<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
- <classpathentry kind="lib" path="lib/min-jaba-client-2.0.jar" sourcepath="/clustengine2"/>
<classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
<classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
<classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
<classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
+ <classpathentry kind="lib" path="lib/VARNAv3-9-dev.jar"/>
+ <classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
+ <classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
- <classpathentry kind="lib" path="/Users/jimp/git/jalview_clean/lib/VARNAv3-9-dev.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="output" path="classes"/>
</classpath>
</dictionary>
</arguments>
</buildCommand>
- <buildCommand>
- <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
- <triggers>full,incremental,</triggers>
- <arguments>
- <dictionary>
- <key>LaunchConfigHandle</key>
- <value><project>/.externalToolBuilders/buildapplet [Builder].launch</value>
- </dictionary>
- </arguments>
- </buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.groovy.core.groovyNature</nature>
<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
<copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+ <copy todir="${outputDir}/lang">
+ <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
<jar destfile="in.jar" index="true">
<manifest>
<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
<include name=".build_properties" />
<include name="images/idwidth.gif" />
<include name="images/link.gif" />
+ <include name="lang/**" />
</fileset>
</jar>
</target>
--- /dev/null
+<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\r
+<!--\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+-->\r
+<html xmlns="http://www.w3.org/1999/xhtml">\r
+ <head>Jalview i18n</head>\r
+ <body>\r
+<h1>Best practices</h1>\r
+<ol>\r
+<li>Follow the standards described in this guide</li>\r
+<li>Always use properties files for user interface text; never include displayable text in code</li>\r
+<li>Use properties files only for user interface text (Messages_xx.properties) and config files for configuration settings (jalview.properties).</li>\r
+<li>Use a proper naming schema for keys in your resource bundles. The name of the keys should provide some information about the context of the displayed text. This helps the translators during the translation process.</li>\r
+<li>Group keys by view, ie. edit.title, edit.instructions, list.title, list.instructions, create.title, etc</li>\r
+<li>Never use displayable text when executing comparisons within the logic of the tool (separate codified values from displayable text)</li>\r
+<li>Always use the MessageManager class for retrieving properties values, and invoke MessageManager methods dynamically, to accommodate dynamic user preferences (see MessageManager below).</li>\r
+<li>All numbers and dates should be formatted specific to the user's locale (e.g. java.text.NumberFormat and java.text.DateFormat)</li>\r
+<li>Test code in more than one language</li>\r
+</ol>\r
+<h1>MessageManager</h1>\r
+<p>The jalview.util.MessageManager class is a wrapper class for the ResourceBundle class. It provides dynamic language/locale support for individual users, and is recommended for all Jalview code.</p>\r
+<p>To use it within your code, you only have to invoke MessageManager with the text key in Messages_xx.properties:</p>\r
+<p>JButton ok = new JButton(MessageManager.getString("button.ok"));</p>\r
+<p>This will set JButton text to the one included at button.ok key. In English JButton text will be OK, while in Spanish will be Aceptar. This is the big thing of i18n. :)</p>\r
+<h1>How to translate Jalview</h1>\r
+<p>Anyone interested in localizing/translating Jalview is strongly encouraged to join the <a href="mailto:jalview-dev@jalview.org">Jalview Development List</a> list. We would recommend that you read this entire page before proceeding.</p>\r
+<p>If you are planning on working on a Jalview translation, please send us an email (<a href="mailto:jalview-dev@jalview.org">Jalview Development List</a>). There may be someone else already working on translating Jalview to your target language.</p>\r
+<p>Once you have downloaded the source code (available at <a href="http://www.jalview.org/download">http://www.jalview.org/download</a>), you must edit {jalview.home}/resources/lang/Messages_xx.properties, where xx refers to your language country code. If it doesn't exits, rename Messages.properties to Messages_xx.properties.</p>\r
+<p>Next step...start transtalation!</p>\r
+<p>Once you have it translated, we would appreciate if you contribute it forwarding the file to <a href="mailto:jalview-dev@jalview.org">Jalview Development List</a>. We will commit it to the code base as soon as possible. Thanks so much for this in advance!</p>\r
+</body>\r
+</html>\r
+\r
--- /dev/null
+CLUSTAL
+
+B.taurus.1/1-64 C-UUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGU
+D.melanogaster.3/1-68 G-UGGCGCU--UAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GC--------GGG
+D.melanogaster.2/1-63 C-AUUCAACU-UAUGAGGAUUAUUUCU-UAAA-GGCCUCU---GGC--U-------CGGA
+D.melanogaster.1/1-65 G-AGCC-CU---AUGAUCGAUGAUUGG-CAAA-UCCUCUC--GAGG--A-------ACCG
+R.norvegicus.7/1-66 C-CGGCACU--CAUGACGGUCUGCCUG-AAAA-CCAGCCC--GCUG-GU--------GGG
+R.norvegicus.6/1-67 G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCA-AAGAC--C-----UGUGGU
+R.norvegicus.5/1-62 G-UUUUUCC---AUGACGGUGUUUCCUCUAAA--UUUAC----AUG-----------GAG
+R.norvegicus.4/1-61 G-UCAGAUG---AUGACGGCCUGUGCA-GAAA-CCCCCAC-GUGGG--C--------UGC
+R.norvegicus.3/1-67 U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAGGGU--------UUG
+R.norvegicus.2/1-64 G-UUACAUU--GAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGU
+R.norvegicus.1/1-61 A-UAUUUGUU-UAUGAUGGUCACAGUG-UAAA--GUUCA----CAC-----------AGC
+O.aries.1/1-68 G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCU-UGGAC-GC------CUGGU
+M.musculus.9/1-66 C-CGGCACU--CAUGAAGGUCUGCUUG-AAAA-CCAGCCU--GCUG-GU--------GGG
+M.musculus.8/1-67 U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAG-GA-------CUUG
+O.niloticus.3/1-65 G-UGUCUCU---GUGAAGUUCGGUUUU-UAAA-AGGGUCA---UCC--A-------GAAA
+M.musculus.7/1-64 G-UGUCUCU---AUGAAGGAGGGGCCC-GAAG-CCCUUGU---GGG--C--------GGG
+O.niloticus.2/1-61 U-GUUUAUU--AAUGACGGCUACAGAU-UAAA--CCUUU----AGC-----------CUC
+M.musculus.6/1-61 G-UCAGAUG---AUGAUGGCCUGGGCA-GAAA-CCCCAUG--UGGG--C--------CGC
+O.niloticus.1/1-59 G-UUUCUCA---GUGAAGGCUACAGAU-UAAA--CCUCU----GGC-----------CUC
+M.musculus.5/1-66 G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUA---GAC--C-----UGUGGU
+M.musculus.4/1-65 G-UGUGCGA---AUGAUAACUACUGAC-GAAA-GAGCUGU-CUGCU--C-------AGUC
+M.musculus.3/1-64 G-GUUCUUC--CAUGAUGGUGUUUCCUCUAAA--UUUGC----ACG-----------GAG
+M.musculus.2/1-64 G-UUACAUU--AAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGU
+M.musculus.1/1-64 G-UCACCGA---AUGAUCUGCUCUGGU-CAAA-UCCUUCU---AUG--C------CAGCC
+C.elegans.1/1-64 G-AGGCAGCUUUGUGACGACCUUUGGC-UAAA-CUCCAUC--GUGA-GC--------GCC
+H.sapiens.15/1-63 U-UUUCAUC--UAUGAGGGUGUUUCCUCUAAA--CCUACG---AGG-----------GAG
+H.sapiens.14/1-62 C-ACUGCUG---AUGACGAACUAUCUC-UAAC-UGGUCUU--GACC--A-------CGAG
+H.sapiens.13/1-64 G-UCACUGC---AUGAUCCGCUCUGGU-CAAA-CCCUUCC---AGG--C------CAGCC
+H.sapiens.12/1-67 C-UCUGUUA---AUGACGUCUCUCCCUCUAAA-CCCCAUU-AAGGA--C--------UGG
+D.rerio.1/1-66 A-UGUGGUCUUUAUGAAGGCAGGUGCA-GAAA-CUAUGCA---CUA-GU--------GGU
+H.sapiens.11/1-63 G-CCGGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CAC
+H.sapiens.10/1-62 C-CGGCACU--CAUGACGGCCUGCCUG-CAAA--CCUGC----UGG--U--------GGG
+S.mansoni.1/1-67 C-UCGCUAU---AUGACGAUGGCAAUC-UCAA--AUGUU----CAU--U--------GGU
+S.scrofa.4/1-64 C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCC----CUG-GU--------GGG
+S.scrofa.3/1-63 A-UUUUAUC--CAUGAAAGUGUUUCCUCUAAA--CCUAU----GUG-----------GAG
+S.scrofa.2/1-65 C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCCC---CUG-GU--------GGG
+S.scrofa.1/1-68 G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUG-UGGAC-GC------CUGGU
+H.sapiens.9/1-58 U-AUUUGUU--UAUGAUGGCCACAGCC-UAAA--GUACA----CAC-----------GGC
+H.sapiens.8/1-67 U-UUGCUUU--AAUGAGAAUAGAAACG-UAAA--CUAUGA-CCUAG-G---------GGU
+X.laevis.1/1-67 G-UGUUUGCA-AAUGACGACCGAUUUU-GAAA-UGGUCUCACGGCC--A-------AAAA
+H.sapiens.7/1-70 U-GGCGUCUU-CAUGAGGGAGGGGCCC--AAA-GCCCUUG--UGGG--C--------GGA
+H.sapiens.6/1-66 G-UGUGCGG---AUGAUAACUACUGAC-GAAAGAGUCAUC---GAC--C-----UCAGUU
+H.sapiens.5/1-57 U-UCACAGA---AUGAUGGCACCUUCC-UAA---ACCCU----CAU-----------GGG
+H.sapiens.4/1-71 G-ACUGACAU-UAUGAAGGCCUGUACU-GAAG-ACAGCAA--GCUG--U-------UAGU
+H.sapiens.3/1-68 G-ACGCUUC---AUGAUAGGAAGGACU-GAAA-AGUCUUG-UGGAC--A-----CCUGGU
+H.sapiens.2/1-65 G-UGUGCGG---AUGAUAACUACUGAC-GAAA-GAGUCAU-CGACU--C-------AGUU
+H.sapiens.1/1-63 G-CCAGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CAC
+M.musculus.14/1-67 C-UCUGAUA---AUGAUGUCUCUCCCU-CUAA-CUCCCAGUAAGGA--C--------UGG
+M.musculus.13/1-60 C-AUGCGUC--CAUGAAGUCACUGGCC-UCAA-GCCCAA----GUG-GU--------GGG
+M.musculus.12/1-65 C-UCAGCAG--GAUGAUGAGAAGGGCU-GAAA-UGCUGCC--AAAC--C-------AGGU
+M.musculus.11/1-63 U-AUUUGUG--UAUGAUGGUCACAGUG-UAAA--GUUCC----CAC-----------AGC
+M.musculus.10/1-66 C-CGGCACU--CAUGAAGGUCUGCCUG-AAAA-CCAGCCU--GCUG-GU--------GGG
+B.taurus.7/1-61 U-UUUGCCC---AUGAAGGUGUUCCCUCUAAA--CCUAC----GUG-----------GAG
+B.taurus.6/1-67 G-AUGCGUC--CAUGAAGUCACCAGCC-CCAA-GCCCCUC---GUG-GU--------GGG
+B.taurus.5/1-61 G-CCAGAUG---AUGAGGACCUGUGCG-GAAA-CCCCCCG--CGGG--C--------UGC
+B.taurus.4/1-64 ACUUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGU
+G.gallus.3/1-73 U-AUUUCUU--UGUGAUGACCGAUUUU-GAAA-UGGGUUU---CUC--UAAUGCCAGGAA
+B.taurus.3/1-66 C-CCGGUGCC-UAUGACGGUCUGUCUG-AAAA-CCAGCCC---CUG-GU--------GGG
+G.gallus.2/1-60 U-AUUUGUC---AUGACAGUCACAGCA-UAAA--GCGCA----GAC-----------GGC
+B.taurus.2/1-64 C-UUGCGUU--AAUGAGAACAGAAACG-AAAA--CUAUAA-CCUAG-G---------GGU
+G.gallus.1/1-63 G-UGUGUUU---AUGAAGAGCACUAAC-AAAA-GAGUAAU-UGACU--C-------AGUU
+
+B.taurus.1/1-64 UUC-U-G-UUGGAU--GGUUG-------GCAAC
+D.melanogaster.3/1-68 CAA-U-U-GCUGAU---UACG---AUUAACCAC
+D.melanogaster.2/1-63 AAU-A-G-UCUGAA---CCU--------UAUUG
+D.melanogaster.1/1-65 AUC-G-U-UGAGAA--CCCCU-----UUGCCUU
+R.norvegicus.7/1-66 GCA-G-U-CCCGAG-GACCUG-------GCGUG
+R.norvegicus.6/1-67 CUU-U-C-UUCGAU--GUUCU-------GCGGC
+R.norvegicus.5/1-62 AAA-C-A-CCUGAU-UUCCAG------AAAAAU
+R.norvegicus.4/1-61 -CA-G-G-UUUGAA---CCC--------CUGGC
+R.norvegicus.3/1-67 UGUCG-A-UCUGCU--AAUUG-------GCAAA
+R.norvegicus.2/1-64 UUC-U-G-UUGGAU--AGCUC-------GUAAU
+R.norvegicus.1/1-61 UGU-G-A-CUUGAU--UUUUA-------AAAAU
+O.aries.1/1-68 CCU-U-C-CUUGAU--GUUCU------CACGGC
+M.musculus.9/1-66 GCA-G-U-CCUGAG-GACCUG-------GCGUG
+M.musculus.8/1-67 UGU-AGA-UCUGAU--AAUUG-------GCAAA
+O.niloticus.3/1-65 ACC-G-ACACUGAU--GUUUC------CGACAC
+M.musculus.7/1-64 CCU-C-C-CCUGAG---CCCG----UCUGUGGU
+O.niloticus.2/1-61 UGG-A-G-CCAGAU--GCAUU------CAAACA
+M.musculus.6/1-61 CCA-G-G-UUUGAA---CCC--------CUGGC
+O.niloticus.1/1-59 UGG-A-G-CCAGAU--GCAUU-------GAAAC
+M.musculus.5/1-66 CUU-U-C-CUCGAU--GUUCC------UGCGGC
+M.musculus.4/1-65 UGU-G-G-UUGGAU---GUAG------UCACAC
+M.musculus.3/1-64 AAA-C-A-CCUGAU-UUCCAG-----GAAAAUC
+M.musculus.2/1-64 UUC-U-G-UUGGAU--AGCUU-------GUAAU
+M.musculus.1/1-64 AGG-G-U-GGUGAU--GACCC-------GUGAC
+C.elegans.1/1-64 UCU-G-G-UCUGAU---GC---------GCCUC
+H.sapiens.15/1-63 GAA-C-A-CCUGAU---CUUA-----CAGAAAA
+H.sapiens.14/1-62 CUA-G-U-UCUGAA---UU-G-------CAGGG
+H.sapiens.13/1-64 AGA-G-U-GGGGAU--GGUCU-------GUGAC
+H.sapiens.12/1-67 GAG-A-G-GCAGAGCAAGCCU-------CAGAG
+D.rerio.1/1-66 GUC-U-G-UCUGAU--GUUUG-------GCCAU
+H.sapiens.11/1-63 CCA-U-G-UCCGAG---CCCC-------CUGGC
+H.sapiens.10/1-62 GCA-G-A-CCCGAA-AAUCCA-------GCGUG
+S.mansoni.1/1-67 UGC-C-A-UUUGAU--GAAAUCAGUUUUGUGUG
+S.scrofa.4/1-64 GCA-G-A-CUCGAG-AACCUG-------GCGUG
+S.scrofa.3/1-63 GAA-C-A-CCUGAU-GUCCAG------GAAAAU
+S.scrofa.2/1-65 GCA-G-A-CUCGAG-AACCUG-------GCGUG
+S.scrofa.1/1-68 CCU-U-C-CCUGAU--GUUCU------CAUGGC
+H.sapiens.9/1-58 UGU-G-A-CUUGAU---UCA--------AAAGA
+H.sapiens.8/1-67 UUC-U-G-UUGGAU-AAUUAG-----CAGUUUA
+X.laevis.1/1-67 CUC-GUG-UCCGAC---AUC--------AACCC
+H.sapiens.7/1-70 CCU-C-C-CCUGAG---CCUGUCUGAGGGGCCA
+H.sapiens.6/1-66 AGU-G-G-UUGGAU---GUAG------UCACAU
+H.sapiens.5/1-57 UGG-U-G-UCUGAG--AGGC--------GUGAA
+H.sapiens.4/1-71 ACA-G-A-CCAGAU--GCUUU--CUUGGCAGGC
+H.sapiens.3/1-68 CUU-U-C-CCUGAU--GUUCU------CGUGGC
+H.sapiens.2/1-65 AGU-G-G-UUGGAU---GUAG------UCACAU
+H.sapiens.1/1-63 CCA-U-G-UCCGAG---CCCC-------CUGGC
+M.musculus.14/1-67 GAG-A-G-GCUGAACAAACCU-------CAGAG
+M.musculus.13/1-60 CAG-U-G-ACAGAA---GA---------GCUGC
+M.musculus.12/1-65 CCU-U-U-UCUGAU--GGUGG-------CUGGG
+M.musculus.11/1-63 UGU-G-A-CUUGAU--UUUUA----AAAAUGUC
+M.musculus.10/1-66 GCA-G-U-CCUGAG-GACCUG-------GCGUG
+B.taurus.7/1-61 GAA-U-G-CCUGAU-GUCCAG-------GAAAA
+B.taurus.6/1-67 UGG-U-G-AUGGAA-CCGUCA-----AAGCAGU
+B.taurus.5/1-61 CCA-U-G-UCUGAG---CCC--------CUGGC
+B.taurus.4/1-64 UUC-U-G-UUGGAU--GGUUG-------GCAA-
+G.gallus.3/1-73 AUC-GUG-UCUGAU---GUUG-----UCAAGUA
+B.taurus.3/1-66 GCA-G-A-CCUGAG-AACCUG-------GCGUG
+G.gallus.2/1-60 UGU-G-A-CCUGAU--UUUAG------AAAAUA
+B.taurus.2/1-64 UUC-U-G-UUGGAU--GGUUG-------GCAAC
+G.gallus.1/1-63 GGU-G-U-UCAGAU--GCU---------CUCAC
+
<mapID target="newsreader" url="html/webServices/newsreader.html"/>
<mapID target="disorder" url="html/webServices/proteinDisorder.html"/>
<mapID target="aacon" url="html/webServices/AACon.html"/>
+ <mapID target="rnaalifold" url="html/webServices/RNAalifold.html"/>
<mapID target="seqfetch" url="html/features/seqfetch.html"/>
<mapID target="dbreffetcher" url="html/webServices/dbreffetcher.html"/>
<mapID target="seqmappings" url="html/features/seqmappings.html"/>
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Protein Disorder Prediction" target="disorder"/>
<tocitem text="Alignment Conservation Analysis" target="aacon"/>
+ <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
<tocitem text="Viewing RNA structure" target="varna" />
<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
<tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
<tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
</tocitem>
<tocitem text="Secondary Structure Prediction" target="jnet"/>
+ <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
<tocitem text="Protein Disorder Prediction" target="disorder"/>
<tocitem text="Alignment Conservation Analysis" target="aacon"/>
<tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
</strong><em>Any columns currently not selected will replace the current
column selection. </em>
</li>
- <li><strong>Undefine Groups (Control U)<br> </strong><em>The
- alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
- This cannot be undone.</em>
- </li>
- <li><strong>Make Groups<br /> </strong> <em>The currently
+ <li><strong>Create Group (Control G)<br></strong>
+ <em>Create a group containing the currently selected sequences.</em></li>
+ <li><strong>Remove Group (Shift Control G)<br></strong>
+ <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
+ <li><strong>Make Groups for selection<br /> </strong> <em>The currently
selected groups of the alignment will be subdivided according to
the contents of the currently selected region. <br />Use this to
subdivide an alignment based on the different combinations of
residues observed at specific positions. (new in jalview 2.5)</em>
</li>
- </ul></li>
+ <li><strong>Undefine Groups (Control U)<br> </strong><em>The
+ alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
+ This cannot be undone.</em>
+ </li>
+ </ul></li>
<li><strong>View</strong>
<ul>
<li><strong>New View (Control T)</strong><em><br>
<li><strong>Invert Column Selection (Control Alt I)<br>
</strong><em>Any columns currently not selected will replace the current
column selection. </em></li>
- <li><strong>Undefine Groups (Control U)<br>
- </strong><em>The alignment will be reset with no defined groups.<br>
- <strong>WARNING</strong>: This cannot be undone.</em></li>
- <li><strong>Make Groups<br/></strong>
+ <li><strong>Create Group (Control G)<br></strong>
+ <em>Create a group containing the currently selected sequences.</em></li>
+ <li><strong>Remove Group (Shift Control G)<br></strong>
+ <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
+ <li><strong>Make Groups for selection<br/></strong>
<em>The currently selected groups of the alignment will be subdivided according to the contents of the currently selected region. <br/>Use this to subdivide an alignment based on the different combinations of residues observed at specific positions. (new in jalview 2.5)</em></li>
+<li><strong>Undefine Groups (Control U)<br>
+ </strong><em>The alignment will be reset with no defined groups.<br>
+ <strong>WARNING</strong>: This cannot be undone.</em></li>
+
</ul>
</body>
</html>
<li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>
<em>Opens the dialog box for creating sequence features over the currently
selected region on each selected sequence.</em></li>
- <li><strong>Group</strong><br>
- <em>Group Operations</em>
- <ul>
- <li><strong>Group</strong><em>This is the first entry in the
- menu, and will display the currently selected group's
- name. Selecting it displays a window allowing the name and
- description for this group to be edited. Click OK to set the
- new name and decription, and cancel to leave the existing
- name and description unchanged.</em></li>
+ <li><strong>Create Group<br>
+ </strong><em>This will define a new group from the current selection.</em><strong>
+ </strong></li>
<li><strong>Remove Group<br>
</strong><em>This will undefine the selected group. </em><strong>
</strong></li>
+ <li><strong>Edit (New) Group</strong><br>
+ <em>Group Editing Menu</em> <br />Options in this menu modify
+ the name and display properties of the currently selected group, or
+ a new group defined using the current selection.
+ <ul>
+ <li><strong>Name: <Group></strong> or <strong>Edit name and description</strong><br><em>The first entry in the
+ menu displays the name for the currently selected group, if it has one. Selecting this option opens a window allowing the name and
+ description for this group to be edited. Click OK to set the
+ new name and decription, and cancel to leave the existing
+ name and description unchanged.</em></li>
<li><strong>Group Colour<br>
</strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
of the group.</em><strong> </strong></li>
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+<meta charset="ISO-8859-1">
+<title>RNAalifold Web Service</title>
+</head>
+<body>
+ <strong>RNAalifold RNA Alignment Secondary Structure
+ Prediction Service</strong>
+ <p>
+ RNAalifold is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
+ RNA</a> Secondary Structure Prediction and Comparison Package. It was
+ described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
+ Gruber, and Peter F. Stadler, <em>RNAalifold: Improved consensus
+ structure prediction for RNA alignments</em>. (<a
+ href=http://www.biomedcentral.com/1471-2105/9/474>BMC
+ Bioinformatics, 9:474, 2008</a>).
+ </p>
+ <p>
+ <strong>Example RNAalifold Output</strong><br />
+ RNAalifold prints a consensus alignment and mfe structure to stdout with its
+ associated energy. Depending on the arguments given, other information such as
+ alternate structures are displayed below while base pairing probabilities (-p or --MEA
+ options) are stored in a separate 'alifold.out' file.<br />
+ <pre><br />
+G_UUUCAUU___AUGACGGCCUGUGCU_UAAA__CCUCC____GAG__C________GGGUCA_G_G_UCUGAU___CUUG_______GAGAC
+(.((((...........(((((((((........(((......)))............))))).).).))..................))))) (-19.16 = -11.80 + -7.36)
+(.((((...........(((((((((........(((......)))............))))).).).))..................))))) [-19.32]
+ frequency of mfe structure in ensemble 0.765639
+(.((((...........(((((((((........(((......)))............))))).).).))..................))))) -19.16 {-11.80 + -7.36}
+(.((((...........(((((((((........(((......)))............))))).).).))..................))))) { 13.20 MEA=92.14}
+
+Alifold.out
+ 6 89 9 99.2% 0.023 CG:29 GC:14 UA:9
+ 4 91 11 99.1% 0.028 CG:20 GC:11 UG:2 UA:17
+ 3 92 18 96.9% 0.090 CG:5 GC:2 GU:1 UG:4 AU:6 UA:25
+ 35 46 3 93.3% 0.195 CG:31 GC:16 UG:2 AU:5 UA:4
+ 36 45 10 93.6% 0.185 CG:16 GC:6 GU:1 UG:2 AU:8 UA:18
+ .
+ .
+ .
+ </pre>
+ </p>
+ <p>
+ <strong>Running RNAalifold from Jalview</strong><br />
+ To run RNAalifold go to <strong>Webservices→RNA Structure Prediction</strong>
+ and choose <strong>RNAalifold Defaults</strong> to run with no arguments or
+ <strong>edit settings and run ...</strong> to adjust the parameters before running.
+ Details of all the RNAalifold parameters can be found in the
+ <a href=http://www.tbi.univie.ac.at/RNA/man/RNAalifold.html>RNAalifold Manpage</a>.
+ JABAWS and Jalview support a selection of the RNAalifold arguments only.
+ </p>
+ <p><strong>Supported Arguments which give alternate structures</strong></p>
+ <p>
+ <em>Partition Function (-p)</em><br />
+ Calculate the Partition Function and base pairing probability matrix in addition to the mfe
+ structure. A coarse representation of the pair probabilities in the from of a psuedo
+ bracket notation, as well as the centroid structure derived from the pair probabilities
+ are displayed. The most likely base pairings are stored in a separate file by RNAalifold
+ and represented in Jalview by a bar graph annotation line labelled 'Contact Probabilities'.
+ </p>
+ <p>
+ <em>Maximum Expected Accuracy Structure (--MEA)</em><br />
+ Calculate an MEA structure where the expected Accuracy is computed from the base pair
+ probabilities. A more detailed description is found in the <a href=http://www.tbi.univie.ac.at/RNA/man/RNAfold.html>
+ RNAfold documentation</a>.
