<classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
<classpathentry kind="lib" path="lib/java-json.jar"/>
<classpathentry kind="lib" path="lib/Jmol-14.2.14_2015.06.11.jar"/>
+ <classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
<classpathentry kind="output" path="classes"/>
</classpath>
<booleanAttribute key="org.eclipse.ant.ui.ATTR_TARGETS_UPDATED" value="true"/>
<booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="false"/>
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/jalview/build.xml"/>
+<listEntry value="/jalview"/>
</listAttribute>
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="1"/>
+<listEntry value="4"/>
</listAttribute>
<booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
.project
/dist
/classes
+/tests
+/test-reports
+/test-output
.externalToolBuilders/Jalview Release indices [Builder].launch
/.DS_Store
.DS_Store
editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true
formatter_profile=_Jalview
formatter_settings_version=12
+org.eclipse.jdt.ui.ignorelowercasenames=true
+org.eclipse.jdt.ui.importorder=jalview;java;javax;org;com;
+org.eclipse.jdt.ui.ondemandthreshold=99
+org.eclipse.jdt.ui.staticondemandthreshold=99
sp_cleanup.add_default_serial_version_id=true
sp_cleanup.add_generated_serial_version_id=false
sp_cleanup.add_missing_annotations=true
<!-- J2SE version needed for webstart launch -->
<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
<property name="j2sev" value="1.7+"/>
-
+ <!-- Java Compilation settings - source and target javac version -->
+ <property name="javac.source" value="1.7"/>
+ <property name="javac.target" value="1.7"/>
+
<!-- Permissions for running Java applets and applications. -->
<!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
<property name="application.codebase" value="*.jalview.org" />
<property name="jsonSimple" value="json_simple-1.1.jar" />
<property name="javaJson" value="java-json.jar" />
<property name="jalviewLiteJar" value="jalviewApplet.jar" />
+ <property name="reportDir" value="test-reports" />
+ <property name="testDir" value="test" />
+ <property name="testOutputDir" value="tests" />
<!-- switch to indicate if we should obfuscate jalviewLite -->
<!-- <property name="donotobfuscate" value="true"/> -->
<!-- switch to exclude associations from generated jnlp files -->
<target name="build" depends="prepare">
<!-- not efficient yet. -->
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
<exclude name="jalview/*applet*" />
<exclude name="jalview/appletgui/**" />
<exclude name="com/stevesoft/**" />
</javac>
</target>
+
+
+ <target name="testclean" depends="init">
+ <delete dir="${testOutputDir}" includes="*,**/*"/>
+ </target>
+
+ <target name="prepareTests" depends="init">
+ <mkdir dir="${testOutputDir}" />
+ <copy todir="${testOutputDir}">
+ <fileset dir=".">
+ <include name="${docDir}/**/*.*" />
+ <include name="${helpDir}/**/*.*" />
+ <include name="${libDir}/*.jar" />
+ </fileset>
+ <fileset dir="${resourceDir}">
+ <include name="**/*.*" />
+ </fileset>
+ </copy>
+ </target>
+
+ <target name="buildTests" depends="prepareTests">
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
+ debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
+ </javac>
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
+ debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
+ </javac>
+ </target>
+
+ <taskdef name="testng" classname="org.testng.TestNGAntTask" >
+ <classpath location="utils/testnglibs/testng.jar" />
+ </taskdef>
+
+ <target name="testng" depends="buildTests">
+ <testng classpathref="build.classpath" outputDir="${reportDir}"
+ haltOnFailure="false">
+ <classpath location="${testOutputDir}" />
+ <xmlfileset dir="utils" includes="jalview_testng.xml" />
+ </testng>
+ </target>
+
<target name="buildindices" depends="init, prepare" unless="help.uptodate">
<java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
<arg line="html" />
<target name="compileApplet" depends="init,clean">
<mkdir dir="${outputDir}" />
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
</target>
--- /dev/null
+Command line: [exonerate --model protein2genome Input_Sequences63/dcsA.fas NewSequencedGenome/A_Ellipt_clc_pe_contigs.fa --bestn 1 --showtargetgff]
+Hostname: [ningal.cluster.lifesci.dundee.ac.uk]
+
+C4 Alignment:
+------------
+ Query: DDB_G0269124
+ Target: contig_1146 [revcomp]
+ Model: protein2genome:local
+ Raw score: 3652
+ Query range: 142 -> 1059
+ Target range: 11269 -> 8533
+
+ 143 : SerProSerSerGluTyrGlyThrThrSerGlyGlyGlnArgPheAspThrLeuValAsp : 162
+ ||||||!:!! !||| !.! ! ! !!.! !! !!.!|||!!:||||||:!!|||
+ SerProAsnMetGluLeuAlaArgAspLeuAlaGlnProHisPheGluThrLeuIleAsp
+ 11269 : TCGCCCAACATGGAGCTGGCGCGCGACCTCGCCCAGCCGCACTTTGAGACGCTGATCGAC : 11212
+
+ 163 : ProAspIleSerLeuAlaGluMetGluGluLysMetArgGlnHisLysValTyrGlnGlu : 182
+ ||||||!!:!!!! !!.!|||!!:||||||||||||||||||||||||!.!:!!! |||
+ ProAspMetThrProGlyGluIleGluGluLysMetArgGlnHisLysAlaHisLeuGlu
+ 11211 : CCCGACATGACGCCCGGCGAGATCGAGGAGAAGATGCGCCAGCACAAGGCGCACCTCGAG : 11152
+
+ 183 : GlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnLysGlnLysAspLysGluLeuSer : 202
+ ..!|||:!!.....!..!:!!! |||:!!|||..!:!! !! ! !
+ ------------MetGlnLysSerSerSerGluLeuLysLysLysSerGlnMetGlnLeu
+ 11151 : ------------ATGCAAAAGTCCTCGTCGGAACTCAAGAAGAAGTCCCAAATGCAACTC : 11104
+
+ 203 : SerGlnLysLysLysProSerSerMetGlnLeuSerLysLysLysHisValAlaLysGlu : 222
+ !.!||| ! :!!:!! !..!..!:!: !!.!||| ::: :!! !:!!!!:
+ LysGlnAspGlnGlnLysGlnGlnValValAlaLysLysProArgSerIleLeuGlnAsp
+ 11103 : AAGCAGGATCAGCAGAAACAACAAGTCGTCGCAAAGAAGCCCCGTTCGATCCTCCAGGAC : 11044
+
+ 223 : AspSerGluThrLeuGluThrIleIleGlyGluGluLysLysGluValValPheGluVal : 242
+ |||! !||||||! !||||||:!!.!!!.!||||||:::|||||||||||||||||||||
+ AspMetGluThrSerGluThrLeuPheAlaGluGluArgLysGluValValPheGluVal
+ 11043 : GACATGGAGACGTCGGAGACCCTTTTCGCCGAGGAACGCAAGGAGGTCGTCTTTGAGGTG : 10984
+
+ 243 : LysProTyrPheSerHisAlaIleLeuGlnAlaThrMetAlaValPheLeuIleTrpAsn : 262
+ :::|||||||||||||||:!!|||||||||||||||||||||||||||||||||||||||
+ ArgProTyrPheSerHisSerIleLeuGlnAlaThrMetAlaValPheLeuIleTrpAsn
+ 10983 : CGTCCCTACTTCTCGCACTCTATCCTCCAGGCGACGATGGCCGTCTTCCTCATCTGGAAC : 10924
+
+ 263 : IlePheTyrPheAlaTyrArgAlaGlyTrpThrMetAsnArgThrAspTyrIle<->Thr : 281
+ ||||||||||||||||||||| !|||||||||||||||! ! !:!! !:!! ..!
+ IlePheTyrPheAlaTyrArgMetGlyTrpThrMetAsnThrGlnAsnGlyValTyrVal
+ 10923 : ATCTTTTACTTTGCCTACCGTATGGGCTGGACCATGAACACCCAGAACGGCGTCTACGTG : 10864
+
+ 282 : PheSerTyrSerIleLeuPheIleIleValGluPheIleSerPheLeuGlySerAlaLeu : 301
+ .!!!!!||||||:!:||||||:!!||||||||||||||||||||||||||||||||||||
+ LeuCysTyrSerValLeuPheLeuIleValGluPheIleSerPheLeuGlySerAlaLeu
+ 10863 : CTCTGCTACTCGGTGCTCTTCCTCATCGTCGAGTTCATCTCTTTCCTCGGCTCCGCGCTC : 10804
+
+ 302 : HisLeuAsnAsnPheThrAsnProCysThrPheValLeuValValThrLeuGluGlnIle : 321
+ |||||||||||||||||||||||||||||||||:!!||||||||||||||||||||||||
+ HisLeuAsnAsnPheThrAsnProCysThrPheIleLeuValValThrLeuGluGlnIle
+ 10803 : CATCTCAACAACTTTACCAATCCGTGCACCTTTATCCTGGTGGTCACGCTGGAGCAGATC : 10744
+
+ 322 : LeuAlaLysArgArgLysLysHisProThrValMetMetTyrValCysThrTyrLysGlu : 341
+ ||||||:::||||||||| !||||||||||||||||||:!!|||||||||||||||
+ LeuAlaArgArgArgLysProPheProThrValMetMetTyrIleCysThrTyrLysGlu
+ 10743 : CTCGCGCGCCGTCGCAAGCCCTTCCCCACCGTCATGATGTACATCTGTACCTACAAGGAG : 10684
+
+ 342 : ProProSerIleValSerArgThrPheArgThrAlaIleSerMetAspTyrProSerGlu : 361
+ |||||||||||||||||||||||||||||||||||||||:!!||||||||||||:!!|||
+ ProProSerIleValSerArgThrPheArgThrAlaIleAlaMetAspTyrProAlaGlu
+ 10683 : CCGCCCTCGATCGTCTCGCGCACGTTCCGCACCGCCATCGCCATGGACTACCCCGCCGAG : 10624
+
+ 362 : AsnLeuTrpIleGlyLeuLeuAspAspSerValAsnTyrArgGluSerArgGlyTrpAla : 381
+ ||||||||||||||||||||||||||||||:!!|||!:!||||||||||||||||||:!!
+ AsnLeuTrpIleGlyLeuLeuAspAspSerIleAsnPheArgGluSerArgGlyTrpSer
+ 10623 : AACCTCTGGATCGGCCTGCTCGACGACTCGATCAACTTCCGCGAGTCGCGCGGCTGGTCG : 10564
+
+ 382 : HisLeuGlnSerValGluLysAsnPheLeuTyrValLeuLeuGlnLysAlaValTyrSer : 401
+ ||||||||||||||||||||||||||||||!:! !|||||||||::::!!||||||:!!
+ HisLeuGlnSerValGluLysAsnPheLeuPheGlnLeuLeuGlnArgSerValTyrAla
+ 10563 : CACCTCCAATCGGTCGAGAAGAACTTCCTCTTCCAGCTGCTCCAGCGCTCCGTGTACGCC : 10504
+
+ 402 : ValHisAsnIleArgProProValThrSerGlnHisGluAspProHisGlyIleLeuAsn : 421
+ |||||||||||| !|||||||||.!!..!||| !|||||||||:!!|||||||||..!
+ ValHisAsnIleAlaProProValAlaGlnGlnAlaGluAspProTyrGlyIleLeuGly
+ 10503 : GTGCACAACATCGCGCCGCCCGTCGCGCAGCAGGCCGAGGACCCGTACGGCATCCTCGGC : 10444
+
+ 422 : GluThrSerSerLysIleGluSerSerThrLysGluValIleGluAlaGluValGlnTrp : 441
+ |||||||||..!:::||||||!.!!!!||||||||||||:!!||||||||||||||||||
+ GluThrSerGluArgIleGluLysThrThrLysGluValValGluAlaGluValGlnTrp
+ 10443 : GAGACGTCCGAGCGCATCGAAAAGACCACGAAAGAGGTCGTCGAGGCCGAGGTGCAGTGG : 10384
+
+ 442 : PheIleGluTyrPheLeuLeuAsnSerTrpPheGlyValGlyGlnGluIleProArgAsp : 461
+ ||||||||||||||||||||||||||||||||||||:!!! !!::||| ! !! !!!:
+ PheIleGluTyrPheLeuLeuAsnSerTrpPheGlyIleAspArgGluProGluIleGlu
+ 10383 : TTCATCGAGTACTTCCTCCTGAACAGCTGGTTCGGCATCGACCGCGAGCCCGAGATCGAG : 10324
+
+ 462 : AlaAspAspAlaGluArgAlaLeuIleAlaLysLeuArgAspAspAsnPheSerProTyr : 481
+ !!..!|||||||||||| !!!!|||:!!! !||||||!!:|||||||||||| !!|||
+ ProSerAspAlaGluArgAsnPheIleSerMetLeuArgGluAspAsnPheSerAlaTyr
+ 10323 : CCCTCCGACGCCGAACGCAACTTTATCTCGATGCTGCGCGAGGACAACTTCTCGGCGTAC : 10264
+
+ 482 : ArgThrPheThrLysSerGluSerGluLysIleSerAsnPheThrIleAspSerLeuGln : 501
+ ||||||.!!||| ! ..!||| !!||| |||! !!..|||:!!! !|||:!!||||||
+ ArgThrIleThrAspGlnGluArgGluLeuIleTyrThrPheSerSerAspAlaLeuGln
+ 10263 : CGCACCATCACCGACCAGGAGCGCGAGCTCATCTACACGTTCTCGAGCGACGCGCTCCAG : 10204
+
+ 502 : SerLeuTrpHisGlySerAlaPhePheArgProLeuIleArgSerIleLeuLeuLysLys : 521
+ |||:!!|||||||||||| !!.!.!:!|||||||||:!:|||!:! !|||!!!:!!:::
+ SerIleTrpHisGlySerProMetTyrArgProLeuValArgAsnAlaLeuPheGlnArg
+ 10203 : TCGATCTGGCACGGCTCGCCCATGTACCGCCCGCTGGTGCGCAACGCCCTGTTCCAGCGC : 10144
+
+ 522 : AspTyrValArgAsnPheValSerGluLeuAsnAsnGlnHisArgLeuArgPheLeuAsn : 541
+ !||||||!:!:!!|||:!!:!!|||! !||| ..!|||||||||||||||||||||
+ ArgTyrValLysAspPheIleAlaGluHisAsnAlaSerHisArgLeuArgPheLeuAsn
+ 10143 : CGCTACGTCAAGGACTTTATCGCCGAGCACAACGCGTCGCACCGTCTGCGCTTCCTCAAC : 10084
+
+ 542 : ThrGluAlaLeuAlaMetAlaGlnTyrGlnValLeuMetMetGlyArgGlnGluLeuPro : 561
+ ..!!!:|||:!! !||||||||||||:!!|||! !||||||||||||||||||:!!|||
+ ValAspAlaIleAsnMetAlaGlnTyrLysValHisMetMetGlyArgGlnGluValPro
+ 10083 : GTCGACGCGATCAACATGGCGCAGTACAAGGTGCACATGATGGGCCGCCAGGAGGTGCCC : 10024
+
+ 562 : TrpAspGluIleSerSerGlyAsnValArgIleAspPheAspThrCysAspGlyProIle : 581
+ !::|||!!::!:|||:!!|||||||||||||||||||||||| !! !||| !!:!!
+ PheAspAspValSerAlaGlyAsnValArgIleAspPheAspPro---ThrGlySerVal
+ 10023 : TTCGACGACGTGTCCGCGGGCAACGTGCGCATCGACTTTGACCCG---ACCGGCTCGGTC : 9967
+
+ 582 : ValSerProLysCysThrTyrLeuArgArgArgLysProProIleProHisAsnLysAla : 601
+ |||!!!|||:::||||||||||||||||||||||||||||||||||||||||||||||||
+ ValThrProArgCysThrTyrLeuArgArgArgLysProProIleProHisAsnLysAla
+ 9966 : GTCACGCCGCGCTGCACCTACCTGCGCCGCCGCAAGCCGCCCATCCCGCACAACAAGGCC : 9907
+
+ 602 : GlyAsnIleAsnAsnAlaLeuPheAsnGluSerThrLysAlaAspTyrGluPheLeuGly : 621
+ |||||||||||||||!.!|||||||||||||||! ! ! |||||||||||||||:!!|||
+ GlyAsnIleAsnAsnGlyLeuPheAsnGluSerIleHisAlaAspTyrGluPheMetGly
+ 9906 : GGCAACATCAACAACGGCCTCTTCAACGAGTCGATCCACGCCGACTACGAGTTCATGGGC : 9847
+
+ 622 : LeuLeuAspAlaAspGlnGlnProHisProAspPheLeuLysArgValLeuProTyrPhe : 641
+ ||||||||||||||||||||||||||||||||||||||||||||||||:!!|||||||||
+ LeuLeuAspAlaAspGlnGlnProHisProAspPheLeuLysArgValMetProTyrPhe
+ 9846 : CTGCTCGATGCCGACCAGCAGCCGCACCCCGACTTCCTCAAGCGCGTCATGCCCTACTTC : 9787
+
+ 642 : TyrSerAspGluGlyGlnAspLeuAlaPheValGlnThrProGlnPhePheSerAsnIle : 661
+ !:!||||||!!:|||!!.!!::!!||||||||||||||||||||||||||||||||||||
+ PheSerAspAspGlyHisGluValAlaPheValGlnThrProGlnPhePheSerAsnIle
+ 9786 : TTCAGCGACGACGGCCACGAGGTCGCCTTTGTCCAGACGCCGCAGTTCTTCTCCAACATC : 9727
+
+ 662 : TyrProValAspAspProLeuGlyHisArgAsnMetGluPheTyrGlyProValMetGlu : 681
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ TyrProValAspAspProLeuGlyHisArgAsnMetGluPheTyrGlyProValMetGlu
+ 9726 : TACCCCGTCGACGACCCGCTCGGCCACAGAAACATGGAGTTCTACGGTCCCGTAATGGAG : 9667
+
+ 682 : GlyArgSerAlaAsnAsnAlaCysProPheValGlyThrAsnAlaIlePheArgArgGln : 701
+ |||||||||.!!|||..!|||||||||||||||||||||||||||||||||||||||:!!
+ GlyArgSerThrAsnGlyAlaCysProPheValGlyThrAsnAlaIlePheArgArgLys
+ 9666 : GGTCGCTCCACCAACGGCGCCTGCCCCTTCGTCGGAACCAACGCCATCTTCCGTCGCAAG : 9607
+
+ 702 : ProLeuTyrAspIleGlyGlyIleMetTyrAsnSerValThrGluAspMetTyrThrGly : 721
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ ProLeuTyrAspIleGlyGlyIleMetTyrAsnSerValThrGluAspMetTyrThrGly
+ 9606 : CCCCTCTACGACATTGGCGGCATCATGTACAACTCTGTCACTGAGGATATGTACACGGGA : 9547
+
+ 722 : MetLysLeuGlnValSerGlyTyrLysSerTrpTyrHisAsnGluValLeuValValGly : 741
+ |||||||||||||||||||||!:!||||||||||||||||||||||||||||||||||||
+ MetLysLeuGlnValSerGlyPheLysSerTrpTyrHisAsnGluValLeuValValGly
+ 9546 : ATGAAGCTCCAGGTCTCGGGATTCAAGTCGTGGTACCACAACGAGGTGCTCGTCGTCGGT : 9487
+
+ 742 : ThrAlaProValAspLeuLysGluThrLeuGluGlnArgLysArgTrpAlaGlnGlyAla : 761
+ |||||||||||||||:!!||||||||||||||||||||||||||||||||||||||||||
+ ThrAlaProValAspIleLysGluThrLeuGluGlnArgLysArgTrpAlaGlnGlyAla
+ 9486 : ACCGCGCCCGTCGATATCAAGGAAACGCTCGAGCAGAGAAAGCGTTGGGCGCAGGGCGCC : 9427
+
+ 762 : ValGluIlePheSerLeuThrProTrpGlyTyrIleArgGlyLysLeuGlyTrpArgLys : 781
+ ||||||||||||||||||||||||||||||||||||||| !||||||||||||||||||
+ ValGluIlePheSerLeuThrProTrpGlyTyrIleArgLysLysLeuGlyTrpArgLys
+ 9426 : GTCGAAATCTTCTCGCTCACGCCGTGGGGCTACATCCGCAAGAAGCTCGGCTGGAGAAAG : 9367
+
+ 782 : MetLeuTyrAsnLeuAspSerCysIleTyrProPheLeuSerProThrAlaPhePheTyr : 801
+ |||||||||||||||||||||||||||||||||||||||||||||||||||.!!||||||
+ MetLeuTyrAsnLeuAspSerCysIleTyrProPheLeuSerProThrAlaIlePheTyr
+ 9366 : ATGCTCTACAACCTCGACTCGTGCATCTACCCGTTCCTCTCGCCGACTGCCATCTTCTAC : 9307
+
+ 802 : GlyAlaSerProLeuIleMetSerIleTrpThrValProIleValValLysAspProIle : 821
+ ||| !:!!||||||||||||!!!:!:|||||||||||||||||||||! :!!||||||
+ GlyLeuAlaProLeuIleMetCysLeuTrpThrValProIleValValThrAsnProIle
+ 9306 : GGTCTGGCGCCGCTGATCATGTGTCTGTGGACCGTGCCCATCGTCGTCACCAACCCCATC : 9247
+
+ 822 : IlePheIleLeuValGlyMetIleProValMetValLeuProArgValIleGlnTyrMet : 841
+ |||||||||||||||||||||||||||||||||:!!||||||||||||!!:|||||||||
+ IlePheIleLeuValGlyMetIleProValMetIleLeuProArgValMetGlnTyrMet
+ 9246 : ATCTTCATCCTCGTCGGTATGATCCCCGTCATGATCCTGCCGCGTGTCATGCAGTACATG : 9187
+
+ 842 : IleLeuArgAlaLysArgProTyrGluAlaGlyLysSerGlyProSerLeuTrpValGlu : 861
+ ||||||||||||! !||||||!:!||||||||||||||||||||||||||||||||||||
+ IleLeuArgAlaThrArgProPheGluAlaGlyLysSerGlyProSerLeuTrpValGlu
+ 9186 : ATCCTCCGCGCCACGCGTCCCTTCGAGGCCGGAAAGTCCGGCCCCTCGCTCTGGGTCGAA : 9127
+
+ 862 : AlaThrAspLeuTrpArgAlaGluGlnThrPhePheGlyPheAlaGlyThrTyrIleSer : 881
+ ||||||||||||||||||||||||||||||||||||!.!|||||||||||||||||||||
+ AlaThrAspLeuTrpArgAlaGluGlnThrPhePheAlaPheAlaGlyThrTyrIleSer
+ 9126 : GCCACCGATCTCTGGCGTGCCGAACAGACCTTCTTTGCGTTCGCCGGAACCTACATCTCT : 9067
+
+ 882 : SerTrpArgGluGlySerAlaSerIleValLysLeuLeuLysAlaArgLysIleSerArg : 901
+ :!!|||!:!! ||||||||||||:!!|||:::|||:!!|||||||||||||||||||||
+ AlaTrpLysAlaGlySerAlaSerValValArgLeuIleLysAlaArgLysIleSerArg
+ 9066 : GCGTGGAAGGCCGGCTCCGCGTCGGTCGTCCGTCTCATCAAGGCGCGCAAGATCTCGCGT : 9007
+
+ 902 : HisLysLeuAlaMetTrpAsnTrpLysArgAspPheValLysLysProValValCysGlu : 921
+ ||||||||||||||||||||||||||||||!!:|||!.!||||||||||||:!! !|||
+ HisLysLeuAlaMetTrpAsnTrpLysArgGluPheAlaLysLysProValIleValGlu
+ 9006 : CACAAACTCGCCATGTGGAACTGGAAGCGTGAGTTTGCCAAGAAGCCCGTCATCGTCGAG : 8947
+
+ 922 : ValPheArgGlnThrLysLeuValAsnGluAsnAspAsnAlaGlnGluSerSerGlyLys : 941
+ !!:!||||||:!!|||||||||:!!.!. !!!: .!!:!!||| !!.!||| !
+ ArgTyrArgGlnSerLysLeuValHisHisAlaGlu---ThrGluGluHisLysGlyPro
+ 8946 : CGCTACCGCCAGTCGAAGCTGGTGCACCACGCCGAG---ACCGAGGAGCACAAGGGCCCG : 8890
+
+ 942 : HisLysAlaGluGlnSerPheArgThrSerAsnLysGluSerAspThrIleLysAsnSer : 961
+ !.!|||||||||||||||||||||:!!|||||||||||||||||||||||||||||||||
+ ArgLysAlaGluGlnSerPheArgSerSerAsnLysGluSerAspThrIleLysAsnSer
+ 8889 : CGCAAGGCCGAGCAGTCGTTCCGTTCCTCCAACAAGGAGTCCGACACCATCAAGAACTCG : 8830
+
+ 962 : ArgLeuPheLeuProAsnIleIleLeuPheValValAsnIleLeuAlaMetMetSerAla : 981
+ ||||||||| !||||||:!!|||:!!|||! !!.!||||||||||||!!::!! !.!!
+ ArgLeuPheAlaProAsnLeuIleMetPheGlyAlaAsnIleLeuAlaIleLeuLeuThr
+ 8829 : CGTCTCTTTGCGCCGAATCTCATCATGTTTGGCGCCAACATCCTCGCCATCCTGCTGACC : 8770
+
+ 982 : ValLeuArgPheAsnCysPheGlnAsnAspMetTrpLeuLeuValValValAlaGlyPhe : 1001
+ :!!||| !||||||||||||! |||||||||||||||:!!:!!|||||||||||||||
+ LeuLeuSerPheAsnCysPheLeuAsnAspMetTrpLeuMetIleValValAlaGlyPhe
+ 8769 : CTGCTCTCGTTCAACTGCTTCCTCAACGACATGTGGCTGATGATTGTCGTCGCCGGTTTC : 8710
+
+ 1002 : SerPheSerThrLeuTrpHisLeuTrpSerPheIleProMetAlaLeuArgGlnSerGlu : 1021
+ :!!|||||||||! !|||||||||||||||||||||||||||||||||||||||||||||
+ AlaPheSerThrCysTrpHisLeuTrpSerPheIleProMetAlaLeuArgGlnSerGlu
+ 8709 : GCCTTCTCCACGTGCTGGCATCTCTGGTCGTTCATCCCTATGGCCCTCAGACAGTCCGAG : 8650
+
+ 1022 : LysGlnTrpProTyrAlaSerSerTyrHisAlaHisAsnIleValLeuPheLeuValLeu : 1041
+ ||||||||||||||||||||||||||||||||||||||||||:!!:!!||||||:!!|||
+ LysGlnTrpProTyrAlaSerSerTyrHisAlaHisAsnIleLeuIlePheLeuIleLeu
+ 8649 : AAGCAGTGGCCCTACGCCTCCTCGTACCACGCGCACAACATTCTCATCTTTCTCATTCTC : 8590
+
+ 1042 : GlyPheLeuValLeuLeuPheValAspValLysValCysIleProArgValGly : 1059
+ |||||||||||||||||||||..! ! ||| |||||||||||||||||||||
+ GlyPheLeuValLeuLeuPheThrLysValAlaValCysIleProArgValGly
+ 8589 : GGTTTCCTGGTGCTCCTGTTCACCAAGGTCGCTGTCTGTATTCCTCGTGTCGGA : 8534
+
+vulgar: DDB_G0269124 142 1059 . contig_1146 11269 8533 - 3652 M 40 120 G 4 0 M 94 282 G 0 3 M 296 888 G 1 0 M 356 1068 G 1 0 M 125 375
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:protein2genome:local 2.2.0
+##date 2015-01-16
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+contig_1146 exonerate:protein2genome:local gene 8534 11269 3652 - . gene_id 0 ; sequence DDB_G0269124 ; gene_orientation .
+contig_1146 exonerate:protein2genome:local cds 8534 11269 . - .
+contig_1146 exonerate:protein2genome:local exon 8534 11269 . - . insertions 3 ; deletions 6
+contig_1146 exonerate:protein2genome:local similarity 8534 11269 3652 - . alignment_id 0 ; Query DDB_G0269124 ; Align 11270 143 120 ; Align 11150 187 282 ; Align 10865 281 888 ; Align 9977 578 1068 ; Align 8909 935 375
+# --- END OF GFF DUMP ---
+#
+-- completed exonerate analysis
--- /dev/null
+##gff-version 2
+##source-version exonerate:protein2genome:local 2.2.0
+##date 2015-01-16
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+contig_1146 exonerate:protein2genome:local gene 8534 11269 3652 - . gene_id 0 ; sequence DDB_G0269124 ; gene_orientation .
+contig_1146 exonerate:protein2genome:local cds 8534 11269 . - .
+contig_1146 exonerate:protein2genome:local exon 8534 11269 . - . insertions 3 ; deletions 6
+contig_1146 exonerate:protein2genome:local similarity 8534 11269 3652 - . alignment_id 0 ; Query DDB_G0269124 ; Align 11270 143 120 ; Align 11150 187 282 ; Align 10865 281 888 ; Align 9977 578 1068 ; Align 8909 935 375
+# --- END OF GFF DUMP ---
--- /dev/null
+>DDB_G0280897
+MTDKINNLINQWLKWDKNEITRKEIEQLKENNNEKELLVRLEERIQFGTAGLRGAMRAGF
+SCMNDLTVTQASQGLCEYVIETIEQSKSKGIVIGYDGRHNSYIFAKITAATFKSKGFKVY
+LFSHIVPTPYVSFAVPNLKAAIGVMITASHNPKNDNGYKVYWETGCQINTPHDKGISKKI
+DENLEPWSNVDATSDIKYGNGDDGESMIDPLSVITELYNKNIKEYSVGSKIELANEPIVY
+TAMHGVGGVYAKKAFETFQLKPFIPVAQQIEPDAEFPTVTYPNPEEGKGALKLSIETAEA
+NNSRLILANDPDADRLAVAEKLADGSWKVFNGNEIGVLLADWAWTNRSTLTKGGSTLENN
+KYFMINTAVSSAMLKTMSEKEGFIHQECLTGFKWIGNAAYNAINNNDGTTFLFGYEEAIG
+FQYGDVSFDKDGVRAAAIFAEFALSLYKKGSSVQDHLESMYKRYGYHISKNRYFFCYEPS
+KMVSIFNKIRNDGKYLTKLGDDDDEQFTITRIRDLTTGYDNGYPDCKARLPVSSSTQMIT
+FYFKNGGIATLRGSGTEPKLKYYVEMIGEVKSNVESTLTKAVELVINQLLKPIENQLEPP
+KDD
+>PPL_06716
+MSNIKELAESWLKWDKNAETRKEIQSLLESDNQSELKSRLEQRIAFGTAGLRGPMKAGFS
+CMNDLTVIQASQGLCIYVEQTLSNSKNSGIVVGYDGRHHSKEFARLTAATFASRGFKVYL
+FSKIVPTPYVVILYLISNYMDCYVHQAFAVPELKASVGVMITASHNPKDDNGYKVYWDNG
+CQINTPHDIRIAMQIDLNLEPWNIDVNELLNGSLVSDPLDTITKSYFGKIAKYSVKNEVK
+LATSEKIVYTAMHGVGGEYAKMAFETFGLPAFIPVDQQIQPDPEFPTVAFPNPEEGKGAL
+KLSIETAERNNSRLILANDPDADRLAVAERQPDGQWKVFNGNEIGVLFADWAWQNARRAD
+STTPAERFCMINTAVSSSMLKTMANKDGYRHEECLTGFKWVGNKARELMDKGYNFLFAYE
+EAIGFMYGDVSLDKDGVRCAPIFAELALTCYQAGKSCQDHLEELYKRYGYHISKNRYFFC
+YDPKKMVAIFDKIRNYGQFPTNCGDFYITRVRDLTVGYDSGYPDHKARLPVSSSTQMITF
+YFENGGIATLRGSGTEPKLKYYVEMIGSDRQLVESTLSQLVEQVINQFLRPVENELTPPK
+DD
+>DFA_03821
+MTDINQLAQNWLKWDRNPKTHKEIEQLVEAKDENELRARLENRIAFGTAGIVSTTIVQSH
+MNIGPMKAGFANMNDLTVIQASQGLSIYVQETISQAQSKGVVVGYDGRYNSEVFAKLTAA
+TFASKGFKVYLFSKIVPTPFVAFAVPELGASVGVMVTASHNPKDDNGYKVYWDNGCQINT
+PHDKGIAKQIDLNLEPWTINIDKLLSSELVNDPLETISNAYFSKIYSYSVKNRSTPLELA
+NEKVVYTAMHGVGGDYVKKAFETFKLPPYVEVAQQIKPDPAFPTVAFPNPEEGKGALKLS
+IETAESVNSRLILANDPDADRLAVAEKLKDGSWKVFNGNEIGILLADWAWTNAKINHPDV
+PAEKFFMINTAVSSAMLKTMAKKEGYICEETLTGFKWVGNKAKEMIDQGYKFLFAYEEAI
+GFMYGDVSLDKDGVRCAPIFAEYALNLYANGSSCQDHLDHLMQRYGYHISKNRYFFCYEP
+SKMVRIFNDIRKSNNGQFPDKCGPYEIIRIRDLTVDYDTAYPDNKARLPVSTSTQMITFY
+FKNGAIATLRGSGTEPKLKYYVEMIGDNKQEVESTLQQVVQQVIDNFLQPVVNQLTPPKD
+D
+>DLA_10096
+MDIYTLANKWLEWDKNEKNRKEIQHFVDEKNEQELRERLENRIQFGTAGLRGPMKAGFAN
+MNDLTVIQASQGLALYVKETIDSALTKGVVVGYDGRHNSQTFARLTAATFLSKGFKVYLF
+SKLVPTPFVAFAVPELGASCGVMITASHNPKDDNGYKVYWDNGCQINTPHDKGISKLIDE
+NLVPWTMNLDDLNKSDLVSDPLERVSKSYFTKISKYSVVKSGATIKQEKVVYTPMHGVGG
+DYAAEAFKVFDLHPFIPVELQIKPDAEFPTVAFPNPEEGKGALKLAIETAESNQSRLILA
+NDPDADRLAVAEKQSSDGSWKVFNGNEIGVLFADWAWRKERALFSEGYNCKPSEYTMIST
+AVSSAMLSTMAKKEGFQHEEVLTGFKWVGNAAKQAMDRGQKFLFAYEEAIGFMYGDVSLD
+KDGVRGASIFAELAFDLYQQGSSCQEHLESLYKKYGYHISNNRYFFCYDPKKMVRIFNEI
+RGNNREYVKELGEFKVERIRDLTTGYDTAFPPEFKAQLPTSSSTQMITFYFTNGSIATLR
+GSGTEPKLKYYVESIGSDKLQVQQTLTKLVSLVIEKLLRPKENELTPPKESVGSERLLAL
+LSEVMSTSMKIQVKYNESITEYNIIKGVKLLTQIDVLCQIFKVDANPDRFVLNYRESNLI
+LSEDNLSKLFSNEISSCSSQSQNGSNGELSSLYSSFGENSSNNNNNSTLKFELILAPIYQ
+VDSVLEHLNNSNLIKKRII
+>DPU1265769
+MSMIRSISGVRGVIGQSWTPTLVSNHIIGFTQLLESEKYYNQKQKKIVVGRDSRVSGPWI
+EMIVNGSLISMGYQVIHIDIAATPTVQYMVEKTKSSGGIVITSSHNPVEWNGLKFVGPDG
+LFIAPVECEVLFSLADNPSSFKFPNYDKLGSVVCNTTANKEHIEAIFKLPFISVDKIKEK
+KFKVCLDSVNGAGGPIMSYLLTELGCEVIGINLEPTGLFAHTPEPVPANLGQLCELVKTH
+KADFGIAVDPDVDRCVFIDDKGVPLGEEYTLAMAVELLLGDCGRRGNVCKNLSSSRAIDD
+ICKKYDSQVICAPVGEIQVAKKMQQVNAVIGGEGNGGVMLPDIHIGRDAPVAATLALQLL
+ANRNAASISEFKRTTLPTYEIVKLKAGIEGLDPDAILAEYTKQYENKEGVVINQEDGLKI
+DSADWWVHLRKSNTEHIIRVISEAKNTKEATDIATKFINEIESKRK
+>440792448
+MASRVSGRMRKISDETQQMVNAWLSVDWDPESREHVKGLVAAGKEEELVAHLGRRISFGT
+AGLRGKMKWGFAFMNAVTVTQASQGLCAYLRTVHPCLTDLRERGVIVGHDGRYNSRMFAR
+LTAAVFLSRKIKVHLFRDDVPTPLVAFGVRHLKCAAGVMVTASHNPKEDNGYKVYWANSA
+QITAPHDAQIARAIEANFSIWDRMPDDKAIDEHPLCLDPTTDVCAAYLAAARHWSFRTPQ
+QNAAAQLRVVYTAMHGVGGQSVERIFDAFGLPPVIAVREQHDPDPDFTTVEFPNPEEANG
+CSLRLAMSTADREGAPLILANDPDADRLAVAERQRDSGEWRILDGNEIALLLADWLWRNY
+TERHPEVDRAKIVMLNSTVSSKALAAMAAKEGFHYRETLTGFKWLGNLADELVRAGYTFL
+FAYEVEIGFMIGDMSLDTDGVRAAPVFVEMANHLYERGLTLSDHLDNLYHKYGYYKMAVG
+YYFCHDPRLMDQIFNEIRNDGLYISTCGDHKVQYVRDLTTGFDNSQPHNRAVLPVSSAAH
+MITFTFENECVATFRGSGTEPKLKYYIEVANASNEQLATDLLDSMKQEIIDRFLQPSQNG
+LRPPAAAEDAHNSPHNSGNSPEQMAPARIARDVIHKEIQALQNLEATLGRDFEKVVEIIE
+SRGSGRVIFTGVGKSGIIAQKISASFSSLGISSFFVHATEAAHGDLGVITAEDVIIAISN
+SGNTPELIFIIPSLRVLAGKIIGITSNKDSLLARYSDASIITGKIMEADQHKIAPTASTI
+VCLAIGDALAVTLSARMKFTLPEFGLRHPGGVLGEKVLGKVFQEFAMKGQGRFLRFWKRM
+TNEERDKLRRDFERIDLAELSRIYLQCRSKAEKGAIDPHSLEPLPSHTWVKLHESDPAAV
+AAWRDAGLRALREGKIGVVLMAGGQATRLGMTMPKGFLDLNLPSHKSLYQLHAEKLLRLQ
+DEVRQTFGGGGGDEEVQQQQQQIQIPFYVMTSPEALQQTHQFFIKHQFFGLCPKQVFFFK
+QRSLPCVAPSGEIIMDTKCSVVFSPDGHGGLFVALKDAKAYEDMKRRGVEYVFAFGVDNP
+LCEVADPAYMGYCIQRNVKMGYKVVDRRDPQETAGVVCVRDGVINCVEYSELPESVAELR
+DEQSGELVYNAANMLNLFFTLRFMRKIADNPSLMEYHLAKKRIPFVNDNGVRTEPLVPNG
+WKFEKYLVDCTPYANNSVAVMFVKREEEFAPIKNGWNSEVDSPRSARRLLAAHYRRRIER
+AGGKLAADDPDKMVEVSPLVTDRKLAQLLQDKHLVTGPAVLQ
+>ENY64621.1
+MALNNYIKKTEMDYLYEQAALWLKWDKTPETRKEIEDLVASKNEEELKKRFCKRIEFGTA
+GLRGKMCAGFNCMNNLIVQQASQGLALAVEELVQNAHEKGVVIGYDGRYHSKEFAAITAK
+VFISKGFKTYLFSTLCPTPWTAFAVGYLKTACGVMVTASHNPKADNGYKVYWENGCQIIE
+PIDANIASKIHSNLEPWDLSNVDISKVIDPLADVSAEYYKQMMLTIPHFECPEQPKVKYV
+YTAMHGVGSKYVQDAFKTAKLPQPILVPLQNEPDPEFPTVPFPNPEEGKGALKCSIEVAE
+ANGATVIIANDPDADRLSVAVKSGNGWRQFTGNEMANLIADWTYNKYIVSGDKTPAFMVR
+STVSSSFISKMGEVEGFDTYETLTGFKWIGNKAKEIVDTQHKKLLMAYEEAIGFVIGNMS
+YDKDGVRAAVCFAAMALEYAEQGFNLEDRLNMLYEKYGYFASNNKYYFCYDPKLMEKIFN
+KMRNNGQYYWKFGKYAVKSIRDLTVGIDTAQPDKKPLLPVSASTQMITYTFENGCKATLR
+GSGTEPKLKYYIELPGKKGVKAEDVIAELMDLSHELLQASLEPEKNGLIPPKAE
+>Ppo014092.000
+MSISPSVQELVGKWLQWDKNPQNIKEIKDLVAANNEAELKNRLATRIAFGTAGLRGPMRA
+GFSCMNDLTVIQASQGLCKYLQQMVSDIKTRGIVVGYDGRHHSKEFAEWTAATFLSQGIT
+VYLFTRLVPTPFVSYATPLLRCAAGIMITASHNPKDDNGYKVYWDNGCQINVPHDKGISD
+CIEQNLTPWDINKAELLKSELVKDPTETVASAYLKEIKAKCCFHHDENSQKIPVTYTAMH
+GVGSEWVARAFEVFGLAPYVPVAPQISADPEFPTVAFPNPEEGKGALKLSMEAADKAGST
+LILATDPDADRLAVAEKLPSGSWKIFTGNEIGALLAYWAWLKYKERNPKVDPSKCVVINS
+TVSSKLLKALADKEGLKYDETLTGFKWIGGQAAIRIKEGYTFIFGFEEAIGFLFGDVNLD
+KDGVRAAAVFAEMNIQLHKQGITVVQQLEKIYKLYGYFITRNRYFFCYDPAKMERIFNAI
+RNYNNSGTYPTSCGPFKIKNTRDLTTGYDDSQTDKKAILPVSKSTQMITFFFENGGVVTL
+RGSGTEPKLKYYTELSGSDPEKVKSTLDEMVQAIIDTCLKPVENQLQPPSDE
+>ADB0001102_3
+MSTTTSINKLAQDWLKWDKNPKTRAEIQELVEQNDVKELTARLENRIAFGTAGLRGPMKA
+GFSCMNDLTVIQASQGLCLYVIDTIPNAIKSGVVIGYDGRYNSKEFAKYTAATFLSKGYK
+VYLFSKVVPTPYVAFAVTDLKASIGVMITASHNPKDDNGYKVYWENGCQINTPHDKGIAK
+LIDLNLEPWEINVDQLLSGPLVEDPLDRIVSSYNTKIAQYSVASHVKFANEKIIYTAMHG
+VGGEYTKMAFEAFKLPPFIPVAQQYQPDPAFPTVTFPNPEEGKGALKLSIETAEANGSRL
+ILANDPDADRLAVAERLKDGTWKVFNGNEIGVLLADWAWQNARRSHPDTPAEKFFMINTA
+VSSAMLKTMAKKDGYRCEETLTGFKWVGNRAREVMDAEGLHFLFAYEEAIGFLYGDVSLD
+KDGVRCAAIFAELALSYYANGSSCEDHLESLYKRYGYHISRNRYFFCYEPPKMVAIFNKI
+RNNRNFPTKCGRFEIERVRDLTIDYDDGFPDKKARLPVSTSTQMITFYFKNGAIATLRGS
+GTEPKLKYYVEMIGQDKAHVQQELAELVQCIINEFLRPVENELTPPKDD
+>Carpum
+MTQSTCITSMVINNYLSIYIFIYTINDYLKRSLFVLCLVAKMSHHKVAITHPISSYNSII
+NELAQNWLRWDKNKETRKEIEQLVEQKNEKELYDCLAKRIAFGTADNEIMMLLTHTLHTG
+LRGQMKAGFSNMNDLTVIQASQGLCKYVKETIPEAQKKGVVVGYDCRHHSETFARLTAAT
+FASQGFTVYLYSKMVPTPFVAFGVTDLKACVGVMVTASHNPKEDNGYKVYWENGCQINSP
+HDKGISQQIELNLEPWTIDVNSLLEKVDDPLERVTKSYMDQISKYSVRGSVDMATENVVY
+TAMHGVGGVFVKDAFAAFGLAPYIPVPAQVGPDAEFPTVTLPNPEEGKGALKLSIETAEA
+NNSRLIVANDPDADRLAAAEKLKDGSWKVFNGNEIGVLFADWAWQNARRQHGGDSINPSE
+YFMVTTAVSSSMLRTMATKEGYGYDETLTGFKWVGNKARDLIDQGKKFLFAYEESIGYMY
+GEVSLDKDGVRGAAVFTEMALSCYARGTSCQEHLESLYVKYGYHLSKNRYYFCYDPSKMV
+SIFNRIRNNGEFPKTCGPFEITRIRDLTVDYDNGYEDKKARLPVSSSTQMITFYFKNGAI
+ATLRGSGTEPKLKYYVEMIGDDKEQVKATLDQVHDQVIQQFLRPTENQLSPPSDE
+>Cephalum
+MTTDIYQIAQNWLRWDRNPKTHKEISQLVQDKNESELKARLESRIAFGTAGLRGPMKAGF
+SCMNDLTVIQASQGLCMYVKQTLAPDAERKGIVVGYDGRYNSEVFAKLTAATFVSQGFKV
+HLFSRLVPTPFVAFAVPFLKACVGVMITASHNPKDDNGYKVYWDNGCQINTPHDKGIAKQ
+IELNLEPWNVFYKEYFDRIERYTVRHNKQMAREKIVYSAMHGVGGEYTKRAFEVFALDPF
+IAVKEQFHPDPAFPTVTFPNPEEGKGALKLSIETAEANNNWAWKNGKPYYEKGLGSFPND
+QYFMINTAVSSAMLKTMAMKEGFTYEEVLTGFKWVGNAAQNLIEKGKHLLFAYEEAIGFM
+YGDVSLDKDGVRCAPIFAELAQHLYSKGSSCQDHLEELYKRYGYHISKNRYFFCYDPLKM
+EKIFNRIRNGGQYPTKCGDFEITRIRDLTTGYDTGYPPENKAQLPTSTSTQMITFYFKNG
+GIATLRGSGTEPKLKYYVEMIGDDKENVELILQSMVDQVINQFLRPIENELIPPKD
+>Violaceum
+MVINPFYPYYLYFCYSPGISYQGVKINKTKLEQSTLTTINQWLNGNYDEQTKKNIQNLLD
+QESYTELTDAFYRNLEFGTGGLRGIMGAGSNRINKYTIGTATQGLSNYLLKKYPGEKIKV
+AIAHDSRNNSDQFAKITADVFSANGIYVYFFKELRPTPELSFAIRELGCRSGVMLTASHN
+PKEYNGYKAYGADGGQFTAPDDRLVMDEVAKITSIDEVKFTRIDANIELIGEEIDQLYLD
+KITALSVSPEAISRQKDLKIVYSPIHGTGITLVPKALAQFGFDNVTIVEEQSKPDGNFPT
+VVYPNPEEKEAMTLALKKAQEIDADLVLATDPDADRVGIAVKNNNNEWILLNGNQTGSLL
+VHYVLTAWEEKGKIDGNQYIVKTVVTSNLIEAIAKAKKVDCYNTLTGFKWIGQLITSLQG
+KKTFVVGGEESYGYSVGELVRDKDAVISCAFIAEMTAYYKDKGSSLYNALIDMYVTHGLY
+KEELVSLTKKGKTGAEEIKAMMEKFRNNPPASLGGSKVSTLKDYELGTETDLNTGKISKL
+SLPKSDVLQFVTEDGSIVSARPSGTEPKIKFYCSVNATLSQASEFDKTDEKLGLKINALM
+EDLQK
+>Deminut
+MTDIYQIAQNWLKWDRNPKTHKEISTLVEKKDEAELRARLETRIAFGTAGLRGPMKAGFS
+CMNDLTVIQASQGLSLYVKKTLAGSESKGAVVGYDGRYNSEVFAKLTAATFASQGFKVYL
+FSKVVPTPYVAFAVPELGASVGVMVTASHNPKDDNGYKVYWDNGCQINTPHDKHISELIE
+SNLEPWNVCIYITLQINIDKLLSGVIDPLQVVTSSYMSKIEKYSVKHLPQPLKLATEQKI
+VYTAMHGVGAEYAKLAFEAFSLPPFIPVTQQVTPDPAFPTVAFPNPEEGKGALKLAIETA
+EANKSRIILANDPDADRLAVAEKQPEYVFLFYLISNNGTWKVFNGNEIGILFADWAWQNC
+RRVYPDVPADQFFMINTAVSSAMLKSMAKKDGYIHEETLTGFKWVGNKARELLDQNKRFL
+FAYEEAIGFMYGDVSLDKDGVRCAAIFAELALYQYANGSSCQRHLDSLYERYGYHISKNR
+YFFCYEPPKMVAIFNAIRNNKNYPTKCGEFEIERIRDLTDDYDNGYPDNKARLPISKSTQ
+MITFFFKNGAIATLRGSGTEPKLKYYVEMIGDNKSEVEAILAKVVTAVIDNFLRPVENQL
+TPPKDD
+>Ellipt
+MADLDKLVEDWMRWDKNTKTRDEVQKMVAQGDKKALAAALQNRIAFGTAGLRGPMKAGFA
+NMNDLTVIQASQGLCIYVSATIADAAKKGVVVGYDGRHNSLQFARLTAATFRSKGFKVYL
+FSTVVPTPYVAFSVPELGACVGVMVTASHNPKDDNGYKIDVEKLLKEDGVEDPLEKITAS
+YMSKVADYSIKSHPATKDIVMSDDKIVYTAMHGVGGEYTRRSFKAFSLPEFIPVVQQFHP
+DPEFPTVTFPNPEEGKGALKLAIETAEKNNSRLILANDPDADRLAVAERQPDGTWKVFNG
+NEIGVLFADWAWKNARARDPTTPASEFFMVNTAVSSAMLKTMAKTEGYTYEETLTGFKWV
+GNKAKEAIDKGGRFLFAYEEAIGFMYGDVSLDKDGVRTAPIFAQMALSLYAKGLSCVDHL
+EQLMKTYGYHISRNRYFFCYEPPKMVAIFDKIRNNGNFPKHCGPFEIVRVRDLTVDYDDA
+YEDKKARLPVSTSTQMITFYFKNGAIATLRGSGTEPKLKYYVEMIGDKSAKKEDVEKTLA
+EVVKQVIDNFLRPVENELTPPKDD
+>Lepto
+MASSERLQQLIQDWLKWDKNPTTLSEIQELVKKNDEKELRARLENRIAFGTAGMFLLGPM
+KAGFSCMNDLTVIQASQGLCIYVSDTIPNALNSGVVVGYDGRYNSKEFAKYTAATFLSKG
+YKVYLFSKVVPTPYVAFAVTELKAAIGVMITASHNPKDDNGYKVYWDNGCQINTPHDKGI
+AKQIQLNLEPWNVCAFFLDINANELLSGSSVVDPLDTIVNSYNSKITSYSVGNSGVKLAN
+EKIVYTAMHGVGGEYTKLAFEAFKLPPFVPVPQQYTPDPAFPTVAFPNPEEGKGALKLSI
+ETAEANGSRLILANDPDADRLAVAERNTNGTWKVFNGNEIGVLLADWAWQNARRAHPDTP
+ANRYFMINTAVSSAMLKTMAKHEGYRCDETLTGFKWVGNQARKVIDEEKLNFLFAYEEAI
+GFMYGDVSLDKDGVRCAPIFAEMALSYYAQGHSCEDHLETLYKRYGYHISRNRYFFCYEP
+PKMVAIFDRIRNGRNFPTKCGRFEIERVRDLTVDYDDAYPDKKARLPVSTSTQMITFWFK
+NGGIATLRGSGTEPKLKYYVEMIGQDKQVVEKELAELVDAVIQQFLRPVENELTPPKDD
--- /dev/null
+<?xml version="1.0"?>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+-->
+<!DOCTYPE rnaml SYSTEM "rnaml.dtd">
+
+<rnaml version="1.0">
+
+ <molecule id="1">
+ <sequence>
+ <numbering-system id="1" used-in-file="false">
+ <numbering-range>
+ <start>1</start>
+ <end>249</end>
+ </numbering-range>
+ </numbering-system>
+ <seq-data>
+ gaggaaaguc cggacUUCGC AGAAAAAGGU GCCAGUGAAA AACUGGGGGC CGUAAGGCUA
+ CGGAAAGUGU AACAGAAAAC AAACCGCUAA UUCUACCUAG GUAAGAUUAG ACAGGAUGAA
+ AAUGUCGAGC UUAUGGCUCG ACCUCUUUGU GGAAACACAA GGACGCUGCA AACCCCACCU
+ GAAGCAAGAA AGAGUUCGUU UCAGUUUUUC GCUCAGGAAC UCUUAGAGUC GCUCGAGGAU
+ UUUGGUGAC
+ </seq-data>
+ </sequence>
+ <structure>
+ <model id="?">
+ <str-annotation>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>15</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>184</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>16</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>183</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>17</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>182</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>18</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
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+ <base-id><position>178</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>18</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>177</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>22</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>212</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>23</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>211</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>24</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>210</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>25</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>209</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>27</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>176</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>28</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>175</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>29</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>174</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>30</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>173</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>31</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>172</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>32</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>46</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>33</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>45</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>34</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>44</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>35</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>43</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>36</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>42</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>47</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>61</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>48</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>59</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>49</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>58</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>50</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>57</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>51</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>56</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>62</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>171</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>63</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>170</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>67</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>169</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>68</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>168</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>69</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>165</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>70</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>164</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>71</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>163</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>83</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>110</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>84</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>109</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>85</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>106</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>86</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>105</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>87</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>104</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>91</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>102</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>92</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>101</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>93</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>100</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>94</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>99</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>118</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>136</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>119</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>135</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>120</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>134</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>121</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>133</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>122</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>132</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>123</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>131</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>137</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>160</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>138</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>158</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>139</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>157</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>140</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>156</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>141</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>155</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>142</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>154</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>143</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>152</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>144</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>151</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>145</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>150</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>184</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>232</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>185</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>231</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>186</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>230</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>187</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>229</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>194</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>223</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>195</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>222</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>196</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>221</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>197</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>220</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>198</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>219</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>199</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>218</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>203</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>217</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>204</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>216</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>205</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>215</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>206</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>214</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>207</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>213</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>239</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>258</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>240</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>257</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>241</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>256</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>242</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>255</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>243</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>254</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>244</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>253</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>245</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>252</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>246</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>251</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ </str-annotation>
+ </model>
+ </structure>
+ </molecule>
+</rnaml>
--- /dev/null
+##gff-version 2
+##source-version exonerate:protein2genome:local 2.2.0
+##date 2015-01-16
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+seq1 exonerate:protein2genome:local gene 8 11 3652 - . gene_id 0 ; sequence seq2 ; gene_orientation .
