureType;
+import jalview.xml.binding.uniprot.LocationType;
+import jalview.xml.binding.uniprot.PositionType;
-import java.io.Reader;
-import java.io.StringReader;
-import java.util.Vector;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+import java.math.BigInteger;
+import java.util.List;
+import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
// adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
- + "<uniprot>"
+ + "<uniprot xmlns=\"http://uniprot.org/uniprot\">"
+ "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
+ "<accession>A9CKP4</accession>"
+ "<accession>A9CKP5</accession>"
+ "<name>A9CKP4_AGRT5</name>"
+ "<name>A9CKP4_AGRT6</name>"
- + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
+ + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName></recommendedName></protein>"
+ "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
+ "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
+ "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
+ "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+ "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+ "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Foo Too\"><variation>LL</variation><variation>LMVK</variation><original>MLML</original><location><begin position=\"42\"/><end position=\"45\"/></location></feature>"
+ "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
+ "</uniprot>";
/**
* Test the method that unmarshals XML to a Uniprot model
+ *
+ * @throws UnsupportedEncodingException
*/
@Test(groups = { "Functional" })
- public void testGetUniprotEntries()
+ public void testGetUniprotEntries() throws UnsupportedEncodingException
{
Uniprot u = new Uniprot();
- Reader reader = new StringReader(UNIPROT_XML);
- Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
+ InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
+ List<Entry> entries = u.getUniprotEntries(is);
assertEquals(1, entries.size());
- UniprotEntry entry = entries.get(0);
+ Entry entry = entries.get(0);
assertEquals(2, entry.getName().size());
assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
assertEquals("A9CKP4", entry.getAccession().get(0));
assertEquals("A9CKP5", entry.getAccession().get(1));
- /*
- * UniprotSequence drops any space characters
- */
- assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
+ assertEquals("MHAPL VSKDL", entry.getSequence().getValue());
- assertEquals(2, entry.getProtein().getName().size());
assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
- .getName().get(0));
- assertEquals("Henry", entry.getProtein().getName().get(1));
+ .getRecommendedName().getFullName().getValue());
/*
* Check sequence features
*/
- Vector<UniprotFeature> features = entry.getFeature();
- assertEquals(6, features.size());
- UniprotFeature sf = features.get(0);
+ List<FeatureType> features = entry.getFeature();
+ assertEquals(9, features.size());
+ FeatureType sf = features.get(0);
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
assertNull(sf.getStatus());
- assertEquals(1, sf.getBegin());
- assertEquals(18, sf.getEnd());
+ assertNull(sf.getLocation().getPosition());
+ assertEquals(1, sf.getLocation().getBegin().getPosition().intValue());
+ assertEquals(18, sf.getLocation().getEnd().getPosition().intValue());
sf = features.get(1);
assertEquals("propeptide", sf.getType());
assertEquals("Activation peptide", sf.getDescription());
- assertEquals(19, sf.getPosition());
- assertEquals(19, sf.getBegin());
- assertEquals(20, sf.getEnd());
+ assertNull(sf.getLocation().getPosition());
+ assertEquals(19, sf.getLocation().getBegin().getPosition().intValue());
+ assertEquals(20, sf.getLocation().getEnd().getPosition().intValue());
sf = features.get(2);
assertEquals("chain", sf.getType());
assertEquals("Granzyme B", sf.getDescription());
- assertEquals(21, sf.getPosition());
- assertEquals(21, sf.getBegin());
- assertEquals(247, sf.getEnd());
+ assertNull(sf.getLocation().getPosition());
+ assertEquals(21, sf.getLocation().getBegin().getPosition().intValue());
+ assertEquals(247, sf.getLocation().getEnd().getPosition().intValue());
sf = features.get(3);
assertEquals("sequence variant", sf.getType());
- assertEquals("Variation: 'L' Original: 'M'", sf.getDescription());
- assertEquals(41, sf.getPosition());
- assertEquals(41, sf.getBegin());
- assertEquals(41, sf.getEnd());
+ assertNull(sf.getDescription());
+ assertEquals(41,
+ sf.getLocation().getPosition().getPosition().intValue());
+ assertNull(sf.getLocation().getBegin());
+ assertNull(sf.getLocation().getEnd());
sf = features.get(4);
assertEquals("sequence variant", sf.getType());
- assertEquals("Pathogenic Variation: 'L' Original: 'M'",
- sf.getDescription());