+ </p>
+ <p><strong>Example RNAalifold Structure Annotation rows</strong><p>
+
+ <div align="center">
+ <img src="RNAalifoldAnnotationRows.png" width="500" height="216"></div>
+
+</body>
+</html>
\ No newline at end of file
--- /dev/null
+action.cancel = Cancel\r
+action.create = Create\r
+action.update = Update\r
+action.delete = Delete\r
+action.snapshot = Snapshot\r
+action.clear = Clear\r
+action.accept = Accept\r
+action.select_ddbb = --- Select Database ---\r
+action.undo = Undo\r
+action.redo = Redo\r
+action.reset = Reset\r
+action.remove_left = Remove left\r
+action.remove_right = Remove right\r
+action.remove_empty_columns = Remove Empty Columns\r
+action.remove_all_gaps = Remove All Gaps\r
+action.boxes = Boxes\r
+action.text = Text\r
+action.by_pairwise_id = by Pairwise Identity\r
+action.by_id = by Id\r
+action.by_length = by Length\r
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+action.pairwise_alignment = Pairwise Alignments...\r
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+action.by_annotation = by Annotation...\r
+action.invert_sequence_selection = Invert Sequence Selection\r
+action.invert_column_selection = Invert Column Selection\r
+action.show = Show\r
+action.hide = Hide\r
+action.ok = OK\r
+action.set_defaults = Defaults\r
+action.create_group = Create Group\r
+action.remove_group = Remove Group\r
+action.edit_group = Edit Group\r
+action.edit_new_group = Edit New Group\r
+action.hide_sequences = Hide Sequences\r
+action.reveal_all = Reveal All\r
+action.reveal_sequences = Reveal Sequences\r
+action.find_all = Find all\r
+action.find_next = Find next\r
+action.file = File\r
+action.view = View\r
+action.change_params = Change Parameters\r
+action.apply = Apply\r
+action.apply_threshold_all_groups = Apply threshold to all groups\r
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+action.by_chain = By chain\r
+action.by_sequence = By Sequence\r
+action.paste_annotations = Paste Annotations\r
+action.format = Format\r
+action.select = Select\r
+action.new_view = New View\r
+action.close = Close\r
+action.add = Add\r
+action.save_as_default = Save as default\r
+action.cancel_fetch = Cancel Fetch\r
+action.save_omit_hidden_columns = Save / Omit Hidden Columns\r
+action.change_font = Change Font\r
+action.colour = Colour\r
+action.calculate = Calculate\r
+action.select_all = Select all\r
+action.deselect_all = Deselect all\r
+action.invert_selection = Invert selection\r
+action.using_jmol = Using Jmol\r
+action.link = Link\r
+action.show_chain = Show Chain\r
+label.str = Str:\r
+label.seq = Seq:\r
+label.structures_manager = Structures Manager\r
+label.nickname = Nickname:\r
+label.url = URL:\r
+label.input_file_url = Enter URL or Input File\r
+label.select_feature = Select feature:\r
+label.name = Name:\r
+label.name_param = Name: {0}\r
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+label.start = Start:\r
+label.end = End:\r
+label.current_parameter_set_name = Current parameter set name:\r
+label.service_action = Service Action:\r
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+label.url_suffix = URL Suffix\r
+label.sequence_source = Sequence Source\r
+label.per_seq = per Sequence\r
+label.result_vertically_separable = Results are vertically separable\r
+label.amend = Amend\r
+label.undo_command = Undo {0}\r
+label.redo_command = Redo {0}\r
+label.principal_component_analysis = Principal Component Analysis\r
+label.average_distance_identity = Average Distance Using % Identity\r
+label.neighbour_joining_identity = Neighbour Joining Using % Identity\r
+label.status_bar = Status bar\r
+label.out_to_textbox = Output to Textbox\r
+label.clustalx = Clustalx\r
+label.zappo = Zappo\r
+label.taylor = Taylor\r
+label.hydrophobicity = Hydrophobicity\r
+label.helix_propensity = Helix Propensity\r
+label.strand_propensity = Strand Propensity\r
+label.turn_propensity = Turn Propensity\r
+label.buried_index = Buried Index\r
+label.purine_pyrimidine = Purine/Pyrimidine\r
+label.percentage_identity = Percentage Identity\r
+label.blosum62_score = BLOSUM62 Score\r
+label.tcoffee_scores = T-Coffee Scores\r
+label.average_distance_bloslum62 = Average Distance Using BLOSUM62\r
+label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62\r
+label.show_annotations = Show annotations\r
+label.colour_text = Colour Text\r
+label.show_non_conversed = Show nonconserved\r
+label.overview_window = Overview Window\r
+label.none = None\r
+label.above_identity_threshold = Above Identity Threshold\r
+label.nucleotide = Nucleotide\r
+label.to_new_alignment = To New Alignment\r
+label.to_this_alignment = Add To This Alignment\r
+label.apply_colour_to_all_groups = Apply Colour To All Groups\r
+label.modify_identity_thereshold = Modify Identity Threshold...\r
+label.modify_conservation_thereshold = Modify Conservation Threshold...\r
+label.input_from_textbox = Input from textbox\r
+label.centre_column_labels = Centre column labels\r
+label.automatic_scrolling = Automatic Scrolling\r
+label.documentation = Documentation\r
+label.about = About...\r
+label.show_sequence_limits = Show Sequence Limits\r
+label.feature_settings = Feature Settings...\r
+label.sequence_features = Sequence Features\r
+label.all_columns = All Columns\r
+label.all_sequences = All Sequences\r
+label.selected_columns = Selected Columns \r
+label.selected_sequences = Selected Sequences\r
+label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H)\r
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+label.group_consensus = Group Consensus\r
+label.group_conservation = Group Conservation\r
+label.show_consensus_histogram = Show Consensus Histogram\r
+label.show_consensus_logo = Show Consensus Logo\r
+label.norm_consensus_logo = Normalise Consensus Logo\r
+label.apply_all_groups = Apply to all groups\r
+label.autocalculated_annotation = Autocalculated Annotation\r
+label.min_colour = Min Colour\r
+label.max_colour = Max Colour\r
+label.use_original_colours = Use Original Colours\r
+label.threshold_minmax = Threshold is min/max\r
+label.represent_group_with = Represent Group with\r
+label.selection = Selection\r
+label.group_colour = Group Colour\r
+label.sequence = Sequence\r
+label.view_pdb_structure = View PDB Structure\r
+label.min = Min:\r
+label.max = Max:\r
+label.colour_by_label = Colour by label\r
+label.new_feature = New Feature\r
+label.match_case = Match Case\r
+label.view_alignment_editor = View in alignment editor\r
+label.labels = Labels\r
+label.output_values = Output Values...\r
+label.input_data = Input Data...\r
+label.nucleotide_matrix = Nucleotide matrix\r
+label.protein_matrix = Protein matrix\r
+label.show_bootstrap_values = Show Bootstrap Values\r
+label.show_distances = Show distances\r
+label.mark_unassociated_leaves = Mark Unassociated Leaves\r
+label.fit_to_window = Fit To Window\r
+label.newick_format = Newick Format\r
+label.colours = Colours\r
+label.view_mapping = View Mapping\r
+label.wireframe = Wireframe\r
+label.depthcue = Depthcue\r
+label.z_buffering = Z Buffering\r
+label.charge_cysteine = Charge & Cysteine\r
+label.all_chains_visible = All Chains Visible\r
+label.successfully_added_features_alignment = Successfully added features to alignment\r
+label.keyboard_editing_mode = Keyboard editing mode is {0}\r
+label.paste_features_annotations_Tcoffee_here = Paste your features / annotations / T-coffee score file here.\r
+label.removed_columns = Removed {0} columns.\r
+label.removed_empty_columns = Removed {0} empty columns.\r
+label.paste_newick_tree_file = Paste your Newick tree file here.\r
+label.order_by_params = Order by {0}\r
+label.html_content = <html>{0}</html>\r
+label.paste_pdb_file= Paste your PDB file here.\r
+label.paste_pdb_file_for_sequence = Paste PDB file for sequence {0}\r
+label.could_not_parse_newick_file = Could not parse Newick file\!\n {0}\r
+label.successfully_pasted_tcoffee_scores_to_alignment= Successfully pasted T-Coffee scores to alignment.\r
+label.failed_add_tcoffee_scores = Failed to add T-Coffee scores: \r
+label.successfully_pasted_annotation_to_alignment= Successfully pasted annotation to alignment.\r
+label.successfully_pasted_alignment_file = Successfully pasted alignment file\r
+label.paste_your_alignment_file = Paste your alignment file here\r
+label.paste_your = Paste your\r
+label.finished_searching = Finished searching\r
+label.search_results= Search results {0} : {1}\r
+label.found_match_for = Found match for {0}\r
+label.font = Font:\r
+label.size = Size:\r
+label.style = Style:\r
+label.enter_redundancy_threshold = Enter the redundancy threshold\r
+label.calculating = Calculating....\r
+label.modify_conservation_visibility = Modify conservation visibility\r
+label.colour_residues_above_occurence = Colour residues above % occurence\r
+label.set_this_label_text = set this label text\r
+label.sequences_from = Sequences from {0}\r
+label.successfully_loaded_file = Successfully loaded file {0}\r
+label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format.\r
+label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.\r
+label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.\r
+label.problem_reading_tcoffee_score_file = Problem reading T-COFFEE score file\r
+label.source_to_target = {0} to '{1}'\r
+label.per_sequence_only= Per-sequence only\r
+label.to_file = to File\r
+label.to_textbox = to Textbox\r
+label.jalview = Jalview\r
+label.csv_spreadsheet = CSV (Spreadsheet)\r
+label.status = [Status]\r
+label.channels = Channels\r
+label.channel_title_item_count = {0} ({1})\r
+label.blog_item_published_on_date = {0} {1} \r
+label.select_das_service_from_table = Select a DAS service from the table to read a full description here.</font></html>\r
+label.session_update = Session Update\r
+label.new_vamsas_session = New Vamsas Session\r
+label.groovy_console = Groovy Console...\r
+label.lineart = Lineart\r
+label.dont_ask_me_again = Don't ask me again\r
+label.select_eps_character_rendering_style = Select EPS character rendering style\r
+label.invert_selection = Invert Selection\r
+label.optimise_order = Optimise Order\r
+label.seq_sort_by_score = Seq sort by Score\r
+label.load_colours = Load Colours\r
+label.save_colours = Save Colours\r
+label.fetch_das_features = Fetch DAS Features\r
+label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2} \r
+label.database_param = Database: {0}\r
+label.example_param = Example: {0}\r
+label.select_file_format_before_saving = You must select a file format before saving!\r
+label.file_format_not_specified = File format not specified\r
+label.alignment_contains_hidden_columns = The Alignment contains hidden columns.\nDo you want to save only the visible alignment?\r
+label.couldnt_save_file = Couldn't save file: {0}\r
+label.error_saving_file = Error Saving File\r
+label.remove_from_default_list = Remove from default list?\r
+label.remove_user_defined_colour = Remove user defined colour\r
+label.you_must_select_least_two_sequences = You must select at least 2 sequences.\r
+label.invalid_selection = Invalid Selection\r
+label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences.\r
+label.sequence_selection_insufficient = Sequence selection insufficient\r
+label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree!\r
+label.not_enough_sequences = Not enough sequences\r
+label.selected_region_to_tree_may_only_contain_residues_or_gaps = The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.\r
+label.sequences_selection_not_aligned = Sequences in selection are not aligned\r
+label.sequences_must_be_aligned_before_creating_tree = The sequences must be aligned before creating a tree.\nTry using the Pad function in the edit menu,\n or one of the multiple sequence alignment web services.\r
+label.sequences_not_aligned = Sequences not aligned\r
+label.problem_reading_tree_file = Problem reading tree file\r
+label.possible_problem_with_tree_file = Possible problem with tree file\r
+label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation.\r
+label.translation_failed = Translation Failed\r
+label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.\r
+label.implementation_error = Implementation error:\r
+label.automatically_associate_pdb_files_with_sequences_same_name = Do you want to automatically associate the {0} PDB files with sequences in the alignment that have the same name?\r
+label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name\r
+label.ignore_unmatched_dropped_files_info = <html>Do you want to <em>ignore</em> the {0} files whose names did not match any sequence IDs ?</html>\r
+label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?\r
+label.enter_view_name = Enter View Name\r
+label.enter_label = Enter label\r
+label.enter_label_for_the_structure = Enter a label for the structure?\r
+label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ?\r
+label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}\r
+label.add_pdbentry_to_view = Do you want to add {0} to the view called\n'{1}'\n\r
+label.align_to_existing_structure_view = Align to existing structure view\r
+label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease try downloading them manually.\r
+label.couldnt_load_file = Couldn't load file\r
+label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.\r
+label.no_pdb_id_in_file = No PDB Id in File\r
+label.couldnt_read_pasted_text = Couldn't read the pasted text {0}\r
+label.error_parsing_text = Error parsing text\r
+label.enter_local_das_source = Enter Nickname & URL of Local DAS Source\r
+label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources!\r
+label.public_das_source = Public DAS source - not editable\r
+label.input_alignment_from_url = Input Alignment From URL\r
+label.couldnt_import_as_vamsas_session = Couldn't import '{0}' as a new vamsas session.\r
+label.vamsas_document_import_failed = Vamsas Document Import Failed\r
+label.couldnt_locate = Couldn't locate {0}\r
+label.url_not_found = URL not found\r
+label.no_link_selected = No link selected\r
+label.new_sequence_url_link = New sequence URL link\r
+label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view\r
+label.wrapped_view_no_edit = Wrapped view - no edit\r
+label.error_retrieving_data = Error Retrieving Data\r
+label.user_colour_scheme_must_have_name = User colour scheme must have a name\r
+label.no_name_colour_scheme = No name for colour scheme\r
+label.invalid_url = Invalid URL !\r
+label.error_loading_file = Error loading file\r
+label.problems_opening_file = Encountered problems opening {0}!!\r
+label.file_open_error = File open error\r
+label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again.\r
+label.no_das_sources_selected_title = No DAS Sources Selected\r
+label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?"\r
+label.duplicate_scheme_name = Duplicate scheme name\r
+label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n\r
+label.jalview_user_survey = Jalview User Survey\r
+label.alignment_properties = Alignment Properties: {0}\r
+label.alignment_props = Alignment Properties\r
+label.input_cut_paste = Cut & Paste Input\r
+label.alignment_output_command = Alignment output - {0}\r
+label.annotations = Annotations\r
+label.features = Features\r
+label.overview_params = Overview {0}\r
+label.paste_newick_file = Paste Newick file\r
+label.load_tree_from_file = From File - \r
+label.colour_by_annotation = Colour by Annotation\r
+label.selection_output_command = Selection output - {0}\r
+label.annotation_for_displayid = <p><h2>Annotation for {0} </h2></p><p>\r
+label.pdb_sequence_mapping = PDB - Sequence Mapping\r
+label.pca_details = PCA details\r
+label.redundancy_threshold_selection = Redundancy threshold selection\r
+label.user_defined_colours = User defined colours\r
+label.jalviewLite_release = JalviewLite - Release {0}\r
+label.jaview_build_date = Build date: {0}\r
+label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,\r
+label.jalview_authors_2 = Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.\r
+label.jalview_dev_managers = Development managed by The Barton Group, University of Dundee, Scotland, UK.\r
+label.jalview_distribution_lists = For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\r
+label.jalview_please_cite = If you use Jalview, please cite:\r
+label.jalview_cite_1_authors = Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)\r
+label.jalview_cite_1_title = Jalview Version 2 - a multiple sequence alignment editor and analysis workbench\r
+label.jalview_cite_1_ref = Bioinformatics doi: 10.1093/bioinformatics/btp033\r
+label.right_click = Right click\r
+label.to_add_annotation = to add annotation\r
+label.alignment_has_no_annotations = Alignment has no annotations\r
+label.retrieving_pdb_data = Retrieving PDB data...\r
+label.label = Label\r
+label.no_features_added_to_this_alignment = No Features added to this alignment!!\r
+label.features_can_be_added_from_searches_1 = (Features can be added from searches or\r
+label.features_can_be_added_from_searches_2 = from Jalview / GFF features files)\r
+label.calculating_pca= Calculating PCA\r
+label.reveal_columns = Reveal Columns\r
+label.jalview_cannot_open_file = Jalview can't open file\r
+label.jalview_applet = Jalview applet\r
+label.loading_data = Loading data\r
+label.memory_stats = Total Free Memory: {0} MB; Max Memory: {1} MB; {2} %\r
+label.calculating_tree = Calculating tree\r
+label.state_queueing = queuing\r
+label.state_running = running\r
+label.state_complete = complete\r
+label.state_job_cancelled = job cancelled!!\r
+label.state_job_error = job error!\r
+label.server_error_try_later = Server Error! (try later)\r
+label.error_loading_pdb_data = Error loading PDB data!!\r
+label.fetching_pdb_data = Fetching PDB data...\r
+label.structure_type = Structure_type\r
+label.settings_for_type = Settings for {0}\r
+label.view_full_application = View in Full Application\r
+label.load_associated_tree = Load Associated Tree ...\r
+label.load_features_annotations = Load Features/Annotations ...\r
+label.export_features = Export Features ...\r
+label.export_annotations = Export Annotations ...\r
+label.jalview_copy = Copy (Jalview Only)\r
+label.jalview_cut = Cut (Jalview Only)\r
+label.to_upper_case = To Upper Case\r
+label.to_lower_case = To Lower Case\r
+label.toggle_case = Toggle Case\r
+label.edit_name_description = Edit Name/Description\r
+label.create_sequence_feature = Create Sequence Feature\r
+label.edit_sequence = Edit Sequence\r
+label.sequence_details = Sequence Details\r
+label.jmol_help = Jmol Help\r
+label.all = All\r
+label.sort_by_score = Sort by Score\r
+label.sort_by_density = Sort by Density\r
+label.reveal = Reveal\r
+label.hide_columns = Hide Columns\r
--- /dev/null
+action.cancel = Cancelar\r
+action.create = Crear\r
+action.update = Actualizar\r
+action.delete = Borrar\r
+action.snapshot = Captura\r
+action.clear = Limpiar\r
+action.accept = Aceptar\r
type="xs:string" />
<xs:attribute name="threshold"
type="xs:float" />
+ <xs:attribute name="perSequence"
+ type="xs:boolean"
+ use="optional" />
+ <xs:attribute name="predefinedColours"
+ type="xs:boolean"
+ use="optional" />
</xs:complexType>
</xs:element>
<xs:element name="hiddenColumns"
import jalview.appletgui.*;
import jalview.structure.*;
+import jalview.util.MessageManager;
public class AppletPDBCanvas extends Panel implements MouseListener,
MouseMotionListener, StructureListener
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading PDB data!!", 50, getSize().height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_pdb_data"), 50, getSize().height / 2);
return;
}
{
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Fetching PDB data...", 50, getSize().height / 2);
+ g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50, getSize().height / 2);
return;
}
import jalview.appletgui.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
public class AppletPDBViewer extends EmbmenuFrame implements
ActionListener, ItemListener
false, null);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
500, 600);
cap.setText(pdbcanvas.mappingDetails.toString());
private void jbInit() throws Exception
{
setMenuBar(jMenuBar1);
- fileMenu.setLabel("File");
- coloursMenu.setLabel("Colours");
- mapping.setLabel("View Mapping");
+ fileMenu.setLabel(MessageManager.getString("action.file"));
+ coloursMenu.setLabel(MessageManager.getString("label.colours"));
+ mapping.setLabel(MessageManager.getString("label.view_mapping"));
mapping.addActionListener(this);
- wire.setLabel("Wireframe");
+ wire.setLabel(MessageManager.getString("label.wireframe"));
wire.addItemListener(this);
depth.setState(true);
- depth.setLabel("Depthcue");
+ depth.setLabel(MessageManager.getString("label.depthcue"));
depth.addItemListener(this);
zbuffer.setState(true);
- zbuffer.setLabel("Z Buffering");
+ zbuffer.setLabel(MessageManager.getString("label.z_buffering"));
zbuffer.addItemListener(this);
- charge.setLabel("Charge & Cysteine");
+ charge.setLabel(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(this);
- hydro.setLabel("Hydrophobicity");
+ hydro.setLabel(MessageManager.getString("label.hydrophobicity"));
hydro.addActionListener(this);
- chain.setLabel("By Chain");
+ chain.setLabel(MessageManager.getString("action.by_chain"));
chain.addActionListener(this);
- seqButton.setLabel("By Sequence");
+ seqButton.setLabel(MessageManager.getString("action.by_sequence"));
seqButton.addActionListener(this);
- allchains.setLabel("All Chains Visible");
+ allchains.setLabel(MessageManager.getString("label.all_chains_visible"));
allchains.addItemListener(this);
- viewMenu.setLabel("View");
- zappo.setLabel("Zappo");
+ viewMenu.setLabel(MessageManager.getString("action.view"));
+ zappo.setLabel(MessageManager.getString("label.zappo"));
zappo.addActionListener(this);
- taylor.setLabel("Taylor");
+ taylor.setLabel(MessageManager.getString("label.taylor"));
taylor.addActionListener(this);
- helix.setLabel("Helix Propensity");
+ helix.setLabel(MessageManager.getString("label.helix_propensity"));
helix.addActionListener(this);
- strand.setLabel("Strand Propensity");
+ strand.setLabel(MessageManager.getString("label.strand_propensity"));
strand.addActionListener(this);
- turn.setLabel("Turn Propensity");
+ turn.setLabel(MessageManager.getString("label.turn_propensity"));
turn.addActionListener(this);
- buried.setLabel("Buried Index");
+ buried.setLabel(MessageManager.getString("label.buried_index"));
buried.addActionListener(this);
- user.setLabel("User Defined...");
+ user.setLabel(MessageManager.getString("action.user_defined"));
user.addActionListener(this);
jMenuBar1.add(fileMenu);
jMenuBar1.add(coloursMenu);
import jalview.gui.*;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
public class PDBViewer extends JInternalFrame implements Runnable
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
+ MessageManager.getString("label.remove_from_default_list"),
+ MessageManager.getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
import java.util.*;
+import jalview.util.Format;
import jalview.datamodel.*;
/**
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
- char c;
+ char c='-';
float percentage;
int[] values = new int[255];
maxResidue = "";
nongap = 0;
values = new int[255];
-
+
for (j = 0; j < jSize; j++)
{
if (sequences[j] == null)
values['-']++;
}
}
-
- for (v = 'A'; v < 'Z'; v++)
+ if (jSize==1)
+ {
+ maxResidue = String.valueOf(c);
+ maxCount=1;
+ } else {for (v = 'A'; v < 'Z'; v++)
{
if (values[v] < 2 || values[v] < maxCount)
{
}
maxCount = values[v];
}
-
+ }
if (maxResidue.length() == 0)
{
maxResidue = "-";
percentage = ((float) maxCount * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
- percentage = ((float) maxCount * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
+ if (nongap>0) {
+ percentage = ((float) maxCount * 100) / nongap;
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+ }
result[i] = residueHash;
}
}
* @param width
* @param ignoreGapsInConsensusCalculation
* @param includeAllConsSymbols
+ * @param nseq
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols)
+ boolean includeAllConsSymbols, long nseq)
{
completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); // new
// char[]
// { 'A', 'C', 'G', 'T', 'U' });
}
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols, char[] alphabet)
+ boolean includeAllConsSymbols, char[] alphabet, long nseq)
{
float tval, value;
if (consensus == null || consensus.annotations == null
// initialised properly
return;
}
+ String fmtstr="%3.1f";
+ int precision=0;
+ while (nseq>=10) {
+ precision++;
+ nseq/=10;
+ }
+ final Format fmt;
+ if (precision>1)
+ {
+ //if (precision>2)
+ {
+ fmtstr = "%"+(2+precision)+"."+(precision)+"f";
+ }
+ fmt = new Format(fmtstr);
+ } else {
+ fmt = null;
+ }
for (int i = iStart; i < width; i++)
{
Hashtable hci;
consensus.annotations[i] = null;
continue;
}
-
value = 0;
Float fv;
if (ignoreGapsInConsensusCalculation)
tval = profile[0][alphabet[c]] * 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
- + ((int) tval) + "%";
+ + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
}
}
else
* 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
- + " " + ((int) tval) + "%";
+ + " " + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
p++;
}
}
else
{
- mouseOver += ((int) value + "%");
+ mouseOver += ((fmt!=null) ? fmt.form(value) : ((int) value)) + "%";
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
import java.util.*;
+import jalview.util.Format;
import jalview.datamodel.*;
/**
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols)
+ boolean includeAllConsSymbols, long nseq)
{
float tval, value;
if (consensus == null || consensus.annotations == null
// initialised properly
return;
}
+ String fmtstr="%3.1f";
+ int precision=2;
+ while (nseq>100) {
+ precision++;
+ nseq/=10;
+ }
+ if (precision>2)
+ {
+ fmtstr = "%"+(2+precision)+"."+precision+"f";
+ }
+ Format fmt = new Format(fmtstr);
+
for (int i = iStart; i < width; i++)
{
Hashtable hci;
tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
- + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%";
+ + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval) + "%";
p++;
}
}
else
{
- mouseOver += ((int) value + "%");
+ mouseOver += (fmt.form(value) + "%");
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
--- /dev/null
+package jalview.api;
+
+/**
+ * prototype abstract controller for a Jalview alignment view
+ * @author jimp
+ *
+ * All operations should return true if the view has changed as a result of the operation
+ * @param <ViewportI>
+ *
+ */
+public interface AlignViewControllerI<ViewportI>
+{
+
+ public boolean makeGroupsFromSelection();
+
+ public boolean createGroup();
+
+ public boolean unGroup();
+
+ public boolean deleteGroups();
+
+ public void setViewportAndAlignmentPanel(AlignViewportI viewport, AlignmentViewPanel alignPanel);
+
+}
void updateGroupAnnotationSettings(boolean applyGlobalSettings,
boolean preserveNewGroupSettings);
+ void setSequenceColour(SequenceI seq, Color col);
+
+ Color getSequenceColour(SequenceI seq);
+
+ void updateSequenceIdColours();
SequenceGroup getSelectionGroup();
SequenceI[] getSequenceSelection();
+ void clearSequenceColours();
CigarArray getViewAsCigars(boolean selectedRegionOnly);
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
import jalview.util.UrlLink;
import jalview.io.AppletFormatAdapter;
import jalview.io.SequenceAnnotationReport;
MenuItem unGroupMenuItem = new MenuItem();
+ MenuItem createGroupMenuItem = new MenuItem();
+
MenuItem nucleotideMenuItem = new MenuItem();
Menu colourMenu = new Menu();
CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
- Menu editMenu = new Menu("Edit");
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
- MenuItem copy = new MenuItem("Copy (Jalview Only)");
+ MenuItem copy = new MenuItem(MessageManager.getString("label.jalview_copy"));
- MenuItem cut = new MenuItem("Cut (Jalview Only)");
+ MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
- MenuItem toUpper = new MenuItem("To Upper Case");
+ MenuItem toUpper = new MenuItem(MessageManager.getString("label.to_upper_case"));
- MenuItem toLower = new MenuItem("To Lower Case");
+ MenuItem toLower = new MenuItem(MessageManager.getString("label.to_lower_case"));
- MenuItem toggleCase = new MenuItem("Toggle Case");
+ MenuItem toggleCase = new MenuItem(MessageManager.getString("label.toggle_case"));
Menu outputmenu = new Menu();
MenuItem repGroup = new MenuItem();
- MenuItem sequenceName = new MenuItem("Edit Name/Description");
+ MenuItem sequenceName = new MenuItem(MessageManager.getString("label.edit_name_description"));
- MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
+ MenuItem sequenceFeature = new MenuItem(MessageManager.getString("label.create_sequence_feature"));
- MenuItem editSequence = new MenuItem("Edit Sequence");
+ MenuItem editSequence = new MenuItem(MessageManager.getString("label.edit_sequence"));
- MenuItem sequenceDetails = new MenuItem("Sequence Details ...");
+ MenuItem sequenceDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
- MenuItem selSeqDetails = new MenuItem("Sequence Details ...");
+ MenuItem selSeqDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
Sequence seq;
if (sg != null && sg.getSize() > 0)
{
- editGroupName.setLabel("Name: " + sg.getName());
+ editGroupName.setLabel(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
displayNonconserved.setState(sg.getShowNonconserved());
if (!ap.av.getAlignment().getGroups().contains(sg))
{
+ menu1.setLabel(MessageManager.getString("action.edit_new_group"));
groupMenu.remove(unGroupMenuItem);
+ } else {
+ menu1.setLabel(MessageManager.getString("action.edit_group"));
+ groupMenu.remove(createGroupMenuItem);
}
}
if (links != null && links.size() > 0)
{
- Menu linkMenu = new Menu("Link");
+ Menu linkMenu = new Menu(MessageManager.getString("action.link"));
String link;
for (int i = 0; i < links.size(); i++)
{
if (seq != null)
{
seqMenu.setLabel(seq.getName());
- repGroup.setLabel("Represent Group with " + seq.getName());
+ repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
}
else
{
unGroupMenuItem_actionPerformed();
}
+ else if (source == createGroupMenuItem)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+
else if (source == sequenceName)
{
editName();
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
- "Selection output - " + e.getActionCommand(), 600, 500);
+ MessageManager.formatMessage("label.selection_output_command", new String[]{e.getActionCommand()}),600, 500);
// JBPNote: getSelectionAsNewSequence behaviour has changed - this method
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
- contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
- + "</h2></p><p>");
+ contents.append(MessageManager.formatMessage("label.annotation_for_displayid",new String[]{seq.getDisplayId(true)}));
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
contents,
jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+ (sequences.length == 1 ? sequences[0].getDisplayId(true)
: "Selection"), 600, 500);
- cap.setText("<html>" + contents.toString() + "</html>");
+ cap.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
}
void editName()
else
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
- cap.setText("Paste your PDB file here.");
+ cap.setText(MessageManager.getString("label.paste_pdb_file"));
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
- "Paste PDB file for sequence " + seq.getName(), 400, 300);
+ MessageManager.formatMessage("label.paste_pdb_file_for_sequence", new String[]{seq.getName()}), 400, 300);
}
}
private void jbInit() throws Exception
{
- groupMenu.setLabel("Group");
- groupMenu.setLabel("Selection");
+ groupMenu.setLabel(MessageManager.getString("label.selection"));
sequenceFeature.addActionListener(this);
editGroupName.addActionListener(this);
- unGroupMenuItem.setLabel("Remove Group");
+ unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(this);
- nucleotideMenuItem.setLabel("Nucleotide");
+ createGroupMenuItem.setLabel(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.addActionListener(this);
+
+ nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(this);
conservationMenuItem.addItemListener(this);
abovePIDColour.addItemListener(this);
- colourMenu.setLabel("Group Colour");
- showBoxes.setLabel("Boxes");
+ colourMenu.setLabel(MessageManager.getString("label.group_colour"));
+ showBoxes.setLabel(MessageManager.getString("label.boxes"));
showBoxes.setState(true);
showBoxes.addItemListener(this);
sequenceName.addActionListener(this);
sequenceDetails.addActionListener(this);
selSeqDetails.addActionListener(this);
- displayNonconserved.setLabel("Show Nonconserved");
+ displayNonconserved.setLabel(MessageManager.getString("label.show_non_conversed"));
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
- showText.setLabel("Text");
+ showText.setLabel(MessageManager.getString("label.text"));
showText.addItemListener(this);
- showColourText.setLabel("Colour Text");
+ showColourText.setLabel(MessageManager.getString("label.colour_text"));
showColourText.addItemListener(this);
- outputmenu.setLabel("Output to Textbox...");
- seqMenu.setLabel("Sequence");
- pdb.setLabel("View PDB Structure");
- hideSeqs.setLabel("Hide Sequences");
- repGroup.setLabel("Represent Group with");
- revealAll.setLabel("Reveal All");
- revealSeq.setLabel("Reveal Sequences");
- menu1.setLabel("Group");
+ outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ seqMenu.setLabel(MessageManager.getString("label.sequence"));
+ pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
+ hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
+ repGroup.setLabel(MessageManager.getString("label.represent_group_with"));
+ revealAll.setLabel(MessageManager.getString("action.reveal_all"));
+ revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
+ menu1.setLabel(MessageManager.getString("label.group"));
add(groupMenu);
this.add(seqMenu);
this.add(hideSeqs);
this.add(revealSeq);
this.add(revealAll);
// groupMenu.add(selSeqDetails);
- groupMenu.add(editGroupName);
groupMenu.add(editMenu);
groupMenu.add(outputmenu);
groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
groupMenu.add(menu1);
colourMenu.add(noColourmenuItem);
seqMenu.add(pdb);
}
seqMenu.add(repGroup);
- menu1.add(unGroupMenuItem);
+ menu1.add(editGroupName);
menu1.add(colourMenu);
menu1.add(showBoxes);
menu1.add(showText);
ap.paintAlignment(true);
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly create group
+ refresh();
+ }
+
public void showColourText_itemStateChanged()
{
getGroup().setColourText(showColourText.getState());
import jalview.analysis.AlignmentSorter;
import jalview.analysis.Conservation;
+import jalview.api.AlignViewControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.ZappoColourScheme;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.Canvas;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener
{
+ public AlignViewControllerI avc;
public AlignmentPanel alignPanel;
public AlignViewport viewport;
viewport = new AlignViewport(al, applet);
alignPanel = new AlignmentPanel(this, viewport);
-
+ avc = new jalview.controller.AlignViewController(viewport, alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
viewport.featureSettings.refreshTable();
}
alignPanel.paintAlignment(true);