+seq1 exonerate:protein2genome:local cds 9 11 . - .
+seq1 exonerate:protein2genome:local exon 9 11 . - . insertions 3 ; deletions 6
+seq1 exonerate:protein2genome:local similarity 8 11 3652 - . alignment_id 0 ; Query seq2 ; Align 11 1 3
+##FASTA
+>seq1
+ACTACGACACGACGACGACGACG
+>seq2
+CDEQEATGTQDAQEQAQC
+
+
*/
package MCview;
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.AlignSeq;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.io.FileParse;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
public class PDBfile extends jalview.io.AlignFile
{
private static String CALC_ID_PREFIX = "JalviewPDB";
"getSeqsAsArray", new Class[]
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]
- { Alignment.class }).invoke(jmf, al);
+ { AlignmentI.class }).invoke(jmf, al);
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
import java.util.Vector;
/**
*/
public class SequenceIdMatcher
{
- private Hashtable names;
+ private HashMap<SeqIdName, SequenceI> names;
- public SequenceIdMatcher(SequenceI[] seqs)
+ public SequenceIdMatcher(List<SequenceI> seqs)
{
- names = new Hashtable();
- for (int i = 0; i < seqs.length; i++)
+ names = new HashMap<SeqIdName, SequenceI>();
+ addAll(seqs);
+ }
+
+ /**
+ * add more sequences to this matcher - also used by the constructor
+ *
+ * @param seqs
+ */
+ public void addAll(List<SequenceI> seqs)
+ {
+ for (SequenceI seq : seqs)
{
// TODO: deal with ID collisions - SequenceI should be appended to list
// associated with this key.
- names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
- SequenceI dbseq = seqs[i];
+ names.put(new SeqIdName(seq.getDisplayId(true)), seq);
+ SequenceI dbseq = seq;
while (dbseq.getDatasetSequence()!=null)
{
dbseq = dbseq.getDatasetSequence();
for (int r = 0; r < dbr.length; r++)
{
sid = new SeqIdName(dbr[r].getAccessionId());
- if (!names.contains(sid))
+ if (!names.containsKey(sid))
{
- names.put(sid, seqs[i]);
+ names.put(sid, seq);
}
}
}
}
/**
+ * convenience method to make a matcher from concrete array
+ *
+ * @param sequences
+ */
+ public SequenceIdMatcher(SequenceI[] sequences)
+ {
+ this(Arrays.asList(sequences));
+ }
+
+ /**
* returns the closest SequenceI in matches to SeqIdName and returns all the
* matches to the names hash.
*
* @param candName
* SeqIdName
* @param matches
- * Vector of SequenceI objects
+ * List of SequenceI objects
* @return SequenceI closest SequenceI to SeqIdName
*/
- private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
+ private SequenceI pickbestMatch(SeqIdName candName,
+ List<SequenceI> matches)
{
- SequenceI[] st = pickbestMatches(candName, matches);
- return st == null || st.length == 0 ? null : st[0];
+ List<SequenceI> st = pickbestMatches(candName, matches);
+ return st == null || st.size() == 0 ? null : st.get(0);
}
/**
* @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[]
* ties }
*/
- private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
+ private List<SequenceI> pickbestMatches(SeqIdName candName,
+ List<SequenceI> matches)
{
- ArrayList best = new ArrayList();
- SequenceI match = null;
+ ArrayList<SequenceI> best = new ArrayList<SequenceI>();
if (candName == null || matches == null || matches.size() == 0)
{
return null;
}
- match = (SequenceI) matches.elementAt(0);
- matches.removeElementAt(0);
+ SequenceI match = matches.remove(0);
best.add(match);
names.put(new SeqIdName(match.getName()), match);
int matchlen = match.getName().length();
while (matches.size() > 0)
{
// look through for a better one.
- SequenceI cand = (SequenceI) matches.elementAt(0);
- matches.remove(0);
+ SequenceI cand = matches.remove(0);
names.put(new SeqIdName(cand.getName()), cand);
int q, w, candlen = cand.getName().length();
// keep the one with an id 'closer' to the given seqnam string
return null;
}
;
- return (SequenceI[]) best.toArray(new SequenceI[0]);
+ return best;
}
/**
*
* @param seqnam
* string to query Matcher with.
+ * @return a new array or (possibly) null
*/
public SequenceI[] findAllIdMatches(String seqnam)
{
SeqIdName nam = new SeqIdName(seqnam);
- return findAllIdMatches(nam);
+ List<SequenceI> m = findAllIdMatches(nam);
+ if (m!=null)
+ {
+ return m.toArray(new SequenceI[m.size()]);
+ }
+ return null;
}
/**
* SeqIdName
* @return SequenceI[]
*/
- private SequenceI[] findAllIdMatches(
+ private List<SequenceI> findAllIdMatches(
jalview.analysis.SequenceIdMatcher.SeqIdName nam)
{
- Vector matches = new Vector();
+ ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
while (names.containsKey(nam))
{
- matches.addElement(names.remove(nam));
+ matches.add(names.remove(nam));
}
- SequenceI[] r = pickbestMatches(nam, matches);
+ List<SequenceI> r = pickbestMatches(nam, matches);
return r;
}
--- /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.api;
+
+/**
+ * Abstract interface implemented by Alignment Export dialog to retrieve user
+ * configurations
+ *
+ * @author tcnofoegbu
+ *
+ */
+public interface AlignExportSettingI
+{
+ /**
+ * Checks if hidden sequences should be exported
+ *
+ * @return
+ */
+ public boolean isExportHiddenSequences();
+
+ /**
+ * Checks if hidden columns shoulb be exported
+ *
+ * @return
+ */
+ public boolean isExportHiddenColumns();
+
+ /**
+ * Checks if Annotations should be exported, note this is available for
+ * complex flat file exports like JSON, HTML, GFF
+ *
+ * @return
+ */
+ public boolean isExportAnnotations();
+
+ /**
+ * Checks if SequenceFeatures should be exported, note this is available for
+ * complex flat file exports like JSON, HTML, GFF
+ *
+ * @return
+ */
+ public boolean isExportFeatures();
+
+ /**
+ * Checks if SequenceGroups should be exported, note this is available for
+ * complex flat file exports like JSON, HTML, GFF
+ *
+ * @return
+ */
+ public boolean isExportGroups();
+
+}
package jalview.api;
import jalview.commands.CommandI;
+import jalview.schemes.ColourSchemeI;
/**
* Interface implemented by gui implementations managing a Jalview Alignment
void addHistoryItem(CommandI command);
+ void setShowSeqFeatures(boolean show);
+
+ void setMenusForViewport();
+
+ void changeColour(ColourSchemeI cs);
+
+ /**
+ * trigger an update of the UI in response to a model data change, and if
+ * necessary enable the display of sequence feature annotation on the view.
+ *
+ * @param enableIfNecessary
+ */
+ void refreshFeatureUI(boolean enableIfNecessary);
+
+ /**
+ * get the Feature Settings control panel for the alignment view if one exists
+ *
+ * @return
+ */
+ FeatureSettingsControllerI getFeatureSettingsUI();
}
*/
void sortAlignmentByFeatureDensity(String[] typ);
+ /**
+ * add a features file of some kind to the current view
+ *
+ * @param file
+ * @param protocol
+ * @param relaxedIdMatching
+ * if true, try harder to match up IDs with local sequence data
+ * @return true if parsing resulted in something being imported to the view or
+ * dataset
+ */
+ public boolean parseFeaturesFile(String file, String protocol,
+ boolean relaxedIdMatching);
+
}
*/
package jalview.api;
-import java.awt.Color;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
/**
* @author jimp
*
* Set whether view should scroll to show the highlighted region of a sequence
*/
void setFollowHighlight(boolean b);
-
- public FeatureRenderer getFeatureRenderer();
-
- public void setFeatureRenderer(FeatureRenderer featureRenderer);
-
- public boolean isIncludeHiddenRegion();
-
}
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
public interface FeatureRenderer
{
+ /**
+ * compute the perceived colour for a given column position in sequenceI,
+ * taking transparency and feature visibility into account.
+ *
+ * @param col
+ * - background colour (due to alignment/group shading schemes, etc).
+ * @param sequenceI
+ * - sequence providing features
+ * @param r
+ * - column position
+ * @return
+ */
Color findFeatureColour(Color col, SequenceI sequenceI, int r);
+ /**
+ * trigger the feature discovery process for a newly created feature renderer.
+ */
void featuresAdded();
+ /**
+ *
+ * @param ft
+ * @return display style for a feature
+ */
Object getFeatureStyle(String ft);
+ /**
+ * update the feature style for a particular feature
+ *
+ * @param ft
+ * @param ggc
+ * - currently allows java.awt.Color and
+ * jalview.schemes.GraduatedColor
+ */
void setColour(String ft, Object ggc);
AlignViewportI getViewport();
+ /**
+ *
+ * @return container managing list of feature types and their visibility
+ */
FeaturesDisplayedI getFeaturesDisplayed();
+ /**
+ * get display style for all features types - visible or invisible
+ *
+ * @return
+ */
Map<String,Object> getFeatureColours();
+ /**
+ * query the alignment view to find all features
+ *
+ * @param newMadeVisible
+ * - when true, automatically make newly discovered types visible
+ */
void findAllFeatures(boolean newMadeVisible);
+ /**
+ * get display style for all features types currently visible
+ *
+ * @return
+ */
Map<String,Object> getDisplayedFeatureCols();
+ /**
+ * get all registered groups
+ *
+ * @return
+ */
List<String> getFeatureGroups();
+ /**
+ * get groups that are visible/invisible
+ *
+ * @param visible
+ * @return
+ */
List<String> getGroups(boolean visible);
+ /**
+ * change visibility for a range of groups
+ *
+ * @param toset
+ * @param visible
+ */
void setGroupVisibility(List<String> toset, boolean visible);
+ /**
+ * change visibiilty of given group
+ *
+ * @param group
+ * @param visible
+ */
void setGroupVisibility(String group, boolean visible);
+ /**
+ * locate features at a particular position on the given sequence
+ *
+ * @param sequence
+ * @param res
+ * @return
+ */
List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
+ /**
+ *
+ * @return true if the rendering platform supports transparency
+ */
boolean isTransparencyAvailable();
+ /**
+ * get current displayed types
+ *
+ * @return
+ */
+
String[] getDisplayedFeatureTypes();
+ /**
+ * get current displayed groups
+ *
+ * @return
+ */
String[] getDisplayedFeatureGroups();
+ /**
+ * display all features of these types
+ *
+ * @param featureTypes
+ */
void setAllVisible(List<String> featureTypes);
+ /**
+ * display featureType
+ *
+ * @param featureType
+ */
void setVisible(String featureType);
}
public interface FeatureSettingsControllerI
{
+
+ void discoverAllFeatureData();
}
*/
package jalview.appletgui;
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
{
// TODO consider using getSequenceSelection instead here
cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
- e.getActionCommand(), ap.av.getShowJVSuffix(), ap.av, true));
+ e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
}
{
if (seq.getPDBId() != null)
{
- PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
+ PDBEntry entry = seq.getPDBId().firstElement();
if (ap.av.applet.jmolAvailable)
{
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
if (hiddenSeqs != null && hiddenSeqs.length > 0)
{
viewport.hideSequence(hiddenSeqs);
- viewport.setHasHiddenRows(true);
}
if (columnSelection != null)
{
{ e.getActionCommand() }), 600, 500);
FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
- viewport.setFeatureRenderer(fr);
- viewport.setIncludeHiddenRegion(false);
- cap.setText(new AppletFormatAdapter(viewport).formatSequences(
+ cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
e.getActionCommand(), viewport.getAlignment(),
viewport.getShowJVSuffix()));
}
public SequenceStructureBinding addStructureViewInstance(
Object jmolviewer, String[] sequenceIds)
{
- // TODO method never called - remove?
Viewer viewer = null;
try
{
{
this.splitFrame = sf;
}
+
+ // may not need this
+ @Override
+ public void setShowSeqFeatures(boolean b)
+ {
+ // showSeqFeatures.setSelected(b);
+ viewport.setShowSequenceFeatures(b);
+
+ }
+
+ @Override
+ public void setMenusForViewport()
+ {
+ // setMenusFromViewport(viewport);
+
+ }
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ if (enableIfNecessary)
+ {
+ sequenceFeatures.setState(true);
+ alignPanel.av.setShowSequenceFeatures(true);
+ }
+ }
+
+ @Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return alignPanel.av.featureSettings;
+ }
+
}
*/
package jalview.appletgui;
-import java.awt.Font;
-
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
import jalview.structure.VamsasSource;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.Font;
+
public class AlignViewport extends AlignmentViewport implements
SelectionSource, VamsasSource, CommandListener
{
private AnnotationColumnChooser annotationColumnSelectionState;
- private FeatureRenderer featureRenderer;
-
- private boolean includeHiddenRegion = true;
-
public void finalize()
{
applet = null;
}
}
- @Override
- public FeatureRenderer getFeatureRenderer()
- {
- return featureRenderer;
- }
-
- @Override
- public void setFeatureRenderer(FeatureRenderer featureRenderer)
- {
- this.featureRenderer = featureRenderer;
-
- }
-
- public boolean isIncludeHiddenRegion()
- {
- return includeHiddenRegion;
- }
-
- public void setIncludeHiddenRegion(boolean includeHiddenRegion)
- {
- this.includeHiddenRegion = includeHiddenRegion;
- }
}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.ColumnSelection;
-import jalview.gui.JvSwingUtils;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
slider.setPreferredSize(new Dimension(100, 32));
thresholdPanel.setBackground(Color.white);
- thresholdPanel.setFont(JvSwingUtils.getLabelFont());
+ // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
// thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
actionPanel.setBackground(Color.white);
- actionPanel.setFont(JvSwingUtils.getLabelFont());
+ // actionPanel.setFont(JvSwingUtils.getLabelFont());
graphFilterView.setLayout(gBorderLayout);
graphFilterView.setBackground(Color.white);
noGraphFilterView.setBackground(Color.white);
annotationComboBoxPanel.setBackground(Color.white);
- annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
+ // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
gSearchPanel = new SearchPanel(this);
ngSearchPanel = new SearchPanel(this);
this.setBackground(Color.white);
this.setTitle("Structure Filter");
- this.setFont(JvSwingUtils.getLabelFont());
+ // this.setFont(JvSwingUtils.getLabelFont());
this.add(all);
this.add(alphaHelix);
description.setEnabled(false);
description.addItemListener(this);
this.setTitle("Search Filter");
- this.setFont(JvSwingUtils.getLabelFont());
+ // this.setFont(JvSwingUtils.getLabelFont());
syncState();
this.add(searchBox);
*/
package jalview.appletgui;
-import java.awt.BorderLayout;
-import java.awt.Button;
-import java.awt.Dialog;
-import java.awt.Font;
-import java.awt.Frame;
-import java.awt.Label;
-import java.awt.Panel;
-import java.awt.TextArea;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-
import jalview.analysis.AlignmentUtils;
import jalview.api.ComplexAlignFile;
import jalview.bin.JalviewLite;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Dialog;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.TextArea;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
public class CutAndPasteTransfer extends Panel implements ActionListener,
MouseListener
{
protected void loadAlignment(String text, boolean newWindow,
AlignViewport viewport)
{
- Alignment al = null;
+ AlignmentI al = null;
String format = new IdentifyFile().Identify(text,
AppletFormatAdapter.PASTE);
- AppletFormatAdapter afa = new AppletFormatAdapter(viewport);
+ AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
try
{
al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
* @param al
* @return
*/
- protected boolean openSplitFrame(Alignment al, String format)
+ protected boolean openSplitFrame(AlignmentI al, String format)
{
final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
if (thisAlignment.isNucleotide() == al.isNucleotide())
*/
package jalview.appletgui;
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.AlignmentSorter;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Image;
+import java.awt.Label;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.ScrollPane;
+import java.awt.Scrollbar;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener
+ AdjustmentListener, FeatureSettingsControllerI
{
FeatureRenderer fr;
fr.findAllFeatures(true); // was default - now true to make all visible
}
- setTableData();
+ discoverAllFeatureData();
this.setLayout(new BorderLayout());
scrollPane = new ScrollPane();
men.show(this.featurePanel, x, y);
}
- public void setTableData()
+ @Override
+ public void discoverAllFeatureData()
{
if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
{
}
// TODO: JAL-964 - smoothly incorporate new group entries if panel already
// displayed and new groups present
- for (String group:(List<String>)fr.getFeatureGroups())
+ for (String group:fr.getFeatureGroups())
{
boolean vis = fr.checkGroupVisibility(group, false);
Checkbox check = new MyCheckbox(group, vis,
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
ap.seqPanel.seqCanvas.repaint();
}
PaintRefresher.Register(this, av.getSequenceSetId());
}
- public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
+ public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
+ int i, int starty,
int ypos)
{
int charHeight = av.getCharHeight();
((i - starty) * charHeight) + ypos + charHeight
- (charHeight / 5));
- if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+ if (hiddenRows)
{
drawMarker(i, starty, ypos);
}
Color currentColor = Color.white;
Color currentTextColor = Color.black;
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows()
+ && av.getShowHiddenMarkers();
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
int cHeight = alheight * avcharHeight + hgap + annotationHeight;
int rowSize = av.getEndRes() - av.getStartRes();
-
// Draw the rest of the panels
for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
&& (row < maxwidth); ypos += cHeight, row += rowSize)
SequenceI s = av.getAlignment().getSequenceAt(i);
gg.setFont(italic);
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+ if (doHiddenCheck)
{
setHiddenFont(s);
}
- drawIdString(gg, s, i, 0, ypos);
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
}
if (labels != null)
}
gg.setFont(italic);
// boolean isrep=false;
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+ if (doHiddenCheck)
{
// isrep =
setHiddenFont(seq);
(((i - starty) * avcharHeight) + avcharHeight)
- (avcharHeight / 5));
- if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+ if (hiddenRows)
{
drawMarker(i, starty, 0);
}
import jalview.datamodel.AlignmentI;
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
public class OverviewPanel extends Panel implements Runnable,
MouseMotionListener, MouseListener
Color color = Color.yellow;
int row, col, sameRow = 0, sameCol = 0;
jalview.datamodel.SequenceI seq;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
boolean hiddenRow = false;
AlignmentI alignment = av.getAlignment();
for (row = 0; row <= sequencesHeight; row++)
}
hiddenRow = false;
- if (av.hasHiddenRows())
+ if (hasHiddenRows)
{
seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
if (seq == null)
}
if (hiddenRow
- || (av.hasHiddenColumns() && !av.getColumnSelection()
+ || (hasHiddenCols && !av.getColumnSelection()
.isVisible(lastcol)))
{
color = color.darker().darker();
*/
package jalview.bin;
-import java.applet.Applet;
-import java.awt.Button;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.EventQueue;
-import java.awt.Font;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.event.ActionEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.URL;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import netscape.javascript.JSException;
-import netscape.javascript.JSObject;
-
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.AlignViewport;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import java.applet.Applet;
+import java.awt.Button;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.EventQueue;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import netscape.javascript.JSException;
+import netscape.javascript.JSObject;
+
/**
* Jalview Applet. Runs in Java 1.18 runtime
*
*/
public AlignFrame loadAlignment(String text, String title)
{
- Alignment al = null;
+ AlignmentI al = null;
String format = new IdentifyFile().Identify(text,
AppletFormatAdapter.PASTE);
*/
package jalview.bin;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
{
System.out.println("User specified Format is " + format);
}
- Alignment al = null;
+ AlignmentI al = null;
try
{
al = new AppletFormatAdapter().readFile(file, protocol, format);
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Alignment implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _annotation.
- */
- private jalview.binding.Annotation _annotation;
-
- /**
- * Field _sequenceSet.
- */
- private jalview.binding.SequenceSet _sequenceSet;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Alignment()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Returns the value of field 'annotation'.
- *
- * @return the value of field 'Annotation'.
- */
- public jalview.binding.Annotation getAnnotation()
- {
- return this._annotation;
- }
-
- /**
- * Returns the value of field 'sequenceSet'.
- *
- * @return the value of field 'SequenceSet'.
- */
- public jalview.binding.SequenceSet getSequenceSet()
- {
- return this._sequenceSet;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+public class Alignment implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _annotation.
+ */
+ private jalview.binding.Annotation _annotation;
+
+ /**
+ * Field _sequenceSet.
+ */
+ private jalview.binding.SequenceSet _sequenceSet;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Alignment() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'annotation'.
+ *
+ * @return the value of field 'Annotation'.
+ */
+ public jalview.binding.Annotation getAnnotation(
+ ) {
+ return this._annotation;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSet'.
+ *
+ * @return the value of field 'SequenceSet'.
+ */
+ public jalview.binding.SequenceSet getSequenceSet(
+ ) {
+ return this._sequenceSet;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'annotation'.
+ *
+ * @param annotation the value of field 'annotation'.
+ */
+ public void setAnnotation(
+ final jalview.binding.Annotation annotation) {
+ this._annotation = annotation;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSet'.
+ *
+ * @param sequenceSet the value of field 'sequenceSet'.
+ */
+ public void setSequenceSet(
+ final jalview.binding.SequenceSet sequenceSet) {
+ this._sequenceSet = sequenceSet;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Alignment
+ */
+ public static jalview.binding.Alignment unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'annotation'.
- *
- * @param annotation
- * the value of field 'annotation'.
- */
- public void setAnnotation(final jalview.binding.Annotation annotation)
- {
- this._annotation = annotation;
- }
-
- /**
- * Sets the value of field 'sequenceSet'.
- *
- * @param sequenceSet
- * the value of field 'sequenceSet'.
- */
- public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet)
- {
- this._sequenceSet = sequenceSet;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Alignment
- */
- public static jalview.binding.Alignment unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Alignment) Unmarshaller.unmarshal(
- jalview.binding.Alignment.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class Annotation implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _graph.
- */
- private boolean _graph;
-
- /**
- * keeps track of state for field: _graph
- */
- private boolean _has_graph;
-
- /**
- * Field _graphType.
- */
- private int _graphType;
-
- /**
- * keeps track of state for field: _graphType
- */
- private boolean _has_graphType;
-
- /**
- * Field _annotationElementList.
- */
- private java.util.Vector _annotationElementList;
-
- /**
- * Field _label.
- */
- private java.lang.String _label;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Annotation()
- {
- super();
- this._annotationElementList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vAnnotationElement
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAnnotationElement(
- final jalview.binding.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- this._annotationElementList.addElement(vAnnotationElement);
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotationElement
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAnnotationElement(final int index,
- final jalview.binding.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- this._annotationElementList.add(index, vAnnotationElement);
- }
-
- /**
- */
- public void deleteGraph()
- {
- this._has_graph = false;
- }
-
- /**
- */
- public void deleteGraphType()
- {
- this._has_graphType = false;
- }
-
- /**
- * Method enumerateAnnotationElement.
- *
- * @return an Enumeration over all jalview.binding.AnnotationElement elements
- */
- public java.util.Enumeration enumerateAnnotationElement()
- {
- return this._annotationElementList.elements();
- }
-
- /**
- * Method getAnnotationElement.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.AnnotationElement at the given
- * index
- */
- public jalview.binding.AnnotationElement getAnnotationElement(
- final int index) throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._annotationElementList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getAnnotationElement",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._annotationElementList.size() - 1)).toString()
- }));
+public class Annotation implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _graph.
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _graphType.
+ */
+ private int _graphType;
+
+ /**
+ * keeps track of state for field: _graphType
+ */
+ private boolean _has_graphType;
+
+ /**
+ * Field _annotationElementList.
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Annotation() {
+ super();
+ this._annotationElementList = new java.util.Vector();
}
- return (jalview.binding.AnnotationElement) _annotationElementList
- .get(index);
- }
-
- /**
- * Method getAnnotationElement.Returns the contents of the collection in an
- * Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.AnnotationElement[] getAnnotationElement()
- {
- jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
- return (jalview.binding.AnnotationElement[]) this._annotationElementList
- .toArray(array);
- }
-
- /**
- * Method getAnnotationElementCount.
- *
- * @return the size of this collection
- */
- public int getAnnotationElementCount()
- {
- return this._annotationElementList.size();
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- }
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return the value of field 'Graph'.
- */
- public boolean getGraph()
- {
- return this._graph;
- }
-
- /**
- * Returns the value of field 'graphType'.
- *
- * @return the value of field 'GraphType'.
- */
- public int getGraphType()
- {
- return this._graphType;
- }
-
- /**
- * Returns the value of field 'label'.
- *
- * @return the value of field 'Label'.
- */
- public java.lang.String getLabel()
- {
- return this._label;
- }
-
- /**
- * Method hasGraph.
- *
- * @return true if at least one Graph has been added
- */
- public boolean hasGraph()
- {
- return this._has_graph;
- }
-
- /**
- * Method hasGraphType.
- *
- * @return true if at least one GraphType has been added
- */
- public boolean hasGraphType()
- {
- return this._has_graphType;
- }
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return the value of field 'Graph'.
- */
- public boolean isGraph()
- {
- return this._graph;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationElementList.addElement(vAnnotationElement);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllAnnotationElement()
- {
- this._annotationElementList.clear();
- }
-
- /**
- * Method removeAnnotationElement.
- *
- * @param vAnnotationElement
- * @return true if the object was removed from the collection.
- */
- public boolean removeAnnotationElement(
- final jalview.binding.AnnotationElement vAnnotationElement)
- {
- boolean removed = _annotationElementList.remove(vAnnotationElement);
- return removed;
- }
-
- /**
- * Method removeAnnotationElementAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.AnnotationElement removeAnnotationElementAt(
- final int index)
- {
- java.lang.Object obj = this._annotationElementList.remove(index);
- return (jalview.binding.AnnotationElement) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotationElement
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setAnnotationElement(final int index,
- final jalview.binding.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._annotationElementList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setAnnotationElement",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._annotationElementList.size() - 1)).toString()
- }));
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final int index,
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationElementList.add(index, vAnnotationElement);
+ }
+
+ /**
+ */
+ public void deleteGraph(
+ ) {
+ this._has_graph= false;
+ }
+
+ /**
+ */
+ public void deleteGraphType(
+ ) {
+ this._has_graphType= false;
+ }
+
+ /**
+ * Method enumerateAnnotationElement.
+ *
+ * @return an Enumeration over all
+ * jalview.binding.AnnotationElement elements
+ */
+ public java.util.Enumeration enumerateAnnotationElement(
+ ) {
+ return this._annotationElementList.elements();
+ }
+
+ /**
+ * Method getAnnotationElement.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.AnnotationElement
+ * at the given index
+ */
+ public jalview.binding.AnnotationElement getAnnotationElement(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size()) {
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.AnnotationElement) _annotationElementList.get(index);
}
- this._annotationElementList.set(index, vAnnotationElement);
- }
-
- /**
- *
- *
- * @param vAnnotationElementArray
- */
- public void setAnnotationElement(
- final jalview.binding.AnnotationElement[] vAnnotationElementArray)
- {
- // -- copy array
- _annotationElementList.clear();
-
- for (int i = 0; i < vAnnotationElementArray.length; i++)
- {
- this._annotationElementList.add(vAnnotationElementArray[i]);
+ /**
+ * Method getAnnotationElement.Returns the contents of the
+ * collection in an Array. <p>Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.AnnotationElement[] getAnnotationElement(
+ ) {
+ jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
+ return (jalview.binding.AnnotationElement[]) this._annotationElementList.toArray(array);
+ }
+
+ /**
+ * Method getAnnotationElementCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationElementCount(
+ ) {
+ return this._annotationElementList.size();
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription(
+ ) {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean getGraph(
+ ) {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'graphType'.
+ *
+ * @return the value of field 'GraphType'.
+ */
+ public int getGraphType(
+ ) {
+ return this._graphType;
+ }
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return the value of field 'Label'.
+ */
+ public java.lang.String getLabel(
+ ) {
+ return this._label;
+ }
+
+ /**
+ * Method hasGraph.
+ *
+ * @return true if at least one Graph has been added
+ */
+ public boolean hasGraph(
+ ) {
+ return this._has_graph;
+ }
+
+ /**
+ * Method hasGraphType.
+ *
+ * @return true if at least one GraphType has been added
+ */
+ public boolean hasGraphType(
+ ) {
+ return this._has_graphType;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean isGraph(
+ ) {
+ return this._graph;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAnnotationElement(
+ ) {
+ this._annotationElementList.clear();
+ }
+
+ /**
+ * Method removeAnnotationElement.
+ *
+ * @param vAnnotationElement
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement) {
+ boolean removed = _annotationElementList.remove(vAnnotationElement);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationElementAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.AnnotationElement removeAnnotationElementAt(
+ final int index) {
+ java.lang.Object obj = this._annotationElementList.remove(index);
+ return (jalview.binding.AnnotationElement) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAnnotationElement(
+ final int index,
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size()) {
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ this._annotationElementList.set(index, vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationElementArray
+ */
+ public void setAnnotationElement(
+ final jalview.binding.AnnotationElement[] vAnnotationElementArray) {
+ //-- copy array
+ _annotationElementList.clear();
+
+ for (int i = 0; i < vAnnotationElementArray.length; i++) {
+ this._annotationElementList.add(vAnnotationElementArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(
+ final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'graph'.
+ *
+ * @param graph the value of field 'graph'.
+ */
+ public void setGraph(
+ final boolean graph) {
+ this._graph = graph;
+ this._has_graph = true;
+ }
+
+ /**
+ * Sets the value of field 'graphType'.
+ *
+ * @param graphType the value of field 'graphType'.
+ */
+ public void setGraphType(
+ final int graphType) {
+ this._graphType = graphType;
+ this._has_graphType = true;
+ }
+
+ /**
+ * Sets the value of field 'label'.
+ *
+ * @param label the value of field 'label'.
+ */
+ public void setLabel(
+ final java.lang.String label) {
+ this._label = label;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Annotation
+ */
+ public static jalview.binding.Annotation unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description
- * the value of field 'description'.
- */
- public void setDescription(final java.lang.String description)
- {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'graph'.
- *
- * @param graph
- * the value of field 'graph'.
- */
- public void setGraph(final boolean graph)
- {
- this._graph = graph;
- this._has_graph = true;
- }
-
- /**
- * Sets the value of field 'graphType'.
- *
- * @param graphType
- * the value of field 'graphType'.
- */
- public void setGraphType(final int graphType)
- {
- this._graphType = graphType;
- this._has_graphType = true;
- }
-
- /**
- * Sets the value of field 'label'.
- *
- * @param label
- * the value of field 'label'.
- */
- public void setLabel(final java.lang.String label)
- {
- this._label = label;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Annotation
- */
- public static jalview.binding.Annotation unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Annotation) Unmarshaller.unmarshal(
- jalview.binding.Annotation.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AnnotationElement implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _position.
- */
- private int _position;
-
- /**
- * keeps track of state for field: _position
- */
- private boolean _has_position;
-
- /**
- * Field _displayCharacter.
- */
- private java.lang.String _displayCharacter;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _secondaryStructure.
- */
- private java.lang.String _secondaryStructure;
-
- /**
- * Field _value.
- */
- private float _value;
-
- /**
- * keeps track of state for field: _value
- */
- private boolean _has_value;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public AnnotationElement()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
+public class AnnotationElement implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _position.
+ */
+ private int _position;
+
+ /**
+ * keeps track of state for field: _position
+ */
+ private boolean _has_position;
+
+ /**
+ * Field _displayCharacter.
+ */
+ private java.lang.String _displayCharacter;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _secondaryStructure.
+ */
+ private java.lang.String _secondaryStructure;
+
+ /**
+ * Field _value.
+ */
+ private float _value;
+
+ /**
+ * keeps track of state for field: _value
+ */
+ private boolean _has_value;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AnnotationElement() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deletePosition(
+ ) {
+ this._has_position= false;
+ }
+
+ /**
+ */
+ public void deleteValue(
+ ) {
+ this._has_value= false;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription(
+ ) {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'displayCharacter'.
+ *
+ * @return the value of field 'DisplayCharacter'.
+ */
+ public java.lang.String getDisplayCharacter(
+ ) {
+ return this._displayCharacter;
+ }
+
+ /**
+ * Returns the value of field 'position'.
+ *
+ * @return the value of field 'Position'.
*/
- public void deletePosition()
- {
- this._has_position = false;
- }
+ public int getPosition(
+ ) {
+ return this._position;
+ }
+
+ /**
+ * Returns the value of field 'secondaryStructure'.
+ *
+ * @return the value of field 'SecondaryStructure'.
+ */
+ public java.lang.String getSecondaryStructure(
+ ) {
+ return this._secondaryStructure;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public float getValue(
+ ) {
+ return this._value;
+ }
+
+ /**
+ * Method hasPosition.
+ *
+ * @return true if at least one Position has been added
+ */
+ public boolean hasPosition(
+ ) {
+ return this._has_position;
+ }
+
+ /**
+ * Method hasValue.
+ *
+ * @return true if at least one Value has been added
+ */
+ public boolean hasValue(
+ ) {
+ return this._has_value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(
+ final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'displayCharacter'.
+ *
+ * @param displayCharacter the value of field 'displayCharacter'
+ */
+ public void setDisplayCharacter(
+ final java.lang.String displayCharacter) {
+ this._displayCharacter = displayCharacter;
+ }
+
+ /**
+ * Sets the value of field 'position'.
+ *
+ * @param position the value of field 'position'.
+ */
+ public void setPosition(
+ final int position) {
+ this._position = position;
+ this._has_position = true;
+ }
+
+ /**
+ * Sets the value of field 'secondaryStructure'.
+ *
+ * @param secondaryStructure the value of field
+ * 'secondaryStructure'.
+ */
+ public void setSecondaryStructure(
+ final java.lang.String secondaryStructure) {
+ this._secondaryStructure = secondaryStructure;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value the value of field 'value'.
+ */
+ public void setValue(
+ final float value) {
+ this._value = value;
+ this._has_value = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.AnnotationElement
+ */
+ public static jalview.binding.AnnotationElement unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);
+ }
- /**
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- public void deleteValue()
- {
- this._has_value = false;
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- }
-
- /**
- * Returns the value of field 'displayCharacter'.
- *
- * @return the value of field 'DisplayCharacter'.
- */
- public java.lang.String getDisplayCharacter()
- {
- return this._displayCharacter;
- }
-
- /**
- * Returns the value of field 'position'.
- *
- * @return the value of field 'Position'.
- */
- public int getPosition()
- {
- return this._position;
- }
-
- /**
- * Returns the value of field 'secondaryStructure'.
- *
- * @return the value of field 'SecondaryStructure'.
- */
- public java.lang.String getSecondaryStructure()
- {
- return this._secondaryStructure;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public float getValue()
- {
- return this._value;
- }
-
- /**
- * Method hasPosition.
- *
- * @return true if at least one Position has been added
- */
- public boolean hasPosition()
- {
- return this._has_position;
- }
-
- /**
- * Method hasValue.
- *
- * @return true if at least one Value has been added
- */
- public boolean hasValue()
- {
- return this._has_value;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description
- * the value of field 'description'.
- */
- public void setDescription(final java.lang.String description)
- {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'displayCharacter'.
- *
- * @param displayCharacter
- * the value of field 'displayCharacter'
- */
- public void setDisplayCharacter(final java.lang.String displayCharacter)
- {
- this._displayCharacter = displayCharacter;
- }
-
- /**
- * Sets the value of field 'position'.
- *
- * @param position
- * the value of field 'position'.
- */
- public void setPosition(final int position)
- {
- this._position = position;
- this._has_position = true;
- }
-
- /**
- * Sets the value of field 'secondaryStructure'.
- *
- * @param secondaryStructure
- * the value of field 'secondaryStructure'.
- */
- public void setSecondaryStructure(
- final java.lang.String secondaryStructure)
- {
- this._secondaryStructure = secondaryStructure;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value
- * the value of field 'value'.
- */
- public void setValue(final float value)
- {
- this._value = value;
- this._has_value = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.AnnotationElement
- */
- public static jalview.binding.AnnotationElement unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(
- jalview.binding.AnnotationElement.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Colour implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _RGB.
- */
- private java.lang.String _RGB;
-
- /**
- * Field _minRGB.
- */
- private java.lang.String _minRGB;
-
- /**
- * loosely specified enumeration: NONE,ABOVE, or BELOW
- */
- private java.lang.String _threshType;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _max.
- */
- private float _max;
-
- /**
- * keeps track of state for field: _max
- */
- private boolean _has_max;
-
- /**
- * Field _min.
- */
- private float _min;
-
- /**
- * keeps track of state for field: _min
- */
- private boolean _has_min;
-
- /**
- * Field _colourByLabel.
- */
- private boolean _colourByLabel;
-
- /**
- * keeps track of state for field: _colourByLabel
- */
- private boolean _has_colourByLabel;
-
- /**
- * Field _autoScale.
- */
- private boolean _autoScale;
-
- /**
- * keeps track of state for field: _autoScale
- */
- private boolean _has_autoScale;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Colour()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- */
- public void deleteAutoScale()
- {
- this._has_autoScale = false;
- }
-
- /**
- */
- public void deleteColourByLabel()
- {
- this._has_colourByLabel = false;
- }
-
- /**
- */
- public void deleteMax()
- {
- this._has_max = false;
- }
-
- /**
- */
- public void deleteMin()
- {
- this._has_min = false;
- }
-
- /**
- */
- public void deleteThreshold()
- {
- this._has_threshold = false;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean getAutoScale()
- {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean getColourByLabel()
- {
- return this._colourByLabel;
- }
-
- /**
- * Returns the value of field 'max'.
- *
- * @return the value of field 'Max'.
- */
- public float getMax()
- {
- return this._max;
- }
-
- /**
- * Returns the value of field 'min'.
- *
- * @return the value of field 'Min'.
- */
- public float getMin()
- {
- return this._min;
- }
-
- /**
- * Returns the value of field 'minRGB'.
- *
- * @return the value of field 'MinRGB'.
- */
- public java.lang.String getMinRGB()
- {
- return this._minRGB;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- }
-
- /**
- * Returns the value of field 'RGB'.
- *
- * @return the value of field 'RGB'.
- */
- public java.lang.String getRGB()
- {
- return this._RGB;
- }
-
- /**
- * Returns the value of field 'threshType'. The field 'threshType' has the
- * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
- *
- * @return the value of field 'ThreshType'.
- */
- public java.lang.String getThreshType()
- {
- return this._threshType;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold()
- {
- return this._threshold;
- }
-
- /**
- * Method hasAutoScale.
- *
- * @return true if at least one AutoScale has been added
- */
- public boolean hasAutoScale()
- {
- return this._has_autoScale;
- }
-
- /**
- * Method hasColourByLabel.
- *
- * @return true if at least one ColourByLabel has been added
- */
- public boolean hasColourByLabel()
- {
- return this._has_colourByLabel;
- }
-
- /**
- * Method hasMax.
- *
- * @return true if at least one Max has been added
- */
- public boolean hasMax()
- {
- return this._has_max;
- }
-
- /**
- * Method hasMin.
- *
- * @return true if at least one Min has been added
- */
- public boolean hasMin()
- {
- return this._has_min;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold()
- {
- return this._has_threshold;
- }
-
- /**
- * Returns the value of field 'autoScale'.
- *
- * @return the value of field 'AutoScale'.
- */
- public boolean isAutoScale()
- {
- return this._autoScale;
- }
-
- /**
- * Returns the value of field 'colourByLabel'.
- *
- * @return the value of field 'ColourByLabel'.
- */
- public boolean isColourByLabel()
- {
- return this._colourByLabel;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'autoScale'.
- *
- * @param autoScale
- * the value of field 'autoScale'.
- */
- public void setAutoScale(final boolean autoScale)
- {
- this._autoScale = autoScale;
- this._has_autoScale = true;
- }
-
- /**
- * Sets the value of field 'colourByLabel'.
- *
- * @param colourByLabel
- * the value of field 'colourByLabel'.
- */
- public void setColourByLabel(final boolean colourByLabel)
- {
- this._colourByLabel = colourByLabel;
- this._has_colourByLabel = true;
- }
-
- /**
- * Sets the value of field 'max'.
- *
- * @param max
- * the value of field 'max'.
- */
- public void setMax(final float max)
- {
- this._max = max;
- this._has_max = true;
- }
-
- /**
- * Sets the value of field 'min'.
- *
- * @param min
- * the value of field 'min'.
- */
- public void setMin(final float min)
- {
- this._min = min;
- this._has_min = true;
- }
-
- /**
- * Sets the value of field 'minRGB'.
- *
- * @param minRGB
- * the value of field 'minRGB'.
