<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>
--- /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
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 = "-";
* @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);
+
+}
*/
package jalview.api;
+import java.awt.Color;
import java.util.Hashtable;
import java.util.Map;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
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);
+
+ AlignmentView getAlignmentView(boolean selectedOnly);
+
+ AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
+
+ String[] getViewAsString(boolean selectedRegionOnly);
+
+ void setSelectionGroup(SequenceGroup sg);
+
+ char getGapCharacter();
+
+
}
MenuItem unGroupMenuItem = new MenuItem();
+ MenuItem createGroupMenuItem = new MenuItem();
+
MenuItem nucleotideMenuItem = new MenuItem();
Menu colourMenu = new Menu();
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);
}
}
unGroupMenuItem_actionPerformed();
}
+ else if (source == createGroupMenuItem)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+
else if (source == sequenceName)
{
editName();
private void jbInit() throws Exception
{
- groupMenu.setLabel(MessageManager.getString("label.group"));
groupMenu.setLabel(MessageManager.getString("label.selection"));
sequenceFeature.addActionListener(this);
unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(this);
+ createGroupMenuItem.setLabel(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.addActionListener(this);
+
nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(this);
conservationMenuItem.addItemListener(this);
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;
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);
}
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())
{
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()
MenuItem grpsFromSelection = new MenuItem();
+ MenuItem createGroup = new MenuItem();
+
+ MenuItem unGroup = new MenuItem();
+
MenuItem delete = new MenuItem();
MenuItem copy = new MenuItem();
deleteGroups.addActionListener(this);
grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
+ 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(MessageManager.getString("action.cut"));
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()
av.setSelectionGroup(null);
av.getAlignment().deleteAllGroups();
- av.sequenceColours = null;
+ av.clearSequenceColours();
colourGroups();
--- /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.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();
-
+
}
/**
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();
}
@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);
+ }
}
/**
@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)
{
alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
viewport = alignPanel.av;
+ avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
}
}
@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
&& 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
{
// 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;
}
{
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())
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();
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);
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!
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ ssm = av.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
{
aps[a].av.setSelectionGroup(null);
aps[a].av.getAlignment().deleteAllGroups();
- aps[a].av.sequenceColours = null;
+ aps[a].av.clearSequenceColours();
}
colourGroups();
}
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
JMenuItem deleteGroups = new JMenuItem();
+
+ JMenuItem createGroup = new JMenuItem();
+ JMenuItem unGroup = new JMenuItem();
JMenuItem delete = new JMenuItem();
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)
{
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;
}
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
+import java.awt.Color;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
*
* @return null or the currently selected sequence region
*/
+ @Override
public SequenceGroup getSelectionGroup()
{
return selectionGroup;
* - group holding references to sequences in this alignment view
*
*/
+ @Override
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
protected boolean showConsensus = true;
+ Hashtable sequenceColours;
+
/**
* Property change listener for changes in alignment
*
*
* @return array of references to sequence objects
*/
+ @Override
public SequenceI[] getSequenceSelection()
{
SequenceI[] sequences = null;
*
* @return String[]
*/
+ @Override
public jalview.datamodel.CigarArray getViewAsCigars(
boolean selectedRegionOnly)
{
* boolean true to just return the selected view
* @return AlignmentView
*/
+ @Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
{
* is true)
* @return AlignmentView
*/
+ @Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
{
*
* @return String[]
*/
+ @Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
String[] selection = null;
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.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;
- }
-
- /**
- * 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;
+ super(service, alignFrame, preset, paramset);
}
- @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());
-
- 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
+ * Recover any existing parameters for this service
*/
- protected boolean bySequence = false;
-
- Map<String, SequenceI> seqNames;
-
- boolean[] gapMap;
-
- int realw;
-
- public List<FastaSequence> getInputSequences(AlignmentI alignment)
+ protected void initViewportParams()
{
- if (alignment == null || alignment.getWidth() <= 0
- || alignment.getSequences() == null
- // || (alignedSeqs && !alignment.isAligned() && !submitGaps)
- || alignment.isNucleotide() ? !nucleotidesAllowed
- : !proteinAllowed)
- {
- return null;
- }
- 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];
- for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
- {
- if (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())));
- }
- 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;
+ ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
+ getCalcId(),
+ new AAConSettings(true, service, this.preset,
+ (arguments != null) ? JabaParamStore
+ .getJwsArgsfromJaba(arguments) : null), true);
}
/**
- * 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;
- }
-
- 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);
- }
- }
+ public abstract String getCalcId();
- 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.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());
+
+ 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;
+
+ public List<FastaSequence> getInputSequences(AlignmentI alignment)
+ {
+ if (alignment == null || alignment.getWidth() <= 0
+ || alignment.getSequences() == null
+ // || (alignedSeqs && !alignment.isAligned() && !submitGaps)
+ || alignment.isNucleotide() ? !nucleotidesAllowed
+ : !proteinAllowed)
+ {
+ return null;
+ }
+ 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];
+ for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
+ {
+ if (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())));
+ }
+ 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