- statusBar.setText("Successfully added features to alignment.");
+ statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
}
return featuresFile;
}
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is "
- + (viewport.cursorMode ? "on" : "off"));
+ statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
}
break;
+ case KeyEvent.VK_G:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
+ {
+ this.unGroup_actionPerformed();
+ }
+ else
+ {
+ this.createGroup_actionPerformed();
+ }
+ }
+ break;
+
case KeyEvent.VK_U:
if (evt.isControlDown())
{
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
- + getTitle(), 400, 250);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
+ 400, 250);
}
else if (source == overviewMenuItem)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
}
protected void outputText_actionPerformed(ActionEvent e)
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
cap.setText(new AppletFormatAdapter().formatSequences(
e.getActionCommand(), viewport.getAlignment(),
viewport.showJVSuffix));
public void loadAnnotations()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your features / annotations / T-coffee score file here.");
+ cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
cap.setAnnotationImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
}
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
cap.setText(annotation);
}
}
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
cap.setText(features);
}
else
{
undoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setLabel("Undo " + command.getDescription());
+ undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
}
else
{
undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
}
if (viewport.redoList.size() > 0)
redoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setLabel("Redo " + command.getDescription());
+ redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
}
else
{
redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
}
}
protected void makeGrpsFromSelection_actionPerformed()
{
- if (viewport.getSelectionGroup() != null)
- {
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
- viewport.getAlignment().deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- // set view properties for each group
- for (int g = 0; g < gps.length; g++)
- {
- // gps[g].setShowunconserved(viewport.getShowUnconserved());
- gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI sq : gps[g].getSequences(null))
- viewport.setSequenceColour(sq, col);
- }
+ if (avc.makeGroupsFromSelection()) {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
}
+ protected void createGroup_actionPerformed()
+ {
+ avc.createGroup();
+ }
+ protected void unGroup_actionPerformed()
+ {
+ if (avc.unGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
protected void deleteGroups_actionPerformed()
{
- viewport.getAlignment().deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
-
- alignPanel.paintAlignment(true);
+ if (avc.deleteGroups())
+ {
+ alignPanel.alignmentChanged();
+ }
}
public void selectAllSequenceMenuItem_actionPerformed()
viewport.getSelectionGroup());
}
- statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
-
+ statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
addHistoryItem(trimRegion);
for (SequenceGroup sg : viewport.getAlignment().getGroups())
addHistoryItem(removeGapCols);
- statusBar.setText("Removed " + removeGapCols.getSize()
- + " empty columns.");
+ statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
// This is to maintain viewport position on first residue
// of first sequence
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
500);
}
}
void loadTree_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your Newick tree file here.");
+ cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
cap.setTreeImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
}
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
- TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
+ TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
.sortByTree(viewport.getAlignment(), treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
- addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
+ addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
// TODO: update this text for each release or centrally store it for
// lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString("JalviewLite - Release " + version, x, y += fh);
+ g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString("Build date: " + builddate, x, y += fh);
+ g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
g.drawString(
- "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
+ MessageManager.getString("label.jalview_authors_1"),
x, y += fh * 1.5);
- g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
+ g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
g.drawString(
- "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
+ MessageManager.getString("label.jalview_dev_managers"),
x, y += fh);
g.drawString(
- "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
+ MessageManager.getString("label.jalview_distribution_lists"),
x, y += fh);
- g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
+ g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
g.drawString(
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+ MessageManager.getString("label.jalview_cite_1_authors"),
x, y += fh);
g.drawString(
- "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
+ MessageManager.getString("label.jalview_cite_1_title"),
x, y += fh);
- g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
+ g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
x, y += fh);
}
}
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
.getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
}
MenuBar alignFrameMenuBar = new MenuBar();
- Menu fileMenu = new Menu("File");
+ Menu fileMenu = new Menu(MessageManager.getString("action.file"));
- MenuItem loadApplication = new MenuItem("View in Full Application");
+ MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+ MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
- MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
+ MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
- MenuItem outputFeatures = new MenuItem("Export Features ...");
+ MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+ MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
- MenuItem closeMenuItem = new MenuItem("Close");
+ MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
- Menu editMenu = new Menu("Edit");
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
- Menu viewMenu = new Menu("View");
+ Menu viewMenu = new Menu(MessageManager.getString("action.view"));
- Menu colourMenu = new Menu("Colour");
+ Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
- Menu calculateMenu = new Menu("Calculate");
+ Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
- MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+ MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
- MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
- MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
+ MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
MenuItem remove2LeftMenuItem = new MenuItem();
CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
- MenuItem alProperties = new MenuItem("Alignment Properties...");
+ MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
MenuItem overviewMenuItem = new MenuItem();
MenuItem grpsFromSelection = new MenuItem();
+ MenuItem createGroup = new MenuItem();
+
+ MenuItem unGroup = new MenuItem();
+
MenuItem delete = new MenuItem();
MenuItem copy = new MenuItem();
selectAllSequenceMenuItem.addActionListener(this);
deselectAllSequenceMenuItem.addActionListener(this);
invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel("Remove Left");
+ remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel("Remove Right");
+ remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
+ removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel("Remove All Gaps");
+ removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel("Boxes");
+ viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel("Text");
+ viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");
+ sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
+ sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel("by Length");
+ sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
sortLengthMenuItem.addActionListener(this);
- sortGroupMenuItem.setLabel("by Group");
+ sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");
+ removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
+ pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel("Principal Component Analysis");
+ PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(this);
averageDistanceTreeMenuItem
- .setLabel("Average Distance Using % Identity");
+ .setLabel(MessageManager.getString("label.average_distance_identity"));
averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
+ neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText("Status bar");
- outputTextboxMenu.setLabel("Output to Textbox");
- clustalColour.setLabel("Clustalx");
+ statusBar.setText(MessageManager.getString("label.status_bar"));
+ outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ clustalColour.setLabel(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
+ hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix Propensity");
+ helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel("Strand Propensity");
+ strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel("Turn Propensity");
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- purinePyrimidineColour.setLabel("Purine/Pyrimidine");
+ purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(this);
- RNAHelixColour.setLabel("by RNA Helices");
+ RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
RNAHelixColour.addActionListener(this);
- userDefinedColour.setLabel("User Defined...");
+ userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
+ PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62 Score");
+ BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(this);
- tcoffeeColour.setLabel("T-Coffee Scores");
+ tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
// provided
tcoffeeColour.addActionListener(this);
avDistanceTreeBlosumMenuItem
- .setLabel("Average Distance Using BLOSUM62");
+ .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
+ njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel("Show Annotations");
+ annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel("Colour Text");
+ colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel("Show nonconserved");
+ displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
displayNonconservedMenuItem.addItemListener(this);
alProperties.addActionListener(this);
- overviewMenuItem.setLabel("Overview Window");
+ overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(this);
undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
undoMenuItem.addActionListener(this);
redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
+ conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel("None");
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
- wrapMenuItem.setLabel("Wrap");
+ wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel("Show Gaps");
+ renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel("Find...");
+ findMenuItem.setLabel(MessageManager.getString("action.find"));
findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel("Above Identity Threshold");
+ abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel("Nucleotide");
+ nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
- deleteGroups.setLabel("Undefine Groups");
+ deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel("Make Groups for selection");
+ grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
- copy.setLabel("Copy");
+ createGroup.setLabel(MessageManager.getString("action.create_group"));
+ unGroup.setLabel(MessageManager.getString("action.remove_group"));
+ copy.setLabel(MessageManager.getString("action.copy"));
copy.addActionListener(this);
- cut.setLabel("Cut");
+ cut.setLabel(MessageManager.getString("action.cut"));
cut.addActionListener(this);
- delete.setLabel("Delete");
+ delete.setLabel(MessageManager.getString("action.delete"));
delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
+ pasteMenu.setLabel(MessageManager.getString("action.paste"));
+ pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
+ pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
+ applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
+ font.setLabel(MessageManager.getString("action.font"));
font.addActionListener(this);
- scaleAbove.setLabel("Scale Above");
+ scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
scaleAbove.setState(true);
scaleAbove.setEnabled(false);
scaleAbove.addItemListener(this);
scaleLeft.setEnabled(false);
scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
+ scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
scaleLeft.addItemListener(this);
scaleRight.setEnabled(false);
scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
+ scaleRight.setLabel(MessageManager.getString("action.scale_right"));
scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
+ modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
+ modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel("By Tree Order");
- sort.setLabel("Sort");
- calculate.setLabel("Calculate Tree");
+ sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
+ sort.setLabel(MessageManager.getString("action.sort"));
+ calculate.setLabel(MessageManager.getString("action.calculate_tree"));
autoCalculate.addItemListener(this);
sortByTree.addItemListener(this);
- inputText.setLabel("Input from textbox");
+ inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel("Centre column labels");
+ centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel("Automatic Scrolling");
+ followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
followMouseOverFlag.addItemListener(this);
- helpMenu.setLabel("Help");
- documentation.setLabel("Documentation");
+ helpMenu.setLabel(MessageManager.getString("action.help"));
+ documentation.setLabel(MessageManager.getString("label.documentation"));
documentation.addActionListener(this);
- about.setLabel("About...");
+ about.setLabel(MessageManager.getString("label.about"));
about.addActionListener(this);
seqLimits.setState(true);
- seqLimits.setLabel("Show Sequence Limits");
+ seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
seqLimits.addItemListener(this);
- featureSettings.setLabel("Feature Settings...");
+ featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
featureSettings.addActionListener(this);
- sequenceFeatures.setLabel("Sequence Features");
+ sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
sequenceFeatures.addItemListener(this);
sequenceFeatures.setState(false);
- annotationColour.setLabel("by Annotation...");
+ annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
annotationColour.addActionListener(this);
- invertSequenceMenuItem.setLabel("Invert Sequence Selection");
- invertColSel.setLabel("Invert Column Selection");
- menu1.setLabel("Show");
- showColumns.setLabel("All Columns ");
- showSeqs.setLabel("All Sequences");
- menu2.setLabel("Hide");
- hideColumns.setLabel("Selected Columns");
- hideSequences.setLabel("Selected Sequences");
- hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
- hideAllSelection.setLabel("Selected Region");
- showAllHidden.setLabel("All Sequences and Columns");
- showGroupConsensus.setLabel("Group Consensus");
- showGroupConservation.setLabel("Group Conservation");
- showConsensusHistogram.setLabel("Show Consensus Histogram");
- showSequenceLogo.setLabel("Show Consensus Logo");
- normSequenceLogo.setLabel("Normalise Consensus Logo");
- applyAutoAnnotationSettings.setLabel("Apply to all groups");
+ invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
+ invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
+ menu1.setLabel(MessageManager.getString("action.show"));
+ showColumns.setLabel(MessageManager.getString("label.all_columns"));
+ showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
+ menu2.setLabel(MessageManager.getString("aciton.hide"));
+ hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
+ hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
+ hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
+ hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
+ showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
+ showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
+ showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
+ showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
+ showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
+ normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
+ applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel("Autocalculated Annotation");
+ autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
normSequenceLogo.addItemListener(this);
applyAutoAnnotationSettings.addItemListener(this);
- formatMenu.setLabel("Format");
- selectMenu.setLabel("Select");
- newView.setLabel("New View");
+ formatMenu.setLabel(MessageManager.getString("action.format"));
+ selectMenu.setLabel(MessageManager.getString("action.select"));
+ newView.setLabel(MessageManager.getString("action.new_view"));
newView.addActionListener(this);
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
public jalview.bin.JalviewLite applet;
- Hashtable sequenceColours;
-
boolean MAC = false;
Stack historyList = new Stack();
showHiddenMarkers = show;
}
- public Color getSequenceColour(SequenceI seq)
- {
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
- }
-
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
- }
-
boolean centreColumnLabels;
public boolean getCentreColumnLabels()
return centreColumnLabels;
}
- public void updateSequenceIdColours()
- {
-
- for (SequenceGroup sg : alignment.getGroups())
- {
- if (sg.idColour != null)
- {
- for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
- {
- this.setSequenceColour(s, sg.idColour);
- }
- }
- }
- }
-
public boolean followHighlight = true;
public boolean getFollowHighlight()
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
setDefaultMinMax();
+ adjusting = true;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.predefinedColours);
- if (!acg.predefinedColours)
+ currentColours.setState(acg.isPredefinedColours() || acg.getBaseColour()!=null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
+ // seqAssociated.setState(acg.isSeqAssociated());
}
- adjusting = true;
Vector list = new Vector();
int index = 1;
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 560,
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.colour_by_annotation"), 560,
175);
validate();
}
private void jbInit() throws Exception
{
minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- minColour.setLabel("Min Colour");
+ minColour.setLabel(MessageManager.getString("label.min_colour"));
minColour.addActionListener(this);
maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- maxColour.setLabel("Max Colour");
+ maxColour.setLabel(MessageManager.getString("label.max_colour"));
maxColour.addActionListener(this);
thresholdIsMin.addItemListener(this);
- ok.setLabel("OK");
+ ok.setLabel(MessageManager.getString("action.ok"));
ok.addActionListener(this);
- cancel.setLabel("Cancel");
+ cancel.setLabel(MessageManager.getString("action.cancel"));
cancel.addActionListener(this);
- defColours.setLabel("Defaults");
+ defColours.setLabel(MessageManager.getString("action.set_defaults"));
defColours.addActionListener(this);
annotations.addItemListener(this);
thresholdValue.setEnabled(false);
thresholdValue.setColumns(5);
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setLabel("Use Original Colours");
+ currentColours.setLabel(MessageManager.getString("label.use_original_colours"));
currentColours.addItemListener(this);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel("Threshold is min/max");
+ thresholdIsMin.setLabel(MessageManager.getString("label.threshold_minmax"));
this.setLayout(borderLayout1);
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.getState();
av.setGlobalColourScheme(acg);
+ // TODO: per group colour propagation not always desired
if (av.getAlignment().getGroups() != null)
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
}
// update colours in linked windows
+ ap.alignmentChanged();
ap.paintAlignment(true);
}
import java.awt.event.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
import jalview.util.ParseHtmlBodyAndLinks;
public class AnnotationLabels extends Panel implements ActionListener,
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- PopupMenu popup = new PopupMenu("Annotations");
+ PopupMenu popup = new PopupMenu(MessageManager.getString("label.annotations"));
MenuItem item = new MenuItem(ADDNEW);
item.addActionListener(this);
if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
{
g.setColor(Color.black);
- g.drawString("Right click", 2, 8);
- g.drawString("to add annotation", 2, 18);
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18);
}
}
}
import jalview.datamodel.*;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.util.MessageManager;
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
AdjustmentListener, ActionListener, MouseListener,
return;
}
- PopupMenu pop = new PopupMenu("Structure type");
+ PopupMenu pop = new PopupMenu(MessageManager.getString("label.structure_type"));
MenuItem item;
/*
* Just display the needed structure options
g.setColor(Color.black);
if (av.validCharWidth)
{
- g.drawString("Alignment has no annotations", 20, 15);
+ g.drawString(MessageManager.getString("label.alignment_has_no_annotations"), 20, 15);
}
return;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
public class AppletJmol extends EmbmenuFrame implements
// StructureListener,
KeyListener, ActionListener, ItemListener, SequenceStructureBinding
{
- Menu fileMenu = new Menu("File");
+ Menu fileMenu = new Menu(MessageManager.getString("action.file"));
- Menu viewMenu = new Menu("View");
+ Menu viewMenu = new Menu(MessageManager.getString("action.view"));
- Menu coloursMenu = new Menu("Colours");
+ Menu coloursMenu = new Menu(MessageManager.getString("action.colour"));
- Menu chainMenu = new Menu("Show Chain");
+ Menu chainMenu = new Menu(MessageManager.getString("action.show_chain"));
- Menu helpMenu = new Menu("Help");
+ Menu helpMenu = new Menu(MessageManager.getString("action.help"));
- MenuItem mappingMenuItem = new MenuItem("View Mapping");
+ MenuItem mappingMenuItem = new MenuItem(MessageManager.getString("label.view_mapping"));
- CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
+ CheckboxMenuItem seqColour = new CheckboxMenuItem(MessageManager.getString("action.by_sequence"), true);
- CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false);
+ CheckboxMenuItem jmolColour = new CheckboxMenuItem(MessageManager.getString("action.using_jmol"), false);
- MenuItem chain = new MenuItem("By Chain");
+ MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
- MenuItem charge = new MenuItem("Charge & Cysteine");
+ MenuItem charge = new MenuItem(MessageManager.getString("label.charge_cysteine"));
- MenuItem zappo = new MenuItem("Zappo");
+ MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
- MenuItem taylor = new MenuItem("Taylor");
+ MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
- MenuItem hydro = new MenuItem("Hydrophobicity");
+ MenuItem hydro = new MenuItem(MessageManager.getString("label.hydrophobicity"));
- MenuItem helix = new MenuItem("Helix Propensity");
+ MenuItem helix = new MenuItem(MessageManager.getString("label.helix_propensity"));
- MenuItem strand = new MenuItem("Strand Propensity");
+ MenuItem strand = new MenuItem(MessageManager.getString("label.strand_propensity"));
- MenuItem turn = new MenuItem("Turn Propensity");
+ MenuItem turn = new MenuItem(MessageManager.getString("label.turn_propensity"));
- MenuItem buried = new MenuItem("Buried Index");
+ MenuItem buried = new MenuItem(MessageManager.getString("label.buried_index"));
- MenuItem purinepyrimidine = new MenuItem("Purine/Pyrimidine");
+ MenuItem purinepyrimidine = new MenuItem(MessageManager.getString("label.purine_pyrimidine"));
- MenuItem user = new MenuItem("User Defined Colours");
+ MenuItem user = new MenuItem(MessageManager.getString("label.user_defined_colours"));
- MenuItem jmolHelp = new MenuItem("Jmol Help");
+ MenuItem jmolHelp = new MenuItem(MessageManager.getString("label.jmol_help"));
Panel scriptWindow;
{
chainMenu.removeAll();
- MenuItem menuItem = new MenuItem("All");
+ MenuItem menuItem = new MenuItem(MessageManager.getString("label.all"));
menuItem.addActionListener(this);
chainMenu.add(menuItem);
.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
return;
}
- jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
550, 600);
}
else if (evt.getSource() == charge)
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
}
else
{
import jalview.datamodel.*;
import jalview.io.*;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.MessageManager;
public class CutAndPasteTransfer extends Panel implements ActionListener,
MouseListener
public void setPDBImport(Sequence seq)
{
this.seq = seq;
- accept.setLabel("Accept");
+ accept.setLabel(MessageManager.getString("action.accept"));
addSequences.setVisible(false);
pdbImport = true;
}
public void setTreeImport()
{
treeImport = true;
- accept.setLabel("Accept");
+ accept.setLabel(MessageManager.getString("action.accept"));
addSequences.setVisible(false);
}
public void setAnnotationImport()
{
annotationImport = true;
- accept.setLabel("Accept");
+ accept.setLabel(MessageManager.getString("action.accept"));
addSequences.setVisible(false);
}
{
// TODO: JAL-1102 - should have a warning message in dialog, not simply
// overwrite the broken input data with the exception
- textarea.setText("Could not parse Newick file!\n" + ex);
+ textarea.setText(MessageManager.formatMessage("label.could_not_parse_newick_file", new String[]{ex.getMessage()}));
return;
}
}
alignFrame.changeColour(new TCoffeeColourScheme(
alignFrame.viewport.getAlignment()));
alignFrame.statusBar
- .setText("Successfully pasted T-Coffee scores to alignment.");
+ .setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
// file valid but didn't get added to alignment for some reason
- alignFrame.statusBar.setText("Failed to add T-Coffee scores: "
- + (tcf.getWarningMessage() != null ? tcf
- .getWarningMessage() : ""));
+ alignFrame.statusBar.setText(MessageManager.formatMessage("label.failed_add_tcoffee_scores", new String[]{(tcf.getWarningMessage() != null ? tcf.getWarningMessage() : "")}));
}
}
else
{
AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
"Cut & Paste input - " + format, false);
- af.statusBar.setText("Successfully pasted alignment file");
+ af.statusBar.setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
}
else
{
alignFrame.addSequences(al.getSequencesArray());
alignFrame.statusBar
- .setText("Successfully pasted alignment file");
+ .setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
}
}
}
private void jbInit() throws Exception
{
textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
- textarea.setText("Paste your alignment file here");
+ textarea.setText(MessageManager.getString("label.paste_your_alignment_file"));
textarea.addMouseListener(this);
this.setLayout(borderLayout1);
accept.addActionListener(this);
public void mousePressed(MouseEvent evt)
{
- if (textarea.getText().startsWith("Paste your"))
+ if (textarea.getText().startsWith(MessageManager.getString("label.paste_your")))
{
textarea.setText("");
}
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
public class FeatureColourChooser extends Panel implements ActionListener,
AdjustmentListener, ItemListener, MouseListener
private void jbInit() throws Exception
{
- Label minLabel = new Label("Min:"), maxLabel = new Label("Max:");
+ Label minLabel = new Label(MessageManager.getString("label.min")), maxLabel = new Label(MessageManager.getString("label.max"));
minLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
maxLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
// minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
jPanel3.setBackground(Color.white);
colourFromLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- colourFromLabel.setLabel("Colour by Label");
+ colourFromLabel.setLabel(MessageManager.getString("label.colour_by_label"));
colourFromLabel.setSize(new Dimension(139, 22));
// threshold.setBounds(new Rectangle(11, 3, 139, 22));
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel("Threshold is min/max");
+ thresholdIsMin.setLabel(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin.setSize(new Dimension(135, 23));
// thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
jPanel1.add(minLabel);
import jalview.datamodel.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
g.setColor(Color.black);
Font f = new Font("Verdana", Font.PLAIN, 10);
g.setFont(f);
- g.drawString("Label", 0, 0);
+ g.drawString(MessageManager.getString("label.label"), 0, 0);
}
else
{
}
else
{
- dialog.ok.setLabel("Amend");
+ dialog.ok.setLabel(MessageManager.getString("label.amend"));
dialog.buttonPanel.add(deleteButton, 1);
deleteButton.addActionListener(new ActionListener()
{
import jalview.datamodel.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
height = Math.max(200, height);
height = Math.min(400, height);
int width = 300;
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", width,
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.feature_settings"), width,
height);
}
public void paint(Graphics g)
{
g.setColor(Color.black);
- g.drawString("No Features added to this alignment!!", 10, 20);
- g.drawString("(Features can be added from searches or", 10, 40);
- g.drawString("from Jalview / GFF features files)", 10, 60);
+ g.drawString(MessageManager.getString("label.no_features_added_to_this_alignment"), 10, 20);
+ g.drawString(MessageManager.getString("label.features_can_be_added_from_searches_1"), 10, 40);
+ g.drawString(MessageManager.getString("label.features_can_be_added_from_searches_2"), 10, 60);
}
protected void popupSort(final MyCheckbox check, final Hashtable minmax,
{
final String type = check.type;
final Object typeCol = fr.getFeatureStyle(type);
- java.awt.PopupMenu men = new PopupMenu("Settings for " + type);
- java.awt.MenuItem scr = new MenuItem("Sort by Score");
+ java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage("label.settings_for_type", new String[]{type}));
+ java.awt.MenuItem scr = new MenuItem(MessageManager.getString("label.sort_by_score"));
men.add(scr);
final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
}
});
- MenuItem dens = new MenuItem("Sort by Density");
+ MenuItem dens = new MenuItem(MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
import java.awt.event.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
public class Finder extends Panel implements ActionListener
{
this.ap = ap;
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.find"), 340, 120);
frame.repaint();
frame.addWindowListener(new WindowAdapter()
{
// 'SelectRegion' selection
if (!haveResults)
{
- ap.alignFrame.statusBar.setText("Finished searching.");
+ ap.alignFrame.statusBar.setText(MessageManager.getString("label.finished_searching"));
resIndex = -1;
seqIndex = 0;
}
{
message += searchResults.getSize() + " subsequence matches.";
}
- ap.alignFrame.statusBar.setText("Search results: " + searchString
- + " : " + message);
+ ap.alignFrame.statusBar.setText(MessageManager.formatMessage("label.search_results", new String[] {searchString, message}));
}
else
{
// TODO: indicate sequence and matching position in status bar
- ap.alignFrame.statusBar.setText("Found match for " + searchString);
+ ap.alignFrame.statusBar.setText(MessageManager.formatMessage("label.found_match_for", new String[]{searchString}));
}
}
}
private void jbInit() throws Exception
{
jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel1.setText("Find");
+ jLabel1.setText(MessageManager.getString("action.find"));
jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
this.setLayout(null);
textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
});
textfield.addActionListener(this);
findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- findAll.setLabel("Find all");
+ findAll.setLabel(MessageManager.getString("action.find_all"));
findAll.addActionListener(this);
findNext.setEnabled(false);
findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- findNext.setLabel("Find Next");
+ findNext.setLabel(MessageManager.getString("action.find_next"));
findNext.addActionListener(this);
jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
jPanel1.setLayout(gridLayout1);
gridLayout1.setVgap(2);
createNewGroup.setEnabled(false);
createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- createNewGroup.setLabel("New Feature");
+ createNewGroup.setLabel(MessageManager.getString("label.new_feature"));
createNewGroup.addActionListener(this);
- caseSensitive.setLabel("Match Case");
+ caseSensitive.setLabel(MessageManager.getString("label.match_case"));
caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
jPanel1.add(findNext, null);
jPanel1.add(findAll, null);
*/
package jalview.appletgui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import java.awt.event.*;
Frame frame = new Frame();
this.frame = frame;
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 115);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.change_font"), 440, 115);
init = false;
}
{
label1.setFont(new java.awt.Font("Verdana", 0, 11));
label1.setAlignment(Label.RIGHT);
- label1.setText("Font: ");
+ label1.setText(MessageManager.getString("label.font"));
this.setLayout(borderLayout4);
fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
fontSize.addItemListener(this);
fontStyle.addItemListener(this);
label2.setAlignment(Label.RIGHT);
label2.setFont(new java.awt.Font("Verdana", 0, 11));
- label2.setText("Size: ");
+ label2.setText(MessageManager.getString("label.size"));
label3.setAlignment(Label.RIGHT);
label3.setFont(new java.awt.Font("Verdana", 0, 11));
- label3.setText("Style: ");
+ label3.setText(MessageManager.getString("label.style"));
fontName.setFont(new java.awt.Font("Verdana", 0, 11));
fontName.addItemListener(this);
ok.setFont(new java.awt.Font("Verdana", 0, 11));
- ok.setLabel("OK");
+ ok.setLabel(MessageManager.getString("action.ok"));
ok.addActionListener(this);
cancel.setFont(new java.awt.Font("Verdana", 0, 11));
- cancel.setLabel("Cancel");
+ cancel.setLabel(MessageManager.getString("action.cancel"));
cancel.addActionListener(this);
this.setBackground(Color.white);
panel1.setLayout(borderLayout1);
import java.awt.event.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
import jalview.viewmodel.PCAModel;
public class PCAPanel extends EmbmenuFrame implements Runnable,
embedMenuIfNeeded(rc);
add(rc, BorderLayout.CENTER);
- jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
+ jalview.bin.JalviewLite.addFrame(this, MessageManager.getString("label.principal_component_analysis"),