- */
- public void setMinRGB(final java.lang.String minRGB)
- {
- this._minRGB = minRGB;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name
- * the value of field 'name'.
- */
- public void setName(final java.lang.String name)
- {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'RGB'.
- *
- * @param RGB
- * the value of field 'RGB'.
- */
- public void setRGB(final java.lang.String RGB)
- {
- this._RGB = RGB;
- }
-
- /**
- * Sets the value of field 'threshType'. The field 'threshType' has the
- * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
- *
- * @param threshType
- * the value of field 'threshType'.
- */
- public void setThreshType(final java.lang.String threshType)
- {
- this._threshType = threshType;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold
- * the value of field 'threshold'.
- */
- public void setThreshold(final float threshold)
- {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Colour
- */
- public static jalview.binding.Colour unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Colour) Unmarshaller.unmarshal(
- jalview.binding.Colour.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class Colour implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _RGB.
+ */
+ private java.lang.String _RGB;
+
+ /**
+ * Field _minRGB.
+ */
+ private java.lang.String _minRGB;
+
+ /**
+ * loosely specified enumeration: NONE,ABOVE, or BELOW
+ */
+ private java.lang.String _threshType;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _max.
+ */
+ private float _max;
+
+ /**
+ * keeps track of state for field: _max
+ */
+ private boolean _has_max;
+
+ /**
+ * Field _min.
+ */
+ private float _min;
+
+ /**
+ * keeps track of state for field: _min
+ */
+ private boolean _has_min;
+
+ /**
+ * Field _colourByLabel.
+ */
+ private boolean _colourByLabel;
+
+ /**
+ * keeps track of state for field: _colourByLabel
+ */
+ private boolean _has_colourByLabel;
+
+ /**
+ * Field _autoScale.
+ */
+ private boolean _autoScale;
+
+ /**
+ * keeps track of state for field: _autoScale
+ */
+ private boolean _has_autoScale;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Colour() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteAutoScale(
+ ) {
+ this._has_autoScale= false;
+ }
+
+ /**
+ */
+ public void deleteColourByLabel(
+ ) {
+ this._has_colourByLabel= false;
+ }
+
+ /**
+ */
+ public void deleteMax(
+ ) {
+ this._has_max= false;
+ }
+
+ /**
+ */
+ public void deleteMin(
+ ) {
+ this._has_min= false;
+ }
+
+ /**
+ */
+ public void deleteThreshold(
+ ) {
+ this._has_threshold= false;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean getAutoScale(
+ ) {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean getColourByLabel(
+ ) {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'max'.
+ *
+ * @return the value of field 'Max'.
+ */
+ public float getMax(
+ ) {
+ return this._max;
+ }
+
+ /**
+ * Returns the value of field 'min'.
+ *
+ * @return the value of field 'Min'.
+ */
+ public float getMin(
+ ) {
+ return this._min;
+ }
+
+ /**
+ * Returns the value of field 'minRGB'.
+ *
+ * @return the value of field 'MinRGB'.
+ */
+ public java.lang.String getMinRGB(
+ ) {
+ return this._minRGB;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'RGB'.
+ *
+ * @return the value of field 'RGB'.
+ */
+ public java.lang.String getRGB(
+ ) {
+ return this._RGB;
+ }
+
+ /**
+ * Returns the value of field 'threshType'. The field
+ * 'threshType' has the following description: loosely
+ * specified enumeration: NONE,ABOVE, or BELOW
+ *
+ * @return the value of field 'ThreshType'.
+ */
+ public java.lang.String getThreshType(
+ ) {
+ return this._threshType;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold(
+ ) {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAutoScale.
+ *
+ * @return true if at least one AutoScale has been added
+ */
+ public boolean hasAutoScale(
+ ) {
+ return this._has_autoScale;
+ }
+
+ /**
+ * Method hasColourByLabel.
+ *
+ * @return true if at least one ColourByLabel has been added
+ */
+ public boolean hasColourByLabel(
+ ) {
+ return this._has_colourByLabel;
+ }
+
+ /**
+ * Method hasMax.
+ *
+ * @return true if at least one Max has been added
+ */
+ public boolean hasMax(
+ ) {
+ return this._has_max;
+ }
+
+ /**
+ * Method hasMin.
+ *
+ * @return true if at least one Min has been added
+ */
+ public boolean hasMin(
+ ) {
+ return this._has_min;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold(
+ ) {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean isAutoScale(
+ ) {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean isColourByLabel(
+ ) {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'autoScale'.
+ *
+ * @param autoScale the value of field 'autoScale'.
+ */
+ public void setAutoScale(
+ final boolean autoScale) {
+ this._autoScale = autoScale;
+ this._has_autoScale = true;
+ }
+
+ /**
+ * Sets the value of field 'colourByLabel'.
+ *
+ * @param colourByLabel the value of field 'colourByLabel'.
+ */
+ public void setColourByLabel(
+ final boolean colourByLabel) {
+ this._colourByLabel = colourByLabel;
+ this._has_colourByLabel = true;
+ }
+
+ /**
+ * Sets the value of field 'max'.
+ *
+ * @param max the value of field 'max'.
+ */
+ public void setMax(
+ final float max) {
+ this._max = max;
+ this._has_max = true;
+ }
+
+ /**
+ * Sets the value of field 'min'.
+ *
+ * @param min the value of field 'min'.
+ */
+ public void setMin(
+ final float min) {
+ this._min = min;
+ this._has_min = true;
+ }
+
+ /**
+ * Sets the value of field 'minRGB'.
+ *
+ * @param minRGB the value of field 'minRGB'.
+ */
+ public void setMinRGB(
+ final java.lang.String minRGB) {
+ this._minRGB = minRGB;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'RGB'.
+ *
+ * @param RGB the value of field 'RGB'.
+ */
+ public void setRGB(
+ final java.lang.String RGB) {
+ this._RGB = RGB;
+ }
+
+ /**
+ * Sets the value of field 'threshType'. The field 'threshType'
+ * has the following description: loosely specified
+ * enumeration: NONE,ABOVE, or BELOW
+ *
+ * @param threshType the value of field 'threshType'.
+ */
+ public void setThreshType(
+ final java.lang.String threshType) {
+ this._threshType = threshType;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold the value of field 'threshold'.
+ */
+ public void setThreshold(
+ final float threshold) {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Colour
+ */
+ public static jalview.binding.Colour unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Feature implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _begin.
- */
- private int _begin;
-
- /**
- * keeps track of state for field: _begin
- */
- private boolean _has_begin;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * Field _status.
- */
- private java.lang.String _status;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Feature()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
+public class Feature implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _begin.
+ */
+ private int _begin;
+
+ /**
+ * keeps track of state for field: _begin
+ */
+ private boolean _has_begin;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _status.
+ */
+ private java.lang.String _status;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Feature() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteBegin(
+ ) {
+ this._has_begin= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ * Returns the value of field 'begin'.
+ *
+ * @return the value of field 'Begin'.
+ */
+ public int getBegin(
+ ) {
+ return this._begin;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription(
+ ) {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
*/
- public void deleteBegin()
- {
- this._has_begin = false;
- }
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'status'.
+ *
+ * @return the value of field 'Status'.
+ */
+ public java.lang.String getStatus(
+ ) {
+ return this._status;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * Method hasBegin.
+ *
+ * @return true if at least one Begin has been added
+ */
+ public boolean hasBegin(
+ ) {
+ return this._has_begin;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'begin'.
+ *
+ * @param begin the value of field 'begin'.
+ */
+ public void setBegin(
+ final int begin) {
+ this._begin = begin;
+ this._has_begin = true;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(
+ final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'status'.
+ *
+ * @param status the value of field 'status'.
+ */
+ public void setStatus(
+ final java.lang.String status) {
+ this._status = status;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Feature
+ */
+ public static jalview.binding.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.class, reader);
+ }
- /**
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- public void deleteEnd()
- {
- this._has_end = false;
- }
-
- /**
- * Returns the value of field 'begin'.
- *
- * @return the value of field 'Begin'.
- */
- public int getBegin()
- {
- return this._begin;
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd()
- {
- return this._end;
- }
-
- /**
- * Returns the value of field 'status'.
- *
- * @return the value of field 'Status'.
- */
- public java.lang.String getStatus()
- {
- return this._status;
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType()
- {
- return this._type;
- }
-
- /**
- * Method hasBegin.
- *
- * @return true if at least one Begin has been added
- */
- public boolean hasBegin()
- {
- return this._has_begin;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd()
- {
- return this._has_end;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'begin'.
- *
- * @param begin
- * the value of field 'begin'.
- */
- public void setBegin(final int begin)
- {
- this._begin = begin;
- this._has_begin = true;
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description
- * the value of field 'description'.
- */
- public void setDescription(final java.lang.String description)
- {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end
- * the value of field 'end'.
- */
- public void setEnd(final int end)
- {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'status'.
- *
- * @param status
- * the value of field 'status'.
- */
- public void setStatus(final java.lang.String status)
- {
- this._status = status;
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type
- * the value of field 'type'.
- */
- public void setType(final java.lang.String type)
- {
- this._type = type;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Feature
- */
- public static jalview.binding.Feature unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Feature) Unmarshaller.unmarshal(
- jalview.binding.Feature.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-import jalview.util.MessageManager;
-
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class FeatureSettings implements java.io.Serializable
-{
+public class FeatureSettings implements java.io.Serializable {
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
- /**
- * Field _settingList.
- */
- private java.util.Vector _settingList;
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
- // ----------------/
- // - Constructors -/
- // ----------------/
+ /**
+ * Field _settingList.
+ */
+ private java.util.Vector _settingList;
- public FeatureSettings()
- {
- super();
- this._settingList = new java.util.Vector();
- }
- // -----------/
- // - Methods -/
- // -----------/
+ //----------------/
+ //- Constructors -/
+ //----------------/
- /**
- *
- *
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSetting(final jalview.binding.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException
- {
- this._settingList.addElement(vSetting);
- }
+ public FeatureSettings() {
+ super();
+ this._settingList = new java.util.Vector();
+ }
- /**
- *
- *
- * @param index
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSetting(final int index,
- final jalview.binding.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException
- {
- this._settingList.add(index, vSetting);
- }
- /**
- * Method enumerateSetting.
- *
- * @return an Enumeration over all jalview.binding.Setting elements
- */
- public java.util.Enumeration enumerateSetting()
- {
- return this._settingList.elements();
- }
+ //-----------/
+ //- Methods -/
+ //-----------/
- /**
- * Method getSetting.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Setting at the given index
- */
- public jalview.binding.Setting getSetting(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._settingList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getSetting",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._settingList.size() - 1)).toString()
- }));
+ /**
+ *
+ *
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSetting(
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException {
+ this._settingList.addElement(vSetting);
}
- return (jalview.binding.Setting) _settingList.get(index);
- }
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSetting(
+ final int index,
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException {
+ this._settingList.add(index, vSetting);
+ }
- /**
- * Method getSetting.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Setting[] getSetting()
- {
- jalview.binding.Setting[] array = new jalview.binding.Setting[0];
- return (jalview.binding.Setting[]) this._settingList.toArray(array);
- }
+ /**
+ * Method enumerateSetting.
+ *
+ * @return an Enumeration over all jalview.binding.Setting
+ * elements
+ */
+ public java.util.Enumeration enumerateSetting(
+ ) {
+ return this._settingList.elements();
+ }
- /**
- * Method getSettingCount.
- *
- * @return the size of this collection
- */
- public int getSettingCount()
- {
- return this._settingList.size();
- }
+ /**
+ * Method getSetting.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Setting at the
+ * given index
+ */
+ public jalview.binding.Setting getSetting(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size()) {
+ throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Setting) _settingList.get(index);
+ }
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+ /**
+ * Method getSetting.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Setting[] getSetting(
+ ) {
+ jalview.binding.Setting[] array = new jalview.binding.Setting[0];
+ return (jalview.binding.Setting[]) this._settingList.toArray(array);
}
- return true;
- }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
+ /**
+ * Method getSettingCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSettingCount(
+ ) {
+ return this._settingList.size();
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
- /**
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- public void removeAllSetting()
- {
- this._settingList.clear();
- }
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
- /**
- * Method removeSetting.
- *
- * @param vSetting
- * @return true if the object was removed from the collection.
- */
- public boolean removeSetting(final jalview.binding.Setting vSetting)
- {
- boolean removed = _settingList.remove(vSetting);
- return removed;
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method removeSettingAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Setting removeSettingAt(final int index)
- {
- java.lang.Object obj = this._settingList.remove(index);
- return (jalview.binding.Setting) obj;
- }
+ /**
+ */
+ public void removeAllSetting(
+ ) {
+ this._settingList.clear();
+ }
- /**
- *
- *
- * @param index
- * @param vSetting
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSetting(final int index,
- final jalview.binding.Setting vSetting)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._settingList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setSetting",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._settingList.size() - 1)).toString()
- }));
+ /**
+ * Method removeSetting.
+ *
+ * @param vSetting
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSetting(
+ final jalview.binding.Setting vSetting) {
+ boolean removed = _settingList.remove(vSetting);
+ return removed;
}
- this._settingList.set(index, vSetting);
- }
+ /**
+ * Method removeSettingAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Setting removeSettingAt(
+ final int index) {
+ java.lang.Object obj = this._settingList.remove(index);
+ return (jalview.binding.Setting) obj;
+ }
- /**
- *
- *
- * @param vSettingArray
- */
- public void setSetting(final jalview.binding.Setting[] vSettingArray)
- {
- // -- copy array
- _settingList.clear();
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSetting(
+ final int index,
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size()) {
+ throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
+ }
+
+ this._settingList.set(index, vSetting);
+ }
- for (int i = 0; i < vSettingArray.length; i++)
- {
- this._settingList.add(vSettingArray[i]);
+ /**
+ *
+ *
+ * @param vSettingArray
+ */
+ public void setSetting(
+ final jalview.binding.Setting[] vSettingArray) {
+ //-- copy array
+ _settingList.clear();
+
+ for (int i = 0; i < vSettingArray.length; i++) {
+ this._settingList.add(vSettingArray[i]);
+ }
}
- }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.FeatureSettings
- */
- public static jalview.binding.FeatureSettings unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(
- jalview.binding.FeatureSettings.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.FeatureSettings
+ */
+ public static jalview.binding.FeatureSettings unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Features extends Feature implements java.io.Serializable
+public class Features extends Feature
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public Features()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Features() {
+ super();
+ }
+
- // -----------/
- // - Methods -/
- // -----------/
+ //-----------/
+ //- Methods -/
+ //-----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
}
- return true;
- }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Feature
- */
- public static jalview.binding.Feature unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Feature) Unmarshaller.unmarshal(
- jalview.binding.Features.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Feature
+ */
+ public static jalview.binding.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Features.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class JGroup implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _colour.
- */
- private java.lang.String _colour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _outlineColour.
- */
- private int _outlineColour;
-
- /**
- * keeps track of state for field: _outlineColour
- */
- private boolean _has_outlineColour;
-
- /**
- * Field _displayBoxes.
- */
- private boolean _displayBoxes;
-
- /**
- * keeps track of state for field: _displayBoxes
- */
- private boolean _has_displayBoxes;
-
- /**
- * Field _displayText.
- */
- private boolean _displayText;
-
- /**
- * keeps track of state for field: _displayText
- */
- private boolean _has_displayText;
-
- /**
- * Field _colourText.
- */
- private boolean _colourText;
-
- /**
- * keeps track of state for field: _colourText
- */
- private boolean _has_colourText;
-
- /**
- * Field _seqList.
- */
- private java.util.Vector _seqList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JGroup()
- {
- super();
- this._seqList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSeq(final int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- this._seqList.addElement(new java.lang.Integer(vSeq));
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSeq(final int index, final int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- this._seqList.add(index, new java.lang.Integer(vSeq));
- }
-
- /**
- */
- public void deleteColourText()
- {
- this._has_colourText = false;
- }
-
- /**
- */
- public void deleteConsThreshold()
- {
- this._has_consThreshold = false;
- }
-
- /**
- */
- public void deleteDisplayBoxes()
- {
- this._has_displayBoxes = false;
- }
-
- /**
- */
- public void deleteDisplayText()
- {
- this._has_displayText = false;
- }
-
- /**
- */
- public void deleteEnd()
- {
- this._has_end = false;
- }
-
- /**
- */
- public void deleteOutlineColour()
- {
- this._has_outlineColour = false;
- }
-
- /**
- */
- public void deletePidThreshold()
- {
- this._has_pidThreshold = false;
- }
-
- /**
- */
- public void deleteStart()
- {
- this._has_start = false;
- }
-
- /**
- * Method enumerateSeq.
- *
- * @return an Enumeration over all int elements
- */
- public java.util.Enumeration enumerateSeq()
- {
- return this._seqList.elements();
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public java.lang.String getColour()
- {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean getColourText()
- {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold()
- {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean getDisplayBoxes()
- {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean getDisplayText()
- {
- return this._displayText;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd()
- {
- return this._end;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- }
-
- /**
- * Returns the value of field 'outlineColour'.
- *
- * @return the value of field 'OutlineColour'.
- */
- public int getOutlineColour()
- {
- return this._outlineColour;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold()
- {
- return this._pidThreshold;
- }
-
- /**
- * Method getSeq.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the int at the given index
- */
- public int getSeq(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getSeq",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._seqList.size() - 1)).toString()
- }));
- }
-
- return ((java.lang.Integer) _seqList.get(index)).intValue();
- }
-
- /**
- * Method getSeq.Returns the contents of the collection in an Array.
- *
- * @return this collection as an Array
- */
- public int[] getSeq()
- {
- int size = this._seqList.size();
- int[] array = new int[size];
- java.util.Iterator iter = _seqList.iterator();
- for (int index = 0; index < size; index++)
- {
- array[index] = ((java.lang.Integer) iter.next()).intValue();
- }
- return array;
- }
-
- /**
- * Method getSeqCount.
- *
- * @return the size of this collection
- */
- public int getSeqCount()
- {
- return this._seqList.size();
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart()
- {
- return this._start;
- }
-
- /**
- * Method hasColourText.
- *
- * @return true if at least one ColourText has been added
- */
- public boolean hasColourText()
- {
- return this._has_colourText;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold()
- {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasDisplayBoxes.
- *
- * @return true if at least one DisplayBoxes has been added
- */
- public boolean hasDisplayBoxes()
- {
- return this._has_displayBoxes;
- }
-
- /**
- * Method hasDisplayText.
- *
- * @return true if at least one DisplayText has been added
- */
- public boolean hasDisplayText()
- {
- return this._has_displayText;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd()
- {
- return this._has_end;
- }
-
- /**
- * Method hasOutlineColour.
- *
- * @return true if at least one OutlineColour has been added
- */
- public boolean hasOutlineColour()
- {
- return this._has_outlineColour;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold()
- {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart()
- {
- return this._has_start;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean isColourText()
- {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean isDisplayBoxes()
- {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean isDisplayText()
- {
- return this._displayText;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllSeq()
- {
- this._seqList.clear();
- }
-
- /**
- * Method removeSeq.
- *
- * @param vSeq
- * @return true if the object was removed from the collection.
- */
- public boolean removeSeq(final int vSeq)
- {
- boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
- return removed;
- }
-
- /**
- * Method removeSeqAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public int removeSeqAt(final int index)
- {
- java.lang.Object obj = this._seqList.remove(index);
- return ((java.lang.Integer) obj).intValue();
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour
- * the value of field 'colour'.
- */
- public void setColour(final java.lang.String colour)
- {
- this._colour = colour;
- }
-
- /**
- * Sets the value of field 'colourText'.
- *
- * @param colourText
- * the value of field 'colourText'.
- */
- public void setColourText(final boolean colourText)
- {
- this._colourText = colourText;
- this._has_colourText = true;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold
- * the value of field 'consThreshold'.
- */
- public void setConsThreshold(final int consThreshold)
- {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'displayBoxes'.
- *
- * @param displayBoxes
- * the value of field 'displayBoxes'.
- */
- public void setDisplayBoxes(final boolean displayBoxes)
- {
- this._displayBoxes = displayBoxes;
- this._has_displayBoxes = true;
- }
-
- /**
- * Sets the value of field 'displayText'.
- *
- * @param displayText
- * the value of field 'displayText'.
- */
- public void setDisplayText(final boolean displayText)
- {
- this._displayText = displayText;
- this._has_displayText = true;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end
- * the value of field 'end'.
- */
- public void setEnd(final int end)
- {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name
- * the value of field 'name'.
- */
- public void setName(final java.lang.String name)
- {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'outlineColour'.
- *
- * @param outlineColour
- * the value of field 'outlineColour'.
- */
- public void setOutlineColour(final int outlineColour)
- {
- this._outlineColour = outlineColour;
- this._has_outlineColour = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold
- * the value of field 'pidThreshold'.
- */
- public void setPidThreshold(final int pidThreshold)
- {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSeq(final int index, final int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setSeq",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._seqList.size() - 1)).toString()
- }));
- }
-
- this._seqList.set(index, new java.lang.Integer(vSeq));
- }
-
- /**
- *
- *
- * @param vSeqArray
- */
- public void setSeq(final int[] vSeqArray)
- {
- // -- copy array
- _seqList.clear();
-
- for (int i = 0; i < vSeqArray.length; i++)
- {
- this._seqList.add(new java.lang.Integer(vSeqArray[i]));
- }
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start
- * the value of field 'start'.
- */
- public void setStart(final int start)
- {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JGroup
- */
- public static jalview.binding.JGroup unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JGroup) Unmarshaller.unmarshal(
- jalview.binding.JGroup.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class JGroup implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _colour.
+ */
+ private java.lang.String _colour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _outlineColour.
+ */
+ private int _outlineColour;
+
+ /**
+ * keeps track of state for field: _outlineColour
+ */
+ private boolean _has_outlineColour;
+
+ /**
+ * Field _displayBoxes.
+ */
+ private boolean _displayBoxes;
+
+ /**
+ * keeps track of state for field: _displayBoxes
+ */
+ private boolean _has_displayBoxes;
+
+ /**
+ * Field _displayText.
+ */
+ private boolean _displayText;
+
+ /**
+ * keeps track of state for field: _displayText
+ */
+ private boolean _has_displayText;
+
+ /**
+ * Field _colourText.
+ */
+ private boolean _colourText;
+
+ /**
+ * keeps track of state for field: _colourText
+ */
+ private boolean _has_colourText;
+
+ /**
+ * Field _seqList.
+ */
+ private java.util.Vector _seqList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JGroup() {
+ super();
+ this._seqList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSeq(
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqList.addElement(new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSeq(
+ final int index,
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqList.add(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ */
+ public void deleteColourText(
+ ) {
+ this._has_colourText= false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold(
+ ) {
+ this._has_consThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteDisplayBoxes(
+ ) {
+ this._has_displayBoxes= false;
+ }
+
+ /**
+ */
+ public void deleteDisplayText(
+ ) {
+ this._has_displayText= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ */
+ public void deleteOutlineColour(
+ ) {
+ this._has_outlineColour= false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold(
+ ) {
+ this._has_pidThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteStart(
+ ) {
+ this._has_start= false;
+ }
+
+ /**
+ * Method enumerateSeq.
+ *
+ * @return an Enumeration over all int elements
+ */
+ public java.util.Enumeration enumerateSeq(
+ ) {
+ return this._seqList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public java.lang.String getColour(
+ ) {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean getColourText(
+ ) {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold(
+ ) {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean getDisplayBoxes(
+ ) {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean getDisplayText(
+ ) {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'outlineColour'.
+ *
+ * @return the value of field 'OutlineColour'.
+ */
+ public int getOutlineColour(
+ ) {
+ return this._outlineColour;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold(
+ ) {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Method getSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the int at the given index
+ */
+ public int getSeq(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size()) {
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ return ((java.lang.Integer) _seqList.get(index)).intValue();
+ }
+
+ /**
+ * Method getSeq.Returns the contents of the collection in an
+ * Array.
+ *
+ * @return this collection as an Array
+ */
+ public int[] getSeq(
+ ) {
+ int size = this._seqList.size();
+ int[] array = new int[size];
+ java.util.Iterator iter = _seqList.iterator();
+ for (int index = 0; index < size; index++) {
+ array[index] = ((java.lang.Integer) iter.next()).intValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSeqCount(
+ ) {
+ return this._seqList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart(
+ ) {
+ return this._start;
+ }
+
+ /**
+ * Method hasColourText.
+ *
+ * @return true if at least one ColourText has been added
+ */
+ public boolean hasColourText(
+ ) {
+ return this._has_colourText;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold(
+ ) {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasDisplayBoxes.
+ *
+ * @return true if at least one DisplayBoxes has been added
+ */
+ public boolean hasDisplayBoxes(
+ ) {
+ return this._has_displayBoxes;
+ }
+
+ /**
+ * Method hasDisplayText.
+ *
+ * @return true if at least one DisplayText has been added
+ */
+ public boolean hasDisplayText(
+ ) {
+ return this._has_displayText;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasOutlineColour.
+ *
+ * @return true if at least one OutlineColour has been added
+ */
+ public boolean hasOutlineColour(
+ ) {
+ return this._has_outlineColour;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold(
+ ) {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart(
+ ) {
+ return this._has_start;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean isColourText(
+ ) {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean isDisplayBoxes(
+ ) {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean isDisplayText(
+ ) {
+ return this._displayText;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllSeq(
+ ) {
+ this._seqList.clear();
+ }
+
+ /**
+ * Method removeSeq.
+ *
+ * @param vSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeq(
+ final int vSeq) {
+ boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+ return removed;
+ }
+
+ /**
+ * Method removeSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public int removeSeqAt(
+ final int index) {
+ java.lang.Object obj = this._seqList.remove(index);
+ return ((java.lang.Integer) obj).intValue();
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour the value of field 'colour'.
+ */
+ public void setColour(
+ final java.lang.String colour) {
+ this._colour = colour;
+ }
+
+ /**
+ * Sets the value of field 'colourText'.
+ *
+ * @param colourText the value of field 'colourText'.
+ */
+ public void setColourText(
+ final boolean colourText) {
+ this._colourText = colourText;
+ this._has_colourText = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(
+ final int consThreshold) {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'displayBoxes'.
+ *
+ * @param displayBoxes the value of field 'displayBoxes'.
+ */
+ public void setDisplayBoxes(
+ final boolean displayBoxes) {
+ this._displayBoxes = displayBoxes;
+ this._has_displayBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'displayText'.
+ *
+ * @param displayText the value of field 'displayText'.
+ */
+ public void setDisplayText(
+ final boolean displayText) {
+ this._displayText = displayText;
+ this._has_displayText = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'outlineColour'.
+ *
+ * @param outlineColour the value of field 'outlineColour'.
+ */
+ public void setOutlineColour(
+ final int outlineColour) {
+ this._outlineColour = outlineColour;
+ this._has_outlineColour = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(
+ final int pidThreshold) {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSeq(
+ final int index,
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size()) {
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ this._seqList.set(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param vSeqArray
+ */
+ public void setSeq(
+ final int[] vSeqArray) {
+ //-- copy array
+ _seqList.clear();
+
+ for (int i = 0; i < vSeqArray.length; i++) {
+ this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start the value of field 'start'.
+ */
+ public void setStart(
+ final int start) {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JGroup
+ */
+ public static jalview.binding.JGroup unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class JSeq implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _id.
- */
- private int _id;
-
- /**
- * keeps track of state for field: _id
- */
- private boolean _has_id;
-
- /**
- * Field _featuresList.
- */
- private java.util.Vector _featuresList;
-
- /**
- * Field _pdbidsList.
- */
- private java.util.Vector _pdbidsList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JSeq()
- {
- super();
- this._featuresList = new java.util.Vector();
- this._pdbidsList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addFeatures(final jalview.binding.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException
- {
- this._featuresList.addElement(vFeatures);
- }
-
- /**
- *
- *
- * @param index
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addFeatures(final int index,
- final jalview.binding.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException
- {
- this._featuresList.add(index, vFeatures);
- }
-
- /**
- *
- *
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addPdbids(final jalview.binding.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException
- {
- this._pdbidsList.addElement(vPdbids);
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addPdbids(final int index,
- final jalview.binding.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException
- {
- this._pdbidsList.add(index, vPdbids);
- }
-
- /**
- */
- public void deleteColour()
- {
- this._has_colour = false;
- }
-
- /**
- */
- public void deleteEnd()
- {
- this._has_end = false;
- }
-
- /**
- */
- public void deleteId()
- {
- this._has_id = false;
- }
-
- /**
- */
- public void deleteStart()
- {
- this._has_start = false;
- }
-
- /**
- * Method enumerateFeatures.
- *
- * @return an Enumeration over all jalview.binding.Features elements
- */
- public java.util.Enumeration enumerateFeatures()
- {
- return this._featuresList.elements();
- }
-
- /**
- * Method enumeratePdbids.
- *
- * @return an Enumeration over all jalview.binding.Pdbids elements
- */
- public java.util.Enumeration enumeratePdbids()
- {
- return this._pdbidsList.elements();
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour()
- {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd()
- {
- return this._end;
- }
-
- /**
- * Method getFeatures.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Features at the given index
- */
- public jalview.binding.Features getFeatures(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._featuresList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getFeatures",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._featuresList.size() - 1)).toString()
- }));
- }
-
- return (jalview.binding.Features) _featuresList.get(index);
- }
-
- /**
- * Method getFeatures.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Features[] getFeatures()
- {
- jalview.binding.Features[] array = new jalview.binding.Features[0];
- return (jalview.binding.Features[]) this._featuresList.toArray(array);
- }
-
- /**
- * Method getFeaturesCount.
- *
- * @return the size of this collection
- */
- public int getFeaturesCount()
- {
- return this._featuresList.size();
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public int getId()
- {
- return this._id;
- }
-
- /**
- * Method getPdbids.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Pdbids at the given index
- */
- public jalview.binding.Pdbids getPdbids(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._pdbidsList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getPdbids",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._pdbidsList.size() - 1)).toString()
- }));
- }
-
- return (jalview.binding.Pdbids) _pdbidsList.get(index);
- }
-
- /**
- * Method getPdbids.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Pdbids[] getPdbids()
- {
- jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
- return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
- }
-
- /**
- * Method getPdbidsCount.
- *
- * @return the size of this collection
- */
- public int getPdbidsCount()
- {
- return this._pdbidsList.size();
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart()
- {
- return this._start;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour()
- {
- return this._has_colour;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd()
- {
- return this._has_end;
- }
-
- /**
- * Method hasId.
- *
- * @return true if at least one Id has been added
- */
- public boolean hasId()
- {
- return this._has_id;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart()
- {
- return this._has_start;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllFeatures()
- {
- this._featuresList.clear();
- }
-
- /**
- */
- public void removeAllPdbids()
- {
- this._pdbidsList.clear();
- }
-
- /**
- * Method removeFeatures.
- *
- * @param vFeatures
- * @return true if the object was removed from the collection.
- */
- public boolean removeFeatures(final jalview.binding.Features vFeatures)
- {
- boolean removed = _featuresList.remove(vFeatures);
- return removed;
- }
-
- /**
- * Method removeFeaturesAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Features removeFeaturesAt(final int index)
- {
- java.lang.Object obj = this._featuresList.remove(index);
- return (jalview.binding.Features) obj;
- }
-
- /**
- * Method removePdbids.
- *
- * @param vPdbids
- * @return true if the object was removed from the collection.
- */
- public boolean removePdbids(final jalview.binding.Pdbids vPdbids)
- {
- boolean removed = _pdbidsList.remove(vPdbids);
- return removed;
- }
-
- /**
- * Method removePdbidsAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Pdbids removePdbidsAt(final int index)
- {
- java.lang.Object obj = this._pdbidsList.remove(index);
- return (jalview.binding.Pdbids) obj;
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour
- * the value of field 'colour'.
- */
- public void setColour(final int colour)
- {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end
- * the value of field 'end'.
- */
- public void setEnd(final int end)
- {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vFeatures
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setFeatures(final int index,
- final jalview.binding.Features vFeatures)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._featuresList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setFeatures",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._featuresList.size() - 1)).toString()
- }));
- }
-
- this._featuresList.set(index, vFeatures);
- }
-
- /**
- *
- *
- * @param vFeaturesArray
- */
- public void setFeatures(final jalview.binding.Features[] vFeaturesArray)
- {
- // -- copy array
- _featuresList.clear();
-
- for (int i = 0; i < vFeaturesArray.length; i++)
- {
- this._featuresList.add(vFeaturesArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id
- * the value of field 'id'.
- */
- public void setId(final int id)
- {
- this._id = id;
- this._has_id = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbids
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setPdbids(final int index,
- final jalview.binding.Pdbids vPdbids)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._pdbidsList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setPdbids",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._pdbidsList.size() - 1)).toString()
- }));
- }
-
- this._pdbidsList.set(index, vPdbids);
- }
-
- /**
- *
- *
- * @param vPdbidsArray
- */
- public void setPdbids(final jalview.binding.Pdbids[] vPdbidsArray)
- {
- // -- copy array
- _pdbidsList.clear();
-
- for (int i = 0; i < vPdbidsArray.length; i++)
- {
- this._pdbidsList.add(vPdbidsArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start
- * the value of field 'start'.
- */
- public void setStart(final int start)
- {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JSeq
- */
- public static jalview.binding.JSeq unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JSeq) Unmarshaller.unmarshal(
- jalview.binding.JSeq.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class JSeq implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _id.
+ */
+ private int _id;
+
+ /**
+ * keeps track of state for field: _id
+ */
+ private boolean _has_id;
+
+ /**
+ * Field _featuresList.
+ */
+ private java.util.Vector _featuresList;
+
+ /**
+ * Field _pdbidsList.
+ */
+ private java.util.Vector _pdbidsList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JSeq() {
+ super();
+ this._featuresList = new java.util.Vector();
+ this._pdbidsList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addFeatures(
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ this._featuresList.addElement(vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addFeatures(
+ final int index,
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ this._featuresList.add(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbids(
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ this._pdbidsList.addElement(vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbids(
+ final int index,
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ this._pdbidsList.add(index, vPdbids);
+ }
+
+ /**
+ */
+ public void deleteColour(
+ ) {
+ this._has_colour= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ */
+ public void deleteId(
+ ) {
+ this._has_id= false;
+ }
+
+ /**
+ */
+ public void deleteStart(
+ ) {
+ this._has_start= false;
+ }
+
+ /**
+ * Method enumerateFeatures.
+ *
+ * @return an Enumeration over all jalview.binding.Features
+ * elements
+ */
+ public java.util.Enumeration enumerateFeatures(
+ ) {
+ return this._featuresList.elements();
+ }
+
+ /**
+ * Method enumeratePdbids.
+ *
+ * @return an Enumeration over all jalview.binding.Pdbids
+ * elements
+ */
+ public java.util.Enumeration enumeratePdbids(
+ ) {
+ return this._pdbidsList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour(
+ ) {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Method getFeatures.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Features at the
+ * given index
+ */
+ public jalview.binding.Features getFeatures(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size()) {
+ throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Features) _featuresList.get(index);
+ }
+
+ /**
+ * Method getFeatures.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Features[] getFeatures(
+ ) {
+ jalview.binding.Features[] array = new jalview.binding.Features[0];
+ return (jalview.binding.Features[]) this._featuresList.toArray(array);
+ }
+
+ /**
+ * Method getFeaturesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getFeaturesCount(
+ ) {
+ return this._featuresList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public int getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Method getPdbids.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Pdbids at the given
+ * index
+ */
+ public jalview.binding.Pdbids getPdbids(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size()) {
+ throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Pdbids) _pdbidsList.get(index);
+ }
+
+ /**
+ * Method getPdbids.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Pdbids[] getPdbids(
+ ) {
+ jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
+ return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
+ }
+
+ /**
+ * Method getPdbidsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbidsCount(
+ ) {
+ return this._pdbidsList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart(
+ ) {
+ return this._start;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour(
+ ) {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasId.
+ *
+ * @return true if at least one Id has been added
+ */
+ public boolean hasId(
+ ) {
+ return this._has_id;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart(
+ ) {
+ return this._has_start;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllFeatures(
+ ) {
+ this._featuresList.clear();
+ }
+
+ /**
+ */
+ public void removeAllPdbids(
+ ) {
+ this._pdbidsList.clear();
+ }
+
+ /**
+ * Method removeFeatures.
+ *
+ * @param vFeatures
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeFeatures(
+ final jalview.binding.Features vFeatures) {
+ boolean removed = _featuresList.remove(vFeatures);
+ return removed;
+ }
+
+ /**
+ * Method removeFeaturesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Features removeFeaturesAt(
+ final int index) {
+ java.lang.Object obj = this._featuresList.remove(index);
+ return (jalview.binding.Features) obj;
+ }
+
+ /**
+ * Method removePdbids.
+ *
+ * @param vPdbids
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbids(
+ final jalview.binding.Pdbids vPdbids) {
+ boolean removed = _pdbidsList.remove(vPdbids);
+ return removed;
+ }
+
+ /**
+ * Method removePdbidsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Pdbids removePdbidsAt(
+ final int index) {
+ java.lang.Object obj = this._pdbidsList.remove(index);
+ return (jalview.binding.Pdbids) obj;
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour the value of field 'colour'.
+ */
+ public void setColour(
+ final int colour) {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setFeatures(
+ final int index,
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size()) {
+ throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+ }
+
+ this._featuresList.set(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vFeaturesArray
+ */
+ public void setFeatures(
+ final jalview.binding.Features[] vFeaturesArray) {
+ //-- copy array
+ _featuresList.clear();
+
+ for (int i = 0; i < vFeaturesArray.length; i++) {
+ this._featuresList.add(vFeaturesArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final int id) {
+ this._id = id;
+ this._has_id = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setPdbids(
+ final int index,
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size()) {
+ throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ this._pdbidsList.set(index, vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbidsArray
+ */
+ public void setPdbids(
+ final jalview.binding.Pdbids[] vPdbidsArray) {
+ //-- copy array
+ _pdbidsList.clear();
+
+ for (int i = 0; i < vPdbidsArray.length; i++) {
+ this._pdbidsList.add(vPdbidsArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start the value of field 'start'.
+ */
+ public void setStart(
+ final int start) {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JSeq
+ */
+ public static jalview.binding.JSeq unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewModel implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _creationDate.
- */
- private java.util.Date _creationDate;
-
- /**
- * Field _version.
- */
- private java.lang.String _version;
-
- /**
- * Field _vamsasModel.
- */
- private jalview.binding.VamsasModel _vamsasModel;
-
- /**
- * Field _jalviewModelSequence.
- */
- private jalview.binding.JalviewModelSequence _jalviewModelSequence;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JalviewModel()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Returns the value of field 'creationDate'.
- *
- * @return the value of field 'CreationDate'.
- */
- public java.util.Date getCreationDate()
- {
- return this._creationDate;
- }
-
- /**
- * Returns the value of field 'jalviewModelSequence'.
- *
- * @return the value of field 'JalviewModelSequence'.
- */
- public jalview.binding.JalviewModelSequence getJalviewModelSequence()
- {
- return this._jalviewModelSequence;
- }
-
- /**
- * Returns the value of field 'vamsasModel'.
- *
- * @return the value of field 'VamsasModel'.
- */
- public jalview.binding.VamsasModel getVamsasModel()
- {
- return this._vamsasModel;
- }
-
- /**
- * Returns the value of field 'version'.
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+public class JalviewModel implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _creationDate.
+ */
+ private java.util.Date _creationDate;
+
+ /**
+ * Field _version.
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _vamsasModel.
+ */
+ private jalview.binding.VamsasModel _vamsasModel;
+
+ /**
+ * Field _jalviewModelSequence.
+ */
+ private jalview.binding.JalviewModelSequence _jalviewModelSequence;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewModel() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'creationDate'.
+ *
+ * @return the value of field 'CreationDate'.
+ */
+ public java.util.Date getCreationDate(
+ ) {
+ return this._creationDate;
+ }
+
+ /**
+ * Returns the value of field 'jalviewModelSequence'.
+ *
+ * @return the value of field 'JalviewModelSequence'.
+ */
+ public jalview.binding.JalviewModelSequence getJalviewModelSequence(
+ ) {
+ return this._jalviewModelSequence;
+ }
+
+ /**
+ * Returns the value of field 'vamsasModel'.
+ *
+ * @return the value of field 'VamsasModel'.
+ */
+ public jalview.binding.VamsasModel getVamsasModel(
+ ) {
+ return this._vamsasModel;
+ }
+
+ /**
+ * Returns the value of field 'version'.
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion(
+ ) {
+ return this._version;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'creationDate'.
+ *
+ * @param creationDate the value of field 'creationDate'.
+ */
+ public void setCreationDate(
+ final java.util.Date creationDate) {
+ this._creationDate = creationDate;
+ }
+
+ /**
+ * Sets the value of field 'jalviewModelSequence'.
+ *
+ * @param jalviewModelSequence the value of field
+ * 'jalviewModelSequence'.
+ */
+ public void setJalviewModelSequence(
+ final jalview.binding.JalviewModelSequence jalviewModelSequence) {
+ this._jalviewModelSequence = jalviewModelSequence;
+ }
+
+ /**
+ * Sets the value of field 'vamsasModel'.
+ *
+ * @param vamsasModel the value of field 'vamsasModel'.
+ */
+ public void setVamsasModel(
+ final jalview.binding.VamsasModel vamsasModel) {
+ this._vamsasModel = vamsasModel;
+ }
+
+ /**
+ * Sets the value of field 'version'.
+ *
+ * @param version the value of field 'version'.
+ */
+ public void setVersion(
+ final java.lang.String version) {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewModel
+ */
+ public static jalview.binding.JalviewModel unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'creationDate'.
- *
- * @param creationDate
- * the value of field 'creationDate'.
- */
- public void setCreationDate(final java.util.Date creationDate)
- {
- this._creationDate = creationDate;
- }
-
- /**
- * Sets the value of field 'jalviewModelSequence'.
- *
- * @param jalviewModelSequence
- * the value of field 'jalviewModelSequence'.
- */
- public void setJalviewModelSequence(
- final jalview.binding.JalviewModelSequence jalviewModelSequence)
- {
- this._jalviewModelSequence = jalviewModelSequence;
- }
-
- /**
- * Sets the value of field 'vamsasModel'.
- *
- * @param vamsasModel
- * the value of field 'vamsasModel'.
- */
- public void setVamsasModel(final jalview.binding.VamsasModel vamsasModel)
- {
- this._vamsasModel = vamsasModel;
- }
-
- /**
- * Sets the value of field 'version'.
- *
- * @param version
- * the value of field 'version'.
- */
- public void setVersion(final java.lang.String version)
- {
- this._version = version;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JalviewModel
- */
- public static jalview.binding.JalviewModel unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(
- jalview.binding.JalviewModel.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewModelSequence implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _JSeqList.
- */
- private java.util.Vector _JSeqList;
-
- /**
- * Field _JGroupList.
- */
- private java.util.Vector _JGroupList;
-
- /**
- * Field _viewportList.
- */
- private java.util.Vector _viewportList;
-
- /**
- * Field _userColoursList.
- */
- private java.util.Vector _userColoursList;
-
- /**
- * Field _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _featureSettings.
- */
- private jalview.binding.FeatureSettings _featureSettings;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JalviewModelSequence()
- {
- super();
- this._JSeqList = new java.util.Vector();
- this._JGroupList = new java.util.Vector();
- this._viewportList = new java.util.Vector();
- this._userColoursList = new java.util.Vector();
- this._treeList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addJGroup(final jalview.binding.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException
- {
- this._JGroupList.addElement(vJGroup);
- }
-
- /**
- *
- *
- * @param index
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addJGroup(final int index,
- final jalview.binding.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException
- {
- this._JGroupList.add(index, vJGroup);
- }
-
- /**
- *
- *
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addJSeq(final jalview.binding.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- this._JSeqList.addElement(vJSeq);
- }
-
- /**
- *
- *
- * @param index
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addJSeq(final int index, final jalview.binding.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- this._JSeqList.add(index, vJSeq);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addTree(final jalview.binding.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addTree(final int index, final jalview.binding.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- this._treeList.add(index, vTree);
- }
-
- /**
- *
- *
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addUserColours(final jalview.binding.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException
- {
- this._userColoursList.addElement(vUserColours);
- }
-
- /**
- *
- *
- * @param index
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addUserColours(final int index,
- final jalview.binding.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException
- {
- this._userColoursList.add(index, vUserColours);
- }
-
- /**
- *
- *
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addViewport(final jalview.binding.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException
- {
- this._viewportList.addElement(vViewport);
- }
-
- /**
- *
- *
- * @param index
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addViewport(final int index,
- final jalview.binding.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException
- {
- this._viewportList.add(index, vViewport);
- }
-
- /**
- * Method enumerateJGroup.
- *
- * @return an Enumeration over all jalview.binding.JGroup elements
- */
- public java.util.Enumeration enumerateJGroup()
- {
- return this._JGroupList.elements();
- }
-
- /**
- * Method enumerateJSeq.
- *
- * @return an Enumeration over all jalview.binding.JSeq elements
- */
- public java.util.Enumeration enumerateJSeq()
- {
- return this._JSeqList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all jalview.binding.Tree elements
- */
- public java.util.Enumeration enumerateTree()
- {
- return this._treeList.elements();
- }
-
- /**
- * Method enumerateUserColours.
- *
- * @return an Enumeration over all jalview.binding.UserColours elements
- */
- public java.util.Enumeration enumerateUserColours()
- {
- return this._userColoursList.elements();
- }
-
- /**
- * Method enumerateViewport.
- *
- * @return an Enumeration over all jalview.binding.Viewport elements
- */
- public java.util.Enumeration enumerateViewport()
- {
- return this._viewportList.elements();
- }
-
- /**
- * Returns the value of field 'featureSettings'.
- *
- * @return the value of field 'FeatureSettings'.
- */
- public jalview.binding.FeatureSettings getFeatureSettings()
- {
- return this._featureSettings;
- }
-
- /**
- * Method getJGroup.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.JGroup at the given index
- */
- public jalview.binding.JGroup getJGroup(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._JGroupList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getJGroup",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._JGroupList.size() - 1)).toString()
- }));
- }
-
- return (jalview.binding.JGroup) _JGroupList.get(index);
- }
-
- /**
- * Method getJGroup.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.JGroup[] getJGroup()
- {
- jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
- return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
- }
-
- /**
- * Method getJGroupCount.
- *
- * @return the size of this collection
- */
- public int getJGroupCount()
- {
- return this._JGroupList.size();
- }
-
- /**
- * Method getJSeq.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.JSeq at the given index
- */
- public jalview.binding.JSeq getJSeq(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._JSeqList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getJSeq",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._JSeqList.size() - 1)).toString()
- }));
- }
-
- return (jalview.binding.JSeq) _JSeqList.get(index);
- }
-
- /**
- * Method getJSeq.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.JSeq[] getJSeq()
- {
- jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
- return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
- }
-
- /**
- * Method getJSeqCount.
- *
- * @return the size of this collection
- */
- public int getJSeqCount()
- {
- return this._JSeqList.size();
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Tree at the given index
- */
- public jalview.binding.Tree getTree(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getJgetTreeSeq",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._treeList.size() - 1)).toString()
- }));
- }
-
- return (jalview.binding.Tree) _treeList.get(index);
- }
-
- /**
- * Method getTree.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Tree[] getTree()
- {
- jalview.binding.Tree[] array = new jalview.binding.Tree[0];
- return (jalview.binding.Tree[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount()
- {
- return this._treeList.size();
- }
-
- /**
- * Method getUserColours.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.UserColours at the given index
- */
- public jalview.binding.UserColours getUserColours(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._userColoursList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getUserColours",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._userColoursList.size() - 1)).toString()
- }));
- }
-
- return (jalview.binding.UserColours) _userColoursList.get(index);
- }
-
- /**
- * Method getUserColours.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.UserColours[] getUserColours()
- {
- jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
- return (jalview.binding.UserColours[]) this._userColoursList
- .toArray(array);
- }
-
- /**
- * Method getUserColoursCount.