- assertEquals(41, sf.getPosition());
- assertEquals(41, sf.getBegin());
- assertEquals(41, sf.getEnd());
+ assertEquals("Pathogenic", sf.getDescription());
+ assertEquals(41,
+ sf.getLocation().getPosition().getPosition().intValue());
+ assertNull(sf.getLocation().getBegin());
+ assertNull(sf.getLocation().getEnd());
sf = features.get(5);
assertEquals("sequence variant", sf.getType());
- assertEquals("Pathogenic Original: 'M'", sf.getDescription());
- assertEquals(41, sf.getPosition());
- assertEquals(41, sf.getBegin());
- assertEquals(41, sf.getEnd());
+ assertEquals("Pathogenic", sf.getDescription());
+ assertEquals(41,
+ sf.getLocation().getPosition().getPosition().intValue());
+ assertNull(sf.getLocation().getBegin());
+ assertNull(sf.getLocation().getEnd());
+
+ sf = features.get(6);
+ assertEquals("sequence variant", sf.getType());
+ assertEquals("Foo",
+ sf.getDescription());
+ assertEquals(42,
+ sf.getLocation().getPosition().getPosition().intValue());
+ assertNull(sf.getLocation().getBegin());
+ assertNull(sf.getLocation().getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "<html>p.Met42Leu" + "<br/> "
+ + "p.Met42LeuMetVal Foo</html>");
+
+ sf = features.get(7);
+ assertNull(sf.getLocation().getPosition());
+ assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
+ assertEquals(43, sf.getLocation().getEnd().getPosition().intValue());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "<html>p.MetLeu42LeuLeu" + "<br/> "
+ + "p.MetLeu42LeuMetVal Foo</html>");
+
+ sf = features.get(8);
+ assertNull(sf.getLocation().getPosition());
+ assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
+ assertEquals(45, sf.getLocation().getEnd().getPosition().intValue());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "<html>p.MLML42LeuLeu" + "<br/> "
+ + "p.MLML42LMVK Foo Too</html>");
+
/*
* Check cross-references
*/
- Vector<PDBEntry> xrefs = entry.getDbReference();
+ List<DbReferenceType> xrefs = entry.getDbReference();
assertEquals(3, xrefs.size());
- PDBEntry xref = xrefs.get(0);
+ DbReferenceType xref = xrefs.get(0);
assertEquals("2FSQ", xref.getId());
assertEquals("PDB", xref.getType());
- assertEquals("X-ray", xref.getProperty("method"));
- assertEquals("1.40", xref.getProperty("resolution"));
+ assertEquals("X-ray",
+ Uniprot.getProperty(xref.getProperty(), "method"));
+ assertEquals("1.40",
+ Uniprot.getProperty(xref.getProperty(), "resolution"));
xref = xrefs.get(1);
assertEquals("2FSR", xref.getId());
assertEquals("PDBsum", xref.getType());
- assertFalse(xref.getProperties().hasMoreElements());
+ assertTrue(xref.getProperty().isEmpty());
xref = xrefs.get(2);
assertEquals("AE007869", xref.getId());
assertEquals("EMBL", xref.getType());
- assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
- assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
+ assertEquals("AAK85932.1",
+ Uniprot.getProperty(xref.getProperty(), "protein sequence ID"));
+ assertEquals("Genomic_DNA",
+ Uniprot.getProperty(xref.getProperty(), "molecule type"));
}
@Test(groups = { "Functional" })
- public void testGetUniprotSequence()
+ public void testGetUniprotSequence() throws UnsupportedEncodingException
{
- UniprotEntry entry = new Uniprot().getUniprotEntries(
- new StringReader(UNIPROT_XML)).get(0);
- SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
+ InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
+ Entry entry = new Uniprot().getUniprotEntries(
+ is).get(0);
+ SequenceI seq = new Uniprot().uniprotEntryToSequence(entry);
assertNotNull(seq);
assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
/**
* Test the method that formats the sequence id
+ *
+ * @throws UnsupportedEncodingException
*/
@Test(groups = { "Functional" })
- public void testGetUniprotEntryId()
+ public void testGetUniprotEntryId() throws UnsupportedEncodingException
{
- UniprotEntry entry = new Uniprot().getUniprotEntries(
- new StringReader(UNIPROT_XML)).get(0);
+ InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
+ Entry entry = new Uniprot().getUniprotEntries(is).get(0);
/*
* name formatted with Uniprot Entry name
/**
* Test the method that formats the sequence description
+ *
+ * @throws UnsupportedEncodingException
*/
@Test(groups = { "Functional" })
public void testGetUniprotEntryDescription()
+ throws UnsupportedEncodingException
+ {
+ InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
+ Entry entry = new Uniprot().getUniprotEntries(is).get(0);
+
+ assertEquals("Mitogen-activated protein kinase 13",
+ Uniprot.getUniprotEntryDescription(entry));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetDescription()
{
- UniprotEntry entry = new Uniprot().getUniprotEntries(
- new StringReader(UNIPROT_XML)).get(0);