475, 400);
Thread worker = new Thread(this);
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pca_details"), 500, 500);
cap.setText(pcaModel.getDetails());
}
xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
xCombobox.addItemListener(this);
resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
- resetButton.setLabel("Reset");
+ resetButton.setLabel(MessageManager.getString("action.reset"));
resetButton.addActionListener(this);
this.setMenuBar(menuBar1);
- menu1.setLabel("File");
- menu2.setLabel("View");
- calcSettings.setLabel("Change Parameters");
- labels.setLabel("Labels");
+ menu1.setLabel(MessageManager.getString("action.file"));
+ menu2.setLabel(MessageManager.getString("action.view"));
+ calcSettings.setLabel(MessageManager.getString("action.change_params"));
+ labels.setLabel(MessageManager.getString("label.labels"));
labels.addItemListener(this);
- values.setLabel("Output Values...");
+ values.setLabel(MessageManager.getString("label.output_values"));
values.addActionListener(this);
- inputData.setLabel("Input Data...");
- nuclSetting.setLabel("Nucleotide matrix");
+ inputData.setLabel(MessageManager.getString("label.input_data"));
+ nuclSetting.setLabel(MessageManager.getString("label.nucleotide_matrix"));
nuclSetting.addItemListener(this);
- protSetting.setLabel("Protein matrix");
+ protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
protSetting.addItemListener(this);
this.add(jPanel2, BorderLayout.SOUTH);
jPanel2.add(jLabel1, null);
import jalview.analysis.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
public class PairwiseAlignPanel extends Panel implements ActionListener
{
textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
textarea.setText("");
viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
- viewInEditorButton.setLabel("View in alignment editor");
+ viewInEditorButton.setLabel(MessageManager.getString("label.view_alignment_editor"));
viewInEditorButton.addActionListener(this);
this.add(scrollPane, BorderLayout.CENTER);
scrollPane.add(textarea);
import jalview.analysis.AlignSeq;
import jalview.commands.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
public class RedundancyPanel extends SliderPanel implements Runnable,
WindowListener
applyButton.setVisible(true);
allGroupsCheck.setVisible(false);
- label.setText("Enter the redundancy threshold");
+ label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
valueField.setText("100");
slider.setVisibleAmount(1);
frame = new Frame();
frame.add(this);
jalview.bin.JalviewLite.addFrame(frame,
- "Redundancy threshold selection", 400, 100);
+ MessageManager.getString("label.redundancy_threshold_selection"), 400, 100);
frame.addWindowListener(this);
*/
public void run()
{
- label.setText("Calculating....");
+ label.setText(MessageManager.getString("label.calculating"));
slider.setVisible(false);
applyButton.setEnabled(false);
redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
omitHidden, start, end, false);
- label.setText("Enter the redundancy threshold");
+ label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
if (points == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString("Calculating PCA....", 20, getSize().height / 2);
+ g.drawString(MessageManager.getString("label.calculating_pca") + "....", 20, getSize().height / 2);
}
else
{
import java.awt.event.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
public class ScalePanel extends Panel implements MouseMotionListener,
MouseListener
PopupMenu pop = new PopupMenu();
if (reveal != null)
{
- MenuItem item = new MenuItem("Reveal");
+ MenuItem item = new MenuItem(MessageManager.getString("label.reveal"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (av.getColumnSelection().getHiddenColumns().size() > 1)
{
- item = new MenuItem("Reveal All");
+ item = new MenuItem(MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
else if (av.getColumnSelection().contains(res))
{
- MenuItem item = new MenuItem("Hide Columns");
+ MenuItem item = new MenuItem(MessageManager.getString("label.hide_columns"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (reveal != null && reveal[0] > startx && reveal[0] < endx)
{
- gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);
+ gg.drawString(MessageManager.getString("label.reveal_columns"), reveal[0] * av.charWidth, 0);
}
}
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
public class SliderPanel extends Panel implements ActionListener,
AdjustmentListener, MouseListener
applyButton.setVisible(false);
if (forConservation)
{
- label.setText("Modify conservation visibility");
+ label.setText(MessageManager.getString("label.modify_conservation_visibility"));
slider.setMinimum(0);
slider.setMaximum(50 + slider.getVisibleAmount());
slider.setUnitIncrement(1);
}
else
{
- label.setText("Colour residues above % occurence");
+ label.setText(MessageManager.getString("label.colour_residues_above_occurence"));
slider.setMinimum(0);
slider.setMaximum(100 + slider.getVisibleAmount());
slider.setBlockIncrement(1);
valueField.setText(" ");
valueField.addActionListener(this);
label.setFont(new java.awt.Font("Verdana", 0, 11));
- label.setText("set this label text");
+ label.setText(MessageManager.getString("label.set_this_label_text"));
jPanel1.setLayout(borderLayout1);
jPanel2.setLayout(flowLayout1);
applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
- applyButton.setLabel("Apply");
+ applyButton.setLabel(MessageManager.getString("action.apply"));
applyButton.addActionListener(this);
undoButton.setEnabled(false);
undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
- undoButton.setLabel("Undo");
+ undoButton.setLabel(MessageManager.getString("action.undo"));
undoButton.addActionListener(this);
allGroupsCheck.setEnabled(false);
allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
- allGroupsCheck.setLabel("Apply threshold to all groups");
- allGroupsCheck.setName("Apply to all Groups");
+ allGroupsCheck.setLabel(MessageManager.getString("action.apply_threshold_all_groups"));
+ allGroupsCheck.setName(MessageManager.getString("action.apply_all_groups"));
this.setBackground(Color.white);
this.setForeground(Color.black);
jPanel2.add(label, null);
av.setSelectionGroup(null);
av.getAlignment().deleteAllGroups();
- av.sequenceColours = null;
+ av.clearSequenceColours();
colourGroups();
import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.io.*;
+import jalview.util.MessageManager;
public class TreePanel extends EmbmenuFrame implements ActionListener,
ItemListener
setLayout(borderLayout1);
this.setBackground(Color.white);
this.setFont(new java.awt.Font("Verdana", 0, 12));
- jMenu2.setLabel("View");
- fontSize.setLabel("Font...");
+ jMenu2.setLabel(MessageManager.getString("action.view"));
+ fontSize.setLabel(MessageManager.getString("action.font"));
fontSize.addActionListener(this);
- bootstrapMenu.setLabel("Show Bootstrap Values");
+ bootstrapMenu.setLabel(MessageManager.getString("label.show_bootstrap_values"));
bootstrapMenu.addItemListener(this);
- distanceMenu.setLabel("Show Distances");
+ distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
distanceMenu.addItemListener(this);
- placeholdersMenu.setLabel("Mark Unassociated Leaves");
+ placeholdersMenu.setLabel(MessageManager.getString("label.mark_unassociated_leaves"));
placeholdersMenu.addItemListener(this);
fitToWindow.setState(true);
- fitToWindow.setLabel("Fit To Window");
+ fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
fitToWindow.addItemListener(this);
- fileMenu.setLabel("File");
- newickOutput.setLabel("Newick Format");
+ fileMenu.setLabel(MessageManager.getString("action.file"));
+ newickOutput.setLabel(MessageManager.getString("label.newick_format"));
newickOutput.addActionListener(this);
- inputData.setLabel("Input Data...");
+ inputData.setLabel(MessageManager.getString("label.input_data"));
add(scrollPane, BorderLayout.CENTER);
jMenuBar1.add(fileMenu);
import jalview.schemes.GraduatedColor;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
import java.awt.Button;
import java.awt.Color;
}
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420,
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.user_defined_colours"), 420,
345);
if (seqGroup != null)
gridLayout.setColumns(6);
gridLayout.setRows(4);
okButton.setFont(new java.awt.Font("Verdana", 0, 11));
- okButton.setLabel("OK");
+ okButton.setLabel(MessageManager.getString("action.ok"));
okButton.addActionListener(this);
applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
- applyButton.setLabel("Apply");
+ applyButton.setLabel(MessageManager.getString("action.apply"));
applyButton.addActionListener(this);
cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
- cancelButton.setLabel("Cancel");
+ cancelButton.setLabel(MessageManager.getString("action.cancel"));
cancelButton.addActionListener(this);
this.setBackground(new Color(212, 208, 223));
okcancelPanel.setBounds(new Rectangle(0, 265, 400, 35));
*/
package jalview.bin;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
import java.awt.Color;
import java.io.*;
import java.text.DateFormat;
-import java.text.SimpleDateFormat;
import java.util.*;
import org.apache.log4j.*;
setProperty(property, jalview.util.Format.getHexString(colour));
}
- public static final DateFormat date_format = SimpleDateFormat
- .getDateTimeInstance();
+ public static final DateFormat date_format = DateFormat.getDateInstance(DateFormat.LONG,MessageManager.getLocale());
/**
* store a date in a jalview property
import jalview.javascript.JsCallBack;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
import java.applet.Applet;
import java.awt.Button;
g.setColor(Color.cyan);
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.red);
- g.drawString("Jalview can't open file", 5, 15);
+ g.drawString(MessageManager.getString("label.jalview_cannot_open_file"), 5, 15);
g.drawString("\"" + file + "\"", 5, 30);
}
else if (embedded)
{
g.setColor(Color.black);
g.setFont(new Font("Arial", Font.BOLD, 24));
- g.drawString("Jalview Applet", 50, getSize().height / 2 - 30);
- g.drawString("Loading Data...", 50, getSize().height / 2);
+ g.drawString(MessageManager.getString("label.jalview_applet"), 50, getSize().height / 2 - 30);
+ g.drawString(MessageManager.getString("label.loading_data") + "...", 50, getSize().height / 2);
}
}
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
- newAlignFrame.setTitle("Sequences from "
- + applet.getDocumentBase());
+ newAlignFrame.setTitle(MessageManager.formatMessage("label.sequences_from", new String[]{applet.getDocumentBase().toString()}));
}
- newAlignFrame.statusBar.setText("Successfully loaded file " + file);
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage("label.successfully_loaded_file", new String []{file}));
String treeFile = applet.getParameter("tree");
if (treeFile == null)
--- /dev/null
+package jalview.controller;
+
+import java.awt.Color;
+
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+public class AlignViewController implements AlignViewControllerI
+{
+ AlignViewportI viewport=null;
+ AlignmentViewPanel alignPanel=null;
+ @Override
+ protected void finalize() throws Throwable {
+ viewport = null;
+ alignPanel = null;
+ };
+
+ public AlignViewController(AlignViewportI viewport,
+ AlignmentViewPanel alignPanel)
+ {
+ this.viewport=viewport;
+ this.alignPanel = alignPanel;
+ }
+ @Override
+ public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
+ {
+ this.alignPanel = alignPanel;
+ this.viewport = viewport;
+
+ }
+ @Override
+ public boolean makeGroupsFromSelection()
+ {
+
+ if (viewport.getSelectionGroup() != null)
+ {
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true).getSequenceStrings(
+ viewport.getGapCharacter()), viewport.getAlignment()
+ .getGroups());
+ viewport.getAlignment().deleteAllGroups();
+ viewport.clearSequenceColours();
+ viewport.setSelectionGroup(null);
+ // set view properties for each group
+ for (int g = 0; g < gps.length; g++)
+ {
+ // gps[g].setShowunconserved(viewport.getShowUnconserved());
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
+ viewport.getAlignment().addGroup(gps[g]);
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ col = col.brighter();
+ for (SequenceI sq : gps[g].getSequences(null))
+ viewport.setSequenceColour(sq, col);
+ }
+ return true;
+ }
+ return false;
+}
+ @Override
+ public boolean createGroup()
+ {
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg!=null)
+ {
+ viewport.getAlignment().addGroup(sg);
+ return true;
+ }
+ return false;
+ }
+ @Override
+ public boolean unGroup()
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg!=null)
+ {
+ viewport.getAlignment().deleteGroup(sg);
+ return true;
+ }
+ return false;
+ }
+ @Override
+ public boolean deleteGroups()
+ {
+ if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
+ {
+ viewport.getAlignment().deleteAllGroups();
+ viewport.clearSequenceColours();
+ viewport.setSelectionGroup(null);
+ return true;
+ }
+ return false;
+ }
+
+ }
{
tmp = new char[i];
System.arraycopy(sequence, 0, tmp, 0, i);
+ j=sequence.length;
}
else
{
System.arraycopy(sequence, j, tmp, i, sequence.length - j);
}
boolean createNewDs = false;
+ // TODO: take a look at the new dataset creation validation method below -
+ // this could become time comsuming for large sequences - consider making it
+ // more efficient
for (int s = i; s < j; s++)
{
if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
endRes + 1, showSequenceLogo);
if (consensus != null)
{
- _updateConsensusRow(cnsns);
+ _updateConsensusRow(cnsns, sequences.size());
}
if (cs != null)
{
public Hashtable[] consensusData = null;
- private void _updateConsensusRow(Hashtable[] cnsns)
+ private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
{
if (consensus == null)
{
consensus.annotations = new Annotation[aWidth]; // should be alignment width
AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
- ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
+ ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting container
// for
// ignoreGapsInConsensusCalculation);
}
import jalview.analysis.NJTree;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
public AlignmentPanel alignPanel;
AlignViewport viewport;
+
+ public AlignViewControllerI avc;
+
Vector alignPanels = new Vector();
*/
void init()
{
+ avc = new jalview.controller.AlignViewController(viewport, alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
}
addKeyListener();
-
+
}
/**
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is "
- + (viewport.cursorMode ? "on" : "off"));
+ statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
{
ap.alignFrame = this;
+ avc = new jalview.controller.AlignViewController(viewport, alignPanel);
alignPanels.addElement(ap);
rnahelicesColour
.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
setShowProductsEnabled();
-
updateEditMenuBar();
}
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton("Cancel");
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
if (currentFileFormat == null)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "You must select a file format before saving!",
- "File format not specified", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.select_file_format_before_saving"),
+ MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
value = chooser.showSaveDialog(this);
return;
}
success = new Jalview2XML().SaveAlignment(this, file, shortName);
- statusBar.setText("Successfully saved to file: " + fileName + " in "
- + format + " format.");
+ statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
+
}
else
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- "The Alignment contains hidden columns."
- + "\nDo you want to save only the visible alignment?",
- "Save / Omit Hidden Columns",
+ MessageManager.getString("label.alignment_contains_hidden_columns"),
+ MessageManager.getString("action.save_omit_hidden_columns"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
out.print(output);
out.close();
this.setTitle(file);
- statusBar.setText("Successfully saved to file: " + fileName
- + " in " + format + " format.");
+ statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
} catch (Exception ex)
{
success = false;
if (!success)
{
- JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
- + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
+ MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
}
return success;
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- "The Alignment contains hidden columns."
- + "\nDo you want to output only the visible alignment?",
- "Save / Omit Hidden Columns",
+ MessageManager.getString("label.alignment_contains_hidden_columns"),
+ MessageManager.getString("action.save_omit_hidden_columns"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
{
undoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setText("Undo " + command.getDescription());
+ undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
}
else
{
undoMenuItem.setEnabled(false);
- undoMenuItem.setText("Undo");
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
}
if (viewport.redoList.size() > 0)
redoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setText("Redo " + command.getDescription());
+ redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
}
else
{
redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
}
}
Desktop.jalviewClipboard = new Object[]
{ seqs, viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
+ statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
}
/**
@Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
- viewport.getAlignment().deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ if (avc.deleteGroups()) {
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
}
/**
viewport.getSelectionGroup());
}
- statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
+ statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
- statusBar.setText("Removed " + removeGapCols.getSize()
- + " empty columns.");
+ statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
// This is to maintain viewport position on first residue
// of first sequence
newap.av.viewName = newViewName;
addAlignmentPanel(newap, true);
-
+ newap.alignmentChanged();
+
if (alignPanels.size() == 2)
{
viewport.gatherViewsHere = true;
editPane.setEditable(false);
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
- editPane.setText("<html>" + contents.toString() + "</html>");
+ editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
+ MessageManager.getString("label.remove_from_default_list"),
+ MessageManager.getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
|| (viewport.getSelectionGroup().getSize() < 2))
{
JOptionPane.showInternalMessageDialog(this,
- "You must select at least 2 sequences.", "Invalid Selection",
+ MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
JOptionPane.WARNING_MESSAGE);
}
else
|| (viewport.getAlignment().getHeight() < 4))
{
JOptionPane.showInternalMessageDialog(this,
- "Principal component analysis must take\n"
- + "at least 4 input sequences.",
- "Sequence selection insufficient",
+ MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+ MessageManager.getString("label.sequence_selection_insufficient"),
JOptionPane.WARNING_MESSAGE);
return;
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "You need to have more than two sequences selected to build a tree!",
- "Not enough sequences", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
+ MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
return;
}
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "The selected region to create a tree may\nonly contain residues or gaps.\n"
- + "Try using the Pad function in the edit menu,\n"
- + "or one of the multiple sequence alignment web services.",
- "Sequences in selection are not aligned",
+ MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
+ MessageManager.getString("label.sequences_selection_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "The sequences must be aligned before creating a tree.\n"
- + "Try using the Pad function in the edit menu,\n"
- + "or one of the multiple sequence alignment web services.",
- "Sequences not aligned",
+ MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
+ MessageManager.getString("label.sequences_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
} catch (Exception ex)
{
JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (fin != null && fin.hasWarningMessage())
{
JOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(), "Possible problem with tree file",
+ fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
JOptionPane.WARNING_MESSAGE);
}
}
@Override
public void run()
{
+ final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
try
{
System.err.println("Building ws menu again "
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// stored or retrieved from elsewhere
- Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+ // No MSAWS used any more:
+ // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services
.get("SecStrPred");
- Vector seqsrch = null; // (Vector)
- // Discoverer.services.get("SeqSearch");
- // TODO: move GUI generation code onto service implementation - so a
- // client instance attaches itself to the GUI with method call like
- // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
- // alignframe)
- if (msaws != null)
- {
- // Add any Multiple Sequence Alignment Services
- for (int i = 0, j = msaws.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(msawsmenu, me);
-
- }
- }
if (secstrpr != null)
{
// Add any secondary structure prediction services
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
+ int p=secstrmenu.getItemCount();
impl.attachWSMenuEntry(secstrmenu, me);
- }
- }
- if (seqsrch != null)
- {
- // Add any sequence search services
- for (int i = 0, j = seqsrch.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
- .elementAt(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(seqsrchmenu, me);
+ int q=secstrmenu.getItemCount();
+ for (int litm=p;litm<q; litm++)
+ {
+ legacyItems.add(secstrmenu.getItem(litm));
+ }
}
}
}
-
+
// Add all submenus in the order they should appear on the web
// services menu
wsmenu.add(msawsmenu);
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
- // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
- // submens.add(msawsmenu);
- // submens.add(secstrmenu);
- // submens.add(dismenu);
- // submens.add(analymenu);
-
// No search services yet
// wsmenu.add(seqsrchmenu);
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
+ boolean new_sspred=false;
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs.hasServices())
{
jws2servs.attachWSMenuEntry(webService, me);
+ for (Jws2Instance sv:jws2servs.getServices()) {
+ if (sv.description.toLowerCase().contains("jpred"))
+ {
+ for (JMenuItem jmi:legacyItems)
+ {
+ jmi.setVisible(false);
+ }
+ }
+ }
+
}
if (jws2servs.isRunning())
{
}
}
}
-
build_urlServiceMenu(me.webService);
build_fetchdbmenu(webService);
for (JMenu item : wsmenu)
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
- "Translation Failed", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+ MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
}
else
{
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.",
- "Implementation error: Translation Failed", JOptionPane.ERROR_MESSAGE);
+ MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
+ MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
return;
}
if (al == null)
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
- "Translation Failed", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+ MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
}
else
{
|| JOptionPane
.showConfirmDialog(
this,
- "Do you want to automatically associate the "
- + filesmatched.size()
- + " PDB files with sequences in the alignment that have the same name ?",
- "Automatically Associate PDB files by name",
+ MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
+ new String[]{Integer.valueOf(filesmatched.size()).toString()}),
+ MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
{
"AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
.showConfirmDialog(
this,
- "<html>Do you want to <em>ignore</em> the "
- + filesnotmatched.size()
- + " files whose names did not match any sequence IDs ?</html>",
- "Ignore unmatched dropped files ?",
+ MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
+ MessageManager.getString("label.ignore_unmatched_dropped_files"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
{
return;
tcoffeeColour.setSelected(true);
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
- statusBar
- .setText("Successfully pasted T-Coffee scores to alignment.");
+ statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
JOptionPane
.showMessageDialog(
Desktop.desktop,
- tcf.getWarningMessage() == null ? "Check that the file matches sequence IDs in the alignment."
+ tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
: tcf.getWarningMessage(),
- "Problem reading T-COFFEE score file",
+ MessageManager.getString("label.problem_reading_tcoffee_score_file"),
JOptionPane.WARNING_MESSAGE);
}
}
{
alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
viewport = alignPanel.av;
+ avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
}
}
if (SwingUtilities.isRightMouseButton(e))
{
String reply = JOptionPane.showInternalInputDialog(this,
- "Enter View Name", "Edit View Name",
+ MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
JOptionPane.QUESTION_MESSAGE);
if (reply != null)
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
{
- ifetch.setText(imname + " to '" + sname + "'");
+ ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
dfetch.add(ifetch);
ifetch = new JMenu();
imname = null;
++dbi;
if (comp >= mcomp || dbi >= (dbclasses.length))
{
- dfetch.setText(mname + " to '" + dbclass + "'");
+ dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
rfetch.add(dfetch);
dfetch = new JMenu();
mname = null;
@Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
- if (viewport.getSelectionGroup() != null)
- {
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
- viewport.getAlignment().deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- // set view properties for each group
- for (int g = 0; g < gps.length; g++)
- {
- gps[g].setShowNonconserved(viewport.getShowUnconserved());
- gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI s : gps[g].getSequences())
- viewport.setSequenceColour(s, col);
- }
+ if (avc.makeGroupsFromSelection()) {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
}
+ @Override
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ if (avc.createGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
+ @Override
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ if (avc.unGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
/**
* make the given alignmentPanel the currently selected tab
*
Stack redoList = new Stack();
- Hashtable sequenceColours;
-
int thresholdTextColour = 0;
Color textColour = Color.black;
showHiddenMarkers = show;
}
- public Color getSequenceColour(SequenceI seq)
- {
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
- }
-
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
- }
-
/**
* returns the visible column regions of the alignment
*
centreColumnLabels = centrecolumnlabels;
}
- public void updateSequenceIdColours()
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
- for (SequenceGroup sg : alignment.getGroups())
- {
- if (sg.idColour != null)
- {
- for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
- {
- sequenceColours.put(s, sg.idColour);
- }
- }
- }
- }
/**
* enable or disable the display of Database Cross References in the sequence
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
+
import java.awt.Dimension;
public class AnnotationColourChooser extends JPanel
// Always get default shading from preferences.
setDefaultMinMax();
+ adjusting = true;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.predefinedColours);
- if (!acg.predefinedColours)
+ currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
seqAssociated.setSelected(acg.isSeqAssociated());
+
}
- adjusting = true;
annotations = new JComboBox(
getAnnotationItems(seqAssociated.isSelected()));
}
});
ok.setOpaque(false);
- ok.setText("OK");
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
cancel.setOpaque(false);
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
defColours.setOpaque(false);
- defColours.setText("Defaults");
+ defColours.setText(MessageManager.getString("action.set_defaults"));
defColours
.setToolTipText("Reset min and max colours to defaults from user preferences.");
defColours.addActionListener(new ActionListener()
thresholdValue.setColumns(7);
currentColours.setFont(JvSwingUtils.getLabelFont());
currentColours.setOpaque(false);
- currentColours.setText("Use Original Colours");
+ currentColours.setText(MessageManager.getString("label.use_original_colours"));
currentColours.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText("Threshold is Min/Max");
+ thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
});
seqAssociated.setBackground(Color.white);
seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText("Per-sequence only");
+ seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
seqAssociated.addActionListener(new ActionListener()
{
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.isSelected();
import jalview.datamodel.*;
import jalview.io.*;
+import jalview.util.MessageManager;
/**
*
{
this.setLayout(new BorderLayout());
- toFile.setText("to File");
+ toFile.setText(MessageManager.getString("label.to_file"));
toFile.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
toFile_actionPerformed(e);
}
});
- toTextbox.setText("to Textbox");
+ toTextbox.setText(MessageManager.getString("label.to_textbox"));
toTextbox.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
toTextbox_actionPerformed(e);
}
});
- close.setText("Close");
+ close.setText(MessageManager.getString("action.close"));
close.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
GFFFormat.setOpaque(false);
GFFFormat.setText("GFF");
CSVFormat.setOpaque(false);
- CSVFormat.setText("CSV(Spreadsheet)");
+ CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
- jLabel1.setText("Format: ");
+ jLabel1.setText(MessageManager.getString("action.format") + " ");
this.setBackground(Color.white);
jPanel3.setBorder(BorderFactory.createEtchedBorder());
jPanel3.setOpaque(false);
import jalview.datamodel.*;
import jalview.io.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
{
- g.drawString("Right click", 2, 8);
- g.drawString("to add annotation", 2, 18);
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18);
}
}
}
import java.awt.*;
import java.awt.event.*;
import java.awt.image.*;
+
import javax.swing.*;
import jalview.datamodel.*;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.util.MessageManager;
/**
* AnnotationPanel displays visible portion of annotation rows below unwrapped
else if (evt.getActionCommand().equals(LABEL))
{
String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
- String label = JOptionPane.showInputDialog(this, "Enter label",
+ String label = JOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"),
exMesg);
if (label == null)
}
String label = JOptionPane.showInputDialog(
- "Enter a label for the structure?", symbol);
+ MessageManager.getString("label.enter_label_for_the_structure"), symbol);
if (label == null)
{
&& aa[row].annotations[res].description != null
&& aa[row].annotations[res].description.length() > 0)
{
- this.setToolTipText(aa[row].annotations[res].description);
+ this.setToolTipText("<html>"+JvSwingUtils.wrapTooltip(aa[row].annotations[res].description)+"</html>");
}
else
{
g.setColor(Color.black);
if (av.validCharWidth)
{
- g.drawString("Alignment has no annotations", 20, 15);
+ g.drawString(MessageManager.getString("label.alignment_has_no_annotations"), 20, 15);
}
return;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
import jalview.util.Platform;
public class AppJmol extends GStructureViewer implements Runnable,
if (alreadyMapped != null)
{
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- pdbentry.getId() + " is already displayed."
- + "\nDo you want to re-use this viewer ?",
- "Map Sequences to Visible Window: " + pdbentry.getId(),
+ MessageManager.formatMessage("label.pdb_entry_is_already_displayed", new String[]{pdbentry.getId()}),
+ MessageManager.formatMessage("label.map_sequences_to_visible_window", new String[]{pdbentry.getId()}),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
AppJmol topJmol = (AppJmol) jm.nextElement();
// TODO: highlight topJmol in view somehow
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "Do you want to add " + pdbentry.getId()
- + " to the view called\n'" + topJmol.getTitle()
- + "'\n", "Align to existing structure view",
+ MessageManager.formatMessage("label.add_pdbentry_to_view", new String[]{pdbentry.getId(),topJmol.getTitle()}),
+ MessageManager.getString("label.align_to_existing_structure_view"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "The following pdb entries could not be retrieved from the PDB:\n"
- + errormsgs.toString()
- + "\nPlease try downloading them manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+ MessageManager.formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[]{errormsgs.toString()}),
+ MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE);
}
long lastnotify = jmb.getLoadNotifiesHandled();
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading file...", 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2);
StringBuffer sb = new StringBuffer();
int lines = 0;
for (int e = 0; e < jmb.pdbentry.length; e++)
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
}
else
{
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
private JTextField _seq = new JTextField();
- private JLabel _strLabel = new JLabel(" Str:");
+ private JLabel _strLabel = new JLabel(MessageManager.getString("label.str"));
- private JLabel _seqLabel = new JLabel(" Seq:");
+ private JLabel _seqLabel = new JLabel(MessageManager.getString("label.seq"));
- private JButton _createButton = new JButton("Create");
+ private JButton _createButton = new JButton(MessageManager.getString("action.create"));
- private JButton _updateButton = new JButton("Update");
+ private JButton _updateButton = new JButton(MessageManager.getString("action.update"));
- private JButton _deleteButton = new JButton("Delete");
+ private JButton _deleteButton = new JButton(MessageManager.getString("action.delete"));
- private JButton _duplicateButton = new JButton("Snapshot");
+ private JButton _duplicateButton = new JButton(MessageManager.getString("action.snapshot"));
protected JPanel _listPanel = new JPanel();
ops.add(_deleteButton);
ops.add(_duplicateButton);
- JLabel j = new JLabel("Structures Manager", JLabel.CENTER);
+ JLabel j = new JLabel(MessageManager.getString("label.structures_manager"), JLabel.CENTER);
_listPanel.setLayout(new BorderLayout());
// _listPanel.add(ops, BorderLayout.SOUTH);
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
/**
* GUI related routines for associating PDB files with sequences
reply = JOptionPane
.showInternalInputDialog(
Desktop.desktop,
- "Couldn't find a PDB id in the file supplied."