- *
- * @return the size of this collection
- */
- public int getUserColoursCount()
- {
- return this._userColoursList.size();
- }
-
- /**
- * Method getViewport.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Viewport at the given index
- */
- public jalview.binding.Viewport getViewport(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._viewportList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getViewport",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._viewportList.size() - 1)).toString()
- }));
- }
-
- return (jalview.binding.Viewport) _viewportList.get(index);
- }
-
- /**
- * Method getViewport.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Viewport[] getViewport()
- {
- jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
- return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
- }
-
- /**
- * Method getViewportCount.
- *
- * @return the size of this collection
- */
- public int getViewportCount()
- {
- return this._viewportList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllJGroup()
- {
- this._JGroupList.clear();
- }
-
- /**
- */
- public void removeAllJSeq()
- {
- this._JSeqList.clear();
- }
-
- /**
- */
- public void removeAllTree()
- {
- this._treeList.clear();
- }
-
- /**
- */
- public void removeAllUserColours()
- {
- this._userColoursList.clear();
- }
-
- /**
- */
- public void removeAllViewport()
- {
- this._viewportList.clear();
- }
-
- /**
- * Method removeJGroup.
- *
- * @param vJGroup
- * @return true if the object was removed from the collection.
- */
- public boolean removeJGroup(final jalview.binding.JGroup vJGroup)
- {
- boolean removed = _JGroupList.remove(vJGroup);
- return removed;
- }
-
- /**
- * Method removeJGroupAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.JGroup removeJGroupAt(final int index)
- {
- java.lang.Object obj = this._JGroupList.remove(index);
- return (jalview.binding.JGroup) obj;
- }
-
- /**
- * Method removeJSeq.
- *
- * @param vJSeq
- * @return true if the object was removed from the collection.
- */
- public boolean removeJSeq(final jalview.binding.JSeq vJSeq)
- {
- boolean removed = _JSeqList.remove(vJSeq);
- return removed;
- }
-
- /**
- * Method removeJSeqAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.JSeq removeJSeqAt(final int index)
- {
- java.lang.Object obj = this._JSeqList.remove(index);
- return (jalview.binding.JSeq) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(final jalview.binding.Tree vTree)
- {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Tree removeTreeAt(final int index)
- {
- java.lang.Object obj = this._treeList.remove(index);
- return (jalview.binding.Tree) obj;
- }
-
- /**
- * Method removeUserColours.
- *
- * @param vUserColours
- * @return true if the object was removed from the collection.
- */
- public boolean removeUserColours(
- final jalview.binding.UserColours vUserColours)
- {
- boolean removed = _userColoursList.remove(vUserColours);
- return removed;
- }
-
- /**
- * Method removeUserColoursAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.UserColours removeUserColoursAt(final int index)
- {
- java.lang.Object obj = this._userColoursList.remove(index);
- return (jalview.binding.UserColours) obj;
- }
-
- /**
- * Method removeViewport.
- *
- * @param vViewport
- * @return true if the object was removed from the collection.
- */
- public boolean removeViewport(final jalview.binding.Viewport vViewport)
- {
- boolean removed = _viewportList.remove(vViewport);
- return removed;
- }
-
- /**
- * Method removeViewportAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Viewport removeViewportAt(final int index)
- {
- java.lang.Object obj = this._viewportList.remove(index);
- return (jalview.binding.Viewport) obj;
- }
-
- /**
- * Sets the value of field 'featureSettings'.
- *
- * @param featureSettings
- * the value of field 'featureSettings'.
- */
- public void setFeatureSettings(
- final jalview.binding.FeatureSettings featureSettings)
- {
- this._featureSettings = featureSettings;
- }
-
- /**
- *
- *
- * @param index
- * @param vJGroup
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setJGroup(final int index,
- final jalview.binding.JGroup vJGroup)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._JGroupList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setJGroup",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._JGroupList.size() - 1)).toString()
- }));
- }
-
- this._JGroupList.set(index, vJGroup);
- }
-
- /**
- *
- *
- * @param vJGroupArray
- */
- public void setJGroup(final jalview.binding.JGroup[] vJGroupArray)
- {
- // -- copy array
- _JGroupList.clear();
-
- for (int i = 0; i < vJGroupArray.length; i++)
- {
- this._JGroupList.add(vJGroupArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vJSeq
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setJSeq(final int index, final jalview.binding.JSeq vJSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._JSeqList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setJSeq",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._JSeqList.size() - 1)).toString()
- }));
- }
-
- this._JSeqList.set(index, vJSeq);
- }
-
- /**
- *
- *
- * @param vJSeqArray
- */
- public void setJSeq(final jalview.binding.JSeq[] vJSeqArray)
- {
- // -- copy array
- _JSeqList.clear();
-
- for (int i = 0; i < vJSeqArray.length; i++)
- {
- this._JSeqList.add(vJSeqArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setTree(final int index, final jalview.binding.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setTree",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._treeList.size() - 1)).toString()
- }));
- }
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(final jalview.binding.Tree[] vTreeArray)
- {
- // -- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++)
- {
- this._treeList.add(vTreeArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vUserColours
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setUserColours(final int index,
- final jalview.binding.UserColours vUserColours)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._userColoursList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setUserColours",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._userColoursList.size() - 1)).toString()
- }));
- }
-
- this._userColoursList.set(index, vUserColours);
- }
-
- /**
- *
- *
- * @param vUserColoursArray
- */
- public void setUserColours(
- final jalview.binding.UserColours[] vUserColoursArray)
- {
- // -- copy array
- _userColoursList.clear();
-
- for (int i = 0; i < vUserColoursArray.length; i++)
- {
- this._userColoursList.add(vUserColoursArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vViewport
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setViewport(final int index,
- final jalview.binding.Viewport vViewport)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._viewportList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setViewport",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._viewportList.size() - 1)).toString()
- }));
- }
-
- this._viewportList.set(index, vViewport);
- }
-
- /**
- *
- *
- * @param vViewportArray
- */
- public void setViewport(final jalview.binding.Viewport[] vViewportArray)
- {
- // -- copy array
- _viewportList.clear();
-
- for (int i = 0; i < vViewportArray.length; i++)
- {
- this._viewportList.add(vViewportArray[i]);
- }
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JalviewModelSequence
- */
- public static jalview.binding.JalviewModelSequence unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(
- jalview.binding.JalviewModelSequence.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class JalviewModelSequence implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _JSeqList.
+ */
+ private java.util.Vector _JSeqList;
+
+ /**
+ * Field _JGroupList.
+ */
+ private java.util.Vector _JGroupList;
+
+ /**
+ * Field _viewportList.
+ */
+ private java.util.Vector _viewportList;
+
+ /**
+ * Field _userColoursList.
+ */
+ private java.util.Vector _userColoursList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _featureSettings.
+ */
+ private jalview.binding.FeatureSettings _featureSettings;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewModelSequence() {
+ super();
+ this._JSeqList = new java.util.Vector();
+ this._JGroupList = new java.util.Vector();
+ this._viewportList = new java.util.Vector();
+ this._userColoursList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJGroup(
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JGroupList.addElement(vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJGroup(
+ final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JGroupList.add(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJSeq(
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JSeqList.addElement(vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJSeq(
+ final int index,
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JSeqList.add(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final int index,
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ this._userColoursList.addElement(vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ this._userColoursList.add(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ this._viewportList.addElement(vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ this._viewportList.add(index, vViewport);
+ }
+
+ /**
+ * Method enumerateJGroup.
+ *
+ * @return an Enumeration over all jalview.binding.JGroup
+ * elements
+ */
+ public java.util.Enumeration enumerateJGroup(
+ ) {
+ return this._JGroupList.elements();
+ }
+
+ /**
+ * Method enumerateJSeq.
+ *
+ * @return an Enumeration over all jalview.binding.JSeq elements
+ */
+ public java.util.Enumeration enumerateJSeq(
+ ) {
+ return this._JSeqList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all jalview.binding.Tree elements
+ */
+ public java.util.Enumeration enumerateTree(
+ ) {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method enumerateUserColours.
+ *
+ * @return an Enumeration over all jalview.binding.UserColours
+ * elements
+ */
+ public java.util.Enumeration enumerateUserColours(
+ ) {
+ return this._userColoursList.elements();
+ }
+
+ /**
+ * Method enumerateViewport.
+ *
+ * @return an Enumeration over all jalview.binding.Viewport
+ * elements
+ */
+ public java.util.Enumeration enumerateViewport(
+ ) {
+ return this._viewportList.elements();
+ }
+
+ /**
+ * Returns the value of field 'featureSettings'.
+ *
+ * @return the value of field 'FeatureSettings'.
+ */
+ public jalview.binding.FeatureSettings getFeatureSettings(
+ ) {
+ return this._featureSettings;
+ }
+
+ /**
+ * Method getJGroup.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JGroup at the given
+ * index
+ */
+ public jalview.binding.JGroup getJGroup(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size()) {
+ throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JGroup) _JGroupList.get(index);
+ }
+
+ /**
+ * Method getJGroup.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.JGroup[] getJGroup(
+ ) {
+ jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
+ return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
+ }
+
+ /**
+ * Method getJGroupCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJGroupCount(
+ ) {
+ return this._JGroupList.size();
+ }
+
+ /**
+ * Method getJSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JSeq at the given
+ * index
+ */
+ public jalview.binding.JSeq getJSeq(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size()) {
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JSeq) _JSeqList.get(index);
+ }
+
+ /**
+ * Method getJSeq.Returns the contents of the collection in an
+ * Array. <p>Note: Just in case the collection contents are
+ * changing in another thread, we pass a 0-length Array of the
+ * correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.JSeq[] getJSeq(
+ ) {
+ jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
+ return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
+ }
+
+ /**
+ * Method getJSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJSeqCount(
+ ) {
+ return this._JSeqList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Tree at the given
+ * index
+ */
+ public jalview.binding.Tree getTree(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an
+ * Array. <p>Note: Just in case the collection contents are
+ * changing in another thread, we pass a 0-length Array of the
+ * correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Tree[] getTree(
+ ) {
+ jalview.binding.Tree[] array = new jalview.binding.Tree[0];
+ return (jalview.binding.Tree[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount(
+ ) {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method getUserColours.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.UserColours at the
+ * given index
+ */
+ public jalview.binding.UserColours getUserColours(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size()) {
+ throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.UserColours) _userColoursList.get(index);
+ }
+
+ /**
+ * Method getUserColours.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.UserColours[] getUserColours(
+ ) {
+ jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
+ return (jalview.binding.UserColours[]) this._userColoursList.toArray(array);
+ }
+
+ /**
+ * Method getUserColoursCount.
+ *
+ * @return the size of this collection
+ */
+ public int getUserColoursCount(
+ ) {
+ return this._userColoursList.size();
+ }
+
+ /**
+ * Method getViewport.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Viewport at the
+ * given index
+ */
+ public jalview.binding.Viewport getViewport(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size()) {
+ throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Viewport) _viewportList.get(index);
+ }
+
+ /**
+ * Method getViewport.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Viewport[] getViewport(
+ ) {
+ jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
+ return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
+ }
+
+ /**
+ * Method getViewportCount.
+ *
+ * @return the size of this collection
+ */
+ public int getViewportCount(
+ ) {
+ return this._viewportList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllJGroup(
+ ) {
+ this._JGroupList.clear();
+ }
+
+ /**
+ */
+ public void removeAllJSeq(
+ ) {
+ this._JSeqList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree(
+ ) {
+ this._treeList.clear();
+ }
+
+ /**
+ */
+ public void removeAllUserColours(
+ ) {
+ this._userColoursList.clear();
+ }
+
+ /**
+ */
+ public void removeAllViewport(
+ ) {
+ this._viewportList.clear();
+ }
+
+ /**
+ * Method removeJGroup.
+ *
+ * @param vJGroup
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJGroup(
+ final jalview.binding.JGroup vJGroup) {
+ boolean removed = _JGroupList.remove(vJGroup);
+ return removed;
+ }
+
+ /**
+ * Method removeJGroupAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JGroup removeJGroupAt(
+ final int index) {
+ java.lang.Object obj = this._JGroupList.remove(index);
+ return (jalview.binding.JGroup) obj;
+ }
+
+ /**
+ * Method removeJSeq.
+ *
+ * @param vJSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJSeq(
+ final jalview.binding.JSeq vJSeq) {
+ boolean removed = _JSeqList.remove(vJSeq);
+ return removed;
+ }
+
+ /**
+ * Method removeJSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JSeq removeJSeqAt(
+ final int index) {
+ java.lang.Object obj = this._JSeqList.remove(index);
+ return (jalview.binding.JSeq) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(
+ final jalview.binding.Tree vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Tree removeTreeAt(
+ final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (jalview.binding.Tree) obj;
+ }
+
+ /**
+ * Method removeUserColours.
+ *
+ * @param vUserColours
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeUserColours(
+ final jalview.binding.UserColours vUserColours) {
+ boolean removed = _userColoursList.remove(vUserColours);
+ return removed;
+ }
+
+ /**
+ * Method removeUserColoursAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.UserColours removeUserColoursAt(
+ final int index) {
+ java.lang.Object obj = this._userColoursList.remove(index);
+ return (jalview.binding.UserColours) obj;
+ }
+
+ /**
+ * Method removeViewport.
+ *
+ * @param vViewport
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeViewport(
+ final jalview.binding.Viewport vViewport) {
+ boolean removed = _viewportList.remove(vViewport);
+ return removed;
+ }
+
+ /**
+ * Method removeViewportAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Viewport removeViewportAt(
+ final int index) {
+ java.lang.Object obj = this._viewportList.remove(index);
+ return (jalview.binding.Viewport) obj;
+ }
+
+ /**
+ * Sets the value of field 'featureSettings'.
+ *
+ * @param featureSettings the value of field 'featureSettings'.
+ */
+ public void setFeatureSettings(
+ final jalview.binding.FeatureSettings featureSettings) {
+ this._featureSettings = featureSettings;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setJGroup(
+ final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size()) {
+ throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+ }
+
+ this._JGroupList.set(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJGroupArray
+ */
+ public void setJGroup(
+ final jalview.binding.JGroup[] vJGroupArray) {
+ //-- copy array
+ _JGroupList.clear();
+
+ for (int i = 0; i < vJGroupArray.length; i++) {
+ this._JGroupList.add(vJGroupArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setJSeq(
+ final int index,
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size()) {
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ this._JSeqList.set(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeqArray
+ */
+ public void setJSeq(
+ final jalview.binding.JSeq[] vJSeqArray) {
+ //-- copy array
+ _JSeqList.clear();
+
+ for (int i = 0; i < vJSeqArray.length; i++) {
+ this._JSeqList.add(vJSeqArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setTree(
+ final int index,
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(
+ final jalview.binding.Tree[] vTreeArray) {
+ //-- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setUserColours(
+ final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size()) {
+ throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+ }
+
+ this._userColoursList.set(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColoursArray
+ */
+ public void setUserColours(
+ final jalview.binding.UserColours[] vUserColoursArray) {
+ //-- copy array
+ _userColoursList.clear();
+
+ for (int i = 0; i < vUserColoursArray.length; i++) {
+ this._userColoursList.add(vUserColoursArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setViewport(
+ final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size()) {
+ throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+ }
+
+ this._viewportList.set(index, vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param vViewportArray
+ */
+ public void setViewport(
+ final jalview.binding.Viewport[] vViewportArray) {
+ //-- copy array
+ _viewportList.clear();
+
+ for (int i = 0; i < vViewportArray.length; i++) {
+ this._viewportList.add(vViewportArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewModelSequence
+ */
+ public static jalview.binding.JalviewModelSequence unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-import jalview.util.MessageManager;
-
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class JalviewUserColours implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _schemeName.
- */
- private java.lang.String _schemeName;
-
- /**
- * Jalview colour scheme document version.
- *
- */
- private java.lang.String _version;
-
- /**
- * Field _colourList.
- */
- private java.util.Vector _colourList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public JalviewUserColours()
- {
- super();
- this._colourList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addColour(final Colour vColour)
- throws java.lang.IndexOutOfBoundsException
- {
- this._colourList.addElement(vColour);
- }
-
- /**
- *
- *
- * @param index
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addColour(final int index, final Colour vColour)
- throws java.lang.IndexOutOfBoundsException
- {
- this._colourList.add(index, vColour);
- }
-
- /**
- * Method enumerateColour.
- *
- * @return an Enumeration over all Colour elements
- */
- public java.util.Enumeration enumerateColour()
- {
- return this._colourList.elements();
- }
-
- /**
- * Method getColour.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the Colour at the given index
- */
- public Colour getColour(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._colourList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getColour",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._colourList.size() - 1)).toString()
- }));
+public class JalviewUserColours implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _schemeName.
+ */
+ private java.lang.String _schemeName;
+
+ /**
+ * Jalview colour scheme document version.
+ *
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _colourList.
+ */
+ private java.util.Vector _colourList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewUserColours() {
+ super();
+ this._colourList = new java.util.Vector();
}
- return (Colour) _colourList.get(index);
- }
-
- /**
- * Method getColour.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public Colour[] getColour()
- {
- Colour[] array = new Colour[0];
- return (Colour[]) this._colourList.toArray(array);
- }
-
- /**
- * Method getColourCount.
- *
- * @return the size of this collection
- */
- public int getColourCount()
- {
- return this._colourList.size();
- }
-
- /**
- * Returns the value of field 'schemeName'.
- *
- * @return the value of field 'SchemeName'.
- */
- public java.lang.String getSchemeName()
- {
- return this._schemeName;
- }
-
- /**
- * Returns the value of field 'version'. The field 'version' has the following
- * description: Jalview colour scheme document version.
- *
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addColour(
+ final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException {
+ this._colourList.addElement(vColour);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addColour(
+ final int index,
+ final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException {
+ this._colourList.add(index, vColour);
+ }
+
+ /**
+ * Method enumerateColour.
+ *
+ * @return an Enumeration over all Colour elements
+ */
+ public java.util.Enumeration enumerateColour(
+ ) {
+ return this._colourList.elements();
+ }
+
+ /**
+ * Method getColour.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the Colour at the given index
+ */
+ public Colour getColour(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size()) {
+ throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
+ }
+
+ return (Colour) _colourList.get(index);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
+
+ /**
+ * Method getColour.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public Colour[] getColour(
+ ) {
+ Colour[] array = new Colour[0];
+ return (Colour[]) this._colourList.toArray(array);
+ }
+
+ /**
+ * Method getColourCount.
+ *
+ * @return the size of this collection
*/
- public void removeAllColour()
- {
- this._colourList.clear();
- }
-
- /**
- * Method removeColour.
- *
- * @param vColour
- * @return true if the object was removed from the collection.
- */
- public boolean removeColour(final Colour vColour)
- {
- boolean removed = _colourList.remove(vColour);
- return removed;
- }
-
- /**
- * Method removeColourAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public Colour removeColourAt(final int index)
- {
- java.lang.Object obj = this._colourList.remove(index);
- return (Colour) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vColour
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setColour(final int index, final Colour vColour)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._colourList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setColour",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._colourList.size() - 1)).toString()
- }));
+ public int getColourCount(
+ ) {
+ return this._colourList.size();
}
- this._colourList.set(index, vColour);
- }
-
- /**
- *
- *
- * @param vColourArray
- */
- public void setColour(final Colour[] vColourArray)
- {
- // -- copy array
- _colourList.clear();
-
- for (int i = 0; i < vColourArray.length; i++)
- {
- this._colourList.add(vColourArray[i]);
+ /**
+ * Returns the value of field 'schemeName'.
+ *
+ * @return the value of field 'SchemeName'.
+ */
+ public java.lang.String getSchemeName(
+ ) {
+ return this._schemeName;
+ }
+
+ /**
+ * Returns the value of field 'version'. The field 'version'
+ * has the following description: Jalview colour scheme
+ * document version.
+ *
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion(
+ ) {
+ return this._version;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllColour(
+ ) {
+ this._colourList.clear();
+ }
+
+ /**
+ * Method removeColour.
+ *
+ * @param vColour
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeColour(
+ final Colour vColour) {
+ boolean removed = _colourList.remove(vColour);
+ return removed;
+ }
+
+ /**
+ * Method removeColourAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Colour removeColourAt(
+ final int index) {
+ java.lang.Object obj = this._colourList.remove(index);
+ return (Colour) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setColour(
+ final int index,
+ final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size()) {
+ throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
+ }
+
+ this._colourList.set(index, vColour);
+ }
+
+ /**
+ *
+ *
+ * @param vColourArray
+ */
+ public void setColour(
+ final Colour[] vColourArray) {
+ //-- copy array
+ _colourList.clear();
+
+ for (int i = 0; i < vColourArray.length; i++) {
+ this._colourList.add(vColourArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'schemeName'.
+ *
+ * @param schemeName the value of field 'schemeName'.
+ */
+ public void setSchemeName(
+ final java.lang.String schemeName) {
+ this._schemeName = schemeName;
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has
+ * the following description: Jalview colour scheme document
+ * version.
+ *
+ *
+ * @param version the value of field 'version'.
+ */
+ public void setVersion(
+ final java.lang.String version) {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewUserColours
+ */
+ public static jalview.binding.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- }
-
- /**
- * Sets the value of field 'schemeName'.
- *
- * @param schemeName
- * the value of field 'schemeName'.
- */
- public void setSchemeName(final java.lang.String schemeName)
- {
- this._schemeName = schemeName;
- }
-
- /**
- * Sets the value of field 'version'. The field 'version' has the following
- * description: Jalview colour scheme document version.
- *
- *
- * @param version
- * the value of field 'version'.
- */
- public void setVersion(final java.lang.String version)
- {
- this._version = version;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JalviewUserColours
- */
- public static jalview.binding.JalviewUserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
- jalview.binding.JalviewUserColours.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-import jalview.util.MessageManager;
-
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class Pdbentry implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _items.
- */
- private java.util.Vector _items;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Pdbentry()
- {
- super();
- this._items = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addPdbentryItem(
- final jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- this._items.addElement(vPdbentryItem);
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addPdbentryItem(final int index,
- final jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- this._items.add(index, vPdbentryItem);
- }
-
- /**
- * Method enumeratePdbentryItem.
- *
- * @return an Enumeration over all jalview.binding.PdbentryItem elements
- */
- public java.util.Enumeration enumeratePdbentryItem()
- {
- return this._items.elements();
- }
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- }
-
- /**
- * Method getPdbentryItem.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.PdbentryItem at the given index
- */
- public jalview.binding.PdbentryItem getPdbentryItem(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._items.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getPdbentryItem",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._items.size() - 1)).toString()
- }));
+public class Pdbentry implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _items.
+ */
+ private java.util.Vector _items;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Pdbentry() {
+ super();
+ this._items = new java.util.Vector();
}
- return (jalview.binding.PdbentryItem) _items.get(index);
- }
-
- /**
- * Method getPdbentryItem.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.PdbentryItem[] getPdbentryItem()
- {
- jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
- return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
- }
-
- /**
- * Method getPdbentryItemCount.
- *
- * @return the size of this collection
- */
- public int getPdbentryItemCount()
- {
- return this._items.size();
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType()
- {
- return this._type;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ this._items.addElement(vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final int index,
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ this._items.add(index, vPdbentryItem);
+ }
+
+ /**
+ * Method enumeratePdbentryItem.
+ *
+ * @return an Enumeration over all jalview.binding.PdbentryItem
+ * elements
+ */
+ public java.util.Enumeration enumeratePdbentryItem(
+ ) {
+ return this._items.elements();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
+
+ /**
+ * Method getPdbentryItem.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.PdbentryItem at the
+ * given index
+ */
+ public jalview.binding.PdbentryItem getPdbentryItem(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size()) {
+ throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
+ }
+
+ return (jalview.binding.PdbentryItem) _items.get(index);
+ }
+
+ /**
+ * Method getPdbentryItem.Returns the contents of the
+ * collection in an Array. <p>Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
*/
- public void removeAllPdbentryItem()
- {
- this._items.clear();
- }
-
- /**
- * Method removePdbentryItem.
- *
- * @param vPdbentryItem
- * @return true if the object was removed from the collection.
- */
- public boolean removePdbentryItem(
- final jalview.binding.PdbentryItem vPdbentryItem)
- {
- boolean removed = _items.remove(vPdbentryItem);
- return removed;
- }
-
- /**
- * Method removePdbentryItemAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.PdbentryItem removePdbentryItemAt(final int index)
- {
- java.lang.Object obj = this._items.remove(index);
- return (jalview.binding.PdbentryItem) obj;
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id
- * the value of field 'id'.
- */
- public void setId(final java.lang.String id)
- {
- this._id = id;
- }
-
- /**
- *
- *
- * @param index
- * @param vPdbentryItem
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setPdbentryItem(final int index,
- final jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._items.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setPdbentryItem",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._items.size() - 1)).toString()
- }));
+ public jalview.binding.PdbentryItem[] getPdbentryItem(
+ ) {
+ jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
+ return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
}
- this._items.set(index, vPdbentryItem);
- }
-
- /**
- *
- *
- * @param vPdbentryItemArray
- */
- public void setPdbentryItem(
- final jalview.binding.PdbentryItem[] vPdbentryItemArray)
- {
- // -- copy array
- _items.clear();
-
- for (int i = 0; i < vPdbentryItemArray.length; i++)
- {
- this._items.add(vPdbentryItemArray[i]);
+ /**
+ * Method getPdbentryItemCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbentryItemCount(
+ ) {
+ return this._items.size();
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllPdbentryItem(
+ ) {
+ this._items.clear();
+ }
+
+ /**
+ * Method removePdbentryItem.
+ *
+ * @param vPdbentryItem
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbentryItem(
+ final jalview.binding.PdbentryItem vPdbentryItem) {
+ boolean removed = _items.remove(vPdbentryItem);
+ return removed;
+ }
+
+ /**
+ * Method removePdbentryItemAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.PdbentryItem removePdbentryItemAt(
+ final int index) {
+ java.lang.Object obj = this._items.remove(index);
+ return (jalview.binding.PdbentryItem) obj;
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setPdbentryItem(
+ final int index,
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size()) {
+ throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
+ }
+
+ this._items.set(index, vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbentryItemArray
+ */
+ public void setPdbentryItem(
+ final jalview.binding.PdbentryItem[] vPdbentryItemArray) {
+ //-- copy array
+ _items.clear();
+
+ for (int i = 0; i < vPdbentryItemArray.length; i++) {
+ this._items.add(vPdbentryItemArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Pdbentry
+ */
+ public static jalview.binding.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type
- * the value of field 'type'.
- */
- public void setType(final java.lang.String type)
- {
- this._type = type;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Pdbentry
- */
- public static jalview.binding.Pdbentry unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
- jalview.binding.Pdbentry.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
-package jalview.binding;
-import jalview.util.MessageManager;
+package jalview.binding;
/**
* Class PdbentryItem.
*
* @version $Revision$ $Date$
*/
-public class PdbentryItem implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _propertyList.
- */
- private java.util.Vector _propertyList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public PdbentryItem()
- {
- super();
- this._propertyList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addProperty(final jalview.binding.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- this._propertyList.addElement(vProperty);
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addProperty(final int index,
- final jalview.binding.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- this._propertyList.add(index, vProperty);
- }
-
- /**
- * Method enumerateProperty.
- *
- * @return an Enumeration over all jalview.binding.Property elements
- */
- public java.util.Enumeration enumerateProperty()
- {
- return this._propertyList.elements();
- }
-
- /**
- * Method getProperty.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Property at the given index
- */
- public jalview.binding.Property getProperty(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getProperty",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._propertyList.size() - 1)).toString()
- }));
+public class PdbentryItem implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public PdbentryItem() {
+ super();
+ this._propertyList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final int index,
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all jalview.binding.Property
+ * elements
+ */
+ public java.util.Enumeration enumerateProperty(
+ ) {
+ return this._propertyList.elements();
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Property at the
+ * given index
+ */
+ public jalview.binding.Property getProperty(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Property) _propertyList.get(index);
+ }
+
+ /**
+ * Method getProperty.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Property[] getProperty(
+ ) {
+ jalview.binding.Property[] array = new jalview.binding.Property[0];
+ return (jalview.binding.Property[]) this._propertyList.toArray(array);
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount(
+ ) {
+ return this._propertyList.size();
}
- return (jalview.binding.Property) _propertyList.get(index);
- }
-
- /**
- * Method getProperty.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Property[] getProperty()
- {
- jalview.binding.Property[] array = new jalview.binding.Property[0];
- return (jalview.binding.Property[]) this._propertyList.toArray(array);
- }
-
- /**
- * Method getPropertyCount.
- *
- * @return the size of this collection
- */
- public int getPropertyCount()
- {
- return this._propertyList.size();
- }
-
- /**
+ /**
*/
- public void removeAllProperty()
- {
- this._propertyList.clear();
- }
-
- /**
- * Method removeProperty.
- *
- * @param vProperty
- * @return true if the object was removed from the collection.
- */
- public boolean removeProperty(final jalview.binding.Property vProperty)
- {
- boolean removed = _propertyList.remove(vProperty);
- return removed;
- }
-
- /**
- * Method removePropertyAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Property removePropertyAt(final int index)
- {
- java.lang.Object obj = this._propertyList.remove(index);
- return (jalview.binding.Property) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setProperty(final int index,
- final jalview.binding.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setProperty",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._propertyList.size() - 1)).toString()
- }));
+ public void removeAllProperty(
+ ) {
+ this._propertyList.clear();
}
- this._propertyList.set(index, vProperty);
- }
-
- /**
- *
- *
- * @param vPropertyArray
- */
- public void setProperty(final jalview.binding.Property[] vPropertyArray)
- {
- // -- copy array
- _propertyList.clear();
-
- for (int i = 0; i < vPropertyArray.length; i++)
- {
- this._propertyList.add(vPropertyArray[i]);
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final jalview.binding.Property vProperty) {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Property removePropertyAt(
+ final int index) {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (jalview.binding.Property) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setProperty(
+ final int index,
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final jalview.binding.Property[] vPropertyArray) {
+ //-- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++) {
+ this._propertyList.add(vPropertyArray[i]);
+ }
}
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Pdbids extends Pdbentry implements java.io.Serializable
+public class Pdbids extends Pdbentry
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public Pdbids()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Pdbids() {
+ super();
+ }
+
- // -----------/
- // - Methods -/
- // -----------/
+ //-----------/
+ //- Methods -/
+ //-----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
}
- return true;
- }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Pdbentry
- */
- public static jalview.binding.Pdbentry unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
- jalview.binding.Pdbids.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Pdbentry
+ */
+ public static jalview.binding.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbids.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Property implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _value.
- */
- private java.lang.String _value;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Property()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- }
-
- /**
- * Returns the value of field 'value'.
- *
- * @return the value of field 'Value'.
- */
- public java.lang.String getValue()
- {
- return this._value;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+public class Property implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _value.
+ */
+ private java.lang.String _value;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Property() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public java.lang.String getValue(
+ ) {
+ return this._value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value the value of field 'value'.
+ */
+ public void setValue(
+ final java.lang.String value) {
+ this._value = value;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Property
+ */
+ public static jalview.binding.Property unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name
- * the value of field 'name'.
- */
- public void setName(final java.lang.String name)
- {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value
- * the value of field 'value'.
- */
- public void setValue(final java.lang.String value)
- {
- this._value = value;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Property
- */
- public static jalview.binding.Property unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Property) Unmarshaller.unmarshal(
- jalview.binding.Property.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Sequence extends SequenceType implements java.io.Serializable
+public class Sequence extends SequenceType
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public Sequence()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Sequence() {
+ super();
+ }
+
- // -----------/
- // - Methods -/
- // -----------/
+ //-----------/
+ //- Methods -/
+ //-----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
}
- return true;
- }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.SequenceType
- */
- public static jalview.binding.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
- jalview.binding.Sequence.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.SequenceType
+ */
+ public static jalview.binding.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceSet implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _gapChar.
- */
- private java.lang.String _gapChar;
-
- /**
- * Field _aligned.
- */
- private boolean _aligned;
-
- /**
- * keeps track of state for field: _aligned
- */
- private boolean _has_aligned;
-
- /**
- * Field _sequenceList.
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _annotationList.
- */
- private java.util.Vector _annotationList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public SequenceSet()
- {
- super();
- this._sequenceList = new java.util.Vector();
- this._annotationList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAnnotation(final jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- this._annotationList.addElement(vAnnotation);
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAnnotation(final int index,
- final jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- this._annotationList.add(index, vAnnotation);
- }
-
- /**
- *
- *
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequence(final jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceList.addElement(vSequence);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequence(final int index,
- final jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceList.add(index, vSequence);
- }
-
- /**
- */
- public void deleteAligned()
- {
- this._has_aligned = false;
- }
-
- /**
- * Method enumerateAnnotation.
- *
- * @return an Enumeration over all jalview.binding.Annotation elements
- */
- public java.util.Enumeration enumerateAnnotation()
- {
- return this._annotationList.elements();
- }
-
- /**
- * Method enumerateSequence.
- *
- * @return an Enumeration over all jalview.binding.Sequence elements
- */
- public java.util.Enumeration enumerateSequence()
- {
- return this._sequenceList.elements();
- }
-
- /**
- * Returns the value of field 'aligned'.
- *
- * @return the value of field 'Aligned'.
- */
- public boolean getAligned()
- {
- return this._aligned;
- }
-
- /**
- * Method getAnnotation.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Annotation at the given index
- */
- public jalview.binding.Annotation getAnnotation(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._annotationList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getAnnotation",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._annotationList.size() - 1)).toString()
- }));
- }
-
- return (jalview.binding.Annotation) _annotationList.get(index);
- }
-
- /**
- * Method getAnnotation.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Annotation[] getAnnotation()
- {
- jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
- return (jalview.binding.Annotation[]) this._annotationList
- .toArray(array);
- }
-
- /**
- * Method getAnnotationCount.
- *
- * @return the size of this collection
- */
- public int getAnnotationCount()
- {
- return this._annotationList.size();
- }
-
- /**
- * Returns the value of field 'gapChar'.
- *
- * @return the value of field 'GapChar'.
- */
- public java.lang.String getGapChar()
- {
- return this._gapChar;
- }
-
- /**
- * Method getSequence.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.binding.Sequence at the given index
- */
- public jalview.binding.Sequence getSequence(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getSequence",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._sequenceList.size() - 1)).toString()
- }));
- }
-
- return (jalview.binding.Sequence) _sequenceList.get(index);
- }
-
- /**
- * Method getSequence.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.binding.Sequence[] getSequence()
- {
- jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
- return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
- }
-
- /**
- * Method getSequenceCount.
- *
- * @return the size of this collection
- */
- public int getSequenceCount()
- {
- return this._sequenceList.size();
- }
-
- /**
- * Method hasAligned.
- *
- * @return true if at least one Aligned has been added
- */
- public boolean hasAligned()
- {
- return this._has_aligned;
- }
-
- /**
- * Returns the value of field 'aligned'.
- *
- * @return the value of field 'Aligned'.
- */
- public boolean isAligned()
- {
- return this._aligned;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllAnnotation()
- {
- this._annotationList.clear();
- }
-
- /**
- */
- public void removeAllSequence()
- {
- this._sequenceList.clear();
- }
-
- /**
- * Method removeAnnotation.
- *
- * @param vAnnotation
- * @return true if the object was removed from the collection.
- */
- public boolean removeAnnotation(
- final jalview.binding.Annotation vAnnotation)
- {
- boolean removed = _annotationList.remove(vAnnotation);
- return removed;
- }
-
- /**
- * Method removeAnnotationAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Annotation removeAnnotationAt(final int index)
- {
- java.lang.Object obj = this._annotationList.remove(index);
- return (jalview.binding.Annotation) obj;
- }
-
- /**
- * Method removeSequence.
- *
- * @param vSequence
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequence(final jalview.binding.Sequence vSequence)
- {
- boolean removed = _sequenceList.remove(vSequence);
- return removed;
- }
-
- /**
- * Method removeSequenceAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.binding.Sequence removeSequenceAt(final int index)
- {
- java.lang.Object obj = this._sequenceList.remove(index);
- return (jalview.binding.Sequence) obj;
- }
-
- /**
- * Sets the value of field 'aligned'.
- *
- * @param aligned
- * the value of field 'aligned'.
- */
- public void setAligned(final boolean aligned)
- {
- this._aligned = aligned;
- this._has_aligned = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setAnnotation(final int index,
- final jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._annotationList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setAnnotation",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._annotationList.size() - 1)).toString()
- }));
- }
-
- this._annotationList.set(index, vAnnotation);
- }
-
- /**
- *
- *
- * @param vAnnotationArray
- */
- public void setAnnotation(
- final jalview.binding.Annotation[] vAnnotationArray)
- {
- // -- copy array
- _annotationList.clear();
-
- for (int i = 0; i < vAnnotationArray.length; i++)
- {
- this._annotationList.add(vAnnotationArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'gapChar'.
- *
- * @param gapChar
- * the value of field 'gapChar'.
- */
- public void setGapChar(final java.lang.String gapChar)
- {
- this._gapChar = gapChar;
- }
-
- /**
- *
- *
- * @param index
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSequence(final int index,
- final jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setSequence",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._sequenceList.size() - 1)).toString()
- }));
- }
-
- this._sequenceList.set(index, vSequence);
- }
-
- /**
- *
- *
- * @param vSequenceArray
- */
- public void setSequence(final jalview.binding.Sequence[] vSequenceArray)
- {
- // -- copy array
- _sequenceList.clear();
-
- for (int i = 0; i < vSequenceArray.length; i++)
- {
- this._sequenceList.add(vSequenceArray[i]);
- }
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.SequenceSet
- */
- public static jalview.binding.SequenceSet unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(
- jalview.binding.SequenceSet.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class SequenceSet implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _gapChar.
+ */
+ private java.lang.String _gapChar;
+
+ /**
+ * Field _aligned.
+ */
+ private boolean _aligned;
+
+ /**
+ * keeps track of state for field: _aligned
+ */
+ private boolean _has_aligned;
+
+ /**
+ * Field _sequenceList.
+ */
+ private java.util.Vector _sequenceList;
+
+ /**
+ * Field _annotationList.
+ */
+ private java.util.Vector _annotationList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceSet() {
+ super();
+ this._sequenceList = new java.util.Vector();
+ this._annotationList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotation(
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationList.addElement(vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotation(
+ final int index,
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationList.add(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequence(
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceList.addElement(vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequence(
+ final int index,
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceList.add(index, vSequence);
+ }
+
+ /**
+ */
+ public void deleteAligned(
+ ) {
+ this._has_aligned= false;
+ }
+
+ /**
+ * Method enumerateAnnotation.
+ *
+ * @return an Enumeration over all jalview.binding.Annotation
+ * elements
+ */
+ public java.util.Enumeration enumerateAnnotation(
+ ) {
+ return this._annotationList.elements();
+ }
+
+ /**
+ * Method enumerateSequence.
+ *
+ * @return an Enumeration over all jalview.binding.Sequence
+ * elements
+ */
+ public java.util.Enumeration enumerateSequence(
+ ) {
+ return this._sequenceList.elements();
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean getAligned(
+ ) {
+ return this._aligned;
+ }
+
+ /**
+ * Method getAnnotation.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Annotation at the
+ * given index
+ */
+ public jalview.binding.Annotation getAnnotation(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size()) {
+ throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Annotation) _annotationList.get(index);
+ }
+
+ /**
+ * Method getAnnotation.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Annotation[] getAnnotation(
+ ) {
+ jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
+ return (jalview.binding.Annotation[]) this._annotationList.toArray(array);
+ }
+
+ /**
+ * Method getAnnotationCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationCount(
+ ) {
+ return this._annotationList.size();
+ }
+
+ /**
+ * Returns the value of field 'gapChar'.
+ *
+ * @return the value of field 'GapChar'.
+ */
+ public java.lang.String getGapChar(
+ ) {
+ return this._gapChar;
+ }
+
+ /**
+ * Method getSequence.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Sequence at the
+ * given index
+ */
+ public jalview.binding.Sequence getSequence(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size()) {
+ throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Sequence) _sequenceList.get(index);
+ }
+
+ /**
+ * Method getSequence.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Sequence[] getSequence(
+ ) {
+ jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
+ return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceCount(
+ ) {
+ return this._sequenceList.size();
+ }
+
+ /**
+ * Method hasAligned.
+ *
+ * @return true if at least one Aligned has been added
+ */
+ public boolean hasAligned(
+ ) {
+ return this._has_aligned;
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean isAligned(
+ ) {
+ return this._aligned;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAnnotation(
+ ) {
+ this._annotationList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequence(
+ ) {
+ this._sequenceList.clear();
+ }
+
+ /**
+ * Method removeAnnotation.
+ *
+ * @param vAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotation(
+ final jalview.binding.Annotation vAnnotation) {
+ boolean removed = _annotationList.remove(vAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Annotation removeAnnotationAt(
+ final int index) {
+ java.lang.Object obj = this._annotationList.remove(index);
+ return (jalview.binding.Annotation) obj;
+ }
+
+ /**
+ * Method removeSequence.
+ *
+ * @param vSequence
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequence(
+ final jalview.binding.Sequence vSequence) {
+ boolean removed = _sequenceList.remove(vSequence);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Sequence removeSequenceAt(
+ final int index) {
+ java.lang.Object obj = this._sequenceList.remove(index);
+ return (jalview.binding.Sequence) obj;
+ }
+
+ /**
+ * Sets the value of field 'aligned'.
+ *
+ * @param aligned the value of field 'aligned'.
+ */
+ public void setAligned(
+ final boolean aligned) {
+ this._aligned = aligned;
+ this._has_aligned = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAnnotation(
+ final int index,
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size()) {
+ throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
+ }
+
+ this._annotationList.set(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationArray
+ */
+ public void setAnnotation(
+ final jalview.binding.Annotation[] vAnnotationArray) {
+ //-- copy array
+ _annotationList.clear();
+
+ for (int i = 0; i < vAnnotationArray.length; i++) {
+ this._annotationList.add(vAnnotationArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'gapChar'.
+ *
+ * @param gapChar the value of field 'gapChar'.
+ */
+ public void setGapChar(
+ final java.lang.String gapChar) {
+ this._gapChar = gapChar;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSequence(
+ final int index,
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size()) {
+ throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
+ }
+
+ this._sequenceList.set(index, vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceArray
+ */
+ public void setSequence(
+ final jalview.binding.Sequence[] vSequenceArray) {
+ //-- copy array
+ _sequenceList.clear();
+
+ for (int i = 0; i < vSequenceArray.length; i++) {
+ this._sequenceList.add(vSequenceArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.SequenceSet
+ */
+ public static jalview.binding.SequenceSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class SequenceType implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _sequence.
- */
- private java.lang.String _sequence;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public SequenceType()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- }
-
- /**
- * Returns the value of field 'sequence'.
- *
- * @return the value of field 'Sequence'.
- */
- public java.lang.String getSequence()
- {
- return this._sequence;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+public class SequenceType implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _sequence.
+ */
+ private java.lang.String _sequence;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceType() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'sequence'.
+ *
+ * @return the value of field 'Sequence'.
+ */
+ public java.lang.String getSequence(
+ ) {
+ return this._sequence;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'sequence'.
+ *
+ * @param sequence the value of field 'sequence'.
+ */
+ public void setSequence(
+ final java.lang.String sequence) {
+ this._sequence = sequence;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.SequenceType
+ */
+ public static jalview.binding.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id
- * the value of field 'id'.
- */
- public void setId(final java.lang.String id)
- {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name
- * the value of field 'name'.
- */
- public void setName(final java.lang.String name)
- {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'sequence'.
- *
- * @param sequence
- * the value of field 'sequence'.
- */
- public void setSequence(final java.lang.String sequence)
- {
- this._sequence = sequence;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.SequenceType
- */
- public static jalview.binding.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
- jalview.binding.SequenceType.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Setting implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _type.
- */
- private java.lang.String _type;
-
- /**
- * Field _colour.
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _display.
- */
- private boolean _display;
-
- /**
- * keeps track of state for field: _display
- */
- private boolean _has_display;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Setting()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
+public class Setting implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _display.
+ */
+ private boolean _display;
+
+ /**
+ * keeps track of state for field: _display
+ */
+ private boolean _has_display;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Setting() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
*/
- public void deleteColour()
- {
- this._has_colour = false;
- }
+ public void deleteColour(
+ ) {
+ this._has_colour= false;
+ }
+
+ /**
+ */
+ public void deleteDisplay(
+ ) {
+ this._has_display= false;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour(
+ ) {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean getDisplay(
+ ) {
+ return this._display;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour(
+ ) {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasDisplay.
+ *
+ * @return true if at least one Display has been added
+ */
+ public boolean hasDisplay(
+ ) {
+ return this._has_display;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean isDisplay(
+ ) {
+ return this._display;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour the value of field 'colour'.
+ */
+ public void setColour(
+ final int colour) {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'display'.
+ *
+ * @param display the value of field 'display'.
+ */
+ public void setDisplay(
+ final boolean display) {
+ this._display = display;
+ this._has_display = true;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Setting
+ */
+ public static jalview.binding.Setting unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader);
+ }
- /**
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- public void deleteDisplay()
- {
- this._has_display = false;
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public int getColour()
- {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean getDisplay()
- {
- return this._display;
- }
-
- /**
- * Returns the value of field 'type'.
- *
- * @return the value of field 'Type'.
- */
- public java.lang.String getType()
- {
- return this._type;
- }
-
- /**
- * Method hasColour.
- *
- * @return true if at least one Colour has been added
- */
- public boolean hasColour()
- {
- return this._has_colour;
- }
-
- /**
- * Method hasDisplay.
- *
- * @return true if at least one Display has been added
- */
- public boolean hasDisplay()
- {
- return this._has_display;
- }
-
- /**
- * Returns the value of field 'display'.
- *
- * @return the value of field 'Display'.
- */
- public boolean isDisplay()
- {
- return this._display;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour
- * the value of field 'colour'.
- */
- public void setColour(final int colour)
- {
- this._colour = colour;
- this._has_colour = true;
- }
-
- /**
- * Sets the value of field 'display'.
- *
- * @param display
- * the value of field 'display'.
- */
- public void setDisplay(final boolean display)
- {
- this._display = display;
- this._has_display = true;
- }
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type
- * the value of field 'type'.
- */
- public void setType(final java.lang.String type)
- {
- this._type = type;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Setting
- */
- public static jalview.binding.Setting unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Setting) Unmarshaller.unmarshal(
- jalview.binding.Setting.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Tree implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _showBootstrap.
- */
- private boolean _showBootstrap;
-
- /**
- * keeps track of state for field: _showBootstrap
- */
- private boolean _has_showBootstrap;
-
- /**
- * Field _showDistances.
- */
- private boolean _showDistances;
-
- /**
- * keeps track of state for field: _showDistances
- */
- private boolean _has_showDistances;
-
- /**
- * Field _markUnlinked.
- */
- private boolean _markUnlinked;
-
- /**
- * keeps track of state for field: _markUnlinked
- */
- private boolean _has_markUnlinked;
-
- /**
- * Field _fitToWindow.
- */
- private boolean _fitToWindow;
-
- /**
- * keeps track of state for field: _fitToWindow
- */
- private boolean _has_fitToWindow;
-
- /**
- * Field _currentTree.