+ FeatureType ft = new FeatureType();
+ assertEquals("", Uniprot.getDescription(ft));
+
+ ft.setDescription("Hello");
+ assertEquals("Hello", Uniprot.getDescription(ft));
+
+ ft.setLocation(new LocationType());
+ ft.getLocation().setPosition(new PositionType());
+ ft.getLocation().getPosition().setPosition(BigInteger.valueOf(23));
+ ft.setOriginal("K");
+ ft.getVariation().add("y");
+ assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(ft));
+
+ // multiple variants generate an html description over more than one line
+ ft.getVariation().add("W");
+ assertEquals("<html>p.Lys23Tyr<br/> p.Lys23Trp Hello</html>",
+ Uniprot.getDescription(ft));
/*
- * recommended names concatenated with space separator
+ * indel cases
+ * up to 3 bases (original or variant) are shown using 3 letter code
*/
- String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
- assertEquals(expectedDescription,
- Uniprot.getUniprotEntryDescription(entry));
+ ft.getVariation().clear();
+ ft.getVariation().add("KWE");
+ ft.setOriginal("KLS");
+ assertEquals("p.LysLeuSer23LysTrpGlu Hello",
+ Uniprot.getDescription(ft));
+
+ // adding a fourth original base switches to single letter code
+ ft.setOriginal("KLST");
+ assertEquals("p.KLST23LysTrpGlu Hello", Uniprot.getDescription(ft));
+
+ // adding a fourth variant switches to single letter code
+ ft.getVariation().clear();
+ ft.getVariation().add("KWES");
+ assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(ft));
+
+ ft.getVariation().clear();
+ ft.getVariation().add("z"); // unknown variant - fails gracefully
+ ft.setOriginal("K");
+ assertEquals("p.Lys23z Hello", Uniprot.getDescription(ft));
+
+ ft.getVariation().clear(); // variant missing - is ignored
+ assertEquals("Hello", Uniprot.getDescription(ft));
}
}
<method name="addElement">
<object class="com.zerog.ia.installer.util.LAXPropertyData" objectID="97fa91cfa6f7">
<property name="propertyValue">
- <string><![CDATA[268400000]]></string>
+ <string><![CDATA[1060000000]]></string>
</property>
<property name="propertyName">
<string><![CDATA[lax.nl.java.option.java.heap.size.max]]></string>
<method name="addElement">
<object class="com.zerog.ia.installer.util.LAXPropertyData" objectID="97f991ffa6f7">
<property name="propertyValue">
- <string><![CDATA[33554432]]></string>
+ <string><![CDATA[1000000000]]></string>
</property>
<property name="propertyName">
<string><![CDATA[lax.nl.java.option.java.heap.size.initial]]></string>
<string><![CDATA[664]]></string>
</property>
<property name="sourceName">
- <string><![CDATA[VAqua4.jar]]></string>
+ <string><![CDATA[VAqua5-patch.jar]]></string>
</property>
<property name="overrideUnixPermissions">
<boolean>false</boolean>
<boolean>true</boolean>
</property>
<property name="destinationName">
- <string><![CDATA[VAqua4.jar]]></string>
+ <string><![CDATA[VAqua5-patch.jar]]></string>
</property>
<property name="fileSize">
- <long>1355141</long>
+ <long>1370564</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
To run application:
-java -Djava.ext.dirs=JALVIEW_HOME/lib -jar JALVIEW_HOME/jalview.jar [-help ... ]
+java -classpath "JALVIEW_HOME/lib/*" -jar JALVIEW_HOME/jalview.jar [-help ... ]
Replace JALVIEW_HOME with the full path to Jalview Installation Directory.
Use -help to see the available command line arguments.
For best results use a Sun java run time environment (not the gcj gnu java, sorry!).
-If you want to the java runtime bundled with Jalview, then launch jalview like this:
+If you want to use the java runtime bundled with Jalview, then launch jalview like this:
-JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -Djava.ext.dirs=JALVIEW_HOME/lib -jar JALVIEW_HOME/jalview.jar
+in Windows:
+JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+
+in Linux:
+JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+
+in macOS:
+JAVA_HOME=JALVIEW_HOME/jre/Contents/Home JALVIEW_HOME/jre/Contents/Home/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+
+Note: ensure the -classpath argument is quoted and only use a terminating wildcard (e.g. 'DIR/*') to refer to all jar files in a directory, don't use e.g. 'DIR/*.jar'
-Please Note: the -jar jalview.jar option launches the jalview.bin.Jalview class in the jalview.jar
##################
<setting id="org.eclipse.jdt.core.formatter.indent_statements_compare_to_body" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch" value="false"/>
-<setting id="org.eclipse.jdt.core.formatter.indentation.size" value="8"/>
+<setting id="org.eclipse.jdt.core.formatter.indentation.size" value="2"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method" value="insert"/>
git://source.jalview.org / jalview.git / commitdiff