- + "Please enter an Id to identify this structure.",
- "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+ MessageManager.getString("label.couldnt_find_pdb_id_in_file"),
+ MessageManager.getString("label.no_pdb_id_in_file"), JOptionPane.QUESTION_MESSAGE);
}
if (reply == null)
{
package jalview.gui;
import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dimension;
java.util.Date earliest = null;
try
{
- earliest = new SimpleDateFormat("YYYY-MM-DD").parse(chan
+ earliest = new SimpleDateFormat("YYYY-MM-DD",MessageManager.getLocale()).parse(chan
.getHTTPLastModified());
} catch (Exception x)
{
topBottomSplitPane.setBottomComponent(bottomPanel);
JScrollPane spTextDescription = new JScrollPane(textDescription);
textDescription.setText("");
- statusBar.setText(" [Status] ");
+ statusBar.setText(MessageManager.getString("label.status"));
buttonRefresh.addActionListener(new ActionListener()
{
_popupChannels);
listItems.addMouseListener(popupAdapter);
listItems.setCellRenderer(new ItemsRenderer());
- lblChannels.setText("Channels");
+ lblChannels.setText(MessageManager.getString("label.channels"));
}
private void postInit()
if (value instanceof Channel)
{
Channel channel = (Channel) value;
- component.setText(channel.getTitle() + " ("
- + channel.getUnreadItemCount() + ")");
+ component.setText(MessageManager.formatMessage("label.channel_title_item_count", new String[]{channel.getTitle(),Integer.valueOf(channel.getUnreadItemCount()).toString()}));
component.setToolTipText(channel.getURL());
}
return component;
Item item = (Item) value;
if (item.getPublishDate() != null)
{
- component.setText(DateFormat.getDateInstance().format(
- item.getPublishDate())
- + " " + item.getTitle());
+ component.setText(MessageManager.formatMessage("label.blog_item_published_on_date", new String[]{DateFormat.getDateInstance(DateFormat.LONG, MessageManager.getLocale()).format(item.getPublishDate()).toString(),item.getTitle()}));
}
component.setToolTipText(item.getLink());
if (!item.isRead())
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.io.*;
import java.awt.*;
import java.awt.event.*;
// textArea = cpt.getTextArea();
textArea = new JTextArea();
textArea.setEditable(false);
- JButton button = new JButton("clear");
+ JButton button = new JButton(MessageManager.getString("action.clear"));
// frame = cpt;
frame.getContentPane().setLayout(new BorderLayout());
import jalview.io.*;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
/**
* Cut'n'paste files into the desktop See JAL-1105
this.viewport = viewport;
if (viewport != null)
{
- ok.setText("Add");
+ ok.setText(MessageManager.getString("action.add"));
}
getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
/**
* Cut'n'paste files into the desktop See JAL-1105
this.viewport = viewport;
if (viewport != null)
{
- ok.setText("Add");
+ ok.setText(MessageManager.getString("action.add"));
}
getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
} catch (java.io.IOException ex)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't read the pasted text.\n" + ex.toString(),
- "Error parsing text", JOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.couldnt_read_pasted_text", new String[]{ex.toString()}),
+ MessageManager.getString("label.error_parsing_text"), JOptionPane.WARNING_MESSAGE);
}
}
af.currentFileFormat = format;
Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
+ af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
try
{
package jalview.gui;
import jalview.jbgui.GDasSourceBrowser;
+import jalview.util.MessageManager;
import jalview.util.TableSorter;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.api.jalviewSourceI;
if (nickName == null)
{
- fullDetails.setText(text + "Select a DAS service from the table"
- + " to read a full description here.</font></html>");
+ fullDetails.setText(text + MessageManager.getString("label.select_das_service_from_table"));
return;
}
JTextField nametf = new JTextField(nickname, 40);
JTextField urltf = new JTextField(url, 40);
- JCheckBox seqs = new JCheckBox("Sequence Source");
+ JCheckBox seqs = new JCheckBox(MessageManager.getString("label.sequence_source"));
seqs.setSelected(seqsrc);
JPanel panel = new JPanel(new BorderLayout());
JPanel pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);
+ pane12.add(new JLabel(MessageManager.getString("label.structure_manager")), BorderLayout.CENTER);
pane12.add(nametf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.NORTH);
pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel("URL: "), BorderLayout.NORTH);
+ pane12.add(new JLabel(MessageManager.getString("label.url")), BorderLayout.NORTH);
pane12.add(seqs, BorderLayout.SOUTH);
pane12.add(urltf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.SOUTH);
int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- panel, "Enter Nickname & URL of Local DAS Source",
+ panel, MessageManager.getString("label.enter_local_das_source"),
JOptionPane.OK_CANCEL_OPTION);
if (reply != JOptionPane.OK_OPTION)
if (!sourceRegistry.getSource(nickname).isLocal())
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "You can only edit or remove local DAS Sources!",
- "Public DAS source - not editable",
+ MessageManager.getString("label.you_can_only_edit_or_remove_local_das_sources"),
+ MessageManager.getString("label.public_das_source"),
JOptionPane.WARNING_MESSAGE);
return;
}
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.util.MessageManager;
import jalview.ws.params.ParamManager;
import java.awt.BorderLayout;
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ if (instance == null || (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true")))
{
return;
}
{
// This construct allows us to have a wider textfield
// for viewing
- JLabel label = new JLabel("Enter URL of Input File");
+ JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
final JComboBox history = new JComboBox();
JPanel panel = new JPanel(new GridLayout(2, 1));
}
int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
- "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION);
+ MessageManager.getString("label.input_alignment_from_url"), JOptionPane.OK_CANCEL_OPTION);
if (reply != JOptionPane.OK_OPTION)
{
if (!vamsasImport(chooser.getSelectedFile()))
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't import '" + fle + "' as a new vamsas session.",
- "Vamsas Document Import Failed",
+ MessageManager.formatMessage("label.couldnt_import_as_vamsas_session", new String[]{fle}),
+ MessageManager.getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
}
}
protected void setupVamsasConnectedGui()
{
- vamsasStart.setText("Session Update");
+ vamsasStart.setText(MessageManager.getString("label.session_update"));
vamsasSave.setVisible(true);
vamsasStop.setVisible(true);
vamsasImport.setVisible(false); // Document import to existing session is
vamsasSave.setVisible(false);
vamsasStop.setVisible(false);
vamsasImport.setVisible(true);
- vamsasStart.setText("New Vamsas Session");
+ vamsasStart.setText(MessageManager.getString("label.new_vamsas_session"));
}
public void vamsasStop_actionPerformed(ActionEvent e)
if (fm != null)
{
g.drawString(
- "Total Free Memory: " + df.format(totalFreeMemory)
- + "MB; Max Memory: " + df.format(maxMemory)
- + "MB; " + df.format(percentUsage) + "%", 10,
+ MessageManager.formatMessage("label.memory_stats", new String[]{df.format(totalFreeMemory),df.format(maxMemory),df.format(percentUsage)}), 10,
getHeight() - fm.getHeight());
}
}
if (jalview.bin.Cache.groovyJarsPresent())
{
groovyShell = new JMenuItem();
- groovyShell.setText("Groovy Console...");
+ groovyShell.setText(MessageManager.getString("label.groovy_console"));
groovyShell.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton("Cancel");
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
{
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
-
+ // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
+ if (true)
+ {
// todo: changesupport handlers need to be transferred
if (discoverer == null)
{
}
// JAL-940 - disabled JWS1 service configuration - always start discoverer
// until we phase out completely
- if (true)
- {
(t0 = new Thread(discoverer)).start();
}
- try
+ // ENFIN services are EOLed as of Jalview 2.8.1 release
+ if (false)
{
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ try
{
- // EnfinEnvision web service menu entries are rebuild every time the
- // menu is shown, so no changeSupport events are needed.
- jalview.ws.EnfinEnvision2OneWay.getInstance();
- (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()))
- .start();
+ if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ {
+ // EnfinEnvision web service menu entries are rebuild every time the
+ // menu is shown, so no changeSupport events are needed.
+ jalview.ws.EnfinEnvision2OneWay.getInstance();
+ (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()))
+ .start();
+ }
+ } catch (Exception e)
+ {
+ Cache.log
+ .info("Exception when trying to launch Envision2 workflow discovery.",
+ e);
+ Cache.log.info(e.getStackTrace());
}
- } catch (Exception e)
- {
- Cache.log
- .info("Exception when trying to launch Envision2 workflow discovery.",
- e);
- Cache.log.info(e.getStackTrace());
}
+
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
private void jbInit() throws Exception
{
lineart.setFont(JvSwingUtils.getLabelFont());
- lineart.setText("Lineart");
+ lineart.setText(MessageManager.getString("label.lineart"));
text.setFont(JvSwingUtils.getLabelFont());
- text.setText("Text");
+ text.setText(MessageManager.getString("action.text"));
text.setSelected(true);
askAgain.setFont(JvSwingUtils.getLabelFont());
- askAgain.setText("Don\'t ask me again");
- ok.setText("OK");
+ askAgain.setText(MessageManager.getString("label.dont_ask_me_again"));
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
ok_actionPerformed(e);
}
});
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
jLabel1.setFont(JvSwingUtils.getLabelFont());
- jLabel1.setText("Select EPS character rendering style");
+ jLabel1.setText(MessageManager.getString("label.select_eps_character_rendering_style"));
this.setLayout(borderLayout1);
jPanel3.setBorder(BorderFactory.createEtchedBorder());
jPanel2.add(text);
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import javax.swing.*;
{
JTextField id, description;
- JButton ok = new JButton("Accept");
+ JButton ok = new JButton(MessageManager.getString("action.accept"));
- JButton cancel = new JButton("Cancel");
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
boolean accept = false;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
+
import java.awt.Dimension;
public class FeatureColourChooser extends JalviewDialog
}
});
maxColour.setBorder(new LineBorder(Color.black));
- minText.setText("Min:");
+ minText.setText(MessageManager.getString("label.min"));
minText.setFont(JvSwingUtils.getLabelFont());
- maxText.setText("Max:");
+ maxText.setText(MessageManager.getString("label.max"));
maxText.setFont(JvSwingUtils.getLabelFont());
this.setLayout(borderLayout1);
jPanel2.setLayout(flowLayout1);
thresholdValue.setColumns(7);
jPanel3.setBackground(Color.white);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setText("Threshold is Min/Max");
+ thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin
.setToolTipText("Toggle between absolute and relative display threshold.");
thresholdIsMin.addActionListener(new ActionListener()
}
});
colourByLabel.setBackground(Color.white);
- colourByLabel.setText("Colour by Label");
+ colourByLabel.setText(MessageManager.getString("label.colour_by_label"));
colourByLabel
.setToolTipText("Display features of the same type with a different label using a different colour. (e.g. domain features)");
colourByLabel.addActionListener(new ActionListener()
import jalview.datamodel.*;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
{
panel = new JPanel(new GridLayout(4, 1));
tmp = new JPanel();
- tmp.add(new JLabel("Select Feature: "));
+ tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
overlaps = new JComboBox();
for (int i = 0; i < features.length; i++)
{
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel("Name: ", JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
tmp.add(name);
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel("Group: ", JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.group"), JLabel.RIGHT));
tmp.add(source);
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.colour"), JLabel.RIGHT));
tmp.add(colour);
colour.setPreferredSize(new Dimension(150, 15));
colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
bigPanel.add(panel, BorderLayout.NORTH);
panel = new JPanel();
- panel.add(new JLabel("Description: ", JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.description"), JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
panel.add(new JScrollPane(description));
bigPanel.add(panel, BorderLayout.SOUTH);
panel = new JPanel();
- panel.add(new JLabel(" Start:", JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.start"), JLabel.RIGHT));
panel.add(start);
- panel.add(new JLabel(" End:", JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.end"), JLabel.RIGHT));
panel.add(end);
bigPanel.add(panel, BorderLayout.CENTER);
}
import jalview.io.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
public class FeatureSettings extends JPanel
dasSettingsPane.setLayout(borderLayout3);
bigPanel.setLayout(borderLayout4);
invert.setFont(JvSwingUtils.getLabelFont());
- invert.setText("Invert Selection");
+ invert.setText(MessageManager.getString("label.invert_selection"));
invert.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
optimizeOrder.setFont(JvSwingUtils.getLabelFont());
- optimizeOrder.setText("Optimise Order");
+ optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
optimizeOrder.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
sortByScore.setFont(JvSwingUtils.getLabelFont());
- sortByScore.setText("Seq sort by Score");
+ sortByScore.setText(MessageManager.getString("label.seq_sort_by_score"));
sortByScore.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
cancel.setFont(JvSwingUtils.getLabelFont());
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
ok.setFont(JvSwingUtils.getLabelFont());
- ok.setText("OK");
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
loadColours.setFont(JvSwingUtils.getLabelFont());
- loadColours.setText("Load Colours");
+ loadColours.setText(MessageManager.getString("label.load_colours"));
loadColours.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
saveColours.setFont(JvSwingUtils.getLabelFont());
- saveColours.setText("Save Colours");
+ saveColours.setText(MessageManager.getString("label.save_colours"));
saveColours.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
transparency.setMaximum(70);
- fetchDAS.setText("Fetch DAS Features");
+ fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
fetchDAS.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
fetchDAS_actionPerformed(e);
}
});
- saveDAS.setText("Save as default");
+ saveDAS.setText(MessageManager.getString("action.save_as_default"));
saveDAS.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
dasSettingsPane.setBorder(null);
cancelDAS.setEnabled(false);
- cancelDAS.setText("Cancel Fetch");
+ cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
cancelDAS.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
complete();
JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "No das sources were selected.\n"
- + "Please select some sources and\n" + " try again.",
- "No Sources Selected", JOptionPane.DEFAULT_OPTION,
+ MessageManager.getString("label.no_das_sources_selected_warn"),
+ MessageManager.getString("label.no_das_sources_selected_title"), JOptionPane.DEFAULT_OPTION,
JOptionPane.INFORMATION_MESSAGE);
}
// width/g.getFontMetrics().stringWidth("Label"),
// height/g.getFontMetrics().getHeight())));
- g.drawString("Label", 0, 0);
+ g.drawString(MessageManager.getString("label.label"), 0, 0);
}
else
package jalview.gui;
import java.util.*;
-
import java.awt.event.*;
+
import javax.swing.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
// 'SelectRegion' selection
if (!haveResults)
{
- JOptionPane.showInternalMessageDialog(this, "Finished searching",
+ JOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"),
null, JOptionPane.INFORMATION_MESSAGE);
resIndex = -1;
seqIndex = 0;
package jalview.gui;
import jalview.bin.Cache;
+import jalview.util.MessageManager;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
JButton getDatabaseSelectorButton()
{
- final JButton viewdbs = new JButton("--- Select Database ---");
+ final JButton viewdbs = new JButton(MessageManager.getString("action.select_ddbb"));
viewdbs.addActionListener(new ActionListener()
{
if (allowMultiSelections)
{
- dbstatus.setText("Selected "
- + srcs.size()
- + " database"
- + (srcs.size() == 1 ? "" : "s")
- + " to fetch from"
- + (srcs.size() > 0 ? " with " + x + " test quer"
- + (x == 1 ? "y" : "ies") : "."));
+ dbstatus.setText(MessageManager.formatMessage("label.selected_database_to_fetch_from", new String[]{Integer.valueOf(srcs.size()).toString(),(srcs.size() == 1 ? "" : "s"),(srcs.size() > 0 ? " with " + x + " test quer" + (x == 1 ? "y" : "ies") : ".")}));
dbstatex.setText(" ");
}
else
{
if (nm.length() > 0)
{
- dbstatus.setText("Database: " + nm);
+ dbstatus.setText(MessageManager.formatMessage("label.database_param",new String[]{nm}));
if (qr.length() > 0)
{
- dbstatex.setText("Example: " + qr);
+ dbstatex.setText(MessageManager.formatMessage("label.example_param", new String[]{qr}));
}
else
{
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
+ object.setVersion(jalview.bin.Cache.getDefault("VERSION","Development Build"));
jalview.datamodel.AlignmentI jal = av.getAlignment();
ac.setMaxColour(acg.getMaxColour().getRGB());
ac.setMinColour(acg.getMinColour().getRGB());
+ ac.setPerSequence(acg.isSeqAssociated());
+ ac.setPredefinedColours(acg.isPredefinedColours());
view.setAnnotationColours(ac);
view.setBgColour("AnnotationColourGradient");
}
.getAnnotationColours().getColourScheme()),
view.getAnnotationColours().getAboveThreshold());
}
-
+ if (view.getAnnotationColours().hasPerSequence())
+ {
+ ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
+ }
+ if (view.getAnnotationColours().hasPredefinedColours())
+ {
+ ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
+ }
// Also use these settings for all the groups
if (al.getGroups() != null)
{
.getAlignment().getAlignmentAnnotation()[i],
sg.cs, view.getAnnotationColours()
.getAboveThreshold());
+ if (cs instanceof AnnotationColourGradient)
+ {
+ if (view.getAnnotationColours().hasPerSequence())
+ {
+ ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
+ }
+ if (view.getAnnotationColours().hasPredefinedColours())
+ {
+ ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
+ }
+ }
}
}
view.getHeight());
af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
reorderAutoannotation(af, al, autoAlan);
+ af.alignPanel.alignmentChanged();
return af;
}
import org.exolab.castor.xml.*;
import jalview.binding.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
/**
System.err.println("Couldn't locate Jalview XML file : " + ex
+ "\n");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + file, "URL not found",
+ MessageManager.formatMessage("label.couldnt_locate", new String[]{file}),
+ MessageManager.getString("label.url_not_found"),
JOptionPane.WARNING_MESSAGE);
}
});
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.awt.Container;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
this.block = block;
ok.setOpaque(false);
- ok.setText("OK");
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
cancel.setOpaque(false);
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
import jalview.datamodel.*;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
import jalview.viewmodel.PCAModel;
/**
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton("Cancel");
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
JMenuItem sequenceSelDetails = new JMenuItem();
SequenceI sequence;
-
+ JMenuItem createGroupMenuItem = new JMenuItem();
JMenuItem unGroupMenuItem = new JMenuItem();
JMenuItem outline = new JMenuItem();
}
SequenceGroup sg = ap.av.getSelectionGroup();
+ boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
if (sg != null && sg.getSize() > 0)
- {
+ {
groupName.setText("Name: " + sg.getName());
groupName.setText("Edit name and description of current group.");
editMenu.setVisible(false);
}
- if (!ap.av.getAlignment().getGroups().contains(sg))
+ if (!isDefinedGroup)
{
+ createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
+ jMenu1.setText("Edit New Group");
+ } else {
+ createGroupMenuItem.setVisible(false);
+ unGroupMenuItem.setVisible(true);
+ jMenu1.setText("Edit Group");
}
if (seq == null)
unGroupMenuItem_actionPerformed();
}
});
+ createGroupMenuItem.setText("Create Group");
+ createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
outline.setText("Border colour");
outline.addActionListener(new java.awt.event.ActionListener()
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
groupMenu.add(jMenu1);
sequenceMenu.add(sequenceName);
sequenceMenu.add(sequenceDetails);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
- jMenu1.add(unGroupMenuItem);
jMenu1.add(colourMenu);
jMenu1.add(showBoxes);
jMenu1.add(showText);
sequence.getAnnotation()[0], null,
AnnotationColourGradient.NO_THRESHOLD);
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
sg.cs = acg;
refresh();
ap.av.setSelectionGroup(null);
refresh();
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
+ refresh();
+ }
/**
* DOCUMENT ME!
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
while (!valid)
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+ MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
if (index == -1)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!", "No link selected",
+ MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+ MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
if (index == -1)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!", "No link selected",
+ MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
package jalview.gui;
import java.util.*;
-
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
import jalview.api.RotatableCanvasI;
import jalview.datamodel.*;
import jalview.math.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
if (points == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString("Calculating PCA....", 20, getHeight() / 2);
+ g.drawString(MessageManager.getString("label.calculating_pca")+ "....", 20, getHeight() / 2);
}
else
{
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
if (reveal != null && reveal[0] > startx && reveal[0] < endx)
{
- gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);
+ gg.drawString(MessageManager.getString("label.reveal_columns"), reveal[0] * av.charWidth, 0);
}
}
import jalview.io.SequenceAnnotationReport;
import jalview.schemes.*;
import jalview.structure.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ ssm = av.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
if (av.wrapAlignment && seq > av.getAlignment().getHeight())
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Cannot edit annotations in wrapped view.",
- "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.cannot_edit_annotations_in_wrapped_view"),
+ MessageManager.getString("label.wrapped_view_no_edit"), JOptionPane.WARNING_MESSAGE);
return;
}
import jalview.datamodel.*;
import jalview.io.*;
import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
- "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.error_retrieving_data"), JOptionPane.WARNING_MESSAGE);
}
});
}
if (tree == null)
{
- g.drawString("Calculating tree....", 20, getHeight() / 2);
+ g.drawString(MessageManager.getString("label.calculating_tree") + "....", 20, getHeight() / 2);
}
else
{
{
aps[a].av.setSelectionGroup(null);
aps[a].av.getAlignment().deleteAllGroups();
- aps[a].av.sequenceColours = null;
+ aps[a].av.clearSequenceColours();
}
colourGroups();
}
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.Font;
if (schemeName.getText().trim().length() < 1)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "User colour scheme must have a name!",
- "No name for colour scheme", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.user_colour_scheme_must_have_name"),
+ MessageManager.getString("label.no_name_colour_scheme"), JOptionPane.WARNING_MESSAGE);
return;
}
{
int reply = JOptionPane.showInternalConfirmDialog(
Desktop.desktop,
- "Colour scheme " + schemeName.getText() + " exists."
- + "\nContinue saving colour scheme as "
- + schemeName.getText() + "?",
- "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
+ MessageManager.formatMessage("label.colour_scheme_exists_overwrite", new String[]{schemeName.getText(),schemeName.getText()}),
+ MessageManager.getString("label.duplicate_scheme_name"), JOptionPane.YES_NO_OPTION);
if (reply != JOptionPane.YES_OPTION)
{
return;
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.io.*;
import java.net.*;
jalview.bin.Cache.log.info("Prompting user for questionnaire at "
+ qurl);
int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "There is a new Questionnaire available."
- + "Would you like to complete it now ?\n",
- "Jalview User Survey", JOptionPane.YES_NO_OPTION,
+ MessageManager.getString("label.jalview_new_questionnaire"),
+ MessageManager.getString("label.jalview_user_survey"), JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
if (reply == JOptionPane.YES_OPTION)
import javax.swing.text.html.StyleSheet;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
import jalview.ws.WSClientI;
/**
switch (currentStatus)
{
case STATE_QUEUING:
- g.drawString(title.concat(" - queuing"), 60, 30);
+ g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_queueing")), 60, 30);
break;
case STATE_RUNNING:
- g.drawString(title.concat(" - running"), 60, 30);
+ g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_running")), 60, 30);
break;
case STATE_STOPPED_OK:
- g.drawString(title.concat(" - complete"), 60, 30);
+ g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_completed")), 60, 30);
break;
case STATE_CANCELLED_OK:
- g.drawString(title.concat(" - job cancelled!"), 60, 30);
+ g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_job_cancelled")), 60, 30);
break;
case STATE_STOPPED_ERROR:
- g.drawString(title.concat(" - job error!"), 60, 30);
+ g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_job_error")), 60, 30);
break;
case STATE_STOPPED_SERVERERROR:
- g.drawString(title.concat(" - Server Error! (try later)"), 60, 30);
+ g.drawString(title.concat(" - ").concat(MessageManager.getString("label.server_error_try_later")), 60, 30);
break;
}
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton("Cancel");
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
import jalview.gui.OptsAndParamsPage.OptionBox;
import jalview.gui.OptsAndParamsPage.ParamBox;
+import jalview.util.MessageManager;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.jws2.Jws2Discoverer;
GridBagLayout gbl = new GridBagLayout();
SetNamePanel.setLayout(gbl);
- JLabel setNameLabel = new JLabel("Current parameter set name :");
+ JLabel setNameLabel = new JLabel(MessageManager.getString("label.current_parameter_set_name"));
setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
setNameInfo.add(setNameLabel);
import jalview.bin.Cache;
import jalview.jbgui.GWsPreferences;
+import jalview.util.MessageManager;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.rest.RestServiceDescription;
JTextField urltf = new JTextField(url, 40);
JPanel panel = new JPanel(new BorderLayout());
JPanel pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel("URL: "), BorderLayout.CENTER);
+ pane12.add(new JLabel(MessageManager.getString("label.url")), BorderLayout.CENTER);
pane12.add(urltf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.NORTH);
boolean valid = false;
{
valid = false;
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Invalid URL !");
+ MessageManager.getString("label.invalid_url"));
}
}
if (valid && resp == JOptionPane.OK_OPTION)
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
public class FileLoader implements Runnable
{
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage, "Error loading file",
+ errorMessage, MessageManager.getString("label.error_loading_file"),
JOptionPane.WARNING_MESSAGE);
}
});
public void run()
{
javax.swing.JOptionPane.showInternalMessageDialog(
- Desktop.desktop, "Encountered problems opening " + file
- + "!!", "File open error",
+ Desktop.desktop, MessageManager.formatMessage("label.problems_opening_file", new String[]{file}),
+ MessageManager.getString("label.file_open_error"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
package jalview.jbgui;
import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.Color;
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
JMenuItem deleteGroups = new JMenuItem();
+
+ JMenuItem createGroup = new JMenuItem();
+ JMenuItem unGroup = new JMenuItem();
JMenuItem delete = new JMenuItem();
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
+ MessageManager.getString("label.remove_from_default_list"),
+ MessageManager.getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
invertSequenceMenuItem_actionPerformed(e);
}
});
- grpsFromSelection.setText("Make Groups for selection");
+ grpsFromSelection.setText("Make Groups For Selection");
grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
deleteGroups_actionPerformed(e);
}
});
+ createGroup.setText("Create group");
+ createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ createGroup.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroup_actionPerformed(e);
+ }
+ });
+ unGroup.setText("Remove Group");
+ unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
+ unGroup.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ unGroup_actionPerformed(e);
+ }
+ });
copy.setText("Copy");
copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
- selectMenu.add(deleteGroups);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
// selectMenu.addSeparator();
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
+
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ }
protected void copy_actionPerformed(ActionEvent e)
{
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
name = new JTextArea(1, 12);
JvSwingUtils.mgAddtoLayout(cpanel,
- "Short descriptive name for service", new JLabel("Name:"),
+ "Short descriptive name for service", new JLabel(MessageManager.getString("label.name")),
name, "wrap");
action = new JComboBox();
JvSwingUtils
.mgAddtoLayout(
cpanel,
"What kind of function the service performs (e.g. alignment, analysis, search, etc).",
- new JLabel("Service Action:"), action, "wrap");
+ new JLabel(MessageManager.getString("label.service_action")), action, "wrap");
descr = new JTextArea(4, 60);
descrVp = new JScrollPane();
descrVp.setViewportView(descr);
.mgAddtoLayout(
cpanel,
"URL to post data to service. Include any special parameters needed here",
- new JLabel("POST URL:"), urlVp, "wrap");
+ new JLabel(MessageManager.getString("label.post_url")), urlVp, "wrap");
urlsuff = new JTextArea();
urlsuff.setColumns(60);
.mgAddtoLayout(
cpanel,
"Optional suffix added to URL when retrieving results from service",
- new JLabel("URL Suffix:"), urlsuff, "wrap");
+ new JLabel(MessageManager.getString("label.url_suffix")), urlsuff, "wrap");
// input options
// details.add(cpanel = new JPanel(), BorderLayout.CENTER);
// cpanel.setLayout(new FlowLayout());
- hSeparable = new JCheckBox("per Sequence");
+ hSeparable = new JCheckBox(MessageManager.getString("label.per_seq"));
hSeparable
.setToolTipText("<html>"
+ JvSwingUtils
}
});
- vSeparable = new JCheckBox("Results are vertically separable");
+ vSeparable = new JCheckBox(MessageManager.getString("label.result_vertically_separable"));
vSeparable
.setToolTipText("<html>"
+ JvSwingUtils
-#Thu Sep 06 17:55:29 BST 2012
+#Thu Oct 17 10:35:33 BST 2013
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
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.schemabinding.version2;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AnnotationColours implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _aboveThreshold.
- */
- private int _aboveThreshold;
-
- /**
- * keeps track of state for field: _aboveThreshold
- */
- private boolean _has_aboveThreshold;
-
- /**
- * Field _annotation.
- */
- private java.lang.String _annotation;
-
- /**
- * Field _minColour.
- */
- private int _minColour;
-
- /**
- * keeps track of state for field: _minColour
- */
- private boolean _has_minColour;
-
- /**
- * Field _maxColour.
- */
- private int _maxColour;
-
- /**
- * keeps track of state for field: _maxColour
- */
- private boolean _has_maxColour;
-
- /**
- * Field _colourScheme.
- */
- private java.lang.String _colourScheme;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public AnnotationColours()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- */
- public void deleteAboveThreshold()
- {
- this._has_aboveThreshold = false;
- }
-
- /**
- */
- public void deleteMaxColour()
- {
- this._has_maxColour = false;
- }
-
- /**
- */
- public void deleteMinColour()
- {
- this._has_minColour = false;
- }
-
- /**
- */
- public void deleteThreshold()
- {
- this._has_threshold = false;
- }
-
- /**
- * Returns the value of field 'aboveThreshold'.
- *
- * @return the value of field 'AboveThreshold'.
- */
- public int getAboveThreshold()
- {
- return this._aboveThreshold;
- }
-
- /**
- * Returns the value of field 'annotation'.