- */
- private boolean _currentTree;
-
- /**
- * keeps track of state for field: _currentTree
- */
- private boolean _has_currentTree;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _newick.
- */
- private java.lang.String _newick;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Tree()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- */
- public void deleteCurrentTree()
- {
- this._has_currentTree = false;
- }
-
- /**
- */
- public void deleteFitToWindow()
- {
- this._has_fitToWindow = false;
- }
-
- /**
- */
- public void deleteFontSize()
- {
- this._has_fontSize = false;
- }
-
- /**
- */
- public void deleteFontStyle()
- {
- this._has_fontStyle = false;
- }
-
- /**
- */
- public void deleteHeight()
- {
- this._has_height = false;
- }
-
- /**
- */
- public void deleteMarkUnlinked()
- {
- this._has_markUnlinked = false;
- }
-
- /**
- */
- public void deleteShowBootstrap()
- {
- this._has_showBootstrap = false;
- }
-
- /**
- */
- public void deleteShowDistances()
- {
- this._has_showDistances = false;
- }
-
- /**
- */
- public void deleteThreshold()
- {
- this._has_threshold = false;
- }
-
- /**
- */
- public void deleteWidth()
- {
- this._has_width = false;
- }
-
- /**
- */
- public void deleteXpos()
- {
- this._has_xpos = false;
- }
-
- /**
- */
- public void deleteYpos()
- {
- this._has_ypos = false;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean getCurrentTree()
- {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean getFitToWindow()
- {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName()
- {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize()
- {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle()
- {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight()
- {
- return this._height;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean getMarkUnlinked()
- {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'newick'.
- *
- * @return the value of field 'Newick'.
- */
- public java.lang.String getNewick()
- {
- return this._newick;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean getShowBootstrap()
- {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean getShowDistances()
- {
- return this._showDistances;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold()
- {
- return this._threshold;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth()
- {
- return this._width;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- }
-
- /**
- * Method hasCurrentTree.
- *
- * @return true if at least one CurrentTree has been added
- */
- public boolean hasCurrentTree()
- {
- return this._has_currentTree;
- }
-
- /**
- * Method hasFitToWindow.
- *
- * @return true if at least one FitToWindow has been added
- */
- public boolean hasFitToWindow()
- {
- return this._has_fitToWindow;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize()
- {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle()
- {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight()
- {
- return this._has_height;
- }
-
- /**
- * Method hasMarkUnlinked.
- *
- * @return true if at least one MarkUnlinked has been added
- */
- public boolean hasMarkUnlinked()
- {
- return this._has_markUnlinked;
- }
-
- /**
- * Method hasShowBootstrap.
- *
- * @return true if at least one ShowBootstrap has been added
- */
- public boolean hasShowBootstrap()
- {
- return this._has_showBootstrap;
- }
-
- /**
- * Method hasShowDistances.
- *
- * @return true if at least one ShowDistances has been added
- */
- public boolean hasShowDistances()
- {
- return this._has_showDistances;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold()
- {
- return this._has_threshold;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth()
- {
- return this._has_width;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos()
- {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos()
- {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean isCurrentTree()
- {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean isFitToWindow()
- {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean isMarkUnlinked()
- {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean isShowBootstrap()
- {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean isShowDistances()
- {
- return this._showDistances;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'currentTree'.
- *
- * @param currentTree
- * the value of field 'currentTree'.
- */
- public void setCurrentTree(final boolean currentTree)
- {
- this._currentTree = currentTree;
- this._has_currentTree = true;
- }
-
- /**
- * Sets the value of field 'fitToWindow'.
- *
- * @param fitToWindow
- * the value of field 'fitToWindow'.
- */
- public void setFitToWindow(final boolean fitToWindow)
- {
- this._fitToWindow = fitToWindow;
- this._has_fitToWindow = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName
- * the value of field 'fontName'.
- */
- public void setFontName(final java.lang.String fontName)
- {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize
- * the value of field 'fontSize'.
- */
- public void setFontSize(final int fontSize)
- {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle
- * the value of field 'fontStyle'.
- */
- public void setFontStyle(final int fontStyle)
- {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height
- * the value of field 'height'.
- */
- public void setHeight(final int height)
- {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'markUnlinked'.
- *
- * @param markUnlinked
- * the value of field 'markUnlinked'.
- */
- public void setMarkUnlinked(final boolean markUnlinked)
- {
- this._markUnlinked = markUnlinked;
- this._has_markUnlinked = true;
- }
-
- /**
- * Sets the value of field 'newick'.
- *
- * @param newick
- * the value of field 'newick'.
- */
- public void setNewick(final java.lang.String newick)
- {
- this._newick = newick;
- }
-
- /**
- * Sets the value of field 'showBootstrap'.
- *
- * @param showBootstrap
- * the value of field 'showBootstrap'.
- */
- public void setShowBootstrap(final boolean showBootstrap)
- {
- this._showBootstrap = showBootstrap;
- this._has_showBootstrap = true;
- }
-
- /**
- * Sets the value of field 'showDistances'.
- *
- * @param showDistances
- * the value of field 'showDistances'.
- */
- public void setShowDistances(final boolean showDistances)
- {
- this._showDistances = showDistances;
- this._has_showDistances = true;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold
- * the value of field 'threshold'.
- */
- public void setThreshold(final float threshold)
- {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title
- * the value of field 'title'.
- */
- public void setTitle(final java.lang.String title)
- {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width
- * the value of field 'width'.
- */
- public void setWidth(final int width)
- {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos
- * the value of field 'xpos'.
- */
- public void setXpos(final int xpos)
- {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos
- * the value of field 'ypos'.
- */
- public void setYpos(final int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Tree
- */
- public static jalview.binding.Tree unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Tree) Unmarshaller.unmarshal(
- jalview.binding.Tree.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class Tree implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _showBootstrap.
+ */
+ private boolean _showBootstrap;
+
+ /**
+ * keeps track of state for field: _showBootstrap
+ */
+ private boolean _has_showBootstrap;
+
+ /**
+ * Field _showDistances.
+ */
+ private boolean _showDistances;
+
+ /**
+ * keeps track of state for field: _showDistances
+ */
+ private boolean _has_showDistances;
+
+ /**
+ * Field _markUnlinked.
+ */
+ private boolean _markUnlinked;
+
+ /**
+ * keeps track of state for field: _markUnlinked
+ */
+ private boolean _has_markUnlinked;
+
+ /**
+ * Field _fitToWindow.
+ */
+ private boolean _fitToWindow;
+
+ /**
+ * keeps track of state for field: _fitToWindow
+ */
+ private boolean _has_fitToWindow;
+
+ /**
+ * Field _currentTree.
+ */
+ private boolean _currentTree;
+
+ /**
+ * keeps track of state for field: _currentTree
+ */
+ private boolean _has_currentTree;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _newick.
+ */
+ private java.lang.String _newick;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Tree() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteCurrentTree(
+ ) {
+ this._has_currentTree= false;
+ }
+
+ /**
+ */
+ public void deleteFitToWindow(
+ ) {
+ this._has_fitToWindow= false;
+ }
+
+ /**
+ */
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteMarkUnlinked(
+ ) {
+ this._has_markUnlinked= false;
+ }
+
+ /**
+ */
+ public void deleteShowBootstrap(
+ ) {
+ this._has_showBootstrap= false;
+ }
+
+ /**
+ */
+ public void deleteShowDistances(
+ ) {
+ this._has_showDistances= false;
+ }
+
+ /**
+ */
+ public void deleteThreshold(
+ ) {
+ this._has_threshold= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean getCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean getFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName(
+ ) {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize(
+ ) {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle(
+ ) {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean getMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'newick'.
+ *
+ * @return the value of field 'Newick'.
+ */
+ public java.lang.String getNewick(
+ ) {
+ return this._newick;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean getShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean getShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold(
+ ) {
+ return this._threshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCurrentTree.
+ *
+ * @return true if at least one CurrentTree has been added
+ */
+ public boolean hasCurrentTree(
+ ) {
+ return this._has_currentTree;
+ }
+
+ /**
+ * Method hasFitToWindow.
+ *
+ * @return true if at least one FitToWindow has been added
+ */
+ public boolean hasFitToWindow(
+ ) {
+ return this._has_fitToWindow;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize(
+ ) {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle(
+ ) {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasMarkUnlinked.
+ *
+ * @return true if at least one MarkUnlinked has been added
+ */
+ public boolean hasMarkUnlinked(
+ ) {
+ return this._has_markUnlinked;
+ }
+
+ /**
+ * Method hasShowBootstrap.
+ *
+ * @return true if at least one ShowBootstrap has been added
+ */
+ public boolean hasShowBootstrap(
+ ) {
+ return this._has_showBootstrap;
+ }
+
+ /**
+ * Method hasShowDistances.
+ *
+ * @return true if at least one ShowDistances has been added
+ */
+ public boolean hasShowDistances(
+ ) {
+ return this._has_showDistances;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold(
+ ) {
+ return this._has_threshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean isCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean isFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean isMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean isShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean isShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'currentTree'.
+ *
+ * @param currentTree the value of field 'currentTree'.
+ */
+ public void setCurrentTree(
+ final boolean currentTree) {
+ this._currentTree = currentTree;
+ this._has_currentTree = true;
+ }
+
+ /**
+ * Sets the value of field 'fitToWindow'.
+ *
+ * @param fitToWindow the value of field 'fitToWindow'.
+ */
+ public void setFitToWindow(
+ final boolean fitToWindow) {
+ this._fitToWindow = fitToWindow;
+ this._has_fitToWindow = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName the value of field 'fontName'.
+ */
+ public void setFontName(
+ final java.lang.String fontName) {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize the value of field 'fontSize'.
+ */
+ public void setFontSize(
+ final int fontSize) {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle the value of field 'fontStyle'.
+ */
+ public void setFontStyle(
+ final int fontStyle) {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'markUnlinked'.
+ *
+ * @param markUnlinked the value of field 'markUnlinked'.
+ */
+ public void setMarkUnlinked(
+ final boolean markUnlinked) {
+ this._markUnlinked = markUnlinked;
+ this._has_markUnlinked = true;
+ }
+
+ /**
+ * Sets the value of field 'newick'.
+ *
+ * @param newick the value of field 'newick'.
+ */
+ public void setNewick(
+ final java.lang.String newick) {
+ this._newick = newick;
+ }
+
+ /**
+ * Sets the value of field 'showBootstrap'.
+ *
+ * @param showBootstrap the value of field 'showBootstrap'.
+ */
+ public void setShowBootstrap(
+ final boolean showBootstrap) {
+ this._showBootstrap = showBootstrap;
+ this._has_showBootstrap = true;
+ }
+
+ /**
+ * Sets the value of field 'showDistances'.
+ *
+ * @param showDistances the value of field 'showDistances'.
+ */
+ public void setShowDistances(
+ final boolean showDistances) {
+ this._showDistances = showDistances;
+ this._has_showDistances = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold the value of field 'threshold'.
+ */
+ public void setThreshold(
+ final float threshold) {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Tree
+ */
+ public static jalview.binding.Tree unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class UserColourScheme extends JalviewUserColours implements
- java.io.Serializable
+public class UserColourScheme extends JalviewUserColours
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public UserColourScheme()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public UserColourScheme() {
+ super();
+ }
+
- // -----------/
- // - Methods -/
- // -----------/
+ //-----------/
+ //- Methods -/
+ //-----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
}
- return true;
- }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.JalviewUserColours
- */
- public static jalview.binding.JalviewUserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
- jalview.binding.UserColourScheme.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewUserColours
+ */
+ public static jalview.binding.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class UserColours implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _id.
- */
- private java.lang.String _id;
-
- /**
- * Field _userColourScheme.
- */
- private jalview.binding.UserColourScheme _userColourScheme;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public UserColours()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Returns the value of field 'id'.
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- }
-
- /**
- * Returns the value of field 'userColourScheme'.
- *
- * @return the value of field 'UserColourScheme'.
- */
- public jalview.binding.UserColourScheme getUserColourScheme()
- {
- return this._userColourScheme;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+public class UserColours implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _userColourScheme.
+ */
+ private jalview.binding.UserColourScheme _userColourScheme;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public UserColours() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'userColourScheme'.
+ *
+ * @return the value of field 'UserColourScheme'.
+ */
+ public jalview.binding.UserColourScheme getUserColourScheme(
+ ) {
+ return this._userColourScheme;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'userColourScheme'.
+ *
+ * @param userColourScheme the value of field 'userColourScheme'
+ */
+ public void setUserColourScheme(
+ final jalview.binding.UserColourScheme userColourScheme) {
+ this._userColourScheme = userColourScheme;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.UserColours
+ */
+ public static jalview.binding.UserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id
- * the value of field 'id'.
- */
- public void setId(final java.lang.String id)
- {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'userColourScheme'.
- *
- * @param userColourScheme
- * the value of field 'userColourScheme'
- */
- public void setUserColourScheme(
- final jalview.binding.UserColourScheme userColourScheme)
- {
- this._userColourScheme = userColourScheme;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.UserColours
- */
- public static jalview.binding.UserColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.UserColours) Unmarshaller.unmarshal(
- jalview.binding.UserColours.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-import jalview.util.MessageManager;
-
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class VAMSAS implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _alignmentList.
- */
- private java.util.Vector _alignmentList;
-
- /**
- * Field _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _sequenceSetList.
- */
- private java.util.Vector _sequenceSetList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public VAMSAS()
- {
- super();
- this._alignmentList = new java.util.Vector();
- this._treeList = new java.util.Vector();
- this._sequenceSetList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAlignment(final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- this._alignmentList.addElement(vAlignment);
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addAlignment(final int index, final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- this._alignmentList.add(index, vAlignment);
- }
-
- /**
- *
- *
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequenceSet(final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceSetList.addElement(vSequenceSet);
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addSequenceSet(final int index, final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- this._sequenceSetList.add(index, vSequenceSet);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addTree(final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addTree(final int index, final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- this._treeList.add(index, vTree);
- }
-
- /**
- * Method enumerateAlignment.
- *
- * @return an Enumeration over all Alignment elements
- */
- public java.util.Enumeration enumerateAlignment()
- {
- return this._alignmentList.elements();
- }
-
- /**
- * Method enumerateSequenceSet.
- *
- * @return an Enumeration over all SequenceSet elements
- */
- public java.util.Enumeration enumerateSequenceSet()
- {
- return this._sequenceSetList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all java.lang.String elements
- */
- public java.util.Enumeration enumerateTree()
- {
- return this._treeList.elements();
- }
-
- /**
- * Method getAlignment.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the Alignment at the given index
- */
- public Alignment getAlignment(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._alignmentList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getAlignment",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._alignmentList.size() - 1)).toString()
- }));
- }
-
- return (Alignment) _alignmentList.get(index);
- }
-
- /**
- * Method getAlignment.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public Alignment[] getAlignment()
- {
- Alignment[] array = new Alignment[0];
- return (Alignment[]) this._alignmentList.toArray(array);
- }
-
- /**
- * Method getAlignmentCount.
- *
- * @return the size of this collection
- */
- public int getAlignmentCount()
- {
- return this._alignmentList.size();
- }
-
- /**
- * Method getSequenceSet.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the SequenceSet at the given index
- */
- public SequenceSet getSequenceSet(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getSequenceSet",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
- }));
- }
-
- return (SequenceSet) _sequenceSetList.get(index);
- }
-
- /**
- * Method getSequenceSet.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public SequenceSet[] getSequenceSet()
- {
- SequenceSet[] array = new SequenceSet[0];
- return (SequenceSet[]) this._sequenceSetList.toArray(array);
- }
-
- /**
- * Method getSequenceSetCount.
- *
- * @return the size of this collection
- */
- public int getSequenceSetCount()
- {
- return this._sequenceSetList.size();
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the java.lang.String at the given index
- */
- public java.lang.String getTree(final int index)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getTree",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._treeList.size() - 1)).toString()
- }));
- }
-
- return (java.lang.String) _treeList.get(index);
- }
-
- /**
- * Method getTree.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public java.lang.String[] getTree()
- {
- java.lang.String[] array = new java.lang.String[0];
- return (java.lang.String[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount()
- {
- return this._treeList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Method removeAlignment.
- *
- * @param vAlignment
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlignment(final Alignment vAlignment)
- {
- boolean removed = _alignmentList.remove(vAlignment);
- return removed;
- }
-
- /**
- * Method removeAlignmentAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public Alignment removeAlignmentAt(final int index)
- {
- java.lang.Object obj = this._alignmentList.remove(index);
- return (Alignment) obj;
- }
-
- /**
- */
- public void removeAllAlignment()
- {
- this._alignmentList.clear();
- }
-
- /**
- */
- public void removeAllSequenceSet()
- {
- this._sequenceSetList.clear();
- }
-
- /**
- */
- public void removeAllTree()
- {
- this._treeList.clear();
- }
-
- /**
- * Method removeSequenceSet.
- *
- * @param vSequenceSet
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequenceSet(final SequenceSet vSequenceSet)
- {
- boolean removed = _sequenceSetList.remove(vSequenceSet);
- return removed;
- }
-
- /**
- * Method removeSequenceSetAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public SequenceSet removeSequenceSetAt(final int index)
- {
- java.lang.Object obj = this._sequenceSetList.remove(index);
- return (SequenceSet) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(final java.lang.String vTree)
- {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public java.lang.String removeTreeAt(final int index)
- {
- java.lang.Object obj = this._treeList.remove(index);
- return (java.lang.String) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setAlignment(final int index, final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._alignmentList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setAlignment",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._alignmentList.size() - 1)).toString()
- }));
- }
-
- this._alignmentList.set(index, vAlignment);
- }
-
- /**
- *
- *
- * @param vAlignmentArray
- */
- public void setAlignment(final Alignment[] vAlignmentArray)
- {
- // -- copy array
- _alignmentList.clear();
-
- for (int i = 0; i < vAlignmentArray.length; i++)
- {
- this._alignmentList.add(vAlignmentArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSequenceSet(final int index, final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setSequenceSet",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
- }));
- }
-
- this._sequenceSetList.set(index, vSequenceSet);
- }
-
- /**
- *
- *
- * @param vSequenceSetArray
- */
- public void setSequenceSet(final SequenceSet[] vSequenceSetArray)
- {
- // -- copy array
- _sequenceSetList.clear();
-
- for (int i = 0; i < vSequenceSetArray.length; i++)
- {
- this._sequenceSetList.add(vSequenceSetArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setTree(final int index, final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setTree",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._treeList.size() - 1)).toString()
- }));
- }
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(final java.lang.String[] vTreeArray)
- {
- // -- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++)
- {
- this._treeList.add(vTreeArray[i]);
- }
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.VAMSAS
- */
- public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
- jalview.binding.VAMSAS.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class VAMSAS implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _alignmentList.
+ */
+ private java.util.Vector _alignmentList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _sequenceSetList.
+ */
+ private java.util.Vector _sequenceSetList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public VAMSAS() {
+ super();
+ this._alignmentList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ this._sequenceSetList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlignment(
+ final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentList.addElement(vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlignment(
+ final int index,
+ final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentList.add(index, vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequenceSet(
+ final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceSetList.addElement(vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequenceSet(
+ final int index,
+ final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceSetList.add(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final int index,
+ final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ * Method enumerateAlignment.
+ *
+ * @return an Enumeration over all Alignment elements
+ */
+ public java.util.Enumeration enumerateAlignment(
+ ) {
+ return this._alignmentList.elements();
+ }
+
+ /**
+ * Method enumerateSequenceSet.
+ *
+ * @return an Enumeration over all SequenceSet elements
+ */
+ public java.util.Enumeration enumerateSequenceSet(
+ ) {
+ return this._sequenceSetList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateTree(
+ ) {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method getAlignment.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the Alignment at the given index
+ */
+ public Alignment getAlignment(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size()) {
+ throw new IndexOutOfBoundsException("getAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
+ }
+
+ return (Alignment) _alignmentList.get(index);
+ }
+
+ /**
+ * Method getAlignment.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public Alignment[] getAlignment(
+ ) {
+ Alignment[] array = new Alignment[0];
+ return (Alignment[]) this._alignmentList.toArray(array);
+ }
+
+ /**
+ * Method getAlignmentCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlignmentCount(
+ ) {
+ return this._alignmentList.size();
+ }
+
+ /**
+ * Method getSequenceSet.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the SequenceSet at the given index
+ */
+ public SequenceSet getSequenceSet(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size()) {
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
+ }
+
+ return (SequenceSet) _sequenceSetList.get(index);
+ }
+
+ /**
+ * Method getSequenceSet.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public SequenceSet[] getSequenceSet(
+ ) {
+ SequenceSet[] array = new SequenceSet[0];
+ return (SequenceSet[]) this._sequenceSetList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceSetCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceSetCount(
+ ) {
+ return this._sequenceSetList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getTree(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (java.lang.String) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an
+ * Array. <p>Note: Just in case the collection contents are
+ * changing in another thread, we pass a 0-length Array of the
+ * correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public java.lang.String[] getTree(
+ ) {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount(
+ ) {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method removeAlignment.
+ *
+ * @param vAlignment
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlignment(
+ final Alignment vAlignment) {
+ boolean removed = _alignmentList.remove(vAlignment);
+ return removed;
+ }
+
+ /**
+ * Method removeAlignmentAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Alignment removeAlignmentAt(
+ final int index) {
+ java.lang.Object obj = this._alignmentList.remove(index);
+ return (Alignment) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlignment(
+ ) {
+ this._alignmentList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequenceSet(
+ ) {
+ this._sequenceSetList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree(
+ ) {
+ this._treeList.clear();
+ }
+
+ /**
+ * Method removeSequenceSet.
+ *
+ * @param vSequenceSet
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceSet(
+ final SequenceSet vSequenceSet) {
+ boolean removed = _sequenceSetList.remove(vSequenceSet);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceSetAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public SequenceSet removeSequenceSetAt(
+ final int index) {
+ java.lang.Object obj = this._sequenceSetList.remove(index);
+ return (SequenceSet) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(
+ final java.lang.String vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeTreeAt(
+ final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAlignment(
+ final int index,
+ final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size()) {
+ throw new IndexOutOfBoundsException("setAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
+ }
+
+ this._alignmentList.set(index, vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param vAlignmentArray
+ */
+ public void setAlignment(
+ final Alignment[] vAlignmentArray) {
+ //-- copy array
+ _alignmentList.clear();
+
+ for (int i = 0; i < vAlignmentArray.length; i++) {
+ this._alignmentList.add(vAlignmentArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSequenceSet(
+ final int index,
+ final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size()) {
+ throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
+ }
+
+ this._sequenceSetList.set(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetArray
+ */
+ public void setSequenceSet(
+ final SequenceSet[] vSequenceSetArray) {
+ //-- copy array
+ _sequenceSetList.clear();
+
+ for (int i = 0; i < vSequenceSetArray.length; i++) {
+ this._sequenceSetList.add(vSequenceSetArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setTree(
+ final int index,
+ final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(
+ final java.lang.String[] vTreeArray) {
+ //-- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.VAMSAS
+ */
+ public static jalview.binding.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class VamsasModel extends VAMSAS implements java.io.Serializable
+public class VamsasModel extends VAMSAS
+implements java.io.Serializable
{
- // ----------------/
- // - Constructors -/
- // ----------------/
- public VamsasModel()
- {
- super();
- }
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public VamsasModel() {
+ super();
+ }
+
- // -----------/
- // - Methods -/
- // -----------/
+ //-----------/
+ //- Methods -/
+ //-----------/
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
}
- return true;
- }
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.VAMSAS
- */
- public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
- jalview.binding.VamsasModel.class, reader);
- }
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.VAMSAS
+ */
+ public static jalview.binding.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * 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.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Viewport implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _conservationSelected.
- */
- private boolean _conservationSelected;
-
- /**
- * keeps track of state for field: _conservationSelected
- */
- private boolean _has_conservationSelected;
-
- /**
- * Field _pidSelected.
- */
- private boolean _pidSelected;
-
- /**
- * keeps track of state for field: _pidSelected
- */
- private boolean _has_pidSelected;
-
- /**
- * Field _bgColour.
- */
- private java.lang.String _bgColour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _showFullId.
- */
- private boolean _showFullId;
-
- /**
- * keeps track of state for field: _showFullId
- */
- private boolean _has_showFullId;
-
- /**
- * Field _showText.
- */
- private boolean _showText;
-
- /**
- * keeps track of state for field: _showText
- */
- private boolean _has_showText;
-
- /**
- * Field _showColourText.
- */
- private boolean _showColourText;
-
- /**
- * keeps track of state for field: _showColourText
- */
- private boolean _has_showColourText;
-
- /**
- * Field _showBoxes.
- */
- private boolean _showBoxes;
-
- /**
- * keeps track of state for field: _showBoxes
- */
- private boolean _has_showBoxes;
-
- /**
- * Field _wrapAlignment.
- */
- private boolean _wrapAlignment;
-
- /**
- * keeps track of state for field: _wrapAlignment
- */
- private boolean _has_wrapAlignment;
-
- /**
- * Field _renderGaps.
- */
- private boolean _renderGaps;
-
- /**
- * keeps track of state for field: _renderGaps
- */
- private boolean _has_renderGaps;
-
- /**
- * Field _showSequenceFeatures.
- */
- private boolean _showSequenceFeatures;
-
- /**
- * keeps track of state for field: _showSequenceFeatures
- */
- private boolean _has_showSequenceFeatures;
-
- /**
- * Field _showAnnotation.
- */
- private boolean _showAnnotation;
-
- /**
- * keeps track of state for field: _showAnnotation
- */
- private boolean _has_showAnnotation;
-
- /**
- * Field _showConservation.
- */
- private boolean _showConservation;
-
- /**
- * keeps track of state for field: _showConservation
- */
- private boolean _has_showConservation;
-
- /**
- * Field _showQuality.
- */
- private boolean _showQuality;
-
- /**
- * keeps track of state for field: _showQuality
- */
- private boolean _has_showQuality;
-
- /**
- * Field _showIdentity.
- */
- private boolean _showIdentity;
-
- /**
- * keeps track of state for field: _showIdentity
- */
- private boolean _has_showIdentity;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _startRes.
- */
- private int _startRes;
-
- /**
- * keeps track of state for field: _startRes
- */
- private boolean _has_startRes;
-
- /**
- * Field _startSeq.
- */
- private int _startSeq;
-
- /**
- * keeps track of state for field: _startSeq
- */
- private boolean _has_startSeq;
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Viewport()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
+public class Viewport implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _conservationSelected.
+ */
+ private boolean _conservationSelected;
+
+ /**
+ * keeps track of state for field: _conservationSelected
+ */
+ private boolean _has_conservationSelected;
+
+ /**
+ * Field _pidSelected.
+ */
+ private boolean _pidSelected;
+
+ /**
+ * keeps track of state for field: _pidSelected
+ */
+ private boolean _has_pidSelected;
+
+ /**
+ * Field _bgColour.
+ */
+ private java.lang.String _bgColour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _showFullId.
+ */
+ private boolean _showFullId;
+
+ /**
+ * keeps track of state for field: _showFullId
+ */
+ private boolean _has_showFullId;
+
+ /**
+ * Field _showText.
+ */
+ private boolean _showText;
+
+ /**
+ * keeps track of state for field: _showText
+ */
+ private boolean _has_showText;
+
+ /**
+ * Field _showColourText.
+ */
+ private boolean _showColourText;
+
+ /**
+ * keeps track of state for field: _showColourText
+ */
+ private boolean _has_showColourText;
+
+ /**
+ * Field _showBoxes.
+ */
+ private boolean _showBoxes;
+
+ /**
+ * keeps track of state for field: _showBoxes
+ */
+ private boolean _has_showBoxes;
+
+ /**
+ * Field _wrapAlignment.
+ */
+ private boolean _wrapAlignment;
+
+ /**
+ * keeps track of state for field: _wrapAlignment
+ */
+ private boolean _has_wrapAlignment;
+
+ /**
+ * Field _renderGaps.
+ */
+ private boolean _renderGaps;
+
+ /**
+ * keeps track of state for field: _renderGaps
+ */
+ private boolean _has_renderGaps;
+
+ /**
+ * Field _showSequenceFeatures.
+ */
+ private boolean _showSequenceFeatures;
+
+ /**
+ * keeps track of state for field: _showSequenceFeatures
+ */
+ private boolean _has_showSequenceFeatures;
+
+ /**
+ * Field _showAnnotation.
+ */
+ private boolean _showAnnotation;
+
+ /**
+ * keeps track of state for field: _showAnnotation
+ */
+ private boolean _has_showAnnotation;
+
+ /**
+ * Field _showConservation.
+ */
+ private boolean _showConservation;
+
+ /**
+ * keeps track of state for field: _showConservation
+ */
+ private boolean _has_showConservation;
+
+ /**
+ * Field _showQuality.
+ */
+ private boolean _showQuality;
+
+ /**
+ * keeps track of state for field: _showQuality
+ */
+ private boolean _has_showQuality;
+
+ /**
+ * Field _showIdentity.
+ */
+ private boolean _showIdentity;
+
+ /**
+ * keeps track of state for field: _showIdentity
+ */
+ private boolean _has_showIdentity;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
- /**
+ /**
+ * keeps track of state for field: _width
*/
- public void deleteConsThreshold()
- {
- this._has_consThreshold = false;
- }
+ private boolean _has_width;
- /**
+ /**
+ * Field _height.
*/
- public void deleteConservationSelected()
- {
- this._has_conservationSelected = false;
- }
+ private int _height;
- /**
+ /**
+ * keeps track of state for field: _height
*/
- public void deleteFontSize()
- {
- this._has_fontSize = false;
- }
+ private boolean _has_height;
- /**
+ /**
+ * Field _startRes.
*/
- public void deleteFontStyle()
- {
- this._has_fontStyle = false;
- }
+ private int _startRes;
- /**
+ /**
+ * keeps track of state for field: _startRes
*/
- public void deleteHeight()
- {
- this._has_height = false;
- }
+ private boolean _has_startRes;
- /**
+ /**
+ * Field _startSeq.
*/
- public void deletePidSelected()
- {
- this._has_pidSelected = false;
- }
+ private int _startSeq;
- /**
+ /**
+ * keeps track of state for field: _startSeq
*/
- public void deletePidThreshold()
- {
- this._has_pidThreshold = false;
- }
+ private boolean _has_startSeq;
- /**
+ /**
+ * Field _fontName.
*/
- public void deleteRenderGaps()
- {
- this._has_renderGaps = false;
- }
+ private java.lang.String _fontName;
- /**
+ /**
+ * Field _fontSize.
*/
- public void deleteShowAnnotation()
- {
- this._has_showAnnotation = false;
- }
+ private int _fontSize;
- /**
+ /**
+ * keeps track of state for field: _fontSize
*/
- public void deleteShowBoxes()
- {
- this._has_showBoxes = false;
- }
+ private boolean _has_fontSize;
- /**
+ /**
+ * Field _fontStyle.
*/
- public void deleteShowColourText()
- {
- this._has_showColourText = false;
- }
+ private int _fontStyle;
- /**
+ /**
+ * keeps track of state for field: _fontStyle
*/
- public void deleteShowConservation()
- {
- this._has_showConservation = false;
- }
+ private boolean _has_fontStyle;
- /**
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Viewport() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteConsThreshold(
+ ) {
+ this._has_consThreshold= false;
+ }
+
+ /**
*/
- public void deleteShowFullId()
- {
- this._has_showFullId = false;
- }
+ public void deleteConservationSelected(
+ ) {
+ this._has_conservationSelected= false;
+ }
- /**
+ /**
*/
- public void deleteShowIdentity()
- {
- this._has_showIdentity = false;
- }
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deletePidSelected(
+ ) {
+ this._has_pidSelected= false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold(
+ ) {
+ this._has_pidThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteRenderGaps(
+ ) {
+ this._has_renderGaps= false;
+ }
+
+ /**
+ */
+ public void deleteShowAnnotation(
+ ) {
+ this._has_showAnnotation= false;
+ }
+
+ /**
+ */
+ public void deleteShowBoxes(
+ ) {
+ this._has_showBoxes= false;
+ }
+
+ /**
+ */
+ public void deleteShowColourText(
+ ) {
+ this._has_showColourText= false;
+ }
+
+ /**
+ */
+ public void deleteShowConservation(
+ ) {
+ this._has_showConservation= false;
+ }
+
+ /**
+ */
+ public void deleteShowFullId(
+ ) {
+ this._has_showFullId= false;
+ }
+
+ /**
+ */
+ public void deleteShowIdentity(
+ ) {
+ this._has_showIdentity= false;
+ }
+
+ /**
+ */
+ public void deleteShowQuality(
+ ) {
+ this._has_showQuality= false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceFeatures(
+ ) {
+ this._has_showSequenceFeatures= false;
+ }
+
+ /**
+ */
+ public void deleteShowText(
+ ) {
+ this._has_showText= false;
+ }
+
+ /**
+ */
+ public void deleteStartRes(
+ ) {
+ this._has_startRes= false;
+ }
+
+ /**
+ */
+ public void deleteStartSeq(
+ ) {
+ this._has_startSeq= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteWrapAlignment(
+ ) {
+ this._has_wrapAlignment= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public java.lang.String getBgColour(
+ ) {
+ return this._bgColour;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold(
+ ) {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean getConservationSelected(
+ ) {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName(
+ ) {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize(
+ ) {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle(
+ ) {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean getPidSelected(
+ ) {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold(
+ ) {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean getRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean getShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean getShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean getShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConservation'.
+ *
+ * @return the value of field 'ShowConservation'.
+ */
+ public boolean getShowConservation(
+ ) {
+ return this._showConservation;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean getShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showIdentity'.
+ *
+ * @return the value of field 'ShowIdentity'.
+ */
+ public boolean getShowIdentity(
+ ) {
+ return this._showIdentity;
+ }
+
+ /**
+ * Returns the value of field 'showQuality'.
+ *
+ * @return the value of field 'ShowQuality'.
+ */
+ public boolean getShowQuality(
+ ) {
+ return this._showQuality;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean getShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean getShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'startRes'.
+ *
+ * @return the value of field 'StartRes'.
+ */
+ public int getStartRes(
+ ) {
+ return this._startRes;
+ }
+
+ /**
+ * Returns the value of field 'startSeq'.
+ *
+ * @return the value of field 'StartSeq'.
+ */
+ public int getStartSeq(
+ ) {
+ return this._startSeq;
+ }
- /**
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
*/
- public void deleteShowQuality()
- {
- this._has_showQuality = false;
- }
-
- /**
- */
- public void deleteShowSequenceFeatures()
- {
- this._has_showSequenceFeatures = false;
- }
-
- /**
- */
- public void deleteShowText()
- {
- this._has_showText = false;
- }
-
- /**
- */
- public void deleteStartRes()
- {
- this._has_startRes = false;
- }
-
- /**
- */
- public void deleteStartSeq()
- {
- this._has_startSeq = false;
- }
-
- /**
- */
- public void deleteWidth()
- {
- this._has_width = false;
- }
-
- /**
- */
- public void deleteWrapAlignment()
- {
- this._has_wrapAlignment = false;
- }
-
- /**
- */
- public void deleteXpos()
- {
- this._has_xpos = false;
- }
-
- /**
- */
- public void deleteYpos()
- {
- this._has_ypos = false;
- }
-
- /**
- * Returns the value of field 'bgColour'.
- *
- * @return the value of field 'BgColour'.
- */
- public java.lang.String getBgColour()
- {
- return this._bgColour;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold()
- {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean getConservationSelected()
- {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName()
- {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize()
- {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle()
- {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight()
- {
- return this._height;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean getPidSelected()
- {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold()
- {
- return this._pidThreshold;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean getRenderGaps()
- {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean getShowAnnotation()
- {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean getShowBoxes()
- {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean getShowColourText()
- {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConservation'.
- *
- * @return the value of field 'ShowConservation'.
- */
- public boolean getShowConservation()
- {
- return this._showConservation;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean getShowFullId()
- {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showIdentity'.
- *
- * @return the value of field 'ShowIdentity'.
- */
- public boolean getShowIdentity()
- {
- return this._showIdentity;
- }
-
- /**
- * Returns the value of field 'showQuality'.
- *
- * @return the value of field 'ShowQuality'.
- */
- public boolean getShowQuality()
- {
- return this._showQuality;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean getShowSequenceFeatures()
- {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean getShowText()
- {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'startRes'.
- *
- * @return the value of field 'StartRes'.
- */
- public int getStartRes()
- {
- return this._startRes;
- }
-
- /**
- * Returns the value of field 'startSeq'.
- *
- * @return the value of field 'StartSeq'.
- */
- public int getStartSeq()
- {
- return this._startSeq;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth()
- {
- return this._width;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean getWrapAlignment()
- {
- return this._wrapAlignment;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold()
- {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasConservationSelected.
- *
- * @return true if at least one ConservationSelected has been added
- */
- public boolean hasConservationSelected()
- {
- return this._has_conservationSelected;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize()
- {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle()
- {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight()
- {
- return this._has_height;
- }
-
- /**
- * Method hasPidSelected.
- *
- * @return true if at least one PidSelected has been added
- */
- public boolean hasPidSelected()
- {
- return this._has_pidSelected;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold()
- {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasRenderGaps.
- *
- * @return true if at least one RenderGaps has been added
- */
- public boolean hasRenderGaps()
- {
- return this._has_renderGaps;
- }
-
- /**
- * Method hasShowAnnotation.
- *
- * @return true if at least one ShowAnnotation has been added
- */
- public boolean hasShowAnnotation()
- {
- return this._has_showAnnotation;
- }
-
- /**
- * Method hasShowBoxes.
- *
- * @return true if at least one ShowBoxes has been added
- */
- public boolean hasShowBoxes()
- {
- return this._has_showBoxes;
- }
-
- /**
- * Method hasShowColourText.
- *
- * @return true if at least one ShowColourText has been added
- */
- public boolean hasShowColourText()
- {
- return this._has_showColourText;
- }
-
- /**
- * Method hasShowConservation.
- *
- * @return true if at least one ShowConservation has been added
- */
- public boolean hasShowConservation()
- {
- return this._has_showConservation;
- }
-
- /**
- * Method hasShowFullId.
- *
- * @return true if at least one ShowFullId has been added
- */
- public boolean hasShowFullId()
- {
- return this._has_showFullId;
- }
-
- /**
- * Method hasShowIdentity.
- *
- * @return true if at least one ShowIdentity has been added
- */
- public boolean hasShowIdentity()
- {
- return this._has_showIdentity;
- }
-
- /**
- * Method hasShowQuality.
- *
- * @return true if at least one ShowQuality has been added
- */
- public boolean hasShowQuality()
- {
- return this._has_showQuality;
- }
-
- /**
- * Method hasShowSequenceFeatures.
- *
- * @return true if at least one ShowSequenceFeatures has been added
- */
- public boolean hasShowSequenceFeatures()
- {
- return this._has_showSequenceFeatures;
- }
-
- /**
- * Method hasShowText.
- *
- * @return true if at least one ShowText has been added
- */
- public boolean hasShowText()
- {
- return this._has_showText;
- }
-
- /**
- * Method hasStartRes.
- *
- * @return true if at least one StartRes has been added
- */
- public boolean hasStartRes()
- {
- return this._has_startRes;
- }
-
- /**
- * Method hasStartSeq.
- *
- * @return true if at least one StartSeq has been added
- */
- public boolean hasStartSeq()
- {
- return this._has_startSeq;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth()
- {
- return this._has_width;
- }
-
- /**
- * Method hasWrapAlignment.
- *
- * @return true if at least one WrapAlignment has been added
- */
- public boolean hasWrapAlignment()
- {
- return this._has_wrapAlignment;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos()
- {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos()
- {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean isConservationSelected()
- {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean isPidSelected()
- {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean isRenderGaps()
- {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean isShowAnnotation()
- {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean isShowBoxes()
- {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean isShowColourText()
- {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConservation'.
- *
- * @return the value of field 'ShowConservation'.
- */
- public boolean isShowConservation()
- {
- return this._showConservation;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean isShowFullId()
- {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showIdentity'.
- *
- * @return the value of field 'ShowIdentity'.
- */
- public boolean isShowIdentity()
- {
- return this._showIdentity;
- }
-
- /**
- * Returns the value of field 'showQuality'.
- *
- * @return the value of field 'ShowQuality'.
- */
- public boolean isShowQuality()
- {
- return this._showQuality;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean isShowSequenceFeatures()
- {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean isShowText()
- {
- return this._showText;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean isWrapAlignment()
- {
- return this._wrapAlignment;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'bgColour'.
- *
- * @param bgColour
- * the value of field 'bgColour'.
- */
- public void setBgColour(final java.lang.String bgColour)
- {
- this._bgColour = bgColour;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold
- * the value of field 'consThreshold'.
- */
- public void setConsThreshold(final int consThreshold)
- {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'conservationSelected'.
- *
- * @param conservationSelected
- * the value of field 'conservationSelected'.
- */
- public void setConservationSelected(final boolean conservationSelected)
- {
- this._conservationSelected = conservationSelected;
- this._has_conservationSelected = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName
- * the value of field 'fontName'.
- */
- public void setFontName(final java.lang.String fontName)
- {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize
- * the value of field 'fontSize'.
- */
- public void setFontSize(final int fontSize)
- {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle
- * the value of field 'fontStyle'.
- */
- public void setFontStyle(final int fontStyle)
- {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height
- * the value of field 'height'.
- */
- public void setHeight(final int height)
- {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'pidSelected'.
- *
- * @param pidSelected
- * the value of field 'pidSelected'.
- */
- public void setPidSelected(final boolean pidSelected)
- {
- this._pidSelected = pidSelected;
- this._has_pidSelected = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold
- * the value of field 'pidThreshold'.
- */
- public void setPidThreshold(final int pidThreshold)
- {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- * Sets the value of field 'renderGaps'.
- *
- * @param renderGaps
- * the value of field 'renderGaps'.
- */
- public void setRenderGaps(final boolean renderGaps)
- {
- this._renderGaps = renderGaps;
- this._has_renderGaps = true;
- }
-
- /**
- * Sets the value of field 'showAnnotation'.
- *
- * @param showAnnotation
- * the value of field 'showAnnotation'.
- */
- public void setShowAnnotation(final boolean showAnnotation)
- {
- this._showAnnotation = showAnnotation;
- this._has_showAnnotation = true;
- }
-
- /**
- * Sets the value of field 'showBoxes'.
- *
- * @param showBoxes
- * the value of field 'showBoxes'.
- */
- public void setShowBoxes(final boolean showBoxes)
- {
- this._showBoxes = showBoxes;
- this._has_showBoxes = true;
- }
-
- /**
- * Sets the value of field 'showColourText'.
- *
- * @param showColourText
- * the value of field 'showColourText'.
- */
- public void setShowColourText(final boolean showColourText)
- {
- this._showColourText = showColourText;
- this._has_showColourText = true;
- }
-
- /**
- * Sets the value of field 'showConservation'.
- *
- * @param showConservation
- * the value of field 'showConservation'
- */
- public void setShowConservation(final boolean showConservation)
- {
- this._showConservation = showConservation;
- this._has_showConservation = true;
- }
-
- /**
- * Sets the value of field 'showFullId'.
- *
- * @param showFullId
- * the value of field 'showFullId'.
- */
- public void setShowFullId(final boolean showFullId)
- {
- this._showFullId = showFullId;
- this._has_showFullId = true;
- }
-
- /**
- * Sets the value of field 'showIdentity'.
- *
- * @param showIdentity
- * the value of field 'showIdentity'.
- */
- public void setShowIdentity(final boolean showIdentity)
- {
- this._showIdentity = showIdentity;
- this._has_showIdentity = true;
- }
-
- /**
- * Sets the value of field 'showQuality'.
- *
- * @param showQuality
- * the value of field 'showQuality'.
- */
- public void setShowQuality(final boolean showQuality)
- {
- this._showQuality = showQuality;
- this._has_showQuality = true;
- }
-
- /**
- * Sets the value of field 'showSequenceFeatures'.
- *
- * @param showSequenceFeatures
- * the value of field 'showSequenceFeatures'.
- */
- public void setShowSequenceFeatures(final boolean showSequenceFeatures)
- {
- this._showSequenceFeatures = showSequenceFeatures;
- this._has_showSequenceFeatures = true;
- }
-
- /**
- * Sets the value of field 'showText'.
- *
- * @param showText
- * the value of field 'showText'.
- */
- public void setShowText(final boolean showText)
- {
- this._showText = showText;
- this._has_showText = true;
- }
-
- /**
- * Sets the value of field 'startRes'.
- *
- * @param startRes
- * the value of field 'startRes'.
- */
- public void setStartRes(final int startRes)
- {
- this._startRes = startRes;
- this._has_startRes = true;
- }
-
- /**
- * Sets the value of field 'startSeq'.
- *
- * @param startSeq
- * the value of field 'startSeq'.
- */
- public void setStartSeq(final int startSeq)
- {
- this._startSeq = startSeq;
- this._has_startSeq = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title
- * the value of field 'title'.
- */
- public void setTitle(final java.lang.String title)
- {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width
- * the value of field 'width'.
- */
- public void setWidth(final int width)
- {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'wrapAlignment'.
- *
- * @param wrapAlignment
- * the value of field 'wrapAlignment'.
- */
- public void setWrapAlignment(final boolean wrapAlignment)
- {
- this._wrapAlignment = wrapAlignment;
- this._has_wrapAlignment = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos
- * the value of field 'xpos'.
- */
- public void setXpos(final int xpos)
- {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos
- * the value of field 'ypos'.
- */
- public void setYpos(final int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Viewport
- */
- public static jalview.binding.Viewport unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Viewport) Unmarshaller.unmarshal(
- jalview.binding.Viewport.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean getWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold(
+ ) {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasConservationSelected.
+ *
+ * @return true if at least one ConservationSelected has been
+ * added
+ */
+ public boolean hasConservationSelected(
+ ) {
+ return this._has_conservationSelected;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize(
+ ) {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle(
+ ) {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasPidSelected.
+ *
+ * @return true if at least one PidSelected has been added
+ */
+ public boolean hasPidSelected(
+ ) {
+ return this._has_pidSelected;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold(
+ ) {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasRenderGaps.
+ *
+ * @return true if at least one RenderGaps has been added
+ */
+ public boolean hasRenderGaps(
+ ) {
+ return this._has_renderGaps;
+ }
+
+ /**
+ * Method hasShowAnnotation.
+ *
+ * @return true if at least one ShowAnnotation has been added
+ */
+ public boolean hasShowAnnotation(
+ ) {
+ return this._has_showAnnotation;
+ }
+
+ /**
+ * Method hasShowBoxes.
+ *
+ * @return true if at least one ShowBoxes has been added
+ */
+ public boolean hasShowBoxes(
+ ) {
+ return this._has_showBoxes;
+ }
+
+ /**
+ * Method hasShowColourText.
+ *
+ * @return true if at least one ShowColourText has been added
+ */
+ public boolean hasShowColourText(
+ ) {
+ return this._has_showColourText;
+ }
+
+ /**
+ * Method hasShowConservation.
+ *
+ * @return true if at least one ShowConservation has been added
+ */
+ public boolean hasShowConservation(
+ ) {
+ return this._has_showConservation;
+ }
+
+ /**
+ * Method hasShowFullId.
+ *
+ * @return true if at least one ShowFullId has been added
+ */
+ public boolean hasShowFullId(
+ ) {
+ return this._has_showFullId;
+ }
+
+ /**
+ * Method hasShowIdentity.
+ *
+ * @return true if at least one ShowIdentity has been added
+ */
+ public boolean hasShowIdentity(
+ ) {
+ return this._has_showIdentity;
+ }
+
+ /**
+ * Method hasShowQuality.