- *
- * @return the value of field 'Annotation'.
- */
- public java.lang.String getAnnotation()
- {
- return this._annotation;
- }
-
- /**
- * Returns the value of field 'colourScheme'.
- *
- * @return the value of field 'ColourScheme'.
- */
- public java.lang.String getColourScheme()
- {
- return this._colourScheme;
- }
-
- /**
- * Returns the value of field 'maxColour'.
- *
- * @return the value of field 'MaxColour'.
- */
- public int getMaxColour()
- {
- return this._maxColour;
- }
-
- /**
- * Returns the value of field 'minColour'.
- *
- * @return the value of field 'MinColour'.
- */
- public int getMinColour()
- {
- return this._minColour;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold()
- {
- return this._threshold;
- }
-
- /**
- * Method hasAboveThreshold.
- *
- * @return true if at least one AboveThreshold has been added
- */
- public boolean hasAboveThreshold()
- {
- return this._has_aboveThreshold;
- }
-
- /**
- * Method hasMaxColour.
- *
- * @return true if at least one MaxColour has been added
- */
- public boolean hasMaxColour()
- {
- return this._has_maxColour;
- }
-
- /**
- * Method hasMinColour.
- *
- * @return true if at least one MinColour has been added
- */
- public boolean hasMinColour()
- {
- return this._has_minColour;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold()
- {
- return this._has_threshold;
- }
-
- /**
- * 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 'aboveThreshold'.
- *
- * @param aboveThreshold
- * the value of field 'aboveThreshold'.
- */
- public void setAboveThreshold(final int aboveThreshold)
- {
- this._aboveThreshold = aboveThreshold;
- this._has_aboveThreshold = true;
- }
-
- /**
- * Sets the value of field 'annotation'.
- *
- * @param annotation
- * the value of field 'annotation'.
- */
- public void setAnnotation(final java.lang.String annotation)
- {
- this._annotation = annotation;
- }
-
- /**
- * Sets the value of field 'colourScheme'.
- *
- * @param colourScheme
- * the value of field 'colourScheme'.
- */
- public void setColourScheme(final java.lang.String colourScheme)
- {
- this._colourScheme = colourScheme;
- }
-
- /**
- * Sets the value of field 'maxColour'.
- *
- * @param maxColour
- * the value of field 'maxColour'.
- */
- public void setMaxColour(final int maxColour)
- {
- this._maxColour = maxColour;
- this._has_maxColour = true;
- }
-
- /**
- * Sets the value of field 'minColour'.
- *
- * @param minColour
- * the value of field 'minColour'.
- */
- public void setMinColour(final int minColour)
- {
- this._minColour = minColour;
- this._has_minColour = 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;
- }
-
- /**
- * 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.schemabinding.version2.AnnotationColours
- */
- public static jalview.schemabinding.version2.AnnotationColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller
- .unmarshal(
- jalview.schemabinding.version2.AnnotationColours.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 AnnotationColours implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _aboveThreshold.
+ */
+ private int _aboveThreshold;
+
+ /**
+ * keeps track of state for field: _aboveThreshold
+ */
+ private boolean _has_aboveThreshold;
+
+ /**
+ * Field _annotation.
+ */
+ private java.lang.String _annotation;
+
+ /**
+ * Field _minColour.
+ */
+ private int _minColour;
+
+ /**
+ * keeps track of state for field: _minColour
+ */
+ private boolean _has_minColour;
+
+ /**
+ * Field _maxColour.
+ */
+ private int _maxColour;
+
+ /**
+ * keeps track of state for field: _maxColour
+ */
+ private boolean _has_maxColour;
+
+ /**
+ * Field _colourScheme.
+ */
+ private java.lang.String _colourScheme;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _perSequence.
+ */
+ private boolean _perSequence;
+
+ /**
+ * keeps track of state for field: _perSequence
+ */
+ private boolean _has_perSequence;
+
+ /**
+ * Field _predefinedColours.
+ */
+ private boolean _predefinedColours;
+
+ /**
+ * keeps track of state for field: _predefinedColours
+ */
+ private boolean _has_predefinedColours;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AnnotationColours() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteAboveThreshold(
+ ) {
+ this._has_aboveThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteMaxColour(
+ ) {
+ this._has_maxColour= false;
+ }
+
+ /**
+ */
+ public void deleteMinColour(
+ ) {
+ this._has_minColour= false;
+ }
+
+ /**
+ */
+ public void deletePerSequence(
+ ) {
+ this._has_perSequence= false;
+ }
+
+ /**
+ */
+ public void deletePredefinedColours(
+ ) {
+ this._has_predefinedColours= false;
+ }
+
+ /**
+ */
+ public void deleteThreshold(
+ ) {
+ this._has_threshold= false;
+ }
+
+ /**
+ * Returns the value of field 'aboveThreshold'.
+ *
+ * @return the value of field 'AboveThreshold'.
+ */
+ public int getAboveThreshold(
+ ) {
+ return this._aboveThreshold;
+ }
+
+ /**
+ * Returns the value of field 'annotation'.
+ *
+ * @return the value of field 'Annotation'.
+ */
+ public java.lang.String getAnnotation(
+ ) {
+ return this._annotation;
+ }
+
+ /**
+ * Returns the value of field 'colourScheme'.
+ *
+ * @return the value of field 'ColourScheme'.
+ */
+ public java.lang.String getColourScheme(
+ ) {
+ return this._colourScheme;
+ }
+
+ /**
+ * Returns the value of field 'maxColour'.
+ *
+ * @return the value of field 'MaxColour'.
+ */
+ public int getMaxColour(
+ ) {
+ return this._maxColour;
+ }
+
+ /**
+ * Returns the value of field 'minColour'.
+ *
+ * @return the value of field 'MinColour'.
+ */
+ public int getMinColour(
+ ) {
+ return this._minColour;
+ }
+
+ /**
+ * Returns the value of field 'perSequence'.
+ *
+ * @return the value of field 'PerSequence'.
+ */
+ public boolean getPerSequence(
+ ) {
+ return this._perSequence;
+ }
+
+ /**
+ * Returns the value of field 'predefinedColours'.
+ *
+ * @return the value of field 'PredefinedColours'.
+ */
+ public boolean getPredefinedColours(
+ ) {
+ return this._predefinedColours;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold(
+ ) {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAboveThreshold.
+ *
+ * @return true if at least one AboveThreshold has been added
+ */
+ public boolean hasAboveThreshold(
+ ) {
+ return this._has_aboveThreshold;
+ }
+
+ /**
+ * Method hasMaxColour.
+ *
+ * @return true if at least one MaxColour has been added
+ */
+ public boolean hasMaxColour(
+ ) {
+ return this._has_maxColour;
+ }
+
+ /**
+ * Method hasMinColour.
+ *
+ * @return true if at least one MinColour has been added
+ */
+ public boolean hasMinColour(
+ ) {
+ return this._has_minColour;
+ }
+
+ /**
+ * Method hasPerSequence.
+ *
+ * @return true if at least one PerSequence has been added
+ */
+ public boolean hasPerSequence(
+ ) {
+ return this._has_perSequence;
+ }
+
+ /**
+ * Method hasPredefinedColours.
+ *
+ * @return true if at least one PredefinedColours has been added
+ */
+ public boolean hasPredefinedColours(
+ ) {
+ return this._has_predefinedColours;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold(
+ ) {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'perSequence'.
+ *
+ * @return the value of field 'PerSequence'.
+ */
+ public boolean isPerSequence(
+ ) {
+ return this._perSequence;
+ }
+
+ /**
+ * Returns the value of field 'predefinedColours'.
+ *
+ * @return the value of field 'PredefinedColours'.
+ */
+ public boolean isPredefinedColours(
+ ) {
+ return this._predefinedColours;
+ }
+
+ /**
+ * 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 'aboveThreshold'.
+ *
+ * @param aboveThreshold the value of field 'aboveThreshold'.
+ */
+ public void setAboveThreshold(
+ final int aboveThreshold) {
+ this._aboveThreshold = aboveThreshold;
+ this._has_aboveThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'annotation'.
+ *
+ * @param annotation the value of field 'annotation'.
+ */
+ public void setAnnotation(
+ final java.lang.String annotation) {
+ this._annotation = annotation;
+ }
+
+ /**
+ * Sets the value of field 'colourScheme'.
+ *
+ * @param colourScheme the value of field 'colourScheme'.
+ */
+ public void setColourScheme(
+ final java.lang.String colourScheme) {
+ this._colourScheme = colourScheme;
+ }
+
+ /**
+ * Sets the value of field 'maxColour'.
+ *
+ * @param maxColour the value of field 'maxColour'.
+ */
+ public void setMaxColour(
+ final int maxColour) {
+ this._maxColour = maxColour;
+ this._has_maxColour = true;
+ }
+
+ /**
+ * Sets the value of field 'minColour'.
+ *
+ * @param minColour the value of field 'minColour'.
+ */
+ public void setMinColour(
+ final int minColour) {
+ this._minColour = minColour;
+ this._has_minColour = true;
+ }
+
+ /**
+ * Sets the value of field 'perSequence'.
+ *
+ * @param perSequence the value of field 'perSequence'.
+ */
+ public void setPerSequence(
+ final boolean perSequence) {
+ this._perSequence = perSequence;
+ this._has_perSequence = true;
+ }
+
+ /**
+ * Sets the value of field 'predefinedColours'.
+ *
+ * @param predefinedColours the value of field
+ * 'predefinedColours'.
+ */
+ public void setPredefinedColours(
+ final boolean predefinedColours) {
+ this._predefinedColours = predefinedColours;
+ this._has_predefinedColours = 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;
+ }
+
+ /**
+ * 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.schemabinding.version2.AnnotationColours
+ */
+ public static jalview.schemabinding.version2.AnnotationColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.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 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.schemabinding.version2.descriptors;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.AnnotationColours;
*
* @version $Revision$ $Date$
*/
-public class AnnotationColoursDescriptor extends
- org.exolab.castor.xml.util.XMLClassDescriptorImpl
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public AnnotationColoursDescriptor()
- {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "AnnotationColours";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- // -- initialize attribute descriptors
-
- // -- _aboveThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasAboveThreshold())
- {
- return null;
+public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AnnotationColoursDescriptor() {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "AnnotationColours";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ //-- initialize attribute descriptors
+
+ //-- _aboveThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AnnotationColours target = (AnnotationColours) object;
+ if (!target.hasAboveThreshold()) { return null; }
+ return new java.lang.Integer(target.getAboveThreshold());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AnnotationColours target = (AnnotationColours) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteAboveThreshold();
+ return;
+ }
+ target.setAboveThreshold( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _aboveThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
- return new java.lang.Integer(target.getAboveThreshold());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteAboveThreshold();
- return;
- }
- target.setAboveThreshold(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _annotation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AnnotationColours target = (AnnotationColours) object;
+ return target.getAnnotation();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AnnotationColours target = (AnnotationColours) object;
+ target.setAnnotation( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _annotation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _aboveThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _annotation
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_annotation", "annotation",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- return target.getAnnotation();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- target.setAnnotation((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _minColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AnnotationColours target = (AnnotationColours) object;
+ if (!target.hasMinColour()) { return null; }
+ return new java.lang.Integer(target.getMinColour());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AnnotationColours target = (AnnotationColours) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteMinColour();
+ return;
+ }
+ target.setMinColour( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _minColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _annotation
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- // -- _minColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_minColour", "minColour",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasMinColour())
- {
- return null;
+ desc.setValidator(fieldValidator);
+ //-- _maxColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AnnotationColours target = (AnnotationColours) object;
+ if (!target.hasMaxColour()) { return null; }
+ return new java.lang.Integer(target.getMaxColour());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AnnotationColours target = (AnnotationColours) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteMaxColour();
+ return;
+ }
+ target.setMaxColour( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _maxColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
}
- return new java.lang.Integer(target.getMinColour());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteMinColour();
- return;
- }
- target.setMinColour(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _colourScheme
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AnnotationColours target = (AnnotationColours) object;
+ return target.getColourScheme();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AnnotationColours target = (AnnotationColours) object;
+ target.setColourScheme( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _colourScheme
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _minColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _maxColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_maxColour", "maxColour",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasMaxColour())
- {
- return null;
+ desc.setValidator(fieldValidator);
+ //-- _threshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AnnotationColours target = (AnnotationColours) object;
+ if (!target.hasThreshold()) { return null; }
+ return new java.lang.Float(target.getThreshold());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AnnotationColours target = (AnnotationColours) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteThreshold();
+ return;
+ }
+ target.setThreshold( ((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _threshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
}
- return new java.lang.Integer(target.getMaxColour());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteMaxColour();
- return;
- }
- target.setMaxColour(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _perSequence
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_perSequence", "perSequence", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AnnotationColours target = (AnnotationColours) object;
+ if (!target.hasPerSequence()) { return null; }
+ return (target.getPerSequence() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AnnotationColours target = (AnnotationColours) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deletePerSequence();
+ return;
+ }
+ target.setPerSequence( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _perSequence
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _maxColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _colourScheme
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_colourScheme", "colourScheme",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- return target.getColourScheme();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- target.setColourScheme((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _predefinedColours
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_predefinedColours", "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AnnotationColours target = (AnnotationColours) object;
+ if (!target.hasPredefinedColours()) { return null; }
+ return (target.getPredefinedColours() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AnnotationColours target = (AnnotationColours) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deletePredefinedColours();
+ return;
+ }
+ target.setPredefinedColours( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _predefinedColours
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _colourScheme
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
}
- desc.setValidator(fieldValidator);
- // -- _threshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Float.TYPE, "_threshold", "threshold",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasThreshold())
- {
- return null;
- }
- return new java.lang.Float(target.getThreshold());
- }
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteThreshold();
- return;
- }
- target.setThreshold(((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
+ //-----------/
+ //- Methods -/
+ //-----------/
- // -- validation code for: _threshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode(
+ ) {
+ return null;
}
- desc.setValidator(fieldValidator);
- // -- initialize element descriptors
-
- }
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- return super.getIdentity();
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no
+ * identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+ ) {
+ return super.getIdentity();
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass()
- {
- return jalview.schemabinding.version2.AnnotationColours.class;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass(
+ ) {
+ return jalview.schemabinding.version2.AnnotationColours.class;
+ }
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix()
- {
- return _nsPrefix;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix(
+ ) {
+ return _nsPrefix;
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI()
- {
- return _nsURI;
- }
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and
+ * unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI(
+ ) {
+ return _nsURI;
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator()
- {
- return this;
- }
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator(
+ ) {
+ return this;
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName()
- {
- return _xmlName;
- }
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName(
+ ) {
+ return _xmlName;
+ }
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition()
- {
- return _elementDefinition;
- }
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that
+ * of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition(
+ ) {
+ return _elementDefinition;
+ }
}
*/
package jalview.schemes;
+import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceI;
import java.awt.Color;
+import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Map;
ColourSchemeI colourScheme;
- public boolean predefinedColours = false;
+ private boolean predefinedColours = false;
- public boolean seqAssociated = false;
+ private boolean seqAssociated = false;
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
return currentColour;
}
+ public boolean isPredefinedColours()
+ {
+ return predefinedColours;
+ }
+
+ public void setPredefinedColours(boolean predefinedColours)
+ {
+ this.predefinedColours = predefinedColours;
+ }
+
public boolean isSeqAssociated()
{
return seqAssociated;
{
seqAssociated = sassoc;
}
+ @Override
+ public void setConsensus(Hashtable[] consensus)
+ {
+ if (colourScheme!=null)
+ {
+ colourScheme.setConsensus(consensus);
+ }
+ }
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ if (colourScheme!=null)
+ {
+ colourScheme.setConservation(cons);
+ }
+ }
+ @Override
+ public void setConservationInc(int i)
+ {
+ if (colourScheme!=null)
+ {
+ colourScheme.setConservationInc(i);
+ }
+ }
}
public void refresh()
{
- if (lastrefresh != annotation._rnasecstr.hashCode()
+ if ((annotation._rnasecstr == null
+ || lastrefresh != annotation._rnasecstr.hashCode())
&& annotation.isValidStruc())
{
annotation.getRNAStruc();
return;
}
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
+ // This loop will find the first rna structure annotation by which to colour
+ // the sequences.
+ AlignmentAnnotation[] annotations = av.getAlignment().getAlignmentAnnotation();
+ for (int i = 0; i < annotations.length; i++) {
+
+ // is this a sensible way of determining type of annotation?
+ if (annotations[i].getRNAStruc() != null) {
+ currentAnnotation = annotations[i];
+ break;
+ }
+ }
+ if (currentAnnotation == null)
+ {
+ System.err.println("Jalview is about to try and colour by RNAHelices even"
+ + " though there are no RNA secondary structure annotations present!");
+ currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
+ }
+
RNAHelicesColour rhc = null;
rhc = new RNAHelicesColour(currentAnnotation);
}
Hashtable mappingData = new Hashtable();
-
+ private static StructureSelectionManager nullProvider = null;
public static StructureSelectionManager getStructureSelectionManager(
StructureSelectionManagerProvider context)
{
- if (context==null)
- {
- throw new Error("Implementation error. Structure selection manager's context is 'null'", new NullPointerException("SSM context is null"));
+ if (context==null) {
+ if (nullProvider == null)
+ {
+ if (instances != null)
+ {
+ throw new Error(
+ "Implementation error. Structure selection manager's context is 'null'",
+ new NullPointerException("SSM context is null"));
+ }
+ else
+ {
+ nullProvider = new StructureSelectionManager();
+ }
+ return nullProvider;
+ }
}
if (instances == null)
{
StructureSelectionManager instance = instances.get(context);
if (instance == null)
{
- instances.put(context, instance = new StructureSelectionManager());
+ if (nullProvider!=null)
+ {
+ instance = nullProvider;
+ } else {
+ instance = new StructureSelectionManager();
+ }
+ instances.put(context, instance);
}
return instance;
}
--- /dev/null
+package jalview.util;
+
+import java.text.MessageFormat;
+import java.util.Locale;
+import java.util.ResourceBundle;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ *
+ * @author David Roldan Martinez
+ * @author Thomas Abeel
+ *
+ *
+ */
+public class MessageManager {
+
+ private static ResourceBundle rb;
+
+ private static Logger log=Logger.getLogger(MessageManager.class.getCanonicalName());
+
+ private static Locale loc;
+
+
+
+ static{
+ try {
+ /* Localize Java dialogs */
+ loc = Locale.getDefault();
+ // Locale.setDefault(loc);
+ /* Getting messages for GV */
+ log.info("Getting messages for lang: "+loc);
+ rb = ResourceBundle.getBundle("lang.Messages", loc);
+ if (log.isLoggable(Level.FINEST)) {
+ // this might take a while, so we only do it if it will be shown
+ log.finest("Language keys: "+rb.keySet());
+ }
+ } catch (Exception q) {
+ log.warning("Exception when initting Locale for i18n messages\n"+q.getMessage());
+ q.printStackTrace();
+ }
+ catch (Error v)
+ {
+ log.warning("Error when initting Locale for i18n messages\n"+v.getMessage());
+ v.printStackTrace();
+ }
+
+
+ }
+
+ public static String getString(String key){
+ String value = "[missing key] " + key;
+ try{
+ value = rb.getString(key);
+ }catch(Exception e){
+ log.warning("I18N missing: "+loc+"\t"+key);
+ }
+ return value;
+ }
+
+ public static Locale getLocale() {
+ return loc;
+ }
+ public static String formatMessage(String key, Object[] params){
+ return MessageFormat.format(rb.getString(key), params);
+ }
+}
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
+import java.awt.Color;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Hashtable;
protected boolean showConsensus = true;
+ Hashtable sequenceColours;
+
/**
* Property change listener for changes in alignment
*
oldrfs.clear();
}
+ @Override
+ public Color getSequenceColour(SequenceI seq)
+ {
+ Color sqc=Color.white;
+ if (sequenceColours != null)
+ {
+ sqc = (Color) sequenceColours.get(seq);
+ if (sqc == null) {
+ sqc = Color.white;
+ }
+ }
+ return sqc;
+ }
+
+ @Override
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+
+ if (col == null)
+ {
+ sequenceColours.remove(seq);
+ }
+ else
+ {
+ sequenceColours.put(seq, col);
+ }
+ }
+
+ @Override
+ public void updateSequenceIdColours()
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+ for (SequenceGroup sg : alignment.getGroups())
+ {
+ if (sg.idColour != null)
+ {
+ for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
+ {
+ sequenceColours.put(s, sg.idColour);
+ }
+ }
+ }
+ }
+
+ @Override
+ public void clearSequenceColours()
+ {
+ sequenceColours = null;
+ };
}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import java.util.Hashtable;
public class ConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
+ private long nseq=-1;
+
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
hconsensus = new Hashtable[aWidth];
try
{
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
+ SequenceI aseqs[] = alignment.getSequencesArray();
+ nseq = aseqs.length;
+ AAFrequency.calculate(aseqs, 0,
alignment.getWidth(), hconsensus, true);
} catch (ArrayIndexOutOfBoundsException x)
{
{
AAFrequency.completeConsensus(consensus, hconsensus, 0,
hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo());
+ alignViewport.isShowSequenceLogo(), nseq);
}
}
}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
public class StrucConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
Hashtable[] hStrucConsensus;
+ private long nseq=-1;
+
@Override
public void run()
{
try
{
- jalview.analysis.StructureFrequency.calculate(
- alignment.getSequencesArray(), 0, alignment.getWidth(),
+ final SequenceI[] arr=
+ alignment.getSequencesArray();
+ nseq = arr.length;
+ jalview.analysis.StructureFrequency.calculate(arr, 0, alignment.getWidth(),
hStrucConsensus, true, rnaStruc);
} catch (ArrayIndexOutOfBoundsException x)
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo());
+ alignViewport.isShowSequenceLogo(), nseq);
}
}
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
import java.util.ArrayList;
import java.util.List;
initViewportParams();
}
- protected void initViewportParams()
- {
- ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
- getCalcId(),
- new AAConSettings(true, service, this.preset,
- (arguments != null) ? JabaParamStore
- .getJwsArgsfromJaba(arguments) : null), true);
- }
-
- @Override
- public void updateParameters(WsParamSetI newpreset,
- java.util.List<Argument> newarguments)
- {
- super.updateParameters(newpreset, newarguments);
- initViewportParams();
- };
-
public String getServiceActionText()
{
return "calculating Amino acid consensus using AACon service";
}
}
+ @Override
public String getCalcId()
{
- return SequenceAnnotationWSClient.AAConCalcId;
+ return CALC_ID;
}
+ private static String CALC_ID="jabaws2.AACon";
- public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
+ public static AlignAnalysisUIText getAlignAnalysisUITest()
{
- for (AlignmentAnnotation aa : alignPanel.getAlignment().findAnnotation(
- SequenceAnnotationWSClient.AAConCalcId))
- {
- alignPanel.getAlignment().deleteAnnotation(aa);
- }
+ return new AlignAnalysisUIText(
+ compbio.ws.client.Services.AAConWS.toString(),
+ jalview.ws.jws2.AAConClient.class, CALC_ID, false, true, true,
+ "AACon Calculations",
+ "When checked, AACon calculations are updated automatically.",
+ "Change AACon Settings...",
+ "Modify settings for AACon calculations.");
}
}
import compbio.data.sequence.ScoreManager.ScoreHolder;
import compbio.metadata.Argument;
-public class AADisorderClient extends JabawsAlignCalcWorker implements
+public class AADisorderClient extends JabawsCalcWorker implements
AlignCalcWorkerI
{
import jalview.bin.Cache;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
import java.util.HashSet;
import java.util.Set;
{ Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
Services.ProbconsWS, Services.TcoffeeWS, Services.AAConWS,
Services.DisemblWS, Services.GlobPlotWS, Services.IUPredWS,
- Services.JronnWS };
+ Services.JronnWS, Services.RNAalifoldWS };
/*
* (non-Javadoc)
jabasws2 = true;
srv_set = registry.getSupportedServices();
+
+ // dan test
+ System.out.println("registry.getSupportedServices: " + srv_set.toString());
+
svccategories = registry.getServiceCategories();
+
+ // dan test
+// System.out.println("registry.getServiceCategories: " + svccategories.toString());
}
} catch (Exception ex)
String description = registry.getServiceDescription(srv);
- svc = new Jws2Instance(jwsservers, srv.toString(),
+ svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
cat.name, description, service);
}
if (svc == null)
{
- svc = new Jws2Instance(jwsservers, srv.toString(),
+ svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
cat.name, "JABAWS 1 Alignment Service", service);
}
jws2Discoverer.addService(jwsservers, svc);
*/
package jalview.ws.jws2;
-import jalview.analysis.AlignSeq;
-import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.gui.IProgressIndicator;
-import jalview.workers.AlignCalcWorker;
-import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
import java.util.List;
-import java.util.Map;
-import compbio.data.msa.SequenceAnnotation;
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.Score;
-import compbio.data.sequence.ScoreManager;
import compbio.metadata.Argument;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Option;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.WrongParameterException;
-public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
+public abstract class JabawsAlignCalcWorker extends JabawsCalcWorker
{
- Jws2Instance service;
-
- @SuppressWarnings("unchecked")
- protected SequenceAnnotation aaservice;
-
- protected ScoreManager scoremanager;
-
- protected WsParamSetI preset;
-
- protected List<Argument> arguments;
public JabawsAlignCalcWorker(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
super(alignViewport, alignPanel);
}
-
- IProgressIndicator guiProgress;
-
+
+
+
+
public JabawsAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
WsParamSetI preset, List<Argument> paramset)
{
- this(alignFrame.getCurrentView(), alignFrame.alignPanel);
- this.guiProgress = alignFrame;
- this.preset = preset;
- this.arguments = paramset;
- this.service = service;
- aaservice = (SequenceAnnotation) service.service;
-
- }
-
- public WsParamSetI getPreset()
- {
- return preset;
- }
-
- public List<Argument> getArguments()
- {
- return arguments;
+ super(service, alignFrame, preset, paramset);
}
/**
- * reconfigure and restart the AAConClient. This method will spawn a new
- * thread that will wait until any current jobs are finished, modify the
- * parameters and restart the conservation calculation with the new values.
- *
- * @param newpreset
- * @param newarguments
+ * Recover any existing parameters for this service
*/
- public void updateParameters(final WsParamSetI newpreset,
- final List<Argument> newarguments)
- {
- preset = newpreset;
- arguments = newarguments;
- calcMan.startWorker(this);
- }
-
- public List<Option> getJabaArguments()
+ protected void initViewportParams()
{
- List<Option> newargs = new ArrayList<Option>();
- if (preset != null && preset instanceof JabaWsParamSet)
- {
- newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
- }
- if (arguments != null && arguments.size() > 0)
- {
- for (Argument rg : arguments)
- {
- if (Option.class.isAssignableFrom(rg.getClass()))
- {
- newargs.add((Option) rg);
- }
- }
- }
- return newargs;
+ ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
+ getCalcId(),
+ new AAConSettings(true, service, this.preset,
+ (arguments != null) ? JabaParamStore
+ .getJwsArgsfromJaba(arguments) : null), true);
}
- @Override
- public void run()
- {
- if (aaservice == null)
- {
- return;
- }
- long progressId = -1;
-
- int serverErrorsLeft = 3;
-
- String rslt = "JOB NOT DEFINED";
- StringBuffer msg = new StringBuffer();
- try
- {
- if (checkDone())
- {
- return;
- }
- List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(alignViewport
- .getAlignment(), bySequence ? alignViewport.getSelectionGroup() : null);
-
- if (seqs == null)
- {
- calcMan.workerComplete(this);
- return;
- }
-
- AlignmentAnnotation[] aa = alignViewport.getAlignment()
- .getAlignmentAnnotation();
- if (guiProgress != null)
- {
- guiProgress.setProgressBar("JABA " + getServiceActionText(),
- progressId = System.currentTimeMillis());
- }
- if (preset == null && arguments == null)
- {
- rslt = aaservice.analize(seqs);
- }
- else
- {
- try
- {
- rslt = aaservice.customAnalize(seqs, getJabaArguments());
- } catch (WrongParameterException x)
- {
- throw new JobSubmissionException(
- "Invalid parameter set. Check Jalview implementation.", x);
-
- }
- }
- boolean finished = false;
- long rpos = 0;
- do
- {
- JobStatus status = aaservice.getJobStatus(rslt);
- if (status.equals(JobStatus.FINISHED))
- {
- finished = true;
- }
- if (calcMan.isPending(this) && this instanceof AAConClient)
- {
- finished = true;
- // cancel this job and yield to the new job
- try
- {
- if (aaservice.cancelJob(rslt))
- {
- System.err.println("Cancelled AACon job: " + rslt);
- }
- else
- {
- System.err.println("FAILED TO CANCEL AACon job: " + rslt);
- }
-
- } catch (Exception x)
- {
-
- }
-
- return;
- }
- long cpos;
- ChunkHolder stats = null;
- do
- {
- cpos = rpos;
- boolean retry = false;
- do
- {
- try
- {
- stats = aaservice.pullExecStatistics(rslt, rpos);
- } catch (Exception x)
- {
-
- if (x.getMessage().contains(
- "Position in a file could not be negative!"))
- {
- // squash index out of bounds exception- seems to happen for
- // disorder predictors which don't (apparently) produce any
- // progress information and JABA server throws an exception
- // because progress length is -1.
- stats = null;
- }
- else
- {
- if (--serverErrorsLeft > 0)
- {
- retry = true;
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException q)
- {
- }
- ;
- }
- else
- {
- throw x;
- }
- }
- }
- } while (retry);
- if (stats != null)
- {
- System.out.print(stats.getChunk());
- msg.append(stats);
- rpos = stats.getNextPosition();
- }
- } while (stats != null && rpos > cpos);
-
- if (!finished && status.equals(JobStatus.FAILED))
- {
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- ;
- }
- } while (!finished);
- if (serverErrorsLeft > 0)
- {
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- ;
- scoremanager = aaservice.getAnnotation(rslt);
- if (scoremanager != null)
- {
- jalview.bin.Cache.log
- .debug("Updating result annotation from Job " + rslt
- + " at " + service.getUri());
- updateResultAnnotation(true);
- ap.adjustAnnotationHeight();
- }
- }
- }
-
- catch (JobSubmissionException x)
- {
-
- System.err.println("submission error with " + getServiceActionText()
- + " :");
- x.printStackTrace();
- calcMan.workerCannotRun(this);
- } catch (ResultNotAvailableException x)
- {
- System.err.println("collection error:\nJob ID: " + rslt);
- x.printStackTrace();
- calcMan.workerCannotRun(this);
-
- } catch (OutOfMemoryError error)
- {
- calcMan.workerCannotRun(this);
-
- // consensus = null;
- // hconsensus = null;
- ap.raiseOOMWarning(getServiceActionText(), error);
- } catch (Exception x)
- {
- calcMan.workerCannotRun(this);
-
- // consensus = null;
- // hconsensus = null;
- System.err
- .println("Blacklisting worker due to unexpected exception:");
- x.printStackTrace();
- } finally
- {
-
- calcMan.workerComplete(this);
- if (ap != null)
- {
- calcMan.workerComplete(this);
- if (guiProgress != null && progressId != -1)
- {
- guiProgress.setProgressBar("", progressId);
- }
- ap.paintAlignment(true);
- }
- if (msg.length() > 0)
- {
- // TODO: stash message somewhere in annotation or alignment view.
- // code below shows result in a text box popup
- /*
- * jalview.gui.CutAndPasteTransfer cap = new
- * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
- * jalview.gui.Desktop.addInternalFrame(cap,
- * "Job Status for "+getServiceActionText(), 600, 400);
- */
- }
- }
-
- }
-
- @Override
- public void updateAnnotation()
- {
- updateResultAnnotation(false);
- }
-
- public abstract void updateResultAnnotation(boolean immediate);
-
- public abstract String getServiceActionText();
-
- boolean submitGaps = true;
-
- boolean alignedSeqs = true;
-
- boolean nucleotidesAllowed = false;
-
- boolean proteinAllowed = false;
-
/**
- * record sequences for mapping result back to afterwards
- */
- protected boolean bySequence = false;
-
- Map<String, SequenceI> seqNames;
-
- boolean[] gapMap;
-
- int realw;
-
- int start,end;
-
- public List<FastaSequence> getInputSequences(AlignmentI alignment, AnnotatedCollectionI inputSeqs)
- {
- if (alignment == null || alignment.getWidth() <= 0
- || alignment.getSequences() == null
- // || (alignedSeqs && !alignment.isAligned() && !submitGaps)
- || alignment.isNucleotide() ? !nucleotidesAllowed
- : !proteinAllowed)
- {
- return null;
- }
- if (inputSeqs==null || inputSeqs.getWidth()<=0 || inputSeqs.getSequences()==null || inputSeqs.getSequences().size()<1)
- {
- inputSeqs = alignment;
- }
-
- List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
-
- int minlen = 10;
- int ln = -1;
- if (bySequence)
- {
- seqNames = new HashMap<String, SequenceI>();
- }
- gapMap = new boolean[0];
- start=inputSeqs.getStartRes();
- end=inputSeqs.getEndRes();
-
- for (SequenceI sq : (List<SequenceI>) inputSeqs.getSequences())
- {
- if (sq.findPosition(end+1) -sq.findPosition(start+1) > minlen - 1)
- {
- String newname = SeqsetUtils.unique_name(seqs.size() + 1);
- // make new input sequence with or without gaps
- if (seqNames != null)
- {
- seqNames.put(newname, sq);
- }
- FastaSequence seq;
- if (submitGaps)
- {
- seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
- sq.getSequenceAsString()));
- if (gapMap == null || gapMap.length < seq.getSequence().length())
- {
- boolean[] tg = gapMap;
- gapMap = new boolean[seq.getLength()];
- System.arraycopy(tg, 0, gapMap, 0, tg.length);
- for (int p = tg.length; p < gapMap.length; p++)
- {
- gapMap[p] = false; // init as a gap
- }
- }
- for (int apos : sq.gapMap())
- {
- gapMap[apos] = true; // aligned.
- }
- }
- else
- {
- seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
- AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
- sq.getSequenceAsString(start,end+1))));
- }
- if (seq.getSequence().length() > ln)
- {
- ln = seq.getSequence().length();
- }
- }
- }
- if (alignedSeqs && submitGaps)
- {
- realw = 0;
- for (int i = 0; i < gapMap.length; i++)
- {
- if (gapMap[i])
- {
- realw++;
- }
- }
- // try real hard to return something submittable
- // TODO: some of AAcon measures need a minimum of two or three amino
- // acids at each position, and AAcon doesn't gracefully degrade.
- for (int p = 0; p < seqs.size(); p++)
- {
- FastaSequence sq = seqs.get(p);
- int l = sq.getSequence().length();
- // strip gapped columns
- char[] padded = new char[realw], orig = sq.getSequence()
- .toCharArray();
- for (int i = 0, pp = 0; i < realw; pp++)
- {
- if (gapMap[pp])
- {
- if (orig.length > pp)
- {
- padded[i++] = orig[pp];
- }
- else
- {
- padded[i++] = '-';
- }
- }
- }
- seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
- new String(padded)));
- }
- }
- return seqs;
- }
-
- /**
- * notify manager that we have started, and wait for a free calculation slot
*
- * @return true if slot is obtained and work still valid, false if another
- * thread has done our work for us.
+ * @return
*/
- boolean checkDone()
- {
- calcMan.notifyStart(this);
- ap.paintAlignment(false);
- while (!calcMan.notifyWorking(this))
- {
- if (calcMan.isWorking(this))
- {
- return true;
- }
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
-
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return true;
- }
- return false;
- }
+ public abstract String getCalcId();
- protected void createAnnotationRowsForScores(
- List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
- Score scr)
- {
- // simple annotation row
- AlignmentAnnotation annotation = alignViewport.getAlignment()
- .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
- null);
- if (alWidth == gapMap.length) // scr.getScores().size())
- {
- constructAnnotationFromScore(annotation, 0, alWidth, scr);
- ourAnnot.add(annotation);
- }
- }
- protected AlignmentAnnotation createAnnotationRowsForScores(
- List<AlignmentAnnotation> ourAnnot, String typeName,
- String calcId, SequenceI dseq, int base, Score scr)
- {
- System.out.println("Creating annotation on dseq:" + dseq.getStart()
- + " base is " + base + " and length=" + dseq.getLength()
- + " == " + scr.getScores().size());
- // AlignmentAnnotation annotation = new AlignmentAnnotation(
- // scr.getMethod(), typeName, new Annotation[]
- // {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
- // annotation.setCalcId(calcId);
- AlignmentAnnotation annotation = alignViewport.getAlignment()
- .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
- constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
- annotation.createSequenceMapping(dseq, base, false);
- annotation.adjustForAlignment();
- dseq.addAlignmentAnnotation(annotation);
- ourAnnot.add(annotation);
- return annotation;
- }
- private void constructAnnotationFromScore(AlignmentAnnotation annotation,
- int base, int alWidth, Score scr)
- {
- Annotation[] elm = new Annotation[alWidth];
- Iterator<Float> vals = scr.getScores().iterator();
- float m = 0f, x = 0f;
- for (int i = 0; vals.hasNext(); i++)
- {
- float val = vals.next().floatValue();
- if (i == 0)
- {
- m = val;
- x = val;
- }
- else
- {
- if (m > val)
- {
- m = val;
- }
- ;
- if (x < val)
- {
- x = val;
- }
- }
- // if we're at a gapped column then skip to next ungapped position
- if (gapMap != null && gapMap.length > 0)
- {
- while (!gapMap[i])
- {
- elm[i++] = new Annotation("", "", ' ', Float.NaN);
- }
- }
- elm[i] = new Annotation("", "" + val, ' ', val);
- }
- annotation.annotations = elm;
- annotation.belowAlignment = true;
- if (x < 0)
- {
- x = 0;
- }
- x += (x - m) * 0.1;
- annotation.graphMax = x;
- annotation.graphMin = m;
- annotation.validateRangeAndDisplay();
- }
-
- protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
+ @Override
+ public void updateParameters(WsParamSetI newpreset, java.util.List<Argument> newarguments)
{
- List<AlignmentAnnotation> our = ourAnnots;
- ourAnnots = ourAnnot;
- AlignmentI alignment = alignViewport.getAlignment();
- if (our != null)
- {
- if (our.size() > 0)
- {
- for (AlignmentAnnotation an : our)
- {
- if (!ourAnnots.contains(an))
- {
- // remove the old annotation
- alignment.deleteAnnotation(an);
- }
- }
- }
- our.clear();
-
- ap.adjustAnnotationHeight();
- }
+ super.updateParameters(newpreset, newarguments);
+ initViewportParams();
}
}
--- /dev/null
+package jalview.ws.jws2;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import compbio.data.msa.SequenceAnnotation;
+import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
+import compbio.metadata.Argument;
+import compbio.metadata.ChunkHolder;
+import compbio.metadata.JobStatus;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.Option;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.metadata.WrongParameterException;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.IProgressIndicator;
+import jalview.workers.AlignCalcWorker;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
+public abstract class JabawsCalcWorker extends AlignCalcWorker
+{
+
+ protected Jws2Instance service;
+ @SuppressWarnings("unchecked")
+ protected SequenceAnnotation aaservice;
+ protected ScoreManager scoremanager;
+ protected WsParamSetI preset;
+ protected List<Argument> arguments;
+ protected IProgressIndicator guiProgress;
+
+ public JabawsCalcWorker(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ public JabawsCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+ WsParamSetI preset, List<Argument> paramset)
+ {
+ this(alignFrame.getCurrentView(), alignFrame.alignPanel);
+ this.guiProgress = alignFrame;
+ this.preset = preset;
+ this.arguments = paramset;
+ this.service = service;
+ aaservice = (SequenceAnnotation) service.service;
+
+ }
+
+ public WsParamSetI getPreset()
+ {
+ return preset;
+ }
+
+ public List<Argument> getArguments()
+ {
+ return arguments;
+ }
+
+ /**
+ * reconfigure and restart the AAConClient. This method will spawn a new
+ * thread that will wait until any current jobs are finished, modify the
+ * parameters and restart the conservation calculation with the new values.
+ *
+ * @param newpreset
+ * @param newarguments
+ */
+ public void updateParameters(final WsParamSetI newpreset, final List<Argument> newarguments)
+ {
+ preset = newpreset;
+ arguments = newarguments;
+ calcMan.startWorker(this);
+ }
+
+ public List<Option> getJabaArguments()
+ {
+ List<Option> newargs = new ArrayList<Option>();
+ if (preset != null && preset instanceof JabaWsParamSet)
+ {
+ newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
+ }
+ if (arguments != null && arguments.size() > 0)
+ {
+ for (Argument rg : arguments)
+ {
+ if (Option.class.isAssignableFrom(rg.getClass()))
+ {
+ newargs.add((Option) rg);
+ }
+ }
+ }
+ return newargs;
+ }
+
+ @Override
+ public void run()
+ {
+ if (aaservice == null)
+ {
+ return;
+ }
+ long progressId = -1;
+
+ int serverErrorsLeft = 3;
+
+ String rslt = "JOB NOT DEFINED";
+ StringBuffer msg = new StringBuffer();
+ try
+ {
+ if (checkDone())
+ {
+ return;
+ }
+ List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(alignViewport
+ .getAlignment(), bySequence ? alignViewport.getSelectionGroup() : null);
+
+ if (seqs == null)
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+
+ AlignmentAnnotation[] aa = alignViewport.getAlignment()
+ .getAlignmentAnnotation();
+ if (guiProgress != null)
+ {
+ guiProgress.setProgressBar("JABA " + getServiceActionText(),
+ progressId = System.currentTimeMillis());
+ }
+ if (preset == null && arguments == null)
+ {
+ rslt = aaservice.analize(seqs);
+ }
+ else
+ {
+ try
+ {
+ rslt = aaservice.customAnalize(seqs, getJabaArguments());
+ } catch (WrongParameterException x)
+ {
+ throw new JobSubmissionException(
+ "Invalid parameter set. Check Jalview implementation.", x);
+
+ }
+ }
+ boolean finished = false;
+ long rpos = 0;
+ do
+ {
+ JobStatus status = aaservice.getJobStatus(rslt);
+ if (status.equals(JobStatus.FINISHED))
+ {
+ finished = true;
+ }
+ if (calcMan.isPending(this) && this instanceof AAConClient)
+ {
+ finished = true;
+ // cancel this job and yield to the new job
+ try
+ {
+ if (aaservice.cancelJob(rslt))
+ {
+ System.err.println("Cancelled AACon job: " + rslt);
+ }
+ else
+ {
+ System.err.println("FAILED TO CANCEL AACon job: " + rslt);
+ }
+
+ } catch (Exception x)
+ {
+
+ }
+
+ return;
+ }
+ long cpos;
+ ChunkHolder stats = null;
+ do
+ {
+ cpos = rpos;
+ boolean retry = false;
+ do
+ {
+ try
+ {
+ stats = aaservice.pullExecStatistics(rslt, rpos);
+ } catch (Exception x)
+ {
+
+ if (x.getMessage().contains(
+ "Position in a file could not be negative!"))
+ {
+ // squash index out of bounds exception- seems to happen for
+ // disorder predictors which don't (apparently) produce any
+ // progress information and JABA server throws an exception
+ // because progress length is -1.
+ stats = null;
+ }
+ else
+ {
+ if (--serverErrorsLeft > 0)
+ {
+ retry = true;
+ try
+ {
+ Thread.sleep(200);
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ }
+ else
+ {
+ throw x;
+ }
+ }
+ }
+ } while (retry);
+ if (stats != null)
+ {
+ System.out.print(stats.getChunk());
+ msg.append(stats);
+ rpos = stats.getNextPosition();
+ }
+ } while (stats != null && rpos > cpos);
+
+ if (!finished && status.equals(JobStatus.FAILED))
+ {
+ try
+ {
+ Thread.sleep(200);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ }
+ } while (!finished);
+ if (serverErrorsLeft > 0)
+ {
+ try
+ {
+ Thread.sleep(200);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ scoremanager = aaservice.getAnnotation(rslt);
+ if (scoremanager != null)
+ {
+ jalview.bin.Cache.log
+ .debug("Updating result annotation from Job " + rslt
+ + " at " + service.getUri());
+ updateResultAnnotation(true);
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
+
+ catch (JobSubmissionException x)
+ {
+
+ System.err.println("submission error with " + getServiceActionText()
+ + " :");
+ x.printStackTrace();
+ calcMan.workerCannotRun(this);
+ } catch (ResultNotAvailableException x)
+ {
+ System.err.println("collection error:\nJob ID: " + rslt);
+ x.printStackTrace();
+ calcMan.workerCannotRun(this);
+
+ } catch (OutOfMemoryError error)
+ {
+ calcMan.workerCannotRun(this);
+
+ // consensus = null;
+ // hconsensus = null;
+ ap.raiseOOMWarning(getServiceActionText(), error);
+ } catch (Exception x)
+ {
+ calcMan.workerCannotRun(this);
+
+ // consensus = null;
+ // hconsensus = null;
+ System.err
+ .println("Blacklisting worker due to unexpected exception:");
+ x.printStackTrace();
+ } finally
+ {
+
+ calcMan.workerComplete(this);
+ if (ap != null)
+ {
+ calcMan.workerComplete(this);
+ if (guiProgress != null && progressId != -1)
+ {
+ guiProgress.setProgressBar("", progressId);
+ }
+ ap.paintAlignment(true);
+ }
+ if (msg.length() > 0)
+ {
+ // TODO: stash message somewhere in annotation or alignment view.
+ // code below shows result in a text box popup
+ /*
+ * jalview.gui.CutAndPasteTransfer cap = new
+ * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
+ * jalview.gui.Desktop.addInternalFrame(cap,
+ * "Job Status for "+getServiceActionText(), 600, 400);
+ */
+ }
+ }
+
+ }
+
+ @Override
+ public void updateAnnotation()
+ {
+ updateResultAnnotation(false);
+ }
+
+ public abstract void updateResultAnnotation(boolean immediate);
+
+ public abstract String getServiceActionText();
+
+ protected boolean submitGaps = true;
+ protected boolean alignedSeqs = true;
+ protected boolean nucleotidesAllowed = false;
+ protected boolean proteinAllowed = false;
+ /**
+ * record sequences for mapping result back to afterwards
+ */
+ protected boolean bySequence = false;
+ protected Map<String, SequenceI> seqNames;
+ protected boolean[] gapMap;
+ int realw;
+ int start,end;
+
+ public List<FastaSequence> getInputSequences(AlignmentI alignment, AnnotatedCollectionI inputSeqs)
+ {
+ if (alignment == null || alignment.getWidth() <= 0
+ || alignment.getSequences() == null
+ || alignment.isNucleotide() ? !nucleotidesAllowed
+ : !proteinAllowed)
+ {
+ return null;
+ }
+ if (inputSeqs==null || inputSeqs.getWidth()<=0 || inputSeqs.getSequences()==null || inputSeqs.getSequences().size()<1)
+ {
+ inputSeqs = alignment;
+ }
+
+ List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
+
+ int minlen = 10;
+ int ln = -1;
+ if (bySequence)
+ {
+ seqNames = new HashMap<String, SequenceI>();
+ }
+ gapMap = new boolean[0];
+ start=inputSeqs.getStartRes();
+ end=inputSeqs.getEndRes();
+
+
+ for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
+ {
+ if (bySequence ? sq.findPosition(end+1) -sq.findPosition(start+1) > minlen - 1 : sq.getEnd() - sq.getStart() > minlen - 1)
+ {
+ String newname = SeqsetUtils.unique_name(seqs.size() + 1);
+ // make new input sequence with or without gaps
+ if (seqNames != null)
+ {
+ seqNames.put(newname, sq);
+ }
+ FastaSequence seq;
+ if (submitGaps)
+ {
+ seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+ sq.getSequenceAsString()));
+ if (gapMap == null || gapMap.length < seq.getSequence().length())
+ {
+ boolean[] tg = gapMap;
+ gapMap = new boolean[seq.getLength()];
+ System.arraycopy(tg, 0, gapMap, 0, tg.length);
+ for (int p = tg.length; p < gapMap.length; p++)
+ {
+ gapMap[p] = false; // init as a gap
+ }
+ }
+ for (int apos : sq.gapMap())
+ {
+ gapMap[apos] = true; // aligned.
+ }
+ }
+ else
+ {
+ seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+ AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ sq.getSequenceAsString(start,end+1))));
+ }
+ if (seq.getSequence().length() > ln)
+ {
+ ln = seq.getSequence().length();
+ }
+ }
+ }
+ if (alignedSeqs && submitGaps)
+ {
+ realw = 0;
+ for (int i = 0; i < gapMap.length; i++)
+ {
+ if (gapMap[i])
+ {
+ realw++;
+ }
+ }
+ // try real hard to return something submittable
+ // TODO: some of AAcon measures need a minimum of two or three amino
+ // acids at each position, and AAcon doesn't gracefully degrade.
+ for (int p = 0; p < seqs.size(); p++)
+ {
+ FastaSequence sq = seqs.get(p);
+ int l = sq.getSequence().length();
+ // strip gapped columns
+ char[] padded = new char[realw], orig = sq.getSequence()
+ .toCharArray();
+ for (int i = 0, pp = 0; i < realw; pp++)
+ {
+ if (gapMap[pp])
+ {
+ if (orig.length > pp)
+ {
+ padded[i++] = orig[pp];
+ }
+ else
+ {
+ padded[i++] = '-';
+ }
+ }
+ }
+ seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
+ new String(padded)));
+ }
+ }
+ return seqs;
+ }
+
+ /**
+ * notify manager that we have started, and wait for a free calculation slot
+ *
+ * @return true if slot is obtained and work still valid, false if another
+ * thread has done our work for us.
+ */
+ boolean checkDone()
+ {
+ calcMan.notifyStart(this);
+ ap.paintAlignment(false);
+ while (!calcMan.notifyWorking(this))
+ {
+ if (calcMan.isWorking(this))
+ {
+ return true;
+ }
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ if (alignViewport.isClosed())
+ {
+ abortAndDestroy();
+ return true;
+ }
+ return false;
+ }
+
+ protected void createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String calcId,
+ int alWidth, Score scr)
+ {
+ // simple annotation row
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
+ null);
+ if (alWidth == gapMap.length) // scr.getScores().size())
+ {
+ constructAnnotationFromScore(annotation, 0, alWidth, scr);
+ ourAnnot.add(annotation);
+ }
+ }
+
+ protected AlignmentAnnotation createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String typeName,
+ String calcId, SequenceI dseq, int base, Score scr)
+ {
+ System.out.println("Creating annotation on dseq:" + dseq.getStart()
+ + " base is " + base + " and length=" + dseq.getLength()
+ + " == " + scr.getScores().size());
+ // AlignmentAnnotation annotation = new AlignmentAnnotation(
+ // scr.getMethod(), typeName, new Annotation[]
+ // {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
+ // annotation.setCalcId(calcId);
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
+ constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
+ annotation.createSequenceMapping(dseq, base, false);
+ annotation.adjustForAlignment();
+ dseq.addAlignmentAnnotation(annotation);
+ ourAnnot.add(annotation);
+ return annotation;
+ }
+
+ private void constructAnnotationFromScore(AlignmentAnnotation annotation, int base,
+ int alWidth, Score scr)
+ {
+ Annotation[] elm = new Annotation[alWidth];
+ Iterator<Float> vals = scr.getScores().iterator();
+ float m = 0f, x = 0f;
+ for (int i = 0; vals.hasNext(); i++)
+ {
+ float val = vals.next().floatValue();
+ if (i == 0)
+ {
+ m = val;
+ x = val;
+ }
+ else
+ {
+ if (m > val)
+ {
+ m = val;
+ }
+ ;
+ if (x < val)
+ {
+ x = val;
+ }
+ }
+ // if we're at a gapped column then skip to next ungapped position
+ if (gapMap != null && gapMap.length > 0)
+ {
+ while (!gapMap[i])
+ {
+ elm[i++] = new Annotation("", "", ' ', Float.NaN);
+ }
+ }
+ elm[i] = new Annotation("", "" + val, ' ', val);
+ }
+
+ annotation.annotations = elm;
+ annotation.belowAlignment = true;
+ if (x < 0)
+ {
+ x = 0;
+ }
+ x += (x - m) * 0.1;
+ annotation.graphMax = x;
+ annotation.graphMin = m;
+ annotation.validateRangeAndDisplay();
+ }
+
+ protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
+ {
+ List<AlignmentAnnotation> our = ourAnnots;
+ ourAnnots = ourAnnot;
+ AlignmentI alignment = alignViewport.getAlignment();
+ if (our != null)
+ {
+ if (our.size() > 0)
+ {
+ for (AlignmentAnnotation an : our)
+ {
+ if (!ourAnnots.contains(an))
+ {
+ // remove the old annotation
+ alignment.deleteAnnotation(an);
+ }
+ }
+ }
+ our.clear();
+
+ ap.adjustAnnotationHeight();
+ }
+ }
+
+}
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.StringTokenizer;
import java.util.Vector;
public void run()
{
+
if (running && oldthread != null && oldthread.isAlive())
{
if (!aborted)
Cache.log.debug("Old discovery thread has finished.");
}
running = true;
+
+ // first set up exclusion list if needed
+ final Set<String> ignoredServices = new HashSet<String>();
+ for (String ignored:jalview.bin.Cache.getDefault("IGNORED_JABAWS_SERVICETYPES", Services.JpredWS.toString()).split("\\|"))
+ {
+ ignoredServices.add(ignored);
+ }
+
+
changeSupport.firePropertyChange("services", services, new Vector());
oldthread = Thread.currentThread();
try
// for all possible services
for (Services sv : squery.JABAWS2SERVERS)
{
- svctypes.add(sv.toString());
+ if (!ignoredServices.contains(sv.toString()))
+ {
+ svctypes.add(sv.toString());
+ }
}
}
;
for (JabaWsServerQuery squery : qrys)
{
- finished = finished && !squery.isRunning();
+ if (squery.isRunning()){
+ finished=false;
+ }
}
if (aborted)
{
services = new Vector<Jws2Instance>();
for (Jws2Instance svc : svcs)
{
- services.add(svc);
+ if (!ignoredServices.contains(svc.serviceType))
+ {
+ services.add(svc);
+ }
}
}
}
*/
package jalview.ws.jws2;
+import java.net.MalformedURLException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
{
copy.setName(option.getName());
copy.setDescription(option.getDescription());
+ copy.setBasicURL(option.getBasicURL());
copy.setFurtherDetails(option.getFurtherDetails());
copy.setRequired(option.isRequired());
List<String> names = option.getOptionNames();
--- /dev/null
+package jalview.ws.jws2;
+
+import jalview.api.AlignCalcWorkerI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.gui.AlignFrame;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
+
+import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.TreeSet;
+import java.util.regex.Pattern;
+
+import compbio.data.sequence.RNAStructReader.AlifoldResult;
+import compbio.data.sequence.RNAStructScoreManager;
+import compbio.data.sequence.Range;
+import compbio.data.sequence.Score;
+import compbio.metadata.Argument;
+
+/**
+ * Client for the JABA RNA Alifold Service
+ * @author daluke - Daniel Barton
+ *
+ */
+
+public class RNAalifoldClient extends JabawsAlignCalcWorker implements
+ AlignCalcWorkerI
+{
+
+ String methodName;
+
+ AlignFrame af;
+
+ // keeps track of whether the RNAalifold result includes base contact
+ // probabilities
+ boolean bpScores;
+
+ public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,
+ WsParamSetI preset, List<Argument> paramset)
+ {
+ super(sh, alignFrame, preset, paramset);
+
+ //if (arguments == null)
+ // arguments = new ArrayList<Argument>();
+
+ af = alignFrame;
+ methodName = sh.serviceType;
+ alignedSeqs=true;
+ submitGaps=true;
+ nucleotidesAllowed = true;
+ proteinAllowed = false;
+ initViewportParams();
+ }
+
+ public String getCalcId()
+ {
+ return CALC_ID;
+ }
+ private static String CALC_ID="jalview.ws.jws2.RNAalifoldClient";
+
+ public static AlignAnalysisUIText getAlignAnalysisUITest()
+ {
+ return new AlignAnalysisUIText(
+ compbio.ws.client.Services.RNAalifoldWS.toString(),
+ jalview.ws.jws2.RNAalifoldClient.class,
+ CALC_ID,
+ true,
+ false,
+ true,
+ "RNAAliFold Prediction",
+ "When checked, RNA secondary structure predictions will be calculated for the alignment, and updated when edits are made.",
+ "Change RNAAliFold settings...",
+ "Modify settings for the RNAAliFold prediction. Use this to hide or show different results of the RNA calculation, and change RNA folding parameters");
+
+ }
+
+ @Override
+ public String getServiceActionText()
+ {
+ return "Submitting RNA alignment for Secondary Structure prediction using "
+ + "RNAalifold Service";
+ }
+
+ @Override
+ public void updateResultAnnotation(boolean immediate)
+ {
+
+ if (immediate || !calcMan.isWorking(this) && scoremanager != null)
+ {
+
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+
+ // Unpack the ScoreManager
+ List<String> structs = ((RNAStructScoreManager) scoremanager)
+ .getStructs();
+ List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager)
+ .getData();
+
+ // test to see if this data object contains base pair contacts
+ Score fscore = data.get(0).first();
+ this.bpScores = (fscore.getMethod()
+ .equals(AlifoldResult.contactProbabilities.toString()));
+
+ // add annotation for the consensus sequence alignment
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
+ structs.get(0), null, null);
+
+ // Add annotations for the mfe Structure
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
+ structs.get(1), data.get(1), null);
+
+ // decide whether to add base pair contact probability histogram
+ int count = 2;
+ if (bpScores)
+ {
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
+ structs.get(2), data.get(0), data.get(2));
+ count++;
+ }
+
+ // Now loop for the rest of the Annotations (if there it isn't stochastic
+ // output
+ // only the centroid and MEA structures remain anyway)
+ for (int i = count; i < structs.size(); i++)
+ {
+ // The ensemble values should be displayed in the description of the
+ // first (or all?) Stochastic Backtrack Structures.