+ *
+ * @return true if at least one ShowQuality has been added
+ */
+ public boolean hasShowQuality(
+ ) {
+ return this._has_showQuality;
+ }
+
+ /**
+ * Method hasShowSequenceFeatures.
+ *
+ * @return true if at least one ShowSequenceFeatures has been
+ * added
+ */
+ public boolean hasShowSequenceFeatures(
+ ) {
+ return this._has_showSequenceFeatures;
+ }
+
+ /**
+ * Method hasShowText.
+ *
+ * @return true if at least one ShowText has been added
+ */
+ public boolean hasShowText(
+ ) {
+ return this._has_showText;
+ }
+
+ /**
+ * Method hasStartRes.
+ *
+ * @return true if at least one StartRes has been added
+ */
+ public boolean hasStartRes(
+ ) {
+ return this._has_startRes;
+ }
+
+ /**
+ * Method hasStartSeq.
+ *
+ * @return true if at least one StartSeq has been added
+ */
+ public boolean hasStartSeq(
+ ) {
+ return this._has_startSeq;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasWrapAlignment.
+ *
+ * @return true if at least one WrapAlignment has been added
+ */
+ public boolean hasWrapAlignment(
+ ) {
+ return this._has_wrapAlignment;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean isConservationSelected(
+ ) {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean isPidSelected(
+ ) {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean isRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean isShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean isShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean isShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConservation'.
+ *
+ * @return the value of field 'ShowConservation'.
+ */
+ public boolean isShowConservation(
+ ) {
+ return this._showConservation;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean isShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showIdentity'.
+ *
+ * @return the value of field 'ShowIdentity'.
+ */
+ public boolean isShowIdentity(
+ ) {
+ return this._showIdentity;
+ }
+
+ /**
+ * Returns the value of field 'showQuality'.
+ *
+ * @return the value of field 'ShowQuality'.
+ */
+ public boolean isShowQuality(
+ ) {
+ return this._showQuality;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean isShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean isShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean isWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour the value of field 'bgColour'.
+ */
+ public void setBgColour(
+ final java.lang.String bgColour) {
+ this._bgColour = bgColour;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(
+ final int consThreshold) {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'conservationSelected'.
+ *
+ * @param conservationSelected the value of field
+ * 'conservationSelected'.
+ */
+ public void setConservationSelected(
+ final boolean conservationSelected) {
+ this._conservationSelected = conservationSelected;
+ this._has_conservationSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName the value of field 'fontName'.
+ */
+ public void setFontName(
+ final java.lang.String fontName) {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize the value of field 'fontSize'.
+ */
+ public void setFontSize(
+ final int fontSize) {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle the value of field 'fontStyle'.
+ */
+ public void setFontStyle(
+ final int fontStyle) {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'pidSelected'.
+ *
+ * @param pidSelected the value of field 'pidSelected'.
+ */
+ public void setPidSelected(
+ final boolean pidSelected) {
+ this._pidSelected = pidSelected;
+ this._has_pidSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(
+ final int pidThreshold) {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'renderGaps'.
+ *
+ * @param renderGaps the value of field 'renderGaps'.
+ */
+ public void setRenderGaps(
+ final boolean renderGaps) {
+ this._renderGaps = renderGaps;
+ this._has_renderGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'showAnnotation'.
+ *
+ * @param showAnnotation the value of field 'showAnnotation'.
+ */
+ public void setShowAnnotation(
+ final boolean showAnnotation) {
+ this._showAnnotation = showAnnotation;
+ this._has_showAnnotation = true;
+ }
+
+ /**
+ * Sets the value of field 'showBoxes'.
+ *
+ * @param showBoxes the value of field 'showBoxes'.
+ */
+ public void setShowBoxes(
+ final boolean showBoxes) {
+ this._showBoxes = showBoxes;
+ this._has_showBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'showColourText'.
+ *
+ * @param showColourText the value of field 'showColourText'.
+ */
+ public void setShowColourText(
+ final boolean showColourText) {
+ this._showColourText = showColourText;
+ this._has_showColourText = true;
+ }
+
+ /**
+ * Sets the value of field 'showConservation'.
+ *
+ * @param showConservation the value of field 'showConservation'
+ */
+ public void setShowConservation(
+ final boolean showConservation) {
+ this._showConservation = showConservation;
+ this._has_showConservation = true;
+ }
+
+ /**
+ * Sets the value of field 'showFullId'.
+ *
+ * @param showFullId the value of field 'showFullId'.
+ */
+ public void setShowFullId(
+ final boolean showFullId) {
+ this._showFullId = showFullId;
+ this._has_showFullId = true;
+ }
+
+ /**
+ * Sets the value of field 'showIdentity'.
+ *
+ * @param showIdentity the value of field 'showIdentity'.
+ */
+ public void setShowIdentity(
+ final boolean showIdentity) {
+ this._showIdentity = showIdentity;
+ this._has_showIdentity = true;
+ }
+
+ /**
+ * Sets the value of field 'showQuality'.
+ *
+ * @param showQuality the value of field 'showQuality'.
+ */
+ public void setShowQuality(
+ final boolean showQuality) {
+ this._showQuality = showQuality;
+ this._has_showQuality = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceFeatures'.
+ *
+ * @param showSequenceFeatures the value of field
+ * 'showSequenceFeatures'.
+ */
+ public void setShowSequenceFeatures(
+ final boolean showSequenceFeatures) {
+ this._showSequenceFeatures = showSequenceFeatures;
+ this._has_showSequenceFeatures = true;
+ }
+
+ /**
+ * Sets the value of field 'showText'.
+ *
+ * @param showText the value of field 'showText'.
+ */
+ public void setShowText(
+ final boolean showText) {
+ this._showText = showText;
+ this._has_showText = true;
+ }
+
+ /**
+ * Sets the value of field 'startRes'.
+ *
+ * @param startRes the value of field 'startRes'.
+ */
+ public void setStartRes(
+ final int startRes) {
+ this._startRes = startRes;
+ this._has_startRes = true;
+ }
+
+ /**
+ * Sets the value of field 'startSeq'.
+ *
+ * @param startSeq the value of field 'startSeq'.
+ */
+ public void setStartSeq(
+ final int startSeq) {
+ this._startSeq = startSeq;
+ this._has_startSeq = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'wrapAlignment'.
+ *
+ * @param wrapAlignment the value of field 'wrapAlignment'.
+ */
+ public void setWrapAlignment(
+ final boolean wrapAlignment) {
+ this._wrapAlignment = wrapAlignment;
+ this._has_wrapAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Viewport
+ */
+ public static jalview.binding.Viewport unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
import jalview.util.MessageManager;
import java.awt.Color;
{
sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
}
+
+ @Override
+ public boolean parseFeaturesFile(String file, String protocol,
+ boolean relaxedIdMatching)
+ {
+ boolean featuresFile = false;
+ try
+ {
+ featuresFile = new FeaturesFile(file, protocol).parse(viewport
+ .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
+ .getFeatureColours(), false, relaxedIdMatching);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (featuresFile)
+ {
+ avcg.refreshFeatureUI(true);
+ if (alignPanel.getFeatureRenderer() != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.getFeatureRenderer().findAllFeatures(true);
+ }
+ if (avcg.getFeatureSettingsUI() != null)
+ {
+ avcg.getFeatureSettingsUI().discoverAllFeatureData();
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ return featuresFile;
+
+ }
}
import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsModelI;
-public class FeatureSettingsController implements jalview.api.FeatureSettingsControllerI
+public class FeatureSettingsController // implements
+ // jalview.api.FeatureSettingsControllerI
{
FeatureSettingsControllerGuiI settingUI;
FeatureRenderer fr;
--- /dev/null
+/**
+ *
+ */
+package jalview.datamodel;
+
+/**
+ * Metadata for a sequence that may or may not be physically present in Jalview
+ * at the moment
+ *
+ * @author jprocter
+ *
+ */
+public class ASequence implements ASequenceI
+{
+
+}
--- /dev/null
+package jalview.datamodel;
+
+/**
+ * interfaces to access the basic metadata for a concrete or virtual sequence
+ *
+ * @author jprocter
+ *
+ */
+public interface ASequenceI
+{
+
+}
*
* Example: in "G-AT-C-GA" the aligned codons are (0, 2, 3) and (5, 7, 8).
*
+ * JBPComment: Is this useful anywhere other than jalview.analysis.Dna ?
+ *
* @author gmcarstairs
*
*/
public class AlignedCodonFrame
{
- /*
+ /**
* tied array of na Sequence objects.
*/
private SequenceI[] dnaSeqs = null;
- /*
+ /**
* tied array of Mappings to protein sequence Objects and SequenceI[]
* aaSeqs=null; MapLists where each maps from the corresponding dnaSeqs
* element to corresponding aaSeqs element
* profileseq marked as hidden.
*/
public static ColumnSelection propagateInsertions(SequenceI profileseq,
- Alignment al, AlignmentView input)
+ AlignmentI al, AlignmentView input)
{
int profsqpos = 0;
* @author $author$
* @version $Revision$
*/
-public class Sequence implements SequenceI
+public class Sequence extends ASequence implements SequenceI
{
SequenceI datasetSequence;
*/
public Sequence(String name, String sequence, int start, int end)
{
- this.name = name;
- this.sequence = sequence.toCharArray();
- this.start = start;
- this.end = end;
- parseId();
- checkValidRange();
+ initSeqAndName(name, sequence.toCharArray(), start, end);
}
public Sequence(String name, char[] sequence, int start, int end)
{
- this.name = name;
- this.sequence = sequence;
- this.start = start;
- this.end = end;
+ initSeqAndName(name, sequence, start, end);
+ }
+
+ /**
+ * Stage 1 constructor - assign name, sequence, and set start and end fields.
+ * start and end are updated values from name2 if it ends with /start-end
+ *
+ * @param name2
+ * @param sequence2
+ * @param start2
+ * @param end2
+ */
+ protected void initSeqAndName(String name2, char[] sequence2, int start2,
+ int end2)
+ {
+ this.name = name2;
+ this.sequence = sequence2;
+ this.start = start2;
+ this.end = end2;
parseId();
checkValidRange();
}
*/
public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
{
- this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+ initSeqFrom(seq, alAnnotation);
+
+ }
+
+ protected void initSeqFrom(SequenceI seq,
+ AlignmentAnnotation[] alAnnotation)
+ {
+ initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
+ seq.getEnd());
description = seq.getDescription();
if (seq.getSequenceFeatures() != null)
{
--- /dev/null
+package jalview.datamodel;
+
+public class SequenceDummy extends Sequence implements SequenceI
+{
+ public SequenceDummy(String sequenceId)
+ {
+ super(sequenceId, "THISAPLACEHOLDER");
+ }
+
+ private boolean dummy = true;
+ /**
+ * become a proxy for mseq, merging any existing annotation on this sequence
+ *
+ * @param mseq
+ */
+ public void become(SequenceI mseq)
+ {
+ initSeqFrom(mseq, null);
+ dummy=false;
+ }
+
+ /**
+ * Test if the SequenceDummy has been promoted to a real sequence via
+ * SequenceDummy.become
+ *
+ * @return true if this is a placeholder and contains no actual sequence data
+ */
+ public boolean isDummy()
+ {
+ return dummy;
+ }
+}
return begin;
}
+ public int getStrand()
+ {
+ String str;
+ if (otherDetails == null
+ || (str = otherDetails.get("STRAND").toString()) == null)
+ {
+ return 0;
+ }
+ if (str.equals("-"))
+ {
+ return -1;
+ }
+ if (str.equals("+"))
+ {
+ return 1;
+ }
+ return 0;
+ }
+
}
import fr.orsay.lri.varna.models.rna.RNA;
/**
- * DOCUMENT ME!
+ * Methods for manipulating a sequence, its metadata and related annotation in
+ * an alignment or dataset.
*
* @author $author$
* @version $Revision$
*/
-public interface SequenceI
+public interface SequenceI extends ASequenceI
{
/**
* Set the display name for the sequence
--- /dev/null
+package jalview.gui;
+
+import jalview.api.AlignExportSettingI;
+import jalview.jbgui.GAlignExportSettings;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JDialog;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
+@SuppressWarnings("serial")
+public class AlignExportSettings extends GAlignExportSettings implements
+ AlignExportSettingI
+{
+ protected JInternalFrame frame;
+
+ boolean cancelled = false;
+
+ JDialog dialog;
+
+ public AlignExportSettings(boolean hasHiddenSeq, boolean hasHiddenCols,
+ String alignFileFormat)
+ {
+ super(hasHiddenSeq, hasHiddenCols, alignFileFormat);
+ if (isShowDialog())
+ {
+ JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
+ JOptionPane.DEFAULT_OPTION, null, new Object[]
+ { this });
+ dialog = pane.createDialog(Desktop.desktop, "Export Settings");
+ dialog.pack();
+ dialog.setVisible(true);
+ dialog.setContentPane(this);
+ dialog.validate();
+ }
+ }
+
+
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ cancelled = false;
+ dialog.setVisible(false);
+ }
+
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ cancelled = true;
+ dialog.setVisible(false);
+ }
+
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return chkHiddenSeqs.isSelected();
+ }
+
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return chkHiddenCols.isSelected();
+ }
+
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return chkExportAnnots.isSelected();
+ }
+
+ @Override
+ public boolean isExportFeatures()
+ {
+ return chkExportFeats.isSelected();
+ }
+
+ @Override
+ public boolean isExportGroups()
+ {
+ return chkExportGrps.isSelected();
+ }
+
+ public boolean isCancelled()
+ {
+ return cancelled;
+ }
+
+}
*/
package jalview.gui;
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
-import jalview.io.FeaturesFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.seqfetcher.DbSourceProxy;
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
/**
* DOCUMENT ME!
*
if (hiddenSeqs != null && hiddenSeqs.length > 0)
{
viewport.hideSequence(hiddenSeqs);
- viewport.setHasHiddenRows(true);
}
alignPanel = new AlignmentPanel(this, viewport);
addAlignmentPanel(alignPanel, true);
return false;
}
- ExportData exportData = getAlignmentForExport();
- FormatAdapter f = new FormatAdapter(viewport);
+ ExportData exportData = getAlignmentForExport(format);
+ FormatAdapter f = new FormatAdapter(alignPanel);
String output = f.formatSequences(format,
exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
protected void outputText_actionPerformed(ActionEvent e)
{
- ExportData exportData = getAlignmentForExport();
+ ExportData exportData = getAlignmentForExport(e.getActionCommand());
+ if (exportData.getSettings().isCancelled())
+ {
+ return;
+ }
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
-
try
{
- cap.setText(new FormatAdapter(viewport).formatSequences(
+ cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
+ .formatSequences(
e.getActionCommand(),
exportData.getAlignment(),
exportData.getOmitHidden(), exportData.getStartEndPostions(),
}
- public ExportData getAlignmentForExport()
+ public ExportData getAlignmentForExport(String exportFomat)
{
AlignmentI alignmentToExport = null;
String[] omitHidden = null;
int[] alignmentStartEnd = new int[2];
- FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
- viewport.setFeatureRenderer(fr);
+
HiddenSequences hiddenSeqs = viewport.getAlignment()
.getHiddenSequences();
alignmentStartEnd = new int[]
{ 0, alignmentToExport.getWidth() - 1 };
- if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
- {
- int reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.alignment_contains_hidden_columns"),
- MessageManager
- .getString("action.save_omit_hidden_columns"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+ AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
+ viewport.hasHiddenColumns(), exportFomat);
+ settings.isExportAnnotations();
- if (reply == JOptionPane.YES_OPTION)
- {
- // export only visible region
- omitHidden = viewport.getViewAsString(false);
- alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
- .getColumnSelection().getHiddenColumns());
- viewport.setIncludeHiddenRegion(false);
- }
- else
- {
- // export all region including visible
- alignmentToExport = hiddenSeqs.getFullAlignment();
- viewport.setIncludeHiddenRegion(true);
- }
+ if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+ {
+ omitHidden = viewport.getViewAsString(false);
}
- return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd);
+ if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ {
+ alignmentToExport = hiddenSeqs.getFullAlignment();
+ }
+ else
+ {
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+ .getColumnSelection().getHiddenColumns());
+ }
+ return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd,
+ settings);
}
private static int[] getStartEnd(int[] aligmentStartEnd,
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- // new HTMLOutput(alignPanel,
- // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
- // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
new HtmlSvgOutput(null, alignPanel);
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel,
- alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
public void createImageMap(File file, String image)
public FeatureSettings featureSettings;
@Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return featureSettings;
+ }
+
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
* contents or path to retrieve file
* @param type
* access mode of file (see jalview.io.AlignFile)
- * @return true if features file was parsed corectly.
+ * @return true if features file was parsed correctly.
*/
public boolean parseFeaturesFile(String file, String type)
{
- boolean featuresFile = false;
- try
- {
- featuresFile = new FeaturesFile(file, type).parse(viewport
- .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer().getFeatureColours(), false,
- jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ return avc.parseFeaturesFile(file, type,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+
+ }
- if (featuresFile)
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ // note - currently this is only still here rather than in the controller
+ // because of the featureSettings hard reference that is yet to be
+ // abstracted
+ if (enableIfNecessary)
{
viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
- if (alignPanel.getSeqPanel().seqCanvas.fr != null)
- {
- // update the min/max ranges where necessary
- alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
- }
- if (featureSettings != null)
- {
- featureSettings.setTableData();
- }
- alignPanel.paintAlignment(true);
}
- return featuresFile;
- }
+ }
@Override
public void dragEnter(DropTargetDragEvent evt)
{
private int[] startEnd;
- public ExportData(AlignmentI align, String[] ommit, int[] startEnd)
+ private AlignExportSettings settings;
+
+ public ExportData(AlignmentI align, String[] ommit, int[] startEnd,
+ AlignExportSettings settings)
{
this.alignment = align;
this.omitHidden = ommit;
this.startEnd = startEnd;
+ this.settings = settings;
}
public AlignmentI getAlignment()
{
this.startEnd = startEnd;
}
+
+ public AlignExportSettings getSettings()
+ {
+ return settings;
+ }
+
+ public void setSettings(AlignExportSettings settings)
+ {
+ this.settings = settings;
+ }
}
}
*/
package jalview.gui;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
/**
* DOCUMENT ME!
*
private Rectangle explodedGeometry;
- private FeatureRenderer featureRenderer;
-
- private boolean includeHiddenRegion = true;
String viewName;
/*
}
}
- @Override
- public FeatureRenderer getFeatureRenderer()
- {
- return featureRenderer;
- }
-
- @Override
- public void setFeatureRenderer(FeatureRenderer featureRenderer)
- {
- this.featureRenderer = featureRenderer;
- }
-
- public boolean isIncludeHiddenRegion()
- {
- return includeHiddenRegion;
- }
-
- public void setIncludeHiddenRegion(boolean includeHiddenRegion)
- {
- this.includeHiddenRegion = includeHiddenRegion;
- }
}
getSize(currentSize);
g.getClipBounds(rectClip);
- if (jmb.fileLoadingError != null)
+ if (jmb != null && jmb.fileLoadingError != null)
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.ComplexAlignFile;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.DataFlavor;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
-import jalview.api.ComplexAlignFile;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GCutAndPasteTransfer;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
/**
* Cut'n'paste files into the desktop See JAL-1105
*
public class CutAndPasteTransfer extends GCutAndPasteTransfer
{
- AlignViewport viewport;
+ AlignmentViewPanel alignpanel;
+
+ AlignViewportI viewport;
FileParse source = null;
public CutAndPasteTransfer()
/**
* DOCUMENT ME!
*/
- public void setForInput(AlignViewport viewport)
+ public void setForInput(AlignmentViewPanel viewpanel)
{
- this.viewport = viewport;
+ this.alignpanel = viewpanel;
+ if (alignpanel != null)
+ {
+ this.viewport = alignpanel.getAlignViewport();
+ }
if (viewport != null)
{
ok.setText(MessageManager.getString("action.add"));
{
String format = new IdentifyFile().Identify(getText(), "Paste");
// TODO: identify feature, annotation or tree file and parse appropriately.
- Alignment al = null;
+ AlignmentI al = null;
if (FormatAdapter.isValidFormat(format))
{
try
{
- FormatAdapter fa = new FormatAdapter(viewport);
+ FormatAdapter fa = new FormatAdapter(alignpanel);
al = fa.readFile(getText(), "Paste", format);
source = fa.getAlignFile();
{ format });
if (viewport != null)
{
- viewport.addAlignment(al, title);
+ ((AlignViewport) viewport).addAlignment(al, title);
}
else
{
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.ParamManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GSplitFrame;
-import jalview.jbgui.GStructureViewer;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-
/**
* Jalview Desktop
*
public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(viewport);
+ cap.setForInput(viewport.getAlignPanel());
Desktop.addInternalFrame(cap,
MessageManager.getString("label.cut_paste_alignmen_file"),
true, 600, 500);
*/
package jalview.gui;
+import jalview.api.FeatureSettingsControllerI;
import jalview.bin.Cache;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
-public class FeatureSettings extends JPanel
+public class FeatureSettings extends JPanel implements
+ FeatureSettingsControllerI
{
DasSourceBrowser dassourceBrowser;
fr.findAllFeatures(true); // display everything!
}
- setTableData();
+ discoverAllFeatureData();
final PropertyChangeListener change;
final FeatureSettings fs = this;
fr.addPropertyChangeListener(change = new PropertyChangeListener()
*/
Hashtable typeWidth = null;
- synchronized public void setTableData()
+ @Override
+ synchronized public void discoverAllFeatureData()
{
Vector allFeatures = new Vector();
Vector allGroups = new Vector();
*
* @param gg
* DOCUMENT ME!
+ * @param hiddenRows
+ * true - check and display hidden row marker if need be
* @param s
* DOCUMENT ME!
* @param i
* @param ypos
* DOCUMENT ME!
*/
- public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
+ public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+ int i, int starty,
int ypos)
{
int xPos = 0;
gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
- if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+ if (hiddenRows)
{
drawMarker(i, starty, ypos);
}
Color currentColor = Color.white;
Color currentTextColor = Color.black;
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows();
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
for (int i = starty; i < alheight; i++)
{
SequenceI s = av.getAlignment().getSequenceAt(i);
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+ if (doHiddenCheck)
{
setHiddenFont(s);
}
gg.setFont(getIdfont());
}
- drawIdString(gg, s, i, 0, ypos);
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
}
if (labels != null && av.isShowAnnotation())
continue;
}
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+ if (doHiddenCheck)
{
setHiddenFont(sequence);
}
(((i - starty) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
- if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+ if (hiddenRows)
{
drawMarker(i, starty, 0);
}
int color = Color.white.getRGB();
int row, col;
jalview.datamodel.SequenceI seq;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
boolean hiddenRow = false;
for (row = 0; row < sequencesHeight; row++)
{
lastrow = (int) (row * sampleRow);
hiddenRow = false;
- if (av.hasHiddenRows())
+ if (hasHiddenRows)
{
seq = av.getAlignment().getHiddenSequences()
.getHiddenSequence(lastrow);
}
if (hiddenRow
- || (av.hasHiddenColumns() && !av.getColumnSelection()
+ || (hasHiddenCols && !av.getColumnSelection()
.isVisible(lastcol)))
{
color = new Color(color).darker().darker().getRGB();
// wysiwig behaviour
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- ap.av, true));
+ ap, true));
}
public void pdbFromFile_actionPerformed()
*/
package jalview.gui;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
import java.awt.BorderLayout;
import java.awt.Font;
import java.awt.event.ActionEvent;
import com.stevesoft.pat.Regex;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.util.DBRefUtils;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
public class SequenceFetcher extends JPanel implements Runnable
{
JLabel dbeg = new JLabel();
AlignmentI parseResult(String result, String title)
{
String format = new IdentifyFile().Identify(result, "Paste");
- Alignment sequences = null;
+ AlignmentI sequences = null;
if (FormatAdapter.isValidFormat(format))
{
sequences = null;
{
boolean srep = av.isDisplayReferenceSeq();
boolean getboxColour = false;
+ boolean isarep = av.getAlignment().getSeqrep() == seq;
+ boolean isgrep = currentSequenceGroup != null ? currentSequenceGroup
+ .getSeqrep() == seq : false;
+ char sr_c;
for (int i = start; i <= end; i++)
{
+
graphics.setColor(av.getTextColour());
getboxColour = false;
s = seq.getCharAt(i);
+
if (!renderGaps && jalview.util.Comparison.isGap(s))
{
continue;
{
graphics.setColor(currentSequenceGroup.textColour);
}
- if (currentSequenceGroup.getShowNonconserved()) // todo optimize
+ if (!isarep && !isgrep
+ && currentSequenceGroup.getShowNonconserved()) // todo
+ // optimize
{
// todo - use sequence group consensus
- s = getDisplayChar(srep, i, s,
- '.');
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
}
graphics.setColor(av.getTextColour2());
}
}
- if (av.getShowUnconserved())
+ if (!isarep && av.getShowUnconserved())
{
- s = getDisplayChar(srep, i, s,
- '.');
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
}
* @return
*/
private char getDisplayChar(final boolean usesrep, int position,
- char sequenceChar, char conservedChar)
+ char sequenceChar, char conservedChar, SequenceGroup currentGroup)
{
// TODO - use currentSequenceGroup rather than alignment
// currentSequenceGroup.getConsensus()
- char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
- .charAt(0);
+ char conschar = (usesrep) ? (currentGroup == null ? av.getAlignment()
+ .getSeqrep().getCharAt(position)
+ : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
+ .getCharAt(position) : av.getAlignment().getSeqrep()
+ .getCharAt(position)))
+ : (currentGroup != null && currentGroup.getConsensus() != null) ? currentGroup
+ .getConsensus().annotations[position].displayCharacter
+ .charAt(0)
+ : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
if (conschar != '-'
&& (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
{
*/
package jalview.io;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
/**
* DOCUMENT ME!
*
*
* @param al
*/
- public void addAnnotations(Alignment al)
+ public void addAnnotations(AlignmentI al)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
}
+ /**
+ * register sequence groups on the alignment for **output**
+ *
+ * @param al
+ */
public void addSeqGroups(AlignmentI al)
{
this.seqGroups = al.getGroups();
* @note implicitly called by addAnnotations()
* @param al
*/
- public void addProperties(Alignment al)
+ public void addProperties(AlignmentI al)
{
if (properties != null && properties.size() > 0)
{
return newickStrings == null ? 0 : newickStrings.size();
}
+ public void addGroups(AlignmentI al)
+ {
+
+ for (SequenceGroup sg : getSeqGroups())
+ {
+ al.addGroup(sg);
+ }
+ }
+
}
*/
package jalview.io;
-import java.io.StringWriter;
import java.io.PrintWriter;
+import java.io.StringWriter;
import java.util.Enumeration;
import java.util.Hashtable;
- alignment.getSequenceAt(i).getStart();
avg += size;
if (size > max)
+ {
max = size;
+ }
if (size < min)
+ {
min = size;
+ }
}
- avg = avg / (float) alignment.getHeight();
+ avg = avg / alignment.getHeight();
pw.print(nl);
pw.print("Sequences: " + alignment.getHeight());
pw.print(nl);
*/
package jalview.io;
-import java.io.File;
-import java.io.InputStream;
-import java.util.List;
-
-import jalview.api.AlignViewportI;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
+import java.io.File;
+import java.io.InputStream;
+import java.util.List;
+
/**
* A low level class for alignment and feature IO with alignment formatting
* methods used by both applet and application for generating flat alignment
*/
public class AppletFormatAdapter
{
- private AlignViewportI viewport;
+ private AlignmentViewPanel viewpanel;
public static String FILE = "File";
*/
protected String newline = System.getProperty("line.separator");
+ private AlignExportSettingI exportSettings;
+
/**
* List of valid format strings used in the isValidFormat method
*/
public static final String[] READABLE_FORMATS = new String[]
{ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
+ "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
"HTML" };
/**
public static final String[] READABLE_EXTENSIONS = new String[]
{ "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
"sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
+ ".gff2,gff3",
"jar,jvp", HtmlFile.FILE_EXT };
/**
*/
public static final String[] READABLE_FNAMES = new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
- "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview",
+ "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview",
HtmlFile.FILE_DESC };
/**
{
}
- public AppletFormatAdapter(AlignViewportI viewport)
+ public AppletFormatAdapter(AlignmentViewPanel viewpanel)
+ {
+ this.viewpanel = viewpanel;
+ }
+
+ public AppletFormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingI settings)
{
- this.viewport = viewport;
+ viewpanel = alignPanel;
+ exportSettings = settings;
}
/**
*
* @return DOCUMENT ME!
*/
- public Alignment readFile(String inFile, String type, String format)
+ public AlignmentI readFile(String inFile, String type, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
this.inFile = inFile;
try
{
- Alignment al;
if (format.equals("FASTA"))
{
alignFile = new FastaFile(inFile, type);
else if (format.equals(JSONFile.FILE_DESC))
{
alignFile = new JSONFile(inFile, type);
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- ((JSONFile) alignFile).setViewport(viewport);
- for (SequenceGroup sg : alignFile.getSeqGroups())
- {
- al.addGroup(sg);
- }
-
- return al;
}
else if (format.equals(HtmlFile.FILE_DESC))
{
alignFile = new HtmlFile(inFile, type);
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- for (SequenceGroup sg : alignFile.getSeqGroups())
- {
- al.addGroup(sg);
- }
- return al;
}
else if (format.equals("RNAML"))
{
alignFile = new RnamlFile(inFile, type);
}
-
- al = new Alignment(alignFile.getSeqsAsArray());
-
- alignFile.addAnnotations(al);
-
- return al;
+ else if (format.equals(IdentifyFile.GFF3File))
+ {
+ alignFile = new Gff3File(inFile, type);
+ }
+ return buildAlignmentFrom(alignFile);
} catch (Exception e)
{
e.printStackTrace();
{
// Possible sequence is just residues with no label
alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- Alignment al = new Alignment(alignFile.getSeqsAsArray());
-
- alignFile.addSeqGroups(al);
- alignFile.addAnnotations(al);
- return al;
+ return buildAlignmentFrom(alignFile);
} catch (Exception ex)
{
String type = source.type;
try
{
- Alignment al;
if (format.equals("FASTA"))
{
alignFile = new FastaFile(source);
{
alignFile = new PhylipFile(source);
}
+ else if (format.equals(IdentifyFile.GFF3File))
+ {
+ alignFile = new Gff3File(inFile, type);
+ }
else if (format.equals(JSONFile.FILE_DESC))
{
alignFile = new JSONFile(source);
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- alignFile.addSeqGroups(al);
- return al;
}
else if (format.equals(HtmlFile.FILE_DESC))
{
alignFile = new HtmlFile(source);
}
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- return al;
+ return buildAlignmentFrom(alignFile);
+
} catch (Exception e)
{
e.printStackTrace();
{
// Possible sequence is just residues with no label
alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- Alignment al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- alignFile.addSeqGroups(al);
- return al;
+ return buildAlignmentFrom(alignFile);
} catch (Exception ex)
{
/**
+ * boilerplate method to handle data from an AlignFile and construct a new
+ * alignment or import to an existing alignment
+ *
+ * @param alignFile2
+ * @return AlignmentI instance ready to pass to a UI constructor
+ */
+ private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
+ {
+ // Standard boilerplate for creating alignment from parser
+ alignFile.configureForView(viewpanel);
+
+ AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
+
+ alignFile.addAnnotations(al);
+
+ alignFile.addGroups(al);
+
+ return al;
+ }
+
+ /**
* create an alignment flatfile from a Jalview alignment view
* @param format
* @param jvsuffix
* @return flatfile in a string
*/
public String formatSequences(String format, boolean jvsuffix,
- AlignViewportI av, boolean selectedOnly)
+ AlignmentViewPanel ap, boolean selectedOnly)
{
- AlignmentView selvew = av.getAlignmentView(selectedOnly, false);
- AlignmentI aselview = selvew.getVisibleAlignment(av
+ AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
+ selectedOnly, false);
+ AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
.getGapCharacter());
- List<AlignmentAnnotation> ala = (av
+ List<AlignmentAnnotation> ala = (ap.getAlignViewport()
.getVisibleAlignmentAnnotation(selectedOnly));
if (ala != null)
{
else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
{
afile = new JSONFile();
- afile.setViewport(viewport);
- // Add groups to AlignFile
- afile.seqGroups = alignment.getGroups();
-
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : alignment.getAlignmentAnnotation())
- {
- if (annot != null && !annot.autoCalculated)
- {
- if (annot.label.equals("PDB.CATempFactor"))
- {
- continue;
- }
- afile.annotations.add(annot);
- }
- }
}
else if (format.equalsIgnoreCase("RNAML"))
{
afile.setNewlineString(newline);
afile.addJVSuffix(jvsuffix);
- afile.setSeqs(alignment.getSequencesArray());
+ afile.setExportSettings(exportSettings);
+ afile.configureForView(viewpanel);
+
+ // check whether we were given a specific alignment to export, rather than
+ // the one in the viewpanel
+ if (viewpanel == null || viewpanel.getAlignment() == null
+ || viewpanel.getAlignment() != alignment)
+ {
+ afile.setSeqs(alignment.getSequencesArray());
+ }
+ else
+ {
+ afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
+ }
String afileresp = afile.print();
if (afile.hasWarningMessage())
System.gc();
long memf = -r.totalMemory() + r.freeMemory();
long t1 = -System.currentTimeMillis();
- Alignment al = afa.readFile(args[i], FILE,
+ AlignmentI al = afa.readFile(args[i], FILE,
new IdentifyFile().Identify(args[i], FILE));
t1 += System.currentTimeMillis();
System.gc();
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
/**
* DOCUMENT ME!
{
line = nextLine();
if (line == null)
+ {
break;
+ }
// seek end of ids
if (line.indexOf("*") > -1)
{
}
} while (!idsFound);
if (line == null)
+ {
break; // end of file.
+ }
int starCol = line.indexOf("*");
seqstrings = new StringBuffer[seqs.size()];
}
if (seqs.size() > 0)
{
- if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is
+ if (headerLines.length() > 1 + numHeaderLines)
+ {
// just whitespace or not.
setAlignmentProperty("Comments", headerLines.toString());
+ }
setAlignmentProperty("iteration", "" + iterationCount);
}
}
package jalview.io;
+import jalview.api.AlignmentViewPanel;
import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
import jalview.json.binding.v1.BioJSReleasePojo;
import jalview.json.binding.v1.BioJSRepositoryPojo;
import jalview.util.MessageManager;
public class BioJsHTMLOutput
{
- private AlignViewport av;
+ private AlignmentViewPanel ap;
private static File currentBJSTemplateFile;
"biojs_template_git_repo",
"https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
- public BioJsHTMLOutput(AlignmentPanel ap, FeatureRenderer fr1)
+ public BioJsHTMLOutput(AlignmentViewPanel ap)
{
if (ap != null)
{
- this.av = ap.av;
- av.setFeatureRenderer(new FeatureRenderer(ap));
+ this.ap = ap;
}
}
try
{
String outputFile = getOutputFile();
- String jalviewAlignmentJson = JSONFile.getJSONData(av);
+ String jalviewAlignmentJson = JSONFile.getJSONData(ap);
String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
.replaceAll(
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
-
import jalview.analysis.SequenceIdMatcher;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.UserColourScheme;
import jalview.util.Format;
+import jalview.util.MapList;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* Parse and create Jalview Features files Detects GFF format features files and
*/
private boolean doGffSource = true;
+ private int gffversion;
+
/**
* Creates a new FeaturesFile object.
*/
}
/**
- * Creates a new FeaturesFile object.
- *
* @param inFile
- * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
- *
* @throws IOException
- * DOCUMENT ME!
*/
public FeaturesFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
+ /**
+ * @param source
+ * @throws IOException
+ */
public FeaturesFile(FileParse source) throws IOException
{
super(source);
}
/**
+ * @param parseImmediately
+ * @param source
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, FileParse source)
+ throws IOException
+ {
+ super(parseImmediately, source);
+ }
+
+ /**
+ * @param parseImmediately
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, String inFile, String type)
+ throws IOException
+ {
+ super(parseImmediately, inFile, type);
+ }
+
+ /**
* Parse GFF or sequence features file using case-independent matching,
* discarding URLs
*
return parse(align, colours, featureLink, removeHTML, false);
}
+ @Override
+ public void addAnnotations(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addAnnotations(al);
+ }
+
+ @Override
+ public void addProperties(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addProperties(al);
+ }
+
+ @Override
+ public void addSeqGroups(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addSeqGroups(al);
+ }
+
/**
* Parse GFF or sequence features file
*
try
{
SequenceI seq = null;
+ /**
+ * keep track of any sequences we try to create from the data if it is a GFF3 file
+ */
+ ArrayList<SequenceI> newseqs = new ArrayList<SequenceI>();
String type, desc, token = null;
int index, start, end;
* when true, assume GFF style features rather than Jalview style.
*/
boolean GFFFile = true;
+ Map<String, String> gffProps = new HashMap<String, String>();
while ((line = nextLine()) != null)
{
+ // skip comments/process pragmas
if (line.startsWith("#"))
{
+ if (line.startsWith("##"))
+ {
+ // possibly GFF2/3 version and metadata header
+ processGffPragma(line, gffProps, align, newseqs);
+ line = "";
+ }
continue;
}
// Still possible this is an old Jalview file,
// which does not have type colours at the beginning
seqId = token = st.nextToken();
- seq = findName(align, seqId, relaxedIdmatching);
+ seq = findName(align, seqId, relaxedIdmatching, newseqs);
if (seq != null)
{
desc = st.nextToken();
if (st.hasMoreTokens())
{
StringBuffer attributes = new StringBuffer();
+ boolean sep = false;
while (st.hasMoreTokens())
{
- attributes.append("\t" + st.nextElement());
+ attributes.append((sep ? "\t" : "") + st.nextElement());
+ sep = true;
}
// TODO validate and split GFF2 attributes field ? parse out
// ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as
sf.setValue("ATTRIBUTES", attributes.toString());
}
- seq.addSequenceFeature(sf);
- while ((seq = align.findName(seq, seqId, true)) != null)
+ if (processOrAddSeqFeature(align, newseqs, seq, sf, GFFFile,
+ relaxedIdmatching))
{
- seq.addSequenceFeature(new SequenceFeature(sf));
+ // check whether we should add the sequence feature to any other
+ // sequences in the alignment with the same or similar
+ while ((seq = align.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
}
break;
}
if (!token.equals("ID_NOT_SPECIFIED"))
{
- seq = findName(align, seqId = token, relaxedIdmatching);
+ seq = findName(align, seqId = token, relaxedIdmatching, null);
st.nextToken();
}
else
resetMatcher();
} catch (Exception ex)
{
+ // should report somewhere useful for UI if necessary
+ warningMessage = ((warningMessage == null) ? "" : warningMessage)
+ + "Parsing error at\n" + line;
System.out.println("Error parsing feature file: " + ex + "\n" + line);
ex.printStackTrace(System.err);
resetMatcher();
return true;
}
+ private enum GffPragmas
+ {
+ gff_version, sequence_region, feature_ontology, attribute_ontology, source_ontology, species_build, fasta, hash
+ };
+
+ private static Map<String, GffPragmas> GFFPRAGMA;
+ static
+ {
+ GFFPRAGMA = new HashMap<String, GffPragmas>();
+ GFFPRAGMA.put("sequence-region", GffPragmas.sequence_region);
+ GFFPRAGMA.put("feature-ontology", GffPragmas.feature_ontology);
+ GFFPRAGMA.put("#", GffPragmas.hash);
+ GFFPRAGMA.put("fasta", GffPragmas.fasta);
+ GFFPRAGMA.put("species-build", GffPragmas.species_build);
+ GFFPRAGMA.put("source-ontology", GffPragmas.source_ontology);
+ GFFPRAGMA.put("attribute-ontology", GffPragmas.attribute_ontology);
+ }
+
+ private void processGffPragma(String line, Map<String, String> gffProps,
+ AlignmentI align, ArrayList<SequenceI> newseqs)
+ throws IOException
+ {
+ // line starts with ##
+ int spacepos = line.indexOf(' ');
+ String pragma = spacepos == -1 ? line.substring(2).trim() : line
+ .substring(2, spacepos);
+ GffPragmas gffpragma = GFFPRAGMA.get(pragma.toLowerCase());
+ if (gffpragma == null)
+ {
+ return;
+ }
+ switch (gffpragma)
+ {
+ case gff_version:
+ try
+ {
+ gffversion = Integer.parseInt(line.substring(spacepos + 1));
+ } finally
+ {
+
+ }
+ break;
+ case feature_ontology:
+ // resolve against specific feature ontology
+ break;
+ case attribute_ontology:
+ // resolve against specific attribute ontology
+ break;
+ case source_ontology:
+ // resolve against specific source ontology
+ break;
+ case species_build:
+ // resolve against specific NCBI taxon version
+ break;
+ case hash:
+ // close off any open feature hierarchies
+ break;
+ case fasta:
+ // process the rest of the file as a fasta file and replace any dummy
+ // sequence IDs
+ process_as_fasta(align, newseqs);
+ break;
+ default:
+ // we do nothing ?
+ System.err.println("Ignoring unknown pragma:\n" + line);
+ }
+ }
+
+ private void process_as_fasta(AlignmentI align, List<SequenceI> newseqs)
+ throws IOException
+ {
+ try
+ {
+ mark();
+ } catch (IOException q)
+ {
+ }
+ FastaFile parser = new FastaFile(this);
+ List<SequenceI> includedseqs = parser.getSeqs();
+ SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);
+ // iterate over includedseqs, and replacing matching ones with newseqs
+ // sequences. Generic iterator not used here because we modify includedseqs
+ // as we go
+ for (int p = 0, pSize = includedseqs.size(); p < pSize; p++)
+ {
+ // search for any dummy seqs that this sequence can be used to update
+ SequenceI dummyseq = smatcher.findIdMatch(includedseqs.get(p));
+ if (dummyseq != null)
+ {
+ // dummyseq was created so it could be annotated and referred to in
+ // alignments/codon mappings
+
+ SequenceI mseq = includedseqs.get(p);
+ // mseq is the 'template' imported from the FASTA file which we'll use
+ // to coomplete dummyseq
+ if (dummyseq instanceof SequenceDummy)
+ {
+ // probably have the pattern wrong
+ // idea is that a flyweight proxy for a sequence ID can be created for
+ // 1. stable reference creation
+ // 2. addition of annotation
+ // 3. future replacement by a real sequence
+ // current pattern is to create SequenceDummy objects - a convenience
+ // constructor for a Sequence.
+ // problem is that when promoted to a real sequence, all references
+ // need
+ // to be updated somehow.
+ ((SequenceDummy) dummyseq).become(mseq);
+ includedseqs.set(p, dummyseq); // template is no longer needed
+ }
+ }
+ }
+ // finally add sequences to the dataset
+ for (SequenceI seq : includedseqs)
+ {
+ align.addSequence(seq);
+ }
+ }
+
+ /**
+ * take a sequence feature and examine its attributes to decide how it should
+ * be added to a sequence
+ *
+ * @param seq
+ * - the destination sequence constructed or discovered in the
+ * current context
+ * @param sf
+ * - the base feature with ATTRIBUTES property containing any
+ * additional attributes
+ * @param gFFFile
+ * - true if we are processing a GFF annotation file
+ * @return true if sf was actually added to the sequence, false if it was
+ * processed in another way
+ */
+ public boolean processOrAddSeqFeature(AlignmentI align, List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
+ boolean gFFFile, boolean relaxedIdMatching)
+ {
+ String attr = (String) sf.getValue("ATTRIBUTES");
+ boolean add = true;
+ if (gFFFile && attr != null)
+ {
+ int nattr=8;
+
+ for (String attset : attr.split("\t"))
+ {
+ if (attset==null || attset.trim().length()==0)
+ {
+ continue;
+ }
+ nattr++;
+ Map<String, List<String>> set = new HashMap<String, List<String>>();
+ // normally, only expect one column - 9 - in this field
+ // the attributes (Gff3) or groups (gff2) field
+ for (String pair : attset.trim().split(";"))
+ {
+ pair = pair.trim();
+ if (pair.length() == 0)
+ {
+ continue;
+ }
+
+ // expect either space seperated (gff2) or '=' separated (gff3)
+ // key/value pairs here
+
+ int eqpos = pair.indexOf('='),sppos = pair.indexOf(' ');
+ String key = null, value = null;
+
+ if (sppos > -1 && (eqpos == -1 || sppos < eqpos))
+ {
+ key = pair.substring(0, sppos);
+ value = pair.substring(sppos + 1);
+ } else {
+ if (eqpos > -1 && (sppos == -1 || eqpos < sppos))
+ {
+ key = pair.substring(0, eqpos);
+ value = pair.substring(eqpos + 1);
+ } else
+ {
+ key = pair;
+ }
+ }
+ if (key != null)
+ {
+ List<String> vals = set.get(key);
+ if (vals == null)
+ {
+ vals = new ArrayList<String>();
+ set.put(key, vals);
+ }
+ if (value != null)
+ {
+ vals.add(value.trim());
+ }
+ }
+ }
+ try
+ {
+ add &= processGffKey(set, nattr, seq, sf, align, newseqs,
+ relaxedIdMatching); // process decides if
+ // feature is actually
+ // added
+ } catch (InvalidGFF3FieldException ivfe)
+ {
+ System.err.println(ivfe);
+ }
+ }
+ }
+ if (add)
+ {
+ seq.addSequenceFeature(sf);
+ }
+ return add;
+ }
+
+ public class InvalidGFF3FieldException extends Exception
+ {
+ String field, value;
+
+ public InvalidGFF3FieldException(String field,
+ Map<String, List<String>> set, String message)
+ {
+ super(message + " (Field was " + field + " and value was "
+ + set.get(field).toString());
+ this.field = field;
+ this.value = set.get(field).toString();
+ }
+
+ }
+
+ /**
+ * take a set of keys for a feature and interpret them
+ *
+ * @param set
+ * @param nattr
+ * @param seq
+ * @param sf
+ * @return
+ */
+ public boolean processGffKey(Map<String, List<String>> set, int nattr,
+ SequenceI seq, SequenceFeature sf, AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching)
+ throws InvalidGFF3FieldException
+ {
+ String attr;
+ // decide how to interpret according to type
+ if (sf.getType().equals("similarity"))
+ {
+ int strand = sf.getStrand();
+ // exonerate cdna/protein map
+ // look for fields
+ List<SequenceI> querySeq = findNames(align, newseqs,
+ relaxedIdMatching, set.get(attr="Query"));
+ if (querySeq==null || querySeq.size()!=1)
+ {
+ throw new InvalidGFF3FieldException( attr, set,
+ "Expecting exactly one sequence in Query field (got "
+ + set.get(attr) + ")");
+ }
+ if (set.containsKey(attr="Align"))
+ {
+ // process the align maps and create cdna/protein maps
+ // ideally, the query sequences are in the alignment, but maybe not...
+
+ AlignedCodonFrame alco = new AlignedCodonFrame();
+ MapList codonmapping = constructCodonMappingFromAlign(set, attr,
+ strand);
+
+ // add codon mapping, and hope!
+ alco.addMap(seq, querySeq.get(0), codonmapping);
+ align.addCodonFrame(alco);
+ // everything that's needed to be done is done
+ // no features to create here !