+ if (!data.get(i).first().getMethod()
+ .equals(AlifoldResult.ensembleValues.toString()))
+ {
+
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
+ structs.get(i), data.get(i), null);
+ }
+ }
+
+ if (ourAnnot.size() > 0)
+ {
+
+ updateOurAnnots(ourAnnot);
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
+
+ protected void createAnnotationRowforScoreHolder(
+ List<AlignmentAnnotation> ourAnnot, String calcId, String struct,
+ TreeSet<Score> data, TreeSet<Score> descriptionData)
+ {
+ /*
+ * If contactProbability information is returned from RNAalifold it is
+ * stored in the first TreeSet<Score> object corresponding to the String Id
+ * which holds the consensus alignment. The method enumeration is then
+ * updated to AlifoldResult.contactProbabilties. This line recreates the
+ * same data object as was overwritten with the contact probabilites data.
+ */
+ if (data == null)
+ data = compbio.data.sequence.RNAStructReader
+ .newEmptyScore(AlifoldResult.consensusAlignment);
+
+ if (descriptionData == null)
+ descriptionData = data;
+
+ String[] typenameAndDescription = constructTypenameAndDescription(descriptionData
+ .first());
+ String typename = typenameAndDescription[0];
+ String description = typenameAndDescription[1];
+
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation(typename, calcId, false, null, null);
+
+ constructAnnotationFromScoreHolder(annotation, struct, data);
+
+ /*
+ * update annotation description with the free Energy, frequency in ensemble
+ * or other data where appropriate.
+ *
+ * Doesnt deal with AlifoldResult.ensembleValues, the free energy of
+ * ensemble and frequency of mfe structure in ensemble. How to deal with
+ * these?
+ */
+ annotation.description = description;
+
+ annotation.belowAlignment = false;
+ // annotation.showAllColLabels = true;
+
+ alignViewport.getAlignment().validateAnnotation(annotation);
+ af.setMenusForViewport();
+
+ ourAnnot.add(annotation);
+ }
+
+ private AlignmentAnnotation constructAnnotationFromScoreHolder(
+ AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
+ {
+ Annotation[] anns = new Annotation[struct.length()];
+
+ if (data != null
+ && data.size() > 1
+ && data.first().getMethod()
+ .equals(AlifoldResult.contactProbabilities.toString()))
+ {
+
+ // The base pair probabilities are stored in a set in scoreholder. we want
+ // a map
+ LinkedHashMap<Range, Float> basePairs = new LinkedHashMap<Range, Float>();
+ for (Score score : data)
+ {
+ // The Score objects contain a set of size one containing the range and
+ // an ArrayList<float> of size one containing the probabilty
+ basePairs.put(score.getRanges().first(), new Float(score
+ .getScores().get(0)));
+ }
+
+ for (int i = 0,ri=0,iEnd=struct.length();i<iEnd; i++,ri++)
+ {
+ if (gapMap!=null)
+ {
+ // skip any gapped columns in the input data
+ while (!gapMap[ri])
+ {
+ ri++;
+ }
+ }
+ // Return all the contacts associated with position i
+ LinkedHashMap<Range, Float> contacts = isContact(basePairs, i + 1);
+
+ String description = "";
+ float prob = 0f;
+
+ if (contacts.size() == 0)
+ {
+ description = "No Data";
+ }
+ else
+ {
+ for (Range contact : contacts.keySet())
+ {
+ float t = contacts.get(contact);
+ if (t > prob)
+ prob = t;
+ description += Integer.toString(contact.from) + "->"
+ + Integer.toString(contact.to) + ": "
+ + Float.toString(t) + "% | ";
+ }
+ }
+
+ anns[ri] = new Annotation(struct.substring(i, i + 1), description,
+ isSS(struct.charAt(i)), prob);
+ }
+ }
+ else if (data == null || data.size() == 1)
+ {
+ for (int i = 0,ri=0,iEnd=struct.length();i<iEnd; i++,ri++)
+ {
+ if (gapMap!=null)
+ {
+ // skip any gapped columns in the input data
+ while (!gapMap[ri])
+ {
+ ri++;
+ }
+ }
+ anns[ri] = new Annotation(struct.substring(i, i + 1), "",
+ isSS(struct.charAt(i)), Float.NaN);
+ }
+
+ annotation.graph = 0; // No graph
+ }
+
+ annotation.annotations = anns;
+
+ return annotation;
+ }
+
+ private String[] constructTypenameAndDescription(Score score)
+ {
+ String description = "";
+ String typename = "";
+ String datatype = score.getMethod();
+
+ // Look up java switch syntax and use one here
+ if (datatype.equals(AlifoldResult.mfeStructure.toString()))
+ {
+
+ description = MessageFormat.format(
+ "Minimum Free Energy Structure. Energy: {0} = {1} + {2}",
+ score.getScores().get(0), score.getScores().get(1), score
+ .getScores().get(2));
+ typename = "MFE Structure";
+ }
+ else if (datatype.equals(AlifoldResult.contactProbabilityStructure
+ .toString()))
+ {
+ description = MessageFormat
+ .format("Base Pair Contact Probabilities. "
+ + "Energy of Ensemble: {0} Frequency of Ensemble: {1}",
+ score.getScores().get(0), score.getScores().get(1));
+ typename = "Contact Probabilities";
+ }
+ else if (datatype.equals(AlifoldResult.centroidStructure.toString()))
+ {
+ description = MessageFormat.format(
+ "Centroid Structure. Energy: {0} = {1} + {2}", score
+ .getScores().get(0), score.getScores().get(1), score
+ .getScores().get(2));
+ typename = "Centroid Structure";
+ }
+ else if (datatype.equals(AlifoldResult.stochBTStructure.toString()))
+ {
+ if (score.getScores().size() > 0)
+ {
+ description = MessageFormat.format("Probability: {0} Energy: {1}",
+ score.getScores().get(0), score.getScores().get(1));
+ }
+ else
+ description = "Stochastic Backtrack Structure";
+ }
+ else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
+ {
+ description = MessageFormat.format(
+ "Maximum Expected Accuracy Values: '{' {0} MEA={1} '}", score
+ .getScores().get(0), score.getScores().get(1));
+ typename = "MEA Structure";
+ }
+ else if (datatype.equals(AlifoldResult.consensusAlignment.toString()))
+ {
+ typename = "RNAalifold Consensus";
+ description = "Consensus Alignment Produced by RNAalifold";
+ }
+ else
+ {
+ typename = datatype;
+ description = typename;
+ }
+
+ return new String[]
+ { typename, description };
+ }
+
+ // Check whether, at position i there is a base contact and return all the
+ // contacts at this position. Should be in order of descending probability.
+ private LinkedHashMap<Range, Float> isContact(
+ LinkedHashMap<Range, Float> basePairs, int i)
+ {
+ LinkedHashMap<Range, Float> contacts = new LinkedHashMap<Range, Float>();
+
+ for (Range contact : basePairs.keySet())
+ {
+ // finds the contacts associtated with position i ordered by the natural
+ // ordering of the Scores TreeSet in ScoreManager which is, descending
+ // probability
+ if (contact.from == i || contact.to == i)
+ contacts.put(contact, basePairs.get(contact));
+ }
+
+ return contacts;
+ }
+
+ private char isSS(char chr)
+ {
+ String regex = "\\(|\\)|\\{|\\}|\\[|\\]";
+ char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
+ return ss;
+ }
+}
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
*/
public class SequenceAnnotationWSClient extends Jws2Client
{
-
- public static final String AAConCalcId = "jabaws2.AACon";
-
/**
* initialise a client so its attachWSMenuEntry method can be called.
*/
initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
}
+ // dan think. Do I need to change this method to run RNAalifold through the GUI
+
public void initSequenceAnnotationWSClient(final Jws2Instance sh,
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
- if (alignFrame.getViewport().getAlignment().isNucleotide())
- {
- JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
- + " can only be used\nfor amino acid alignments.",
- "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
- return;
-
- }
- if (sh.action.toLowerCase().contains("conservation"))
+ // dan changed! dan test. comment out if conditional
+// if (alignFrame.getViewport().getAlignment().isNucleotide())
+// {
+// JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+// + " can only be used\nfor amino acid alignments.",
+// "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
+// return;
+//
+// }
+ AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
+ if (aaui!=null)
{
+ Class clientClass = aaui.getClient();
+
// Build an AACon style client - take alignment, return annotation for
// columns
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
.getCalcManager()
- .getRegisteredWorkersOfClass(AAConClient.class);
+ .getRegisteredWorkersOfClass(clientClass);
+ JabawsAlignCalcWorker worker;
if (clnts == null || clnts.size() == 0)
{
if (!processParams(sh, editParams))
{
return;
}
- AAConClient worker;
+ try {
+ worker = (JabawsAlignCalcWorker) (clientClass.getConstructor(
+ new Class[] { Jws2Instance.class,
+ AlignFrame.class, WsParamSetI.class,
+ List.class }).newInstance(new Object[] { sh, alignFrame, this.preset, paramset}));
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ throw new Error("Implementation error",x);
+ }
alignFrame
.getViewport()
.getCalcManager()
.registerWorker(
- worker = new AAConClient(sh, alignFrame,
- this.preset, paramset));
+ worker);
alignFrame.getViewport().getCalcManager().startWorker(worker);
}
else
{
- AAConClient worker = (AAConClient) clnts.get(0);
+ worker = (JabawsAlignCalcWorker) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
// invalid parameters)
alignFrame.getViewport().getCalcManager().workerMayRun(worker);
worker.updateParameters(this.preset, paramset);
-
}
}
if (sh.action.toLowerCase().contains("disorder"))
.startWorker(
new AADisorderClient(sh, alignFrame, preset, paramset));
}
-
}
public SequenceAnnotationWSClient(AAConSettings fave,
public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame)
{
- if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
- .toString()))
- {
- registerAAConWSInstance(wsmenu, service, alignFrame);
+ if (registerAAConWSInstance(wsmenu, service, alignFrame)) {
+ // Alignment dependent analysis calculation WS gui
return;
}
boolean hasparams = service.hasParameters();
}
}
- private final String AAconToggle = "AACon Calculations",
- AAconToggleTooltip = "When checked, AACon calculations are updated automatically.",
- AAeditSettings = "Change AACon Settings...",
- AAeditSettingsTooltip = "Modify settings for AACon calculations.";
-
- private void registerAAConWSInstance(final JMenu wsmenu,
+
+ private boolean registerAAConWSInstance(final JMenu wsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
- // register this in the AACon settings set
+ final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
+ if (aaui==null)
+ {
+ // not an instantaneous calculation GUI type service
+ return false;
+ }
+ // create the instaneous calculation GUI bits and update state if existing GUI elements already present
+
JCheckBoxMenuItem _aaConEnabled = null;
for (int i = 0; i < wsmenu.getItemCount(); i++)
{
JMenuItem item = wsmenu.getItem(i);
if (item instanceof JCheckBoxMenuItem
- && item.getText().equals(AAconToggle))
+ && item.getText().equals(aaui.getAAconToggle()))
{
_aaConEnabled = (JCheckBoxMenuItem) item;
}
{
List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
.getCalcManager()
- .getRegisteredWorkersOfClass(AAConClient.class);
+ .getRegisteredWorkersOfClass(aaui.getClient());
if (aaconClient != null && aaconClient.size() > 0)
{
- AAConClient worker = (AAConClient) aaconClient.get(0);
+ JabawsAlignCalcWorker worker = (JabawsAlignCalcWorker) aaconClient.get(0);
if (!worker.service.hosturl.equals(service.hosturl))
{
// javax.swing.SwingUtilities.invokeLater(new Runnable()
// @Override
// public void run()
{
- removeCurrentAAConWorkerFor(alignFrame);
- buildCurrentAAConWorkerFor(alignFrame, service);
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ buildCurrentAAConWorkerFor(aaui, alignFrame, service);
}
}// );
}
if (_aaConEnabled == null)
{
final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
- AAconToggle);
- wsmenu.addMenuListener(new MenuListener()
- {
+ aaui.getAAconToggle());
+ aaConEnabled.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip() + "</p>")
+ + "</html>");
+ aaConEnabled.addActionListener(new ActionListener()
+ {
@Override
- public void menuSelected(MenuEvent arg0)
+ public void actionPerformed(ActionEvent arg0)
{
- wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
- .isNucleotide());
List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
.getCalcManager()
- .getRegisteredWorkersOfClass(AAConClient.class);
+ .getRegisteredWorkersOfClass(aaui.getClient());
if (aaconClient != null && aaconClient.size() > 0)
{
- aaConEnabled.setSelected(true);
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
}
else
{
- aaConEnabled.setSelected(false);
+ buildCurrentAAConWorkerFor(aaui, alignFrame);
+
}
}
- @Override
- public void menuDeselected(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
+ });
+ wsmenu.add(aaConEnabled);
+ final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
+ modifyParams.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip() + "</p>")
+ + "</html>");
+ modifyParams.addActionListener(new ActionListener()
+ {
@Override
- public void menuCanceled(MenuEvent arg0)
+ public void actionPerformed(ActionEvent arg0)
{
- // TODO Auto-generated method stub
-
+ showAAConAnnotationSettingsFor(aaui, alignFrame);
}
});
- aaConEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(AAconToggleTooltip + "</p>")
- + "</html>");
- aaConEnabled.addActionListener(new ActionListener()
+ wsmenu.add(modifyParams);
+ wsmenu.addMenuListener(new MenuListener()
{
+
@Override
- public void actionPerformed(ActionEvent arg0)
+ public void menuSelected(MenuEvent arg0)
{
+ // TODO: refactor to the implementing class.
+ if (alignFrame.getViewport().getAlignment()
+ .isNucleotide() ? aaui.isNa() : aaui.isPr()) {
+ aaConEnabled.setEnabled(true);
+ modifyParams.setEnabled(true);
+ }
+ else {
+ aaConEnabled.setEnabled(false);
+ modifyParams.setEnabled(false);
+ }
List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
.getCalcManager()
- .getRegisteredWorkersOfClass(AAConClient.class);
+ .getRegisteredWorkersOfClass(aaui.getClient());
if (aaconClient != null && aaconClient.size() > 0)
{
- removeCurrentAAConWorkerFor(alignFrame);
+ aaConEnabled.setSelected(true);
}
else
{
- buildCurrentAAConWorkerFor(alignFrame);
-
+ aaConEnabled.setSelected(false);
}
}
- });
- wsmenu.add(aaConEnabled);
- JMenuItem modifyParams = new JMenuItem(AAeditSettings);
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
- + "</html>");
- modifyParams.addActionListener(new ActionListener()
- {
+ @Override
+ public void menuDeselected(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
@Override
- public void actionPerformed(ActionEvent arg0)
+ public void menuCanceled(MenuEvent arg0)
{
- showAAConAnnotationSettingsFor(alignFrame);
+ // TODO Auto-generated method stub
+
}
});
- wsmenu.add(modifyParams);
}
+ return true;
}
- private static void showAAConAnnotationSettingsFor(AlignFrame alignFrame)
+ private static void showAAConAnnotationSettingsFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
{
/*
* preferred settings Whether AACon is automatically recalculated Which
*/
// could actually do a class search for this too
AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(AAConCalcId);
+ .getCalcIdSettingsFor(aaui.getCalcId());
if (fave == null)
{
- fave = createDefaultAAConSettings();
+ fave = createDefaultAAConSettings(aaui);
}
new SequenceAnnotationWSClient(fave, alignFrame, true);
}
- private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame)
+ private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
{
- buildCurrentAAConWorkerFor(alignFrame, null);
+ buildCurrentAAConWorkerFor(aaui, alignFrame, null);
}
- private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame,
+ private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame,
Jws2Instance service)
{
/*
* AACon server to use What parameters to use
*/
AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(AAConCalcId);
+ .getCalcIdSettingsFor(aaui.getCalcId());
if (fave == null)
{
- fave = createDefaultAAConSettings(service);
+ fave = createDefaultAAConSettings(aaui, service);
}
else
{
new SequenceAnnotationWSClient(fave, alignFrame, false);
}
- private static AAConSettings createDefaultAAConSettings()
+ private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui)
{
- return createDefaultAAConSettings(null);
+ return createDefaultAAConSettings(aaui, null);
}
- private static AAConSettings createDefaultAAConSettings(
+ private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui,
Jws2Instance service)
{
if (service != null)
{
// get the default service for AACon
service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
- compbio.ws.client.Services.AAConWS.toString());
+ aaui.getServiceType());
}
if (service == null)
{
return new AAConSettings(true, service, null, null);
}
- private static void removeCurrentAAConWorkerFor(AlignFrame alignFrame)
+ private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui, AlignFrame alignFrame)
{
alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(AAConClient.class);
+ .removeRegisteredWorkersOfClass(aaui.getClient());
}
}
import jalview.ws.jws2.ParameterUtils;
import jalview.ws.params.OptionI;
+import java.net.MalformedURLException;
import java.net.URL;
import java.util.List;
@Override
public URL getFurtherDetails()
{
- return opt.getFurtherDetails();
+ try {
+ return new URL(opt.getBasicURL().toExternalForm()+"/"+opt.getFurtherDetails());
+ }
+ catch (NullPointerException q) {}
+ catch (MalformedURLException q)
+ {
+
+ }
+ return null;
}
@Override
public String docUrl;
+ /**
+ *
+ * @param hosturl Service endpoint
+ * @param serviceType Category for this service's analysis
+ * @param action text describing their action that service performs (eg 'aligning', 'analysing')
+ * @param description Description from JABAWS registry
+ * @param service JABAWS registry ID for service
+ */
public Jws2Instance(String hosturl, String serviceType, String action,
String description, JABAService service)
{
{
return "java:" + serviceType;
}
+ jalview.ws.uimodel.AlignAnalysisUIText aaui;
+ public jalview.ws.uimodel.AlignAnalysisUIText getAlignAnalysisUI()
+ {
+ return aaui;
+ }
}
--- /dev/null
+package jalview.ws.jws2.jabaws2;
+
+import java.util.HashMap;
+
+import compbio.data.msa.JABAService;
+
+import jalview.ws.jws2.AAConClient;
+import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.uimodel.AlignAnalysisUIText;
+
+public class Jws2InstanceFactory
+{
+ private static HashMap<String, AlignAnalysisUIText> aaConGUI;
+ private static String category_rewrite(String cat_name)
+ {
+ return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction" : cat_name;
+ }
+ private static void init()
+ {
+ if (aaConGUI == null)
+ {
+ aaConGUI = new HashMap<String, AlignAnalysisUIText>();
+ aaConGUI.put(compbio.ws.client.Services.AAConWS.toString(),
+ AAConClient.getAlignAnalysisUITest());
+ aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
+ RNAalifoldClient.getAlignAnalysisUITest());
+ }
+ }
+
+ /**
+ * construct a service instance and configure it with any additional
+ * properties needed so Jalview can access it correctly
+ *
+ * @param jwsservers
+ * @param serviceType
+ * @param name
+ * @param description
+ * @param service
+ * @return
+ */
+ public static Jws2Instance newJws2Instance(String jwsservers,
+ String serviceType, String name, String description,
+ JABAService service)
+ {
+ init();
+ Jws2Instance svc = new Jws2Instance(jwsservers, serviceType, category_rewrite(name),
+ description, service);
+
+ svc.aaui = aaConGUI.get(serviceType.toString());
+ return svc;
+ }
+
+}
--- /dev/null
+package jalview.ws.uimodel;
+
+import java.util.HashMap;
+
+public class AlignAnalysisUIText
+{
+
+ private String serviceType;
+
+ public String getServiceType()
+ {
+ return serviceType;
+ }
+
+ private Class client;
+
+ private String calcId;
+
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ private String AAconToggle, AAconToggleTooltip, AAeditSettings,
+ AAeditSettingsTooltip;
+
+ private boolean isNa;
+
+ public boolean isNa()
+ {
+ return isNa;
+ }
+
+ public boolean isPr()
+ {
+ return isPr;
+ }
+
+ public boolean isAA()
+ {
+ return isAA;
+ }
+
+ private boolean isPr;
+
+ private boolean isAA;
+
+ public AlignAnalysisUIText(String serviceType, Class<?> client,
+ String calcId, boolean acceptNucl, boolean acceptProt,
+ boolean acceptGaps, String toggle, String toggleTooltip,
+ String settings, String settingsTooltip)
+ {
+ this.serviceType = serviceType;
+ this.calcId = calcId;
+ isNa = acceptNucl;
+ isPr = acceptProt;
+ isAA = acceptGaps;
+ this.client = client;
+ this.AAconToggle = toggle;
+ this.AAconToggleTooltip = toggleTooltip;
+ this.AAeditSettings = settings;
+ this.AAeditSettingsTooltip = settingsTooltip;
+ }
+
+ public Class getClient()
+ {
+ return client;
+ }
+
+ public void setClient(Class client)
+ {
+ this.client = client;
+ }
+
+ public String getAAconToggle()
+ {
+ return AAconToggle;
+ }
+
+ public void setAAconToggle(String aAconToggle)
+ {
+ AAconToggle = aAconToggle;
+ }
+
+ public String getAAconToggleTooltip()
+ {
+ return AAconToggleTooltip;
+ }
+
+ public void setAAconToggleTooltip(String aAconToggleTooltip)
+ {
+ AAconToggleTooltip = aAconToggleTooltip;
+ }
+
+ public String getAAeditSettings()
+ {
+ return AAeditSettings;
+ }
+
+ public void setAAeditSettings(String aAeditSettings)
+ {
+ AAeditSettings = aAeditSettings;
+ }
+
+ public String getAAeditSettingsTooltip()
+ {
+ return AAeditSettingsTooltip;
+ }
+
+ public void setAAeditSettingsTooltip(String aAeditSettingsTooltip)
+ {
+ AAeditSettingsTooltip = aAeditSettingsTooltip;
+ }
+
+}
\ No newline at end of file
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.*;
+import jalview.bin.Cache;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
+import javax.swing.JDesktopPane;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class JAL1353bugdemo
+{
+
+ @BeforeClass
+ public static void setUpBeforeClass() throws Exception
+ {
+ }
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception
+ {
+ }
+ volatile boolean finish=false;
+
+ @Test
+ public void test()
+ {
+ Cache.initLogger();
+ // final Desktop foo = new Desktop();
+ final JFrame cfoo = new JFrame("Crash Java");
+ final JDesktopPane foo=new JDesktopPane();
+ foo.setPreferredSize(new Dimension(600,800));
+ cfoo.setSize(600, 800);
+ final JInternalFrame cont = new JInternalFrame("My Frame");
+ JTextArea evt;
+ cont.setPreferredSize(new Dimension(400, 300));
+ cont.add(evt=new JTextArea("Click here and drag text over this window to freeze java.\n\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\n"));
+ cont.pack();
+ foo.add("A frame",cont);
+ foo.setVisible(true);
+ foo.setEnabled(true);
+ foo.doLayout();
+ cfoo.add(foo);
+ final JMenu jm = new JMenu("Do");
+ JMenuItem jmi=new JMenuItem("this");
+ jm.add(jmi);
+ evt.addMouseListener(new MouseListener()
+ {
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+// JFrame parent = new JFrame();
+// parent.setBounds(foo.getBounds());
+// JPanel oo = new JPanel();
+// parent.add(oo);
+// oo.setVisible(true);
+// parent.setVisible(true);
+ EditNameDialog end =new EditNameDialog("Sequence Name", "Sequence Description","label 1", "Label 2", "Try and drag between the two text fields", foo);//);cont.getRootPane());
+ assert(end!=null);
+ finish=true;
+ }
+ });
+ cont.setVisible(true);
+
+ jmi.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ EditNameDialog end =new EditNameDialog("Sequence Name", "Sequence Description","label 1", "Label 2", "Try and drag between the two text fields", cont);
+ assert(end!=null);
+ finish=true;
+ }
+ });
+ foo.setVisible(true);
+ cfoo.setVisible(true);
+ while (!finish)
+ {
+ try {
+ Thread.sleep(100);
+ } catch (InterruptedException x) {}
+ }
+ }
+
+}
--- /dev/null
+package jalview.ws.jabaws;
+
+import static org.junit.Assert.*;
+
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import jalview.api.AlignCalcManagerI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.AADisorderClient;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.dm.JabaOption;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import compbio.metadata.WrongParameterException;
+
+public class RNAStructExportImport
+{
+ public static String testseqs = "examples/unfolded_RF00031.aln";
+
+ public static Jws2Discoverer disc;
+
+ public static Jws2Instance rnaalifoldws;
+
+ jalview.ws.jws2.RNAalifoldClient alifoldClient;
+
+ public static jalview.gui.AlignFrame af = null;
+
+ @BeforeClass
+ public static void setUpBeforeClass() throws Exception
+ {
+
+ jalview.bin.Cache.initLogger();
+ disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+
+ for (Jws2Instance svc : disc.getServices())
+ {
+
+ if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+ {
+ rnaalifoldws = svc;
+ }
+ }
+
+ System.out.println("State of rnaalifoldws: " + rnaalifoldws);
+
+ if (rnaalifoldws == null)
+ System.exit(0);
+
+ jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+
+ af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+
+ assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
+
+ }
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception
+ {
+ if (af != null)
+ {
+ af.setVisible(false);
+ af.dispose();
+ }
+ }
+
+ @Test
+ public void testRNAStructExport()
+ {
+
+ alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+
+ af.getViewport().getCalcManager().startWorker(alifoldClient);
+
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ } while (af.getViewport().getCalcManager().isWorking());
+
+ AlignmentI orig_alig = af.getViewport().getAlignment();
+
+ testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
+
+ }
+
+ public static void testAnnotationFileIO(String testname, AlignmentI al)
+ {
+ try
+ {
+ // what format would be appropriate for RNAalifold annotations?
+ String aligfileout = new FormatAdapter().formatSequences("PFAM",
+ al.getSequencesArray());
+
+ String anfileout = new AnnotationFile().printAnnotations(
+ al.getAlignmentAnnotation(), al.getGroups(),
+ al.getProperties());
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment annotation file was not regenerated. Null string",
+ anfileout != null);
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment annotation file was not regenerated. Empty string",
+ anfileout.length() > "JALVIEW_ANNOTATION".length());
+
+ System.out.println("Output annotation file:\n" + anfileout
+ + "\n<<EOF\n");
+
+ // again what format would be appropriate?
+ AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
+ FormatAdapter.PASTE, "PFAM");
+ assertTrue(
+ "Test "
+ + testname
+ + "\nregenerated annotation file did not annotate alignment.",
+ new AnnotationFile().readAnnotationFile(al_new, anfileout,
+ FormatAdapter.PASTE));
+
+ // test for consistency in io
+ StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ return;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ fail("Test "
+ + testname
+ + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
+ }
+
+ @Test
+ public void testRnaalifoldSettingsRecovery()
+ {
+ List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
+ for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) rnaalifoldws
+ .getRunnerConfig().getArguments())
+ {
+ if (rg.getDescription().contains("emperature"))
+ {
+ try
+ {
+ rg.setValue("292");
+ } catch (WrongParameterException q)
+ {
+ fail("Couldn't set the temperature parameter "
+ + q.getStackTrace());
+ }
+ opts.add(rg);
+ }
+ if (rg.getDescription().contains("max"))
+ {
+ opts.add(rg);
+ }
+ }
+ alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+
+ af.getViewport().getCalcManager().startWorker(alifoldClient);
+
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ } while (af.getViewport().getCalcManager().isWorking());
+ AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
+ String oldsettings = oldacs.getWsParamFile();
+ // write out parameters
+ jalview.gui.AlignFrame nalf=null;
+ assertTrue("Couldn't write out the Jar file",new Jalview2XML(false).SaveAlignment(af, "testRnalifold_param.jar","trial parameter writeout"));
+ assertTrue("Couldn't read back the Jar file",(nalf = new Jalview2XML(false).LoadJalviewAlign("testRnalifold_param.jar"))!=null);
+ if (nalf!=null)
+ {
+ AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
+ assertTrue("Calc ID settings not recovered from viewport stash", acs.equals(oldacs));
+ assertTrue("Serialised Calc ID settings not identical to those recovered from viewport stash", acs.getWsParamFile().equals(oldsettings));
+ JMenu nmenu=new JMenu();
+ new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu, rnaalifoldws, af);
+ assertTrue("Couldn't get menu entry for service",nmenu.getItemCount()>0);
+ for (Component itm: nmenu.getMenuComponents())
+ {
+ if (itm instanceof JMenuItem)
+ {
+ JMenuItem i = (JMenuItem) itm;
+ if (i.getText().equals(rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
+ {
+ i.doClick();
+ break;
+ }
+ }
+ }
+ while (af.getViewport().isCalcInProgress())
+ {
+ try { Thread.sleep(200);
+ } catch (Exception x) {};
+ }
+ AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
+ assertTrue("Calc ID settings after recalculation has not been recovered.", acs2.getWsParamFile().equals(oldsettings));
+ }
+ }
+}
<string><![CDATA[664]]></string>
</property>
<property name="sourceName">
- <string><![CDATA[min-jaba-client-2.0.jar]]></string>
+ <string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
</property>
<property name="overrideUnixPermissions">
<boolean>false</boolean>
<boolean>true</boolean>
</property>
<property name="destinationName">
- <string><![CDATA[min-jaba-client-2.0.jar]]></string>
+ <string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
</property>
<property name="fileSize">
<long>133065</long>
git://source.jalview.org / jalview.git / commitdiff