+ return false;
+ }
+
+ }
+ return true;
+ }
+
+ private MapList constructCodonMappingFromAlign(
+ Map<String, List<String>> set,
+ String attr, int strand) throws InvalidGFF3FieldException
+ {
+ if (strand == 0)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid strand for a codon mapping (cannot be 0)");
+ }
+ List<Integer> fromrange = new ArrayList<Integer>(), torange = new ArrayList<Integer>();
+ int lastppos = 0, lastpframe = 0;
+ for (String range : set.get(attr))
+ {
+ List<Integer> ints = new ArrayList<Integer>();
+ StringTokenizer st = new StringTokenizer(range, " ");
+ while (st.hasMoreTokens())
+ {
+ String num = st.nextToken();
+ try
+ {
+ ints.add(new Integer(num));
+ } catch (NumberFormatException nfe)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid number in field " + num);
+ }
+ }
+ // Align positionInRef positionInQuery LengthInRef
+ // contig_1146 exonerate:protein2genome:local similarity 8534 11269
+ // 3652 - . alignment_id 0 ;
+ // Query DDB_G0269124
+ // Align 11270 143 120
+ // corresponds to : 120 bases align at pos 143 in protein to 11270 on
+ // dna in strand direction
+ // Align 11150 187 282
+ // corresponds to : 282 bases align at pos 187 in protein to 11150 on
+ // dna in strand direction
+ //
+ // Align 10865 281 888
+ // Align 9977 578 1068
+ // Align 8909 935 375
+ //
+ if (ints.size() != 3)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid number of fields for this attribute ("
+ + ints.size() + ")");
+ }
+ fromrange.add(new Integer(ints.get(0).intValue()));
+ fromrange.add(new Integer(ints.get(0).intValue() + strand
+ * ints.get(2).intValue()));
+ // how are intron/exon boundaries that do not align in codons
+ // represented
+ if (ints.get(1).equals(lastppos) && lastpframe > 0)
+ {
+ // extend existing to map
+ lastppos += ints.get(2) / 3;
+ lastpframe = ints.get(2) % 3;
+ torange.set(torange.size() - 1, new Integer(lastppos));
+ }
+ else
+ {
+ // new to map range
+ torange.add(ints.get(1));
+ lastppos = ints.get(1) + ints.get(2) / 3;
+ lastpframe = ints.get(2) % 3;
+ torange.add(new Integer(lastppos));
+ }
+ }
+ // from and to ranges must end up being a series of start/end intervals
+ if (fromrange.size() % 2 == 1)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Couldn't parse the DNA alignment range correctly");
+ }
+ if (torange.size() % 2 == 1)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Couldn't parse the protein alignment range correctly");
+ }
+ // finally, build the map
+ int[] frommap = new int[fromrange.size()], tomap = new int[torange
+ .size()];
+ int p = 0;
+ for (Integer ip : fromrange)
+ {
+ frommap[p++] = ip.intValue();
+ }
+ p = 0;
+ for (Integer ip : torange)
+ {
+ tomap[p++] = ip.intValue();
+ }
+
+ return new MapList(frommap, tomap, 3, 1);
+ }
+
+ private List<SequenceI> findNames(AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching,
+ List<String> list)
+ {
+ List<SequenceI> found = new ArrayList<SequenceI>();
+ for (String seqId : list)
+ {
+ SequenceI seq = findName(align, seqId, relaxedIdMatching, newseqs);
+ if (seq != null)
+ {
+ found.add(seq);
+ }
+ }
+ return found;
+ }
+
private AlignmentI lastmatchedAl = null;
private SequenceIdMatcher matcher = null;
}
private SequenceI findName(AlignmentI align, String seqId,
- boolean relaxedIdMatching)
+ boolean relaxedIdMatching, List<SequenceI> newseqs)
{
SequenceI match = null;
if (relaxedIdMatching)
{
matcher = new SequenceIdMatcher(
(lastmatchedAl = align).getSequencesArray());
+ if (newseqs != null)
+ {
+ matcher.addAll(newseqs);
+ }
}
match = matcher.findIdMatch(seqId);
}
else
{
match = align.findName(seqId, true);
+ if (match == null && newseqs != null)
+ {
+ for (SequenceI m : newseqs)
+ {
+ if (seqId.equals(m.getName()))
+ {
+ return m;
+ }
+ }
+ }
+
+ }
+ if (match==null && newseqs!=null)
+ {
+ match = new SequenceDummy(seqId);
+ if (relaxedIdMatching)
+ {
+ matcher.addAll(Arrays.asList(new SequenceI[]
+ { match }));
+ }
+ // add dummy sequence to the newseqs list
+ newseqs.add(match);
}
return match;
}
-
public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
{
if (sf.getDescription() == null)
// open a new source and read from it
FormatAdapter fa = new FormatAdapter();
al = fa.readFile(file, protocol, format);
- source = fa.getAlignFile(); // keep reference for later if necessary.
+ source = fa.getAlignFile(); // keep reference for later if
+ // necessary.
}
} catch (java.io.IOException ex)
{
alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
- }
- // add metadata and update ui
- if (!protocol.equals(AppletFormatAdapter.PASTE))
- {
- alignFrame.setFileName(file, format);
- }
+ // add metadata and update ui
+ if (!protocol.equals(AppletFormatAdapter.PASTE))
+ {
+ alignFrame.setFileName(file, format);
+ }
- alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new String[]
- { title }));
+ alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new String[]
+ { title }));
- if (raiseGUI)
- {
- // add the window to the GUI
- // note - this actually should happen regardless of raiseGUI
- // status in Jalview 3
- // TODO: define 'virtual desktop' for benefit of headless scripts
- // that perform queries to find the 'current working alignment'
- Desktop.addInternalFrame(alignFrame, title,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- }
+ if (raiseGUI)
+ {
+ // add the window to the GUI
+ // note - this actually should happen regardless of raiseGUI
+ // status in Jalview 3
+ // TODO: define 'virtual desktop' for benefit of headless scripts
+ // that perform queries to find the 'current working alignment'
+ Desktop.addInternalFrame(alignFrame, title,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
- try
- {
- alignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
- } catch (java.beans.PropertyVetoException ex)
- {
+ try
+ {
+ alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
}
}
else
final String errorMessage = "Couldn't load file " + title + "\n"
+ error;
- if (raiseGUI)
+ // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
+ // bits ?
+ if (raiseGUI && Desktop.desktop != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
{
public void run()
{
- javax.swing.JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.formatMessage("warn.out_of_memory_loading_file", new String[]{file}),
- MessageManager.getString("label.out_of_memory"),
- javax.swing.JOptionPane.WARNING_MESSAGE);
+ javax.swing.JOptionPane.showInternalMessageDialog(
+ Desktop.desktop, MessageManager.formatMessage(
+ "warn.out_of_memory_loading_file", new String[]
+ { file }), MessageManager
+ .getString("label.out_of_memory"),
+ javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
}
*/
package jalview.io;
+import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.util.MessageManager;
import java.io.BufferedReader;
public File inFile = null;
+ /**
+ * a viewport associated with the current file operation. May be null. May
+ * move to different object.
+ */
private AlignViewportI viewport;
- public int index = 1; // sequence counter for FileParse object created from
+ /**
+ * specific settings for exporting data from the current context
+ */
+ private AlignExportSettingI exportSettings;
- // same data source
+ /**
+ * sequence counter for FileParse object created from same data source
+ */
+ public int index = 1;
+ /**
+ * separator for extracting specific 'frame' of a datasource for formats that
+ * support multiple records (e.g. BLC, Stockholm, etc)
+ */
protected char suffixSeparator = '#';
/**
throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
}
+ /**
+ *
+ * @return true if this FileParse is configured for Export only
+ */
+ public boolean isExporting()
+ {
+ return !error && dataIn == null;
+ }
+
+ /**
+ *
+ * @return true if the data source is valid
+ */
public boolean isValid()
{
return !error;
{
this.viewport = viewport;
}
+
+ /**
+ * @return the currently configured exportSettings for writing data.
+ */
+ public AlignExportSettingI getExportSettings()
+ {
+ return exportSettings;
+ }
+
+ /**
+ * Set configuration for export of data.
+ *
+ * @param exportSettings
+ * the exportSettings to set
+ */
+ public void setExportSettings(AlignExportSettingI exportSettings)
+ {
+ this.exportSettings = exportSettings;
+ }
+
+ /**
+ * method overridden by complex file exporter/importers which support
+ * exporting visualisation and layout settings for a view
+ *
+ * @param avpanel
+ */
+ public void configureForView(AlignmentViewPanel avpanel)
+ {
+ if (avpanel!=null) {
+ setViewport(avpanel.getAlignViewport());
+ }
+ // could also set export/import settings
+ }
}
*/
package jalview.io;
-import jalview.api.AlignViewportI;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
/**
* Additional formatting methods used by the application in a number of places.
*/
public class FormatAdapter extends AppletFormatAdapter
{
- public FormatAdapter(AlignViewportI viewport)
+ public FormatAdapter(AlignmentViewPanel viewpanel)
{
- super(viewport);
+ super(viewpanel);
init();
}
init();
}
+ public FormatAdapter(AlignmentPanel alignPanel,
+ AlignExportSettingI settings)
+ {
+ super(alignPanel, settings);
+ }
+
private void init()
{
if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
return this.formatSequences(format, alignment, suffix);
}
- public Alignment readFile(String inFile, String type, String format)
+ public AlignmentI readFile(String inFile, String type, String format)
throws java.io.IOException
{
- Alignment al = super.readFile(inFile, type, format);
+ AlignmentI al = super.readFile(inFile, type, format);
return al;
}
public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
- Alignment al = (Alignment) super.readFromFile(source, format);
+ AlignmentI al = super.readFromFile(source, format);
return al;
}
}
/**
- * Create a flat file representation of a given view or selected region of a view
+ * Create a flat file representation of a given view or selected region of a
+ * view
+ *
* @param format
- * @param av
+ * @param ap
+ * alignment panel originating the view
* @return String containing flat file
*/
- public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+ public String formatSequences(String format, AlignmentViewPanel ap,
+ boolean selectedOnly)
{
- return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+ return formatSequences(format, getCacheSuffixDefault(format), ap,
+ selectedOnly);
}
--- /dev/null
+package jalview.io;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.List;
+
+/**
+ * A GFF3 File parsing wrapper for the tangled mess that is FeaturesFile.
+ *
+ * This class implements the methods relied on by FileLoader/FormatAdapter in
+ * order to allow them to load alignments directly from GFF2 and GFF3 files that
+ * contain sequence data and alignment information.
+ *
+ * Major issues:
+ *
+ * 1. GFF3 files commonly include mappings between DNA, RNA and Protein - so
+ * this class needs a dataset AlignmentI context to create alignment codon
+ * mappings.
+ *
+ * 2. A single GFF3 file can generate many distinct alignments. Support will be
+ * needed to allow several AlignmentI instances to be generated from a single
+ * file.
+ *
+ *
+ * @author jprocter
+ *
+ */
+public class Gff3File extends FeaturesFile
+{
+
+ /**
+ *
+ */
+ public Gff3File()
+ {
+ super();
+ }
+
+ /**
+ * @param source
+ * @throws IOException
+ */
+ public Gff3File(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public Gff3File(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * @param parseImmediately
+ * @param source
+ * @throws IOException
+ */
+ public Gff3File(boolean parseImmediately, FileParse source)
+ throws IOException
+ {
+ super(parseImmediately, source);
+ }
+
+ /**
+ * @param parseImmediately
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public Gff3File(boolean parseImmediately, String inFile, String type)
+ throws IOException
+ {
+ super(parseImmediately, inFile, type);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.FeaturesFile#print()
+ */
+ @Override
+ public String print()
+ {
+ // TODO GFF3 writer with sensible defaults for writing alignment data
+
+ // return super.printGFFFormat(seqs, visible);
+ return ("Not yet implemented.");
+ }
+
+ AlignmentI dataset;
+
+ List<AlignmentI> alignments;
+ @Override
+ public void parse()
+ {
+ AlignViewportI av = getViewport();
+ if (av != null)
+ {
+ if (av.getAlignment() != null)
+ {
+ dataset = av.getAlignment().getDataset();
+ }
+ if (dataset == null)
+ {
+ // working in the applet context ?
+ dataset = av.getAlignment();
+ }
+ }
+ else
+ {
+ dataset = new Alignment(new SequenceI[]
+ {});
+ }
+
+ boolean parseResult = parse(dataset, null, null, false, true);
+ if (!parseResult)
+ {
+ // pass error up somehow
+ }
+ if (av != null)
+ {
+ // update viewport with the dataset data ?
+ }
+ else
+ {
+ setSeqs(dataset.getSequencesArray());
+ }
+
+ }
+
+ @Override
+ public void addProperties(AlignmentI al)
+ {
+ super.addProperties(al);
+ if (dataset.getCodonFrames() != null)
+ {
+ AlignmentI ds = (al.getDataset() == null) ? al : al.getDataset();
+ for (AlignedCodonFrame codons : dataset.getCodonFrames())
+ {
+ ds.addCodonFrame(codons);
+ }
+ }
+ }
+}
package jalview.io;
import java.io.IOException;
+import java.io.StringReader;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
{
try
{
- StringBuilder htmlData = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null)
- {
- htmlData.append(currentLine);
+ Element content = null;
+ Document doc = null;
+ try {
+ StringBuilder htmlData = new StringBuilder();
+ String currentLine;
+ while ((currentLine = nextLine()) != null)
+ {
+ htmlData.append(currentLine);
+ }
+
+ doc = Jsoup.parse(htmlData.toString());
+ } catch (OutOfMemoryError oom) {
+ errormessage = "Not enough memory to process HTML document";
+ throw new IOException(errormessage);
}
-
- Document doc = Jsoup.parse(htmlData.toString());
- Element content = doc.getElementById("seqData");
- String alignmentJsonString = content.val();
-
- JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
+ content = doc.getElementById("seqData");
+
+ JSONFile jsonFile = new JSONFile().parse(new StringReader(content.val()));
this.seqs = jsonFile.getSeqs();
this.seqGroups = jsonFile.getSeqGroups();
this.annotations = jsonFile.getAnnotations();
this.columnSelection = jsonFile.getColumnSelection();
} catch (Exception e)
{
- e.printStackTrace();
+ errormessage = "Failed to extract data from HTML document.";
+ throw new IOException("Unexpected exception whilst extracting JSon from HTML.",e);
}
}
package jalview.io;
+import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
-import jalview.gui.AnnotationPanel;
-import jalview.gui.FeatureRenderer;
import jalview.gui.HTMLOptions;
import jalview.math.AlignmentDimension;
import jalview.util.MessageManager;
FeatureRenderer fr;
AlignmentPanel ap;
- AnnotationPanel annotationPanel;
public HtmlSvgOutput(File file, AlignmentPanel ap)
{
-
- this.av = ap.av;
- this.ap = ap;
- av.setFeatureRenderer(new FeatureRenderer(ap));
- this.annotationPanel = ap.getAnnotationPanel();
+ this.av = ap.av;
+ this.ap = ap;
+ fr = ap.cloneFeatureRenderer();
generateHtmlSvgOutput(file);
}
String titleSvgData = g1.getSVGDocument();
String alignSvgData = g2.getSVGDocument();
- String jsonData = JSONFile.getJSONData(av);
+ String jsonData = JSONFile.getJSONData(ap);
String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
out.write(htmlData.getBytes());
*/
public class IdentifyFile
{
+ public static final String GFF3File = "GFF v2 or v3";
+
/**
* Identify a datasource's file content.
*
}
data = data.toUpperCase();
- if ((data.indexOf("# STOCKHOLM") > -1))
+ if (data.startsWith("##GFF-VERSION"))
+ {
+ reply = GFF3File;
+ break;
+ }
+ if (data.indexOf("# STOCKHOLM") > -1)
{
reply = "STH";
break;
package jalview.io;
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-
-import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureRenderer;
import jalview.api.FeaturesDisplayedI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import java.awt.Color;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+
public class JSONFile extends AlignFile implements ComplexAlignFile
{
private ColourSchemeI colourScheme;
private FeatureRenderer fr;
- private JSONExportSettings jsonExportSettings;
-
private List<int[]> hiddenColumns;
private ColumnSelection columnSelection;
@Override
public void parse() throws IOException
{
- StringBuilder jsonStringBuilder = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null)
- {
- jsonStringBuilder.append(currentLine);
- }
- parse(jsonStringBuilder.toString());
+ parse(getReader());
}
-
@Override
public String print()
{
String jsonOutput = null;
try
{
- if (getJsonExportSettings() == null)
- {
- jsonExportSettings = new JSONExportSettings();
- jsonExportSettings.setExportAnnotations(true);
- jsonExportSettings.setExportGroups(true);
- jsonExportSettings.setExportJalviewSettings(true);
- jsonExportSettings.setExportSequenceFeatures(true);
- }
-
AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
- if (getViewport() != null)
- {
- globalColorScheme = ColourSchemeProperty
- .getColourName(getViewport()
- .getGlobalColourScheme());
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- showSeqFeatures = getViewport().isShowSequenceFeatures();
- fr = getViewport().getFeatureRenderer();
- }
int count = 0;
for (SequenceI seq : seqs)
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
- if (jsonExportSettings.isExportJalviewSettings())
+ jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+ jsonAlignmentPojo.getAppSettings().put("application", application);
+ jsonAlignmentPojo.getAppSettings().put("version", version);
+ jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
+ jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
+ String.valueOf(showSeqFeatures));
+
+ String[] hiddenSections = getHiddenSections();
+ if (hiddenSections != null)
{
- jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
- jsonAlignmentPojo.getAppSettings().put("application", application);
- jsonAlignmentPojo.getAppSettings().put("version", version);
- jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
- jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
- String.valueOf(showSeqFeatures));
-
- String[] hiddenSections = exportHiddenSections();
- if (hiddenSections != null && getViewport().isIncludeHiddenRegion())
+ if (hiddenSections[0] != null
+ && getExportSettings()
+ .isExportHiddenColumns())
{
- if (hiddenSections[0] != null)
- {
- jsonAlignmentPojo.getAppSettings().put("hiddenCols",
- String.valueOf(hiddenSections[0]));
- }
- if (hiddenSections[1] != null)
- {
- jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
- String.valueOf(hiddenSections[1]));
- }
+ jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+ String.valueOf(hiddenSections[0]));
+ }
+ if (hiddenSections[1] != null
+ && getExportSettings()
+ .isExportHiddenSequences())
+ {
+ jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+ String.valueOf(hiddenSections[1]));
}
}
- if (jsonExportSettings.isExportAnnotations())
+ if (getExportSettings().isExportAnnotations())
{
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
- if (jsonExportSettings.isExportSequenceFeatures())
+ if (getExportSettings().isExportFeatures())
{
jsonAlignmentPojo
.setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
}
- if (jsonExportSettings.isExportGroups() && seqGroups != null
+ if (getExportSettings().isExportGroups()
+ && seqGroups != null
&& seqGroups.size() > 0)
{
for (SequenceGroup seqGrp : seqGroups)
return jsonOutput;
}
- public String[] exportHiddenSections()
+ public String[] getHiddenSections()
{
String[] hiddenSections = new String[2];
if (getViewport() == null)
}
@SuppressWarnings("unchecked")
- public JSONFile parse(String jsonAlignmentString)
+ public JSONFile parse(Reader jsonAlignmentString)
{
try
{
this.displayedFeatures = displayedFeatures;
}
- public JSONExportSettings getJsonExportSettings()
- {
- return jsonExportSettings;
- }
-
- public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
+ @Override
+ public void configureForView(AlignmentViewPanel avpanel)
{
- this.jsonExportSettings = jsonExportSettings;
- }
-
+ super.configureForView(avpanel);
+ if (isExporting())
+ {
+ setViewport(avpanel.getAlignViewport());
+ seqGroups = avpanel.getAlignment().getGroups();
+ setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+ fr = avpanel.cloneFeatureRenderer();
- public static String getJSONData(AlignViewportI av)
- {
- JSONFile jsonFile = new JSONFile();
- jsonFile.setViewport(av);
- jsonFile.seqGroups = av.getAlignment().getGroups();
- jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
+ for (SequenceI seq : getViewport().getAlignment().getSequences())
+ {
+ seqs.add(seq);
+ }
- for (SequenceI seq : av.getAlignment().getSequences())
- {
- jsonFile.seqs.add(seq);
- }
-
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : av.getAlignment()
- .getAlignmentAnnotation())
- {
- if (annot != null && !annot.autoCalculated)
+ // Add non auto calculated annotation to AlignFile
+ for (AlignmentAnnotation annot : getViewport().getAlignment()
+ .getAlignmentAnnotation())
{
- if (annot.label.equals("PDB.CATempFactor"))
+ if (annot != null && !annot.autoCalculated)
{
- continue;
+ if (annot.label.equals("PDB.CATempFactor"))
+ {
+ continue;
+ }
+ annotations.add(annot);
}
- jsonFile.annotations.add(annot);
}
+
+ globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
+ .getGlobalColourScheme());
+ setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+ showSeqFeatures = getViewport().isShowSequenceFeatures();
}
+ }
+
+
+ public static String getJSONData(AlignmentViewPanel av)
+ {
+ JSONFile jsonFile = new JSONFile();
+ jsonFile.configureForView(av);
String jsonString = jsonFile.print();
return jsonString;
}
*/
package jalview.io;
-import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
seqs.add(sequenceElements[i]);
}
- // create an alignment based on the sequences
- Alignment a = new Alignment(sequenceElements);
- // add annotations - although comments say addAnnotations
- // is used by AppletFormatAdapter, it doesn't say other
- // classes should/can not use it
- addAnnotations(a);
-
} catch (IOException e)
{
System.err.println("Exception parsing PHYLIP file " + e);
--- /dev/null
+package jalview.jbgui;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JPanel;
+
+@SuppressWarnings("serial")
+public abstract class GAlignExportSettings extends JPanel
+{
+ protected JPanel hiddenRegionConfPanel = new JPanel();
+
+ protected JPanel complexExportPanel = new JPanel();
+
+ protected JPanel optionsPanel = new JPanel();
+
+ protected JPanel actionPanel = new JPanel();
+
+ protected BorderLayout hiddenRegionLayout = new BorderLayout();
+
+ protected BorderLayout complexExportLayout = new BorderLayout();
+
+ protected BorderLayout mainLayout = new BorderLayout();
+
+ protected JCheckBox chkAll = new JCheckBox("Check All");
+
+ protected JCheckBox chkHiddenSeqs = new JCheckBox(
+ "Export Hidden Sequences");
+
+ protected JCheckBox chkHiddenCols = new JCheckBox("Export Hidden Columns");
+
+ protected JCheckBox chkExportAnnots = new JCheckBox("Export Annotations");
+
+ protected JCheckBox chkExportFeats = new JCheckBox("Export Features");
+
+ protected JCheckBox chkExportGrps = new JCheckBox("Export Groups");
+
+ JButton btnOk = new JButton("Ok");
+
+ JButton btnCancel = new JButton("Cancel");
+
+ private boolean hasHiddenSeq, hasHiddenCols, isComplexAlignFile,
+ showDialog;
+
+ public GAlignExportSettings(boolean hasHiddenSeq, boolean hasHiddenCols,
+ String alignFileFormat)
+ {
+ this.hasHiddenSeq = hasHiddenSeq;
+ this.hasHiddenCols = hasHiddenCols;
+ String[] complexFormats =
+ { "JSON", "HTML" };
+
+ for (String format : complexFormats)
+ {
+ if (format.equalsIgnoreCase(alignFileFormat))
+ {
+ this.isComplexAlignFile = true;
+ break;
+ }
+ }
+ if (this.hasHiddenCols || this.hasHiddenSeq || this.isComplexAlignFile)
+ {
+ this.showDialog = true;
+ }
+ init();
+ }
+
+ public void init()
+ {
+ hiddenRegionConfPanel.setLayout(hiddenRegionLayout);
+ complexExportPanel.setLayout(complexExportLayout);
+ setLayout(mainLayout);
+
+ chkAll.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ checkAllAction();
+ }
+ });
+
+ btnOk.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+
+ btnCancel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+
+ hiddenRegionConfPanel.add(chkAll, BorderLayout.NORTH);
+ hiddenRegionConfPanel.add(chkHiddenSeqs, BorderLayout.CENTER);
+ hiddenRegionConfPanel.add(chkHiddenCols, BorderLayout.SOUTH);
+ chkHiddenSeqs.setEnabled(hasHiddenSeq);
+ chkHiddenCols.setEnabled(hasHiddenCols);
+
+ complexExportPanel.add(chkExportAnnots, BorderLayout.NORTH);
+ complexExportPanel.add(chkExportFeats, BorderLayout.CENTER);
+ complexExportPanel.add(chkExportGrps, BorderLayout.SOUTH);
+
+ if (hasHiddenSeq || hasHiddenCols)
+ {
+ optionsPanel.add(hiddenRegionConfPanel);
+ }
+
+ if (this.isComplexAlignFile)
+ {
+ optionsPanel.add(complexExportPanel);
+ }
+ actionPanel.add(btnCancel);
+ actionPanel.add(btnOk);
+
+ add(optionsPanel, BorderLayout.NORTH);
+ add(actionPanel, BorderLayout.SOUTH);
+
+ }
+
+ private void checkAllAction()
+ {
+ boolean isSelected = chkAll.isSelected();
+ chkHiddenSeqs.setSelected(chkHiddenSeqs.isEnabled() && isSelected);
+ chkHiddenCols.setSelected(chkHiddenCols.isEnabled() && isSelected);
+ chkExportAnnots.setSelected(isComplexAlignFile
+ && chkExportAnnots.isEnabled() && isSelected);
+ chkExportFeats.setSelected(isComplexAlignFile
+ && chkExportFeats.isEnabled() && isSelected);
+ chkExportGrps.setSelected(isComplexAlignFile
+ && chkExportGrps.isEnabled() && isSelected);
+ }
+
+ public boolean isShowDialog()
+ {
+ return showDialog;
+ }
+
+ public void setShowDialog(boolean showDialog)
+ {
+ this.showDialog = showDialog;
+ }
+
+ public abstract void ok_actionPerformed(ActionEvent e);
+
+ public abstract void cancel_actionPerformed(ActionEvent e);
+}
*/
package jalview.jbgui;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.io.FormatAdapter;
import jalview.util.MessageManager;
public void run()
{
String str = textfield.getText();
- Alignment al = null;
+ AlignmentI al = null;
try
{
al = new FormatAdapter().readFile(str, "Paste", "FASTA");
-#Wed Jun 17 15:04:02 BST 2015
+#Fri Jun 26 14:22:47 BST 2015
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
//--------------------------/
/**
- * handle for the calculation which uses this parameter set
+ * handle for the calculation which uses
+ * this parameter set
+ *
*/
private java.lang.String _calcId;
/**
- * should the calculation be performed immediately after
- * loading in order to refresh results
+ * should the calculation be performed
+ * immediately after loading in order to refresh results
+ *
*/
private boolean _needsUpdate = false;
private boolean _has_needsUpdate;
/**
- * should the calculation be automatically performed on edits
+ * should the calculation be automatically
+ * performed on edits
+ *
*/
private boolean _autoUpdate;
/**
* Returns the value of field 'autoUpdate'. The field
* 'autoUpdate' has the following description: should the
- * calculation be automatically performed on edits
+ * calculation be automatically
+ * performed on edits
+ *
*
* @return the value of field 'AutoUpdate'.
*/
/**
* Returns the value of field 'calcId'. The field 'calcId' has
* the following description: handle for the calculation which
- * uses this parameter set
+ * uses
+ * this parameter set
+ *
*
* @return the value of field 'CalcId'.
*/
/**
* Returns the value of field 'needsUpdate'. The field
* 'needsUpdate' has the following description: should the
- * calculation be performed immediately after loading in order
- * to refresh results
+ * calculation be performed
+ * immediately after loading in order to refresh results
+ *
*
* @return the value of field 'NeedsUpdate'.
*/
/**
* Returns the value of field 'autoUpdate'. The field
* 'autoUpdate' has the following description: should the
- * calculation be automatically performed on edits
+ * calculation be automatically
+ * performed on edits
+ *
*
* @return the value of field 'AutoUpdate'.
*/
/**
* Returns the value of field 'needsUpdate'. The field
* 'needsUpdate' has the following description: should the
- * calculation be performed immediately after loading in order
- * to refresh results
+ * calculation be performed
+ * immediately after loading in order to refresh results
+ *
*
* @return the value of field 'NeedsUpdate'.
*/
/**
* Sets the value of field 'autoUpdate'. The field 'autoUpdate'
* has the following description: should the calculation be
- * automatically performed on edits
+ * automatically
+ * performed on edits
+ *
*
* @param autoUpdate the value of field 'autoUpdate'.
*/
/**
* Sets the value of field 'calcId'. The field 'calcId' has the
* following description: handle for the calculation which uses
- * this parameter set
+ * this parameter set
+ *
*
* @param calcId the value of field 'calcId'.
*/
/**
* Sets the value of field 'needsUpdate'. The field
* 'needsUpdate' has the following description: should the
- * calculation be performed immediately after loading in order
- * to refresh results
+ * calculation be performed
+ * immediately after loading in order to refresh results
+ *
*
* @param needsUpdate the value of field 'needsUpdate'.
*/
/**
* Optional sequence group ID (only
- * needs to be unique for this
+ * needs to be
+ * unique for this
* alignment)
*
*/
/**
* Returns the value of field 'id'. The field 'id' has the
* following description: Optional sequence group ID (only
- * needs to be unique for this
+ * needs to be
+ * unique for this
* alignment)
*
*
/**
* Sets the value of field 'id'. The field 'id' has the
* following description: Optional sequence group ID (only
- * needs to be unique for this
+ * needs to be
+ * unique for this
* alignment)
*
*
/**
* Optional minimum colour
- * for graduated feature
+ * for graduated
+ * feature
* colour
*
*/
* Returns the value of field 'mincolour'. The field
* 'mincolour' has the following description: Optional minimum
* colour
- * for graduated feature
+ * for graduated
+ * feature
* colour
*
*
/**
* Sets the value of field 'mincolour'. The field 'mincolour'
* has the following description: Optional minimum colour
- * for graduated feature
+ * for graduated
+ * feature
* colour
*
*
private boolean _has_colourByJmol;
/**
- * An identifier for the viewer type, currently either
- * JMOL or CHIMERA
+ * An
+ * identifier
+ * for
+ * the
+ * viewer
+ * type,
+ * currently
+ * either
+ * JMOL
+ * or
+ * CHIMERA
*
*/
private java.lang.String _type;
/**
* Returns the value of field 'type'. The field 'type' has the
- * following description: An identifier for the viewer type,
- * currently either
- * JMOL or CHIMERA
+ * following description: An
+ * identifier
+ * for
+ * the
+ * viewer
+ * type,
+ * currently
+ * either
+ * JMOL
+ * or
+ * CHIMERA
*
*
* @return the value of field 'Type'.
/**
* Sets the value of field 'type'. The field 'type' has the
- * following description: An identifier for the viewer type,
- * currently either
- * JMOL or CHIMERA
+ * following description: An
+ * identifier
+ * for
+ * the
+ * viewer
+ * type,
+ * currently
+ * either
+ * JMOL
+ * or
+ * CHIMERA
*
*
* @param type the value of field 'type'.
/**
* Tree ID added for binding tree
- * visualization settings to vamsas
+ * visualization
+ * settings to vamsas
* document trees in jalview 2.4.1
*
*/
/**
* Returns the value of field 'id'. The field 'id' has the
* following description: Tree ID added for binding tree
- * visualization settings to vamsas
+ * visualization
+ * settings to vamsas
* document trees in jalview 2.4.1
*
*
/**
* Sets the value of field 'id'. The field 'id' has the
* following description: Tree ID added for binding tree
- * visualization settings to vamsas
+ * visualization
+ * settings to vamsas
* document trees in jalview 2.4.1
*
*
/**
* unique id used by jalview to
- * synchronize between stored and
+ * synchronize
+ * between stored and
* instantiated views
*
*/
private java.lang.String _id;
/**
- * The viewport id of this viewport's (cdna/protein) coding
- * complement, if any
+ * The viewport id of this viewport's
+ * (cdna/protein) coding complement, if any
*
*/
private java.lang.String _complementId;
/**
* Returns the value of field 'complementId'. The field
* 'complementId' has the following description: The viewport
- * id of this viewport's (cdna/protein) coding complement, if
- * any
+ * id of this viewport's
+ * (cdna/protein) coding complement, if any
*
*
* @return the value of field 'ComplementId'.
/**
* Returns the value of field 'id'. The field 'id' has the
* following description: unique id used by jalview to
- * synchronize between stored and
+ * synchronize
+ * between stored and
* instantiated views
*
*
/**
* Sets the value of field 'complementId'. The field
* 'complementId' has the following description: The viewport
- * id of this viewport's (cdna/protein) coding complement, if
- * any
+ * id of this viewport's
+ * (cdna/protein) coding complement, if any
*
*
* @param complementId the value of field 'complementId'.
/**
* Sets the value of field 'id'. The field 'id' has the
* following description: unique id used by jalview to
- * synchronize between stored and
+ * synchronize
+ * between stored and
* instantiated views
*
*
*/
package jalview.viewmodel;
-import java.awt.Color;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
+import java.awt.Color;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
// hasHiddenColumns = colSel.hasHiddenColumns();
}
- protected boolean hasHiddenRows = false;
-
@Override
public boolean hasHiddenRows()
{
- return hasHiddenRows;
+ return alignment.getHiddenSequences().getSize() > 0;
}
- public void setHasHiddenRows(boolean hasHiddenRows)
- {
- this.hasHiddenRows = hasHiddenRows;
- }
protected SequenceGroup selectionGroup;
setSequenceAnnotationsVisible(seq, true);
}
- hasHiddenRows = false;
hiddenRepSequences = null;
firePropertyChange("alignment", null, alignment.getSequences());
selectionGroup.addSequence(seq, false);
setSequenceAnnotationsVisible(seq, true);
}
- // JBPNote: refactor: only update flag if we modified visiblity (used to
- // do this regardless)
- if (alignment.getHiddenSequences().getSize() < 1)
- {
- hasHiddenRows = false;
- }
firePropertyChange("alignment", null, alignment.getSequences());
sendSelection();
}
alignment.getHiddenSequences().hideSequence(seq[i]);
setSequenceAnnotationsVisible(seq[i], false);
}
- hasHiddenRows = true;
firePropertyChange("alignment", null, alignment.getSequences());
}
}
import jalview.api.FeatureSettingsModelI;
-public class FeatureSettingsModel implements FeatureSettingsModelI
+public abstract class FeatureSettingsModel implements FeatureSettingsModelI
{
}
if (af != null && af.featureSettings != null)
{
- af.featureSettings.setTableData();
+ af.featureSettings.discoverAllFeatureData();
}
if (getFeatSettings() != null)
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
+
import jalview.ws.seqfetcher.DbSourceProxyImpl;
public abstract class EbiFileRetrievedProxy extends DbSourceProxyImpl
public StringBuffer getRawRecords()
{
if (file == null)
+ {
return null;
+ }
StringBuffer bf = null;
try
{
*/
package jalview.ws.dbsources;
-import java.io.File;
-import java.io.FileReader;
-import java.io.Reader;
-import java.util.Vector;
-
-import org.exolab.castor.xml.Unmarshaller;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
+import java.io.File;
+import java.io.FileReader;
+import java.io.Reader;
+import java.util.Vector;
+
+import org.exolab.castor.xml.Unmarshaller;
+
+import com.stevesoft.pat.Regex;
+
/**
* @author JimP
*
{
queries = queries.toUpperCase().replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
- Alignment al = null;
+ AlignmentI al = null;
EBIFetchClient ebi = new EBIFetchClient();
// uniprotxml parameter required since december 2007
// uniprotkb dbname changed introduced december 2008
* @param entries
* a list of n uniprot entries to be analysed.
*/
- public void addUniprotXrefs(Alignment al, Vector<UniprotEntry> entries)
+ public void addUniprotXrefs(AlignmentI al, Vector<UniprotEntry> entries)
{
final String dbVersion = getDbVersion();
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
{
return null;
}
- Alignment al = null;
+ AlignmentI al = null;
ColumnSelection alcsel = null;
int FirstSeq = -1; // the position of the query sequence in Alignment al
* @param al
* @param profileseq
*/
- private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+ private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
{
char gc = al.getGapCharacter();
int[] gapMap = profileseq.gapMap();
}
else
{
+ // TODO 2.9.x feature
System.out.println("MERGE WITH OLD FRAME");
// TODO: modify alignment in original frame, replacing old for new
// alignment using the commands.EditCommand model to ensure the update can
addSortByMenuItems(af, alorders);
}
+ // TODO: refactor retrieve and show as new splitFrame as Desktop method
+
/*
* If alignment was requested from one half of a SplitFrame, show in a
* SplitFrame with the other pane similarly aligned.
*/
AlignFrame requestedBy = getRequestingAlignFrame();
- if (requestedBy != null && requestedBy.getSplitViewContainer() != null)
+ if (requestedBy != null && requestedBy.getSplitViewContainer() != null
+ && requestedBy.getSplitViewContainer().getComplement(requestedBy)!=null)
{
AlignmentI complement = requestedBy.getSplitViewContainer()
.getComplement(requestedBy);
String complementTitle = requestedBy.getSplitViewContainer()
.getComplementTitle(requestedBy);
+ // becomes null if the alignment window was closed before the alignment
+ // job finished.
AlignmentI copyComplement = new Alignment(complement);
copyComplement.alignAs(al);
if (copyComplement.getHeight() > 0)
*/
package jalview.ws.seqfetcher;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
* @return null or a valid alignment
* @throws Exception
*/
- protected Alignment parseResult(String result) throws Exception
+ protected AlignmentI parseResult(String result) throws Exception
{
- Alignment sequences = null;
+ AlignmentI sequences = null;
String format = new IdentifyFile().Identify(result, "Paste");
if (FormatAdapter.isValidFormat(format))
{
package MCview;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertEquals;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.Test;
public class AtomTest
{
{
new Atom(
"ATOM 34N NE2 GLN A 48 22.290 8.595 17.680 1.00 14.30 N");
- fail("Expected exception");
+ Assert.fail("Expected exception");
} catch (NumberFormatException e)
{
// expected
package MCview;
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class BondTest
{
package MCview;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.util.Vector;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TaylorColourScheme;
+import java.awt.Color;
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
public class PDBChainTest
{
PDBChain c = new PDBChain("1GAQ", "A");
+
Atom a1 = new Atom(1f, 2f, 3f);
Atom a2 = new Atom(5f, 6f, 4f);
package MCview;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import java.io.IOException;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class PDBfileTest
{
*
* @throws IOException
*/
- @Test
- @Ignore
+
+ @Test(enabled = false)
public void testParse_withAnnotate3D() throws IOException
{
// TODO requires a mock for Annotate3D processing
package MCview;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
import java.util.Vector;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class ResidueTest
{
package com.stevesoft.pat;
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
import java.io.IOException;
import java.io.StringWriter;
-import org.junit.Test;
+import org.testng.annotations.Test;
/**
* Test class refactored from RegexWriter main method
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import java.util.Hashtable;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class AAFrequencyTest
{
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
-import org.junit.Before;
-import org.junit.Test;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class AlignmentAnnotationUtilsTest
{
*
* @throws IOException
*/
- @Before
+ @BeforeMethod
public void setUp() throws IOException
{
alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA,
*/
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.util.MapList;
import jalview.util.MappingUtils;
-public class AlignmentUtilsTests
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.testng.annotations.Test;
+
+public class AlignmentUtilsTests
{
// @formatter:off
private static final String TEST_DATA =
*/
protected AlignmentI loadAlignment(final String data, String format) throws IOException
{
- Alignment a = new FormatAdapter().readFile(data,
+ AlignmentI a = new FormatAdapter().readFile(data,
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
+
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import java.util.List;
import java.util.Random;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class AnnotationSorterTest
{
/*
* Set up 6 sequences and 7 annotations.
*/
- @Before
+ @BeforeMethod
public void setUp()
{
al = buildAlignment(NUM_SEQS);
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
import java.util.Arrays;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class CodingUtilsTest
{
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
import jalview.datamodel.DBRefEntry;
+import org.testng.annotations.Test;
+
public class CrossRefTest
{
@Test
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.Alignment;
import java.io.IOException;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class DnaTest
{
import java.util.ArrayList;
import java.util.Arrays;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
public class GroupingTest
{
alignment.getSequencesArray(), cs,
Arrays.asList(new SequenceGroup[]
{ sg1, sg2 }));
- Assert.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
+ AssertJUnit.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
for (int p = 0; p < seqgroupsString.length; p++)
{
- Assert.assertEquals(seqgroupsString[p].getName(),
+ AssertJUnit.assertEquals(seqgroupsString[p].getName(),
seqgroupsColSel[p].getName());
- Assert.assertArrayEquals(
+ AssertJUnit.assertArrayEquals(
seqgroupsString[p].getSequencesInOrder(alignment),
seqgroupsColSel[p].getSequencesInOrder(alignment));
if (seqgroupsString[p].getSequences().contains(s2))
{
- Assert.assertTrue(seqgroupsString[p].getSize() == 2);
+ AssertJUnit.assertTrue(seqgroupsString[p].getSize() == 2);
}
}
}
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import java.util.List;
-
-import org.junit.Before;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
public class ParsePropertiesTest
{
/**
* Construct an alignment with 4 sequences with varying description format
*/
- @Before
+ @BeforeMethod
public void setUp()
{
SequenceI[] seqs = new SequenceI[]
*/
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import java.io.PrintStream;
-
-import org.junit.Before;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import java.io.PrintStream;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
/**
* Test the alignment -> Mapping routines
*
/**
* @throws java.lang.Exception
*/
- @Before
+ @BeforeMethod
public void setUp() throws Exception
{
s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
public class FeatureScoreModelTest
{
AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(alntestFile,
FormatAdapter.PASTE);
AlignmentI al = alf.getViewport().getAlignment();
- Assert.assertEquals(4, al.getHeight());
- Assert.assertEquals(5, al.getWidth());
+ AssertJUnit.assertEquals(4, al.getHeight());
+ AssertJUnit.assertEquals(5, al.getWidth());
for (int i = 0; i < 4; i++)
{
SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
alf.getFeatureRenderer().setVisible("sf2");
alf.getFeatureRenderer().setVisible("sf3");
alf.getFeatureRenderer().findAllFeatures(true);
- Assert.assertEquals("Number of feature types", 3, alf
+ AssertJUnit.assertEquals("Number of feature types", 3, alf
.getFeatureRenderer().getDisplayedFeatureTypes().length);
- Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+ AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
FeatureScoreModel fsm = new FeatureScoreModel();
- Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+ AssertJUnit.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
.getAlignPanel()));
alf.selectAllSequenceMenuItem_actionPerformed(null);
float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
true));
- Assert.assertTrue("FER1_MESCR should be identical with RAPSA (2)",
+ AssertJUnit.assertTrue("FER1_MESCR should be identical with RAPSA (2)",
dm[0][2] == 0f);
- Assert.assertTrue(
+ AssertJUnit.assertTrue(
"FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)",
dm[0][1] > dm[0][2]);
*/
package jalview.bin;
-import static org.junit.Assert.*;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class CommandLineOperations
{
System.out.println("Testing with Headless argument: '" + harg
+ "'\n");
Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000);
- assertTrue("Didn't create an output EPS file.[" + harg + "]",
- new File("test_uniref50_out.eps").exists());
- assertTrue("Didn't create an EPS file with any content[" + harg
- + "]", new File("test_uniref50_out.eps").length() > 4096);
+ AssertJUnit.assertTrue("Didn't create an output EPS file.[" + harg
+ + "]", new File("test_uniref50_out.eps").exists());
+ AssertJUnit.assertTrue(
+ "Didn't create an EPS file with any content[" + harg + "]",
+ new File("test_uniref50_out.eps").length() > 4096);
if (worker.exit == null)
{
worker.interrupt();
Thread.currentThread().interrupt();
worker.process.destroy();
- fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["
+ Assert.fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["
+ harg + "]");
}
} while (!withAwt);
package jalview.commands;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
+
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.datamodel.Alignment;
import java.util.Map;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
/**
* Unit tests for EditCommand
private Alignment al;
- @Before
+ @BeforeMethod
public void setUp()
{
testee = new EditCommand();
/**
* Test a Paste action, where this adds sequences to an alignment.
*/
- @Test
- @Ignore
+ @Test(enabled = false)
// TODO fix so it works
public void testPaste_addToAlignment()
{
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
import jalview.util.MapList;
import java.util.Arrays;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class AlignedCodonFrameTest
{
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+
import jalview.util.MapList;
import java.util.Iterator;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.Test;
/**
* Unit tests for Mapping$AlignedCodonIterator
try
{
codon = codons.next();
- fail("expected exception");
+ Assert.fail("expected exception");
} catch (IncompleteCodonException e)
{
// expected
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class AlignedCodonTest
{
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
import jalview.analysis.AlignSeq;
import jalview.io.AppletFormatAdapter;
+import org.testng.annotations.Test;
+
public class AlignmentAnnotationTests
{
@Test
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
import java.io.IOException;
import java.util.Iterator;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
/**
* Unit tests for Alignment datamodel.
protected AlignmentI loadAlignment(final String data, String format)
throws IOException
{
- Alignment a = new FormatAdapter().readFile(data,
+ AlignmentI a = new FormatAdapter().readFile(data,
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
* Read in Stockholm format test data including secondary structure
* annotations.
*/
- @Before
+ @BeforeMethod
public void setUp() throws IOException
{
al = loadAlignment(TEST_DATA, "STH");
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
import java.util.List;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class ColumnSelectionTest
{
package jalview.datamodel;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.util.MapList;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class DBRefEntryTest
{
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
-import java.util.Arrays;
+import jalview.util.MapList;
-import org.junit.Test;
+import java.util.Arrays;
-import jalview.util.MapList;
+import org.testng.annotations.Test;
/**
* Test class refactored from main method
package jalview.datamodel;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertTrue;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class PDBEntryTest
{
- @Before
+ @BeforeMethod
public void setUp() throws Exception
{
}
- @After
+ @AfterMethod
public void tearDown() throws Exception
{
}
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class SearchResultsTest
{
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
-import org.junit.Test;
+import org.testng.annotations.Test;
/**
* Unit tests for SeqCigar
* String
* @return String
*/
+
+
protected void testCigar_string(Sequence seq, String ex_cs_gapped)
{
SeqCigar c_sgapped = new SeqCigar(seq);
cs_gapped);
}
+
protected void testSeqRecovery(SeqCigar gen_sgapped,
SequenceI s_gapped)
{
--- /dev/null
+package jalview.datamodel;
+
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class SequenceDummyTest
+{
+ /**
+ * test for become method
+ */
+ @Test
+ public void testBecome()
+ {
+ SequenceI seq = new Sequence("OrigSeq", "ASEQUENCE");
+ SequenceFeature ofeat = new SequenceFeature("NewFeat", "somedesc", 3,
+ 12, 2.3f, "none");
+
+ SequenceDummy dummySeq = new SequenceDummy("OrigSeq");
+ dummySeq.addSequenceFeature(ofeat);
+ dummySeq.become(seq);
+ Assert.assertFalse("Dummy sequence did not become a full sequence",
+ dummySeq.isDummy());
+ Assert.assertTrue("Sequence was not updated from template", seq
+ .getSequenceAsString().equals(dummySeq.getSequenceAsString()));
+ boolean found = false;
+ for (SequenceFeature sf : dummySeq.getSequenceFeatures())
+ {
+ if (sf == ofeat)
+ {
+ found = true;
+ break;
+ }
+ }
+ Assert.assertTrue("Didn't retain original sequence feature", found);
+
+ // todo - should test all aspect of copy constructor
+ }
+}
package jalview.datamodel;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
import java.util.Arrays;
import java.util.List;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class SequenceTest
{
SequenceI seq;
- @Before
+ @BeforeMethod
public void setUp()
{
seq = new Sequence("FER1", "AKPNGVL");
package jalview.datamodel.xdb.embl;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.DBRefEntry;
import java.io.StringReader;
import java.util.Vector;
-import org.junit.Test;
-
-import jalview.datamodel.DBRefEntry;
+import org.testng.annotations.Test;
public class EmblFileTest
{
*/
package jalview.ext.jmol;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.util.Vector;
-
-import org.junit.Before;
-import org.junit.Test;
-
-import MCview.PDBfile;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileLoader;
+import java.util.Vector;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
+
/**
* @author jimp
*
// "./examples/DNMT1_MOUSE.pdb"
// };
- @Before
+ @BeforeMethod
public void setUp()
{
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
*/
package jalview.ext.paradise;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
import java.io.BufferedReader;
import java.io.File;
import java.io.Reader;
import java.util.Iterator;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
import MCview.PDBfile;
-import compbio.util.FileUtil;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.io.FastaFile;
-import jalview.io.FormatAdapter;
+import compbio.util.FileUtil;
public class TestAnnotate3D
{
- @Test
+ @Test(enabled = false)
public void test1GIDbyId() throws Exception
{
// use same ID as standard tests given at
testRNAMLcontent(ids, null);
}
- @Test
+ @Test(enabled = false)
public void testIdVsContent2GIS() throws Exception
{
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
*
* @throws Exception
*/
- @Test
+ @Test(enabled = false)
public void testPDBfileVsRNAML() throws Exception
{
PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
testRNAMLcontent(readers, pdbf);
}
+ @Test(enabled = false)
private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
throws Exception
{
}
if (struseq == null)
{
- Assert.fail("Couldn't find this sequence in original input:\n"
+ AssertJUnit.fail("Couldn't find this sequence in original input:\n"
+ new FastaFile().print(new SequenceI[]
{ sq })
+ "\n\nOriginal input:\n"
package jalview.ext.rbvi.chimera;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
import java.awt.Color;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class ChimeraCommandsTest
{
package jalview.ext.rbvi.chimera;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
-import org.junit.Test;
+import org.testng.annotations.Test;
import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
package jalview.ext.rbvi.chimera;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.FormatAdapter;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
public class JalviewChimeraView
{
package jalview.gui;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
-
-import org.junit.Before;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
public class AlignViewportTest
{
AlignmentI al;
AlignViewport testee;
- @Before
+ @BeforeMethod
public void setUp()
{
SequenceI seq1 = new Sequence("Seq1", "ABC");
package jalview.gui;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.Checkbox;
import javax.swing.JButton;
import javax.swing.JPanel;
-import org.junit.Before;
-import org.junit.Test;
-
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.util.MessageManager;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
/**
* Unit tests for AnnotationChooser
AlignFrame af;
- @Before
+ @BeforeMethod
public void setUp() throws IOException
{
// pin down annotation sort order for test
import java.awt.Font;
import java.awt.FontMetrics;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class FontChooserTest
{
package jalview.gui;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.gui.Help.HelpId;
import java.net.URL;
import javax.help.HelpSetException;
import javax.help.Map;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class HelpTest
{
import javax.swing.JMenuItem;
import javax.swing.JTextArea;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class JAL1353bugdemo
{
volatile boolean finish = false;
- @Test
- @Ignore
- // comment out @Ignore to enable this test
+ @Test(enabled = false)
public void test()
{
Cache.initLogger();
package jalview.gui;
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
import javax.swing.JScrollBar;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class JvSwingUtilsTest
{
package jalview.gui;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
import javax.swing.JInternalFrame;
import javax.swing.JTextField;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class PDBSearchPanelTest
{
- @Before
+ @BeforeMethod
public void setUp() throws Exception
{
}
- @After
+ @AfterMethod
public void tearDown() throws Exception
{
}
package jalview.gui;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import javax.swing.JPanel;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class PaintRefresherTest
{
// TODO would prefer PaintRefresher to be a single rather than static
- @Before
+ @BeforeMethod
public void setUp()
{
PaintRefresher.components.clear();
}
- @After
+ @AfterMethod
public void tearDown()
{
PaintRefresher.components.clear();
package jalview.gui;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
import java.awt.Component;
import java.io.IOException;
import javax.swing.JPopupMenu;
import javax.swing.JSeparator;
-import org.junit.Before;
-import org.junit.Test;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FormatAdapter;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class PopupMenuTest
{
PopupMenu testee = null;
- @Before
+ @BeforeMethod
public void setUp() throws IOException
{
alignment = new FormatAdapter().readFile(TEST_DATA,
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
- String expected = "<html><table width=350 border=0><tr><td>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
+ String expected = "<html><table width=350 border=0><tr><td align=justify>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
assertEquals(expected, menu.getToolTipText());
}
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
- String expected = "<html><table width=350 border=0><tr><td>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
+ String expected = "<html><table width=350 border=0><tr><td align=justify>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
assertEquals(expected, menu.getToolTipText());
}
package jalview.gui;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
import java.awt.Component;
import java.awt.FlowLayout;
import javax.swing.JLabel;
import javax.swing.JPanel;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.Test;
public class ProgressBarTest
{
try
{
new ProgressBar(null, null);
- fail("Expected exception");
+ Assert.fail("Expected exception");
} catch (NullPointerException e)
{
// expected
try
{
new ProgressBar(statusPanel, null);
- fail("expected exception");
+ Assert.fail("expected exception");
} catch (IllegalArgumentException e)
{
// expected
package jalview.gui;
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import java.awt.Color;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class SequenceRendererTest
{
package jalview.gui;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import java.util.Vector;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class StructureChooserTest
{
Sequence seq;
- @Before
+ @BeforeMethod
public void setUp() throws Exception
{
seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
seq.setPDBId(pdbIds);
}
- @After
+ @AfterMethod
public void tearDown() throws Exception
{
seq = null;
package jalview.io;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.File;
-
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import java.io.File;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
public class AnnotatedPDBFileInputTest
{
String pdbId;
- @Before
+ @BeforeMethod
public void setup() throws Exception
{
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
{
for (int q = p + 1; q < avec.length; q++)
{
- assertNotEquals(
+ Assert.assertNotEquals(
"Found a duplicate annotation row " + avec[p].label,
avec[p], avec[q]);
}
*/
package jalview.io;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.io.AnnotationFile.ViewDef;
import java.io.File;
import java.util.Hashtable;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.Test;
public class AnnotationFileIOTest
{
{
e.printStackTrace();
}
- fail("Couln't read the alignment in file '" + f.toString() + "'");
+ Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
return null;
}
* - label for IO class used to write and read back in the data from
* f
*/
+
+ // @Test
public static void testAnnotationFileIO(String testname, File f,
File annotFile)
{
{
e.printStackTrace();
}
- fail("Test "
+ Assert.fail("Test "
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ annotFile + "'.");
import java.net.URLConnection;
import java.util.TreeMap;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
public class BioJsHTMLOutputTest
Assert.assertNotNull(bjsTemplate);
}
- @Test(expected = NullPointerException.class)
+ @Test(expectedExceptions = NullPointerException.class)
public void expectedNullPointerException()
{
try
BioJsHTMLOutput.refreshBioJSVersionsInfo(null);
} catch (URISyntaxException e)
{
- Assert.fail("Expception occured while testing!");
+ AssertJUnit.fail("Expception occured while testing!");
e.printStackTrace();
}
}
versions = BioJsHTMLOutput.getBioJsMSAVersions();
} catch (URISyntaxException e)
{
- Assert.fail("Expception occured while testing!");
+ AssertJUnit.fail("Expception occured while testing!");
e.printStackTrace();
}
- Assert.assertNotNull("No versions found", versions);
- Assert.assertTrue("One or more Templates required", versions.size() > 0);
+ AssertJUnit.assertNotNull("No versions found", versions);
+ AssertJUnit.assertTrue("One or more Templates required", versions.size() > 0);
System.out
.println("Number of discovered versions : "
+ versions.size());
System.out.println("\nCurrent latest version : "
+ BioJsHTMLOutput.getCurrentBJSTemplateFile());
- Assert.assertNotNull("Latest BioJsMSA version NOT found!",
+ AssertJUnit.assertNotNull("Latest BioJsMSA version NOT found!",
BioJsHTMLOutput.getCurrentBJSTemplateFile());
}
public void testBioJsUpdate()
{
String url = BioJsHTMLOutput.BJS_TEMPLATE_GIT_REPO;
- Assert.assertTrue("URL not reacable : " + url, urlIsReachable(url));
+ AssertJUnit.assertTrue("URL not reacable : " + url, urlIsReachable(url));
String response = BioJsHTMLOutput.getURLContentAsString(url);
- Assert.assertNotNull("Null response read from url!", response);
+ AssertJUnit.assertNotNull("Null response read from url!", response);
BioJSRepositoryPojo repository = new BioJSRepositoryPojo(response);
System.out.println(">>> description : " + repository.getDescription());
System.out
*/
package jalview.io;
-import static org.junit.Assert.*;
-
import java.io.File;
import java.io.IOException;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
/**
* @author jimp
private void assertValidFormat(String fmt, String src, FileParse fp)
{
- assertTrue("Couldn't resolve " + src + " as a valid file", fp.isValid());
+ AssertJUnit.assertTrue("Couldn't resolve " + src + " as a valid file", fp.isValid());
String type = new IdentifyFile().Identify(fp);
- assertTrue("Data from '" + src + "' Expected to be '" + fmt
+ AssertJUnit.assertTrue("Data from '" + src + "' Expected to be '" + fmt
+ "' identified as '" + type + "'", type.equalsIgnoreCase(fmt));
}
--- /dev/null
+package jalview.io;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+
+import java.io.IOException;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class Gff3tests
+{
+
+ private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
+ exonerateOutput = "examples/testdata/exonerateoutput.gff",
+ simpleGff3file = "examples/testdata/simpleGff3.gff";
+
+ @Test
+ public void testExonerateImport()
+ {
+ // exonerate does not tag sequences after features, so we have a more
+ // conventional annotation import test here
+
+ FileLoader loader = new FileLoader(false);
+
+ AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
+ FormatAdapter.FILE);
+
+ Assert.assertEquals("Unexpected number of DNA protein associations", 0,
+ af.getViewport().getAlignment().getCodonFrames().size());
+
+ af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
+
+ Assert.assertNotEquals("Expected at least one DNA protein association",
+ 0, af.getViewport().getAlignment().getDataset()
+ .getCodonFrames().size());
+
+ }
+
+ @Test
+ public void simpleGff3FileIdentify()
+ {
+ Assert.assertEquals("Didn't recognise file correctly.",
+ IdentifyFile.GFF3File,
+ new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
+ }
+
+ @Test
+ public void simpleGff3FileClass() throws IOException
+ {
+ AlignmentI dataset = new Alignment(new SequenceI[]
+ {});
+ FeaturesFile ffile = new FeaturesFile(simpleGff3file,
+ FormatAdapter.FILE);
+
+ boolean parseResult = ffile.parse(dataset, null, null, false, false);
+ Assert.assertTrue("return result should be true", parseResult);
+ checkDatasetfromSimpleGff3(dataset);
+ }
+
+ @Test
+ public void simpleGff3FileLoader() throws IOException
+ {
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ simpleGff3file, FormatAdapter.FILE);
+ Assert.assertTrue(
+ "Didn't read the alignment into an alignframe from Gff3 File",
+ af != null);
+ checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
+ }
+
+ @Test
+ public void simpleGff3RelaxedIdMatching() throws IOException
+ {
+ AlignmentI dataset = new Alignment(new SequenceI[]
+ {});
+ FeaturesFile ffile = new FeaturesFile(simpleGff3file,
+ FormatAdapter.FILE);
+
+ boolean parseResult = ffile.parse(dataset, null, null, false, true);
+ Assert.assertTrue("return result (relaxedID matching) should be true",
+ parseResult);
+ checkDatasetfromSimpleGff3(dataset);
+ }
+
+ @Test
+ public void readGff3File() throws IOException
+ {
+ Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
+ Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
+ gff3reader.addProperties(dataset);
+ checkDatasetfromSimpleGff3(dataset);
+
+ }
+
+ private void checkDatasetfromSimpleGff3(AlignmentI dataset)
+ {
+ Assert.assertEquals("no sequences extracted from GFF3 file", 2,
+ dataset.getHeight());
+
+ SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
+ .findName("seq2");
+ Assert.assertNotNull(seq1);
+ Assert.assertNotNull(seq2);
+ Assert.assertFalse(
+ "Failed to replace dummy seq1 with real sequence",
+ seq1 instanceof SequenceDummy
+ && ((SequenceDummy) seq1).isDummy());
+ Assert.assertFalse(
+ "Failed to replace dummy seq2 with real sequence",
+ seq2 instanceof SequenceDummy
+ && ((SequenceDummy) seq2).isDummy());
+ String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
+ Assert.assertFalse("dummy replacement buggy for seq1",
+ placeholderseq.equals(seq1.getSequenceAsString()));
+ Assert.assertNotEquals("dummy replacement buggy for seq2",
+ placeholderseq.equals(seq2.getSequenceAsString()));
+ Assert.assertNotNull("No features added to seq1",
+ seq1.getSequenceFeatures());// != null);
+ Assert.assertEquals("Wrong number of features", 3,
+ seq1.getSequenceFeatures().length);
+ Assert.assertNull(seq2.getSequenceFeatures());
+ Assert.assertEquals("Wrong number of features", 0, seq2
+ .getSequenceFeatures() == null ? 0
+ : seq2.getSequenceFeatures().length);
+ Assert.assertTrue(
+ "Expected at least one CDNA/Protein mapping for seq1",
+ dataset.getCodonFrame(seq1) != null
+ && dataset.getCodonFrame(seq1).size() > 0);
+
+ }
+ // @Test
+ // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
+ // {
+ // fail("Not yet implemented");
+ // }
+ //
+ // @Test
+ // public final void testAlignFileBooleanStringString()
+ // {
+ // fail("Not yet implemented");
+ // }
+
+}
import static org.junit.Assert.fail;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class HtmlFileTest
{
- @Test
- @Ignore
+ @Test(enabled = false)
public void test()
{
fail("Not yet implemented");
package jalview.io;
-import static org.junit.Assert.assertNotNull;
-import jalview.datamodel.Alignment;
+import static org.testng.AssertJUnit.assertNotNull;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import java.util.ArrayList;
import java.util.HashMap;
-import org.junit.After;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class JSONFileTest
{
HashMap<String, AlignmentAnnotation> testAnnots = new HashMap<String, AlignmentAnnotation>();
HashMap<String, SequenceGroup> testGrps = new HashMap<String, SequenceGroup>();
- @Before
+ @BeforeMethod
public void setup() throws Exception
{
// create and add sequences
TEST_ANOT_HEIGHT = testAnnots.size();
}
- @After
+ @AfterMethod
public void tearDown() throws Exception
{
}
{
String jsonFile = "examples/example.json";
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = null;
+ AlignmentI al = null;
try
{
al = rf.readFile(jsonFile, AppletFormatAdapter.FILE,
for (SequenceI seq : al.getSequences())
{
SequenceI expectedSeq = testSeqs.get(seq.getName());
- Assert.assertTrue("Failed Sequence Test for >>> " + seq.getName(),
+ AssertJUnit.assertTrue("Failed Sequence Test for >>> " + seq.getName(),
isSeqMatched(expectedSeq, seq));
passedCount++;
}
- Assert.assertEquals("Some Sequences did not pass the test",
+ AssertJUnit.assertEquals("Some Sequences did not pass the test",
TEST_SEQ_HEIGHT, passedCount);
passedCount = 0;
for (SequenceGroup seqGrp : al.getGroups())
{
SequenceGroup expectedGrp = testGrps.get(seqGrp.getName());
- Assert.assertTrue(
+ AssertJUnit.assertTrue(
"Failed SequenceGroup Test for >>> " + seqGrp.getName(),
isGroupMatched(expectedGrp, seqGrp));
passedCount++;
}
- Assert.assertEquals("Some SequenceGroups did not pass the test",
+ AssertJUnit.assertEquals("Some SequenceGroups did not pass the test",
TEST_GRP_HEIGHT, passedCount);
passedCount = 0;
for (AlignmentAnnotation annot : al.getAlignmentAnnotation())
{
AlignmentAnnotation expectedAnnot = testAnnots.get(annot.label);
- Assert.assertTrue("Failed AlignmentAnnotation Test for >>> "
+ AssertJUnit.assertTrue("Failed AlignmentAnnotation Test for >>> "
+ annot.label, isAnnotationMatched(expectedAnnot, annot));
passedCount++;
}
- Assert.assertEquals("Some Sequences did not pass the test",
+ AssertJUnit.assertEquals("Some Sequences did not pass the test",
TEST_ANOT_HEIGHT, passedCount);
// af = new AlignFrame(al, 700, 500);
*/
package jalview.io;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.File;
-
-import org.junit.AfterClass;
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
+import java.io.File;
+
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
public class Jalview2xmlTests
{
}
catch (NullPointerException q)
{
- fail("Mismatch of alignment annotations at position " + p
+ Assert.fail("Mismatch of alignment annotations at position " + p
+ " Ref seq ann: " + refan.annotations[p]
+ " alignment " + alaa.annotations[p]);
}
{
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", FormatAdapter.FILE);
- Assert.assertTrue("Didn't read in the example file correctly.", af != null);
+ assertTrue("Didn't read in the example file correctly.", af != null);
AlignmentViewPanel sps = null, groups = null;
for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
{
ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
- Assert.assertFalse(structureStyle.sameStyle(groupStyle));
+ AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
groups.getAlignViewport().setViewStyle(structureStyle);
- Assert.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
+ AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
.getViewStyle()));
Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
.getViewStyle()));
*/
package jalview.io;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.ConversionUtils.wrapDataProvider;
+
+import jalview.analysis.NJTree;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
import java.util.Arrays;
import java.util.Collection;
import java.util.Vector;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
-
-import jalview.analysis.NJTree;
-import jalview.analysis.SequenceIdMatcher;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.SequenceNode;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Factory;
+import org.testng.annotations.Test;
/**
* @author jimp
*
*/
-@RunWith(Parameterized.class)
public class NewickFileTests
{
+ @Factory
+ public static Object[] factoryData()
+ {
+ return wrapDataProvider(NewickFileTests.class, data());
+ }
+
@Parameters
public static Collection data()
{
System.out.println(treename + "\n" + testTree);
NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE);
nf.parse();
- assertTrue(stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
+ AssertJUnit.assertTrue(stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
nf.isValid());
SequenceNode tree = nf.getTree();
- assertTrue(stage + "Null Tree", tree != null);
+ AssertJUnit.assertTrue(stage + "Null Tree", tree != null);
stage = "Creating newick file from testTree " + treename;
String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
nf.HasDistances());
- assertTrue(stage + "Empty string generated", gentree != null
+ AssertJUnit.assertTrue(stage + "Empty string generated", gentree != null
&& gentree.trim().length() > 0);
stage = "Parsing regenerated testTree " + treename;
NewickFile nf_regen = new NewickFile(gentree, FormatAdapter.PASTE);
nf_regen.parse();
- assertTrue(
+ AssertJUnit.assertTrue(
stage + "Newick file is invalid ('"
+ nf_regen.getWarningMessage() + "')",
nf_regen.isValid());
SequenceNode tree_regen = nf.getTree();
- assertTrue(stage + "Null Tree", tree_regen != null);
+ AssertJUnit.assertTrue(stage + "Null Tree", tree_regen != null);
stage = "Compare original and generated tree" + treename;
Vector oseqs, nseqs;
oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree(),
new Vector());
- assertTrue(stage + "No nodes in original tree.", oseqs.size() > 0);
+ AssertJUnit.assertTrue(stage + "No nodes in original tree.", oseqs.size() > 0);
SequenceI[] olsqs = new SequenceI[oseqs.size()];
for (int i = 0, iSize = oseqs.size(); i < iSize; i++)
{
}
nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(
nf_regen.getTree(), new Vector());
- assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0);
+ AssertJUnit.assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0);
SequenceI[] nsqs = new SequenceI[nseqs.size()];
for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
{
nsqs[i] = (SequenceI) ((SequenceNode) nseqs.get(i)).element();
}
- assertTrue(stage + " Different number of leaves (original "
+ AssertJUnit.assertTrue(stage + " Different number of leaves (original "
+ olsqs.length + " and regen " + nsqs.length + ")",
olsqs.length == nsqs.length);
SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs), nmatcher = new SequenceIdMatcher(
if (warns.length() > 0)
{
- fail(stage + warns);
+ Assert.fail(stage + warns);
}
} catch (Exception x)
{
package jalview.io;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import jalview.datamodel.Alignment;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
-import org.junit.Test;
+import org.testng.annotations.Test;
/**
* Test file for {@link PhylipFile}.
private void testDataExtraction(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
PhylipFile.FILE_DESC);
assertNotNull("Couldn't read supplied alignment data.", al);
public void testIO(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
PhylipFile.FILE_DESC);
assertNotNull("Couldn't read supplied alignment data.", al);
String outputfile = rf.formatSequences(PhylipFile.FILE_DESC, al, true);
- Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+ AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
import java.io.File;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class RNAMLfileTest
{
public void testRnamlToStockholmIO()
{
StockholmFileTest.testFileIOwithFormat(new File(
- "examples/rna-alignment.xml"), "STH", -1, -1);
+ "examples/testdata/rna-alignment.xml"), "STH", -1, -1);
}
*/
package jalview.io;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import jalview.datamodel.Alignment;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import java.util.HashMap;
import java.util.Map;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class StockholmFileTest
{
* - label for IO class used to write and read back in the data from
* f
*/
+
public static void testFileIOwithFormat(File f, String ioformat,
int naliannot, int nminseqann)
{
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
assertNotNull("Couldn't read supplied alignment data.", al);
System.out.println("Output file in '" + ioformat + "':\n"
+ outputfile + "\n<<EOF\n");
// test for consistency in io
- Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+ AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
AppletFormatAdapter.PASTE, ioformat);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
an_new.displayCharacter.trim())
|| !("" + an_or.secondaryStructure).trim().equals(
("" + an_new.secondaryStructure).trim())
- || (an_or.description != an_new.description && (an_or.description == null
- || an_new.description == null || !an_or.description
- .equals(an_new.description))))
+ || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
+ .trim().length() == 0)
+ || (an_new.description == null && an_or.description
+ .trim().length() == 0) || an_or.description
+ .trim().equals(an_new.description.trim()))))
{
System.err.println("Annotation Element Mismatch\nElement " + i
+ " in original: " + annot_or.annotations[i].toString()
*/
package jalview.io;
-import static org.junit.Assert.*;
import jalview.io.TCoffeeScoreFile.Block;
import jalview.io.TCoffeeScoreFile.Header;
import java.io.IOException;
import java.util.List;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.junit.Test;
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
public class TCoffeeScoreFileTest
{
TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
AppletFormatAdapter.FILE);
- assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
+ AssertJUnit.assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
Header header = scoreFile.header;
- assertNotNull(header);
- assertEquals(
+ AssertJUnit.assertNotNull(header);
+ AssertJUnit.assertEquals(
"T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
header.head);
- assertEquals(90, header.score);
- assertEquals(89, header.getScoreFor("1PHT"));
- assertEquals(90, header.getScoreFor("1BB9"));
- assertEquals(94, header.getScoreFor("1UHC"));
- assertEquals(94, header.getScoreFor("1YCS"));
- assertEquals(93, header.getScoreFor("1OOT"));
- assertEquals(94, header.getScoreFor("1ABO"));
- assertEquals(94, header.getScoreFor("1FYN"));
- assertEquals(94, header.getScoreFor("1QCF"));
- assertEquals(90, header.getScoreFor("cons"));
+ AssertJUnit.assertEquals(90, header.score);
+ AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
+ AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
+ AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
+ AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
}
@Test
{
TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
FormatAdapter.FILE);
- assertFalse(result.isValid());
+ AssertJUnit.assertFalse(result.isValid());
} catch (IOException x)
{
- assertTrue("File not found exception thrown",
+ AssertJUnit.assertTrue("File not found exception thrown",
x instanceof FileNotFoundException);
}
}
{
TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
FormatAdapter.FILE);
- assertTrue(result.isValid());
- assertEquals(8, result.getHeight());
- assertEquals(83, result.getWidth());
+ AssertJUnit.assertTrue(result.isValid());
+ AssertJUnit.assertEquals(8, result.getHeight());
+ AssertJUnit.assertEquals(83, result.getWidth());
}
@Test
FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
Block block = TCoffeeScoreFile.readBlock(source, 0);
- assertNotNull(block);
- assertEquals("999999999999999999999999998762112222543211112134",
+ AssertJUnit.assertNotNull(block);
+ AssertJUnit.assertEquals("999999999999999999999999998762112222543211112134",
block.getScoresFor("1PHT"));
- assertEquals("99999999999999999999999999987-------4322----2234",
+ AssertJUnit.assertEquals("99999999999999999999999999987-------4322----2234",
block.getScoresFor("1BB9"));
- assertEquals("99999999999999999999999999987-------5321----2246",
+ AssertJUnit.assertEquals("99999999999999999999999999987-------5321----2246",
block.getScoresFor("1UHC"));
- assertEquals("99999999999999999999999999986-------4321----1-35",
+ AssertJUnit.assertEquals("99999999999999999999999999986-------4321----1-35",
block.getScoresFor("1YCS"));
- assertEquals("999999999999999999999999999861-------3------1135",
+ AssertJUnit.assertEquals("999999999999999999999999999861-------3------1135",
block.getScoresFor("1OOT"));
- assertEquals("99999999999999999999999999986-------422-------34",
+ AssertJUnit.assertEquals("99999999999999999999999999986-------422-------34",
block.getScoresFor("1ABO"));
- assertEquals("99999999999999999999999999985-------32--------35",
+ AssertJUnit.assertEquals("99999999999999999999999999985-------32--------35",
block.getScoresFor("1FYN"));
- assertEquals("99999999999999999999999999974-------2---------24",
+ AssertJUnit.assertEquals("99999999999999999999999999974-------2---------24",
block.getScoresFor("1QCF"));
- assertEquals("999999999999999999999999999851000110321100001134",
+ AssertJUnit.assertEquals("999999999999999999999999999851000110321100001134",
block.getConsensus());
}
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
FormatAdapter.FILE);
- assertEquals(
+ AssertJUnit.assertEquals(
"999999999999999999999999998762112222543211112134----------5666642367889999999999889",
parser.getScoresFor("1PHT"));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
parser.getScoresFor("1BB9"));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
parser.getScoresFor("1UHC"));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
parser.getScoresFor("1YCS"));
- assertEquals(
+ AssertJUnit.assertEquals(
"999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
parser.getScoresFor("1OOT"));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999986-------422-------34----------687774--56779999999999889",
parser.getScoresFor("1ABO"));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999985-------32--------35----------6888842356789999999999889",
parser.getScoresFor("1FYN"));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999974-------2---------24----------6878742356789999999999889",
parser.getScoresFor("1QCF"));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
parser.getScoresFor("cons"));
}
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
FormatAdapter.FILE);
- assertTrue(parser.getWarningMessage(), parser.isValid());
+ AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
List<String> scores = parser.getScoresList();
- assertEquals(
+ AssertJUnit.assertEquals(
"999999999999999999999999998762112222543211112134----------5666642367889999999999889",
scores.get(0));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
scores.get(1));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
scores.get(2));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
scores.get(3));
- assertEquals(
+ AssertJUnit.assertEquals(
"999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
scores.get(4));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999986-------422-------34----------687774--56779999999999889",
scores.get(5));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999985-------32--------35----------6888842356789999999999889",
scores.get(6));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999974-------2---------24----------6878742356789999999999889",
scores.get(7));
- assertEquals(
+ AssertJUnit.assertEquals(
"99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
scores.get(8));
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
FormatAdapter.FILE);
- assertTrue(parser.getWarningMessage(), parser.isValid());
+ AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
byte[][] scores = parser.getScoresArray();
- assertEquals(9, scores[0][0]);
- assertEquals(9, scores[1][0]);
- assertEquals(9, scores[2][0]);
- assertEquals(9, scores[3][0]);
- assertEquals(9, scores[4][0]);
- assertEquals(9, scores[5][0]);
- assertEquals(9, scores[6][0]);
- assertEquals(9, scores[7][0]);
- assertEquals(9, scores[8][0]);
-
- assertEquals(5, scores[0][36]);
- assertEquals(4, scores[1][36]);
- assertEquals(5, scores[2][36]);
- assertEquals(4, scores[3][36]);
- assertEquals(-1, scores[4][36]);
- assertEquals(4, scores[5][36]);
- assertEquals(3, scores[6][36]);
- assertEquals(2, scores[7][36]);
- assertEquals(3, scores[8][36]);
+ AssertJUnit.assertEquals(9, scores[0][0]);
+ AssertJUnit.assertEquals(9, scores[1][0]);
+ AssertJUnit.assertEquals(9, scores[2][0]);
+ AssertJUnit.assertEquals(9, scores[3][0]);
+ AssertJUnit.assertEquals(9, scores[4][0]);
+ AssertJUnit.assertEquals(9, scores[5][0]);
+ AssertJUnit.assertEquals(9, scores[6][0]);
+ AssertJUnit.assertEquals(9, scores[7][0]);
+ AssertJUnit.assertEquals(9, scores[8][0]);
+
+ AssertJUnit.assertEquals(5, scores[0][36]);
+ AssertJUnit.assertEquals(4, scores[1][36]);
+ AssertJUnit.assertEquals(5, scores[2][36]);
+ AssertJUnit.assertEquals(4, scores[3][36]);
+ AssertJUnit.assertEquals(-1, scores[4][36]);
+ AssertJUnit.assertEquals(4, scores[5][36]);
+ AssertJUnit.assertEquals(3, scores[6][36]);
+ AssertJUnit.assertEquals(2, scores[7][36]);
+ AssertJUnit.assertEquals(3, scores[8][36]);
}
{
String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
- assertTrue(result.isValid());
- assertEquals(5, result.getHeight());
- assertEquals(84, result.getWidth());
+ AssertJUnit.assertTrue(result.isValid());
+ AssertJUnit.assertEquals(5, result.getHeight());
+ AssertJUnit.assertEquals(84, result.getWidth());
}
}
*/
package jalview.schemes;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertTrue;
import java.util.Map;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class DnaCodonTests
{
package jalview.schemes;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
import java.util.Collections;
import java.util.List;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class ResiduePropertiesTest
{
import java.util.Map;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class ScoreMatrixPrinter
{
package jalview.structure;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.Assert;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import MCview.PDBfile;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
+
public class Mapping
{
* 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in
* msd numbering, not pdb res numbering.
*/
- @Test
- @Ignore
+ @Test(enabled = false)
public void pdbEntryPositionMap() throws Exception
{
- fail("This test intentionally left to fail");
+ Assert.fail("This test intentionally left to fail");
for (int offset = 0; offset < 20; offset += 6)
{
// check we put the secondary structure in the right position
}
}
- @Test
- @Ignore
+ @Test(enabled = false)
public void testPDBentryMapping() throws Exception
{
- fail("This test intentionally left to fail");
+ Assert.fail("This test intentionally left to fail");
Sequence sq = new Sequence(
"1GAQ A subseq 126 to 219",
"EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
jalview.io.FormatAdapter.FILE);
if (pmap == null)
{
- Assert.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
+ AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
}
}
package jalview.structure;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignedCodonFrame;
import java.util.HashSet;
import java.util.Set;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class StructureSelectionManagerTest
{
private StructureSelectionManager ssm;
- @Before
+ @BeforeMethod
public void setUp()
{
ssm = new StructureSelectionManager();
package jalview.structures.models;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.util.Arrays;
-import java.util.List;
-
-import org.junit.Before;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel.SuperposeData;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
/**
* Unit tests for non-abstract methods of abstract base class
*
/**
* Set up test conditions with three aligned sequences,
*/
- @Before
+ @BeforeMethod
public void setUp()
{
SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
package jalview.util;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
import java.awt.Color;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class ColorUtilsTest
{
package jalview.util;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import org.testng.annotations.Test;
+
public class ComparisonTest
{
package jalview.util;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+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.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class DBRefUtilsTest
{
package jalview.util;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class MapListTest
{
private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
{
int[] frm = mldna.locateInFrom(i, j);
- Assert.assertEquals("Failed test locate from " + i + " to " + j,
+ assertEquals("Failed test locate from " + i + " to " + j,
Arrays.toString(frm), Arrays.toString(ks));
}
package jalview.util;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
-import java.awt.Color;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
+import java.awt.Color;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.Test;
+
public class MappingUtilsTest
{
private AlignViewportI dnaView;
protected AlignmentI loadAlignment(final String data, String format)
throws IOException
{
- Alignment a = new FormatAdapter().readFile(data,
+ AlignmentI a = new FormatAdapter().readFile(data,
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
package jalview.util;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
import java.util.Arrays;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class QuickSortTest
{
private final Object[] sortedThings = new Object[]
{ c4, c2, c1, c3 };
- @Before
+ @BeforeMethod
public void setUp()
{
things = new Object[]
/**
* Test whether sort is stable i.e. equal values retain their mutual ordering.
*/
- @Test
- @Ignore
+ @Test(enabled = false)
public void testSort_withDuplicates()
{
int[] values = new int[]
package jalview.util;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
import java.util.Arrays;
import java.util.List;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class ShiftListTest
{
package jalview.util;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
import java.util.Arrays;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class StringUtilsTest
{
package jalview.viewmodel.styles;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
import java.awt.Color;
import java.lang.reflect.Field;
import java.util.Random;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
public class ViewStyleTest
}
else
{
- Assert.fail("Unhandled field type (add to test): " + field.getName()
+ AssertJUnit.fail("Unhandled field type (add to test): " + field.getName()
+ ":" + type);
}
}
*/
package jalview.ws;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import org.junit.Before;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.ws.seqfetcher.DbSourceProxy;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
public class PDBSequenceFetcherTest
{
SequenceFetcher sf;
- @Before
+ @BeforeMethod
public void setUp() throws Exception
{
// ensure 'add annotation from structure' is selected
sf = new SequenceFetcher(false);
}
- @Test
+ @Test(enabled = false)
public void testRnaSeqRetrieve() throws Exception
{
List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
package jalview.ws.dbsources;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import jalview.ws.uimodel.PDBRestRequest;
import jalview.ws.uimodel.PDBRestResponse;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.ClientResponse;
public class PDBRestClientTest
{
- @Before
+ @BeforeMethod
public void setUp() throws Exception
{
}
- @After
+ @AfterMethod
public void tearDown() throws Exception
{
}
} catch (Exception e)
{
e.printStackTrace();
- fail("Couldn't execute webservice call!");
+ Assert.fail("Couldn't execute webservice call!");
return;
}
assertTrue(response.getNumberOfItemsFound() > 99);
assertEquals(expectedErrorMsg, parsedErrorResponse);
}
- @Test(expected = Exception.class)
+ @Test(expectedExceptions = Exception.class)
public void testForExpectedRuntimeException() throws Exception
{
List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
// Check the response status and report exception if one occurs
if (clientResponse.getStatus() != 200)
{
- fail("Webservice call failed!!!");
+ Assert.fail("Webservice call failed!!!");
}
else
{
}
} catch (ParseException e)
{
- fail(">>> Test failed due to exception while parsing pdb response json !!!");
+ Assert.fail(">>> Test failed due to exception while parsing pdb response json !!!");
e.printStackTrace();
}
}
package jalview.ws.dbsources;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.UniprotEntry;
import java.io.Reader;
import java.io.StringReader;
import java.util.Vector;
-import org.junit.Test;
-
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.UniprotEntry;
+import org.testng.annotations.Test;
public class UniprotTest
{
*/
package jalview.ws.gui;
+import jalview.bin.Cache;
+import jalview.gui.WsJobParameters;
+import jalview.util.MessageManager;
+import jalview.ws.jabaws.JalviewJabawsTestUtils;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
import java.awt.BorderLayout;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import javax.swing.JFrame;
import javax.swing.JPanel;
-import org.junit.BeforeClass;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
-import jalview.bin.Cache;
-import jalview.gui.WsJobParameters;
-import jalview.util.MessageManager;
-import jalview.ws.jabaws.JalviewJabawsTestUtils;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-
public class Jws2ParamView
{
/**
* This test marked Ignore as it appears to need user action to complete
* rather than hang
*/
- @Test
- @Ignore
+
+ @Test(enabled = false)
public void testJws2Gui()
{
Iterator<String> presetEnum = presetTests.iterator();
*/
package jalview.ws.jabaws;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.io.AnnotationFile;
import java.util.ArrayList;
import java.util.List;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class DisorderAnnotExportImport
{
{
e.printStackTrace();
}
- fail("Test "
+ Assert.fail("Test "
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import java.util.Vector;
+import jalview.ws.jws2.Jws2Discoverer;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Ignore;
-import org.junit.Test;
+import java.util.Vector;
-import jalview.ws.jws2.Jws2Discoverer;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class JalviewJabawsTestUtils
{
{ "http://localhost:8080/jabaws",
"http://www.compbio.dundee.ac.uk/jabaws" };
- @Test
- @Ignore
+ @Test(enabled = false)
public void testAnnotExport()
{
fail("Not yet implemented");
*/
package jalview.ws.jabaws;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Component;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
-
-import compbio.metadata.Argument;
-import compbio.metadata.WrongParameterException;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.AutoCalcSetting;
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import compbio.metadata.Argument;
+import compbio.metadata.WrongParameterException;
+
public class JpredJabaStructExportImport
{
public static String testseqs = "examples/uniref50.fa";
if (jpredws == null)
{
- fail("jpredws is null");
+ Assert.fail("jpredws is null");
}
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
if (!success)
{
jpredClient.cancelCurrentJob();
- fail("Jpred Client didn't run with hardwired default parameters.");
+ Assert.fail("Jpred Client didn't run with hardwired default parameters.");
}
} catch (InterruptedException x)
{
e.printStackTrace();
}
- fail("Test "
+ Assert.fail("Test "
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
- // @Test
+ @Test
public void testJpredwsSettingsRecovery()
{
- fail("not implemnented");
+ Assert.fail("not implemnented");
List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) jpredws
.getRunnerConfig().getArguments())
rg.setValue("292");
} catch (WrongParameterException q)
{
- fail("Couldn't set the temperature parameter "
+ Assert.fail("Couldn't set the temperature parameter "
+ q.getStackTrace());
}
opts.add(rg);
package jalview.ws.jabaws;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertEquals;
import java.util.ArrayList;
import java.util.List;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.Test;
import compbio.data.msa.MsaWS;
import compbio.data.msa.RegistryWS;
import compbio.ws.client.Jws2Client;
import compbio.ws.client.Services;
-public class MinJabawsClientTests {
+public class MinJabawsClientTests
+{
/**
* simple test for the benefit of JAL-1338
}
}
if (msaservice == null) {
- fail("couldn't find a clustalO service on the public registry");
+ Assert.fail("couldn't find a clustalO service on the public registry");
}
FastaSequence fsq = new FastaSequence("seqA",
"SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
*/
package jalview.ws.jabaws;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import org.junit.AfterClass;
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
import compbio.metadata.WrongParameterException;
if (rnaalifoldws == null)
{
- fail("no web service");
+ Assert.fail("no web service");
}
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
{
if (aa.isRNA())
{
- Assert.assertTrue("Did not create valid structure from RNAALiFold prediction", aa.isValidStruc());
+ assertTrue(
+ "Did not create valid structure from RNAALiFold prediction",
+ aa.isValidStruc());
}
}
}
{
e.printStackTrace();
}
- fail("Test "
+ Assert.fail("Test "
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
rg.setValue("292");
} catch (WrongParameterException q)
{
- fail("Couldn't set the temperature parameter "
+ Assert.fail("Couldn't set the temperature parameter "
+ q.getStackTrace());
}
opts.add(rg);
*/
package jalview.ws.jws2;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
+import jalview.ws.jabaws.JalviewJabawsTestUtils;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
import compbio.metadata.Option;
import compbio.metadata.Parameter;
import compbio.metadata.PresetManager;
import compbio.metadata.WrongParameterException;
-import jalview.bin.Cache;
-import jalview.ws.jabaws.JalviewJabawsTestUtils;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-
public class ParameterUtilsTest
{
/*
package jalview.ws.rest;
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
-import java.util.Vector;
+import jalview.bin.Cache;
-import org.junit.Test;
+import java.util.Vector;
-import jalview.bin.Cache;
+import org.testng.annotations.Test;
public class RestClientTest
{
*/
package jalview.ws.rest;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
-import java.util.Map;
+import jalview.gui.AlignFrame;
-import org.junit.Test;
+import java.util.Map;
-import jalview.gui.AlignFrame;
-import jalview.util.StringUtils;
+import org.testng.annotations.Test;
/**
* @author jimp
package jalview.ws.seqfetcher;
-import static org.junit.Assert.*;
-
-import org.junit.Test;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
public class DasSequenceFetcher
{
public void testDasRegistryContact()
{
jalview.bin.Cache.getDasSourceRegistry().refreshSources();
- assertTrue(
+ AssertJUnit.assertTrue(
"Expected to find at least one DAS source at the registry. Check config.",
jalview.bin.Cache.getDasSourceRegistry().getSources().size() > 0);
}
*/
package jalview.ws.seqfetcher;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.analysis.CrossRef;
import jalview.datamodel.AlignmentI;
import jalview.util.DBRefUtils;
import jalview.ws.SequenceFetcher;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
/**
* @author jimp
*
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-import java.io.*;
-import java.util.*;
+import java.io.DataInputStream;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
versions.put("48.0", "1.4");
versions.put("49.0", "1.5");
versions.put("50.0", "1.6");
+ versions.put("51.0", "1.7");
+ versions.put("52.0", "1.8");
+
}
String version = (String) versions.get(major + "."
+ minor);
version = (String) versions.get(major + ".0");
}
// System.err.println("Version "+version);
+ if (version == null)
+ {
+ versions.put(major + "." + minor, "Class v" + major + ".0");
+ }
return version;
}
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
+<suite name="Suite" parallel="none">
+ <test verbose="2" name="Test">
+ <classes>
+ <class name="jalview.gui.AlignViewportTest"/>
+ <class name="jalview.util.ShiftListTest"/>
+ <class name="jalview.util.ColorUtilsTest"/>
+ <class name="jalview.gui.PDBSearchPanelTest"/>
+ <class name="MCview.PDBfileTest"/>
+ <class name="jalview.io.BioJsHTMLOutputTest"/>
+ <class name="jalview.io.JSONFileTest"/>
+ <class name="jalview.ext.jmol.PDBFileWithJmolTest"/>
+ <class name="jalview.ws.jabaws.RNAStructExportImport"/>
+ <class name="jalview.ext.paradise.TestAnnotate3D"/>
+ <class name="MCview.PDBChainTest"/>
+ <class name="jalview.io.StockholmFileTest"/>
+ <class name="jalview.schemes.ScoreMatrixPrinter"/>
+ <class name="jalview.datamodel.SearchResultsTest"/>
+ <class name="jalview.ws.seqfetcher.DasSequenceFetcher"/>
+ <class name="jalview.util.DBRefUtilsTest"/>
+ <class name="jalview.analysis.CrossRefTest"/>
+ <class name="jalview.ws.jabaws.MinJabawsClientTests"/>
+ <class name="jalview.datamodel.AlignedCodonTest"/>
+ <class name="MCview.AtomTest"/>
+ <class name="jalview.gui.PopupMenuTest"/>
+ <class name="jalview.viewmodel.styles.ViewStyleTest"/>
+ <class name="jalview.io.AnnotationFileIOTest"/>
+ <class name="jalview.ws.jws2.ParameterUtilsTest"/>
+ <class name="jalview.io.RNAMLfileTest"/>
+ <class name="jalview.analysis.AlignmentUtilsTests"/>
+ <class name="jalview.gui.SequenceRendererTest"/>
+ <class name="jalview.bin.CommandLineOperations"/>
+ <class name="jalview.gui.PaintRefresherTest"/>
+ <class name="jalview.ws.seqfetcher.DbRefFetcherTest"/>
+ <class name="jalview.datamodel.AlignmentAnnotationTests"/>
+ <class name="jalview.schemes.ResiduePropertiesTest"/>
+ <class name="jalview.ext.rbvi.chimera.ChimeraCommandsTest"/>
+ <class name="MCview.ResidueTest"/>
+ <class name="jalview.io.PhylipFileTests"/>
+ <class name="jalview.util.MappingUtilsTest"/>
+ <class name="jalview.ws.jabaws.DisorderAnnotExportImport"/>
+ <class name="jalview.analysis.GroupingTest"/>
+ <class name="jalview.analysis.AnnotationSorterTest"/>
+ <class name="jalview.io.FileIOTester"/>
+ <class name="jalview.util.MapListTest"/>
+ <class name="jalview.datamodel.ColumnSelectionTest"/>
+ <class name="jalview.ext.rbvi.chimera.ChimeraConnect"/>
+ <class name="jalview.gui.ProgressBarTest"/>
+ <class name="jalview.analysis.AlignmentAnnotationUtilsTest"/>
+ <class name="jalview.structure.StructureSelectionManagerTest"/>
+ <class name="jalview.io.TCoffeeScoreFileTest"/>
+ <class name="jalview.analysis.AAFrequencyTest"/>
+ <class name="jalview.ws.dbsources.PDBRestClientTest"/>
+ <class name="jalview.analysis.DnaTest"/>
+ <class name="jalview.util.StringUtilsTest"/>
+ <class name="jalview.structures.models.AAStructureBindingModelTest"/>
+ <class name="jalview.gui.JvSwingUtilsTest"/>
+ <class name="jalview.analysis.CodingUtilsTest"/>
+ <class name="jalview.io.AnnotatedPDBFileInputTest"/>
+ <class name="jalview.ws.rest.ShmmrRSBSService"/>
+ <class name="jalview.io.NewickFileTests"/>
+ <class name="jalview.analysis.ParsePropertiesTest"/>
+ <class name="MCview.BondTest"/>
+ <class name="jalview.commands.EditCommandTest"/>
+ <class name="jalview.ext.rbvi.chimera.JalviewChimeraView"/>
+ <class name="jalview.ws.jabaws.JpredJabaStructExportImport"/>
+ <class name="jalview.gui.HelpTest"/>
+ <class name="jalview.datamodel.AlignedCodonIteratorTest"/>
+ <class name="jalview.datamodel.xdb.embl.EmblFileTest"/>
+ <class name="jalview.util.ComparisonTest"/>
+ <class name="jalview.util.QuickSortTest"/>
+ <class name="jalview.ws.PDBSequenceFetcherTest"/>
+ <class name="jalview.analysis.scoremodels.FeatureScoreModelTest"/>
+ <class name="jalview.io.Jalview2xmlTests"/>
+ <class name="jalview.ws.rest.RestClientTest"/>
+ <class name="jalview.datamodel.AlignedCodonFrameTest"/>
+ <class name="jalview.datamodel.MappingTest"/>
+ <class name="jalview.datamodel.AlignmentTest"/>
+ <class name="jalview.ws.dbsources.UniprotTest"/>
+ <class name="jalview.gui.AnnotationChooserTest"/>
+ <class name="jalview.structure.Mapping"/>
+ <class name="jalview.datamodel.SequenceTest"/>
+ <class name="jalview.datamodel.PDBEntryTest"/>
+ <class name="jalview.gui.StructureChooserTest"/>
+ <class name="jalview.schemes.DnaCodonTests"/>
+ <class name="com.stevesoft.pat.RegexWriterTest"/>
+ <class name="jalview.datamodel.DBRefEntryTest"/>
+ <class name="jalview.gui.FontChooserTest"/>
+ <class name="jalview.analysis.TestAlignSeq"/>
+ <class name="jalview.datamodel.SeqCigarTest"/>
+ <class name="jalview.gui.JAL1353bugdemo"/>
+ </classes>
+ </test> <!-- Test -->
+</suite> <!-- Suite -->
git://source.jalview.org / jalview.git / commitdiff