Jim Procter
Andrew Waterhouse
+Mungo Carstairs
+Tochukwu 'Charles' Ofoegbu
Jan Engelhardt
Lauren Lui
Anne Menard
JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
Jmol-12.1.13.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+VARNAv3-91.jar GPL licenced software by Kévin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
activation.jar
apache-mime4j-0.6.jar
axis.jar
xercesImpl.jar
xml-apis.jar
json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
+jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfree.org/jfreesvg/
Additional dependencies
--- /dev/null
+T-COFFEE, Version_8.99(Fri Feb 18 08:27:45 CET 2011 - Revision 596)
+Cedric Notredame
+CPU TIME:0 sec.
+SCORE=94
+*
+ BAD AVG GOOD
+*
+FER_CAPAA : 99
+FER_CAPAN : 94
+FER1_SOLLC : 94
+Q93XJ9_SOLTU : 93
+FER1_PEA : 93
+Q7XA98_TRIPR : 92
+FER1_MESCR : 92
+FER1_SPIOL : 92
+FER3_RAPSA : 99
+FER1_ARATH : 93
+FER_BRANA : 99
+FER2_ARATH : 93
+Q93Z60_ARATH : 92
+FER1_MAIZE : 91
+O80429_MAIZE : 91
+cons : 94
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+FER3_RAPSA ------------------------------------------------
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+FER2_ARATH 9965----344556888888876665555233333345--6778876-
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+FER1_SPIOL 422--2334599999999999999999999999999999999999999
+FER3_RAPSA -----------9999999999999999999999999999999999999
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+FER_BRANA -----------9999999999999999999999999999999999999
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+FER2_ARATH 99999998764--
+Q93Z60_ARATH -------------
+FER1_MAIZE 9999999998620
+O80429_MAIZE 99999999874--
+cons 9999999987550
+
+
+
+
+
<mapID target="varna" url="html/features/varna.html"/>
<mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
<mapID target="preferences" url="html/features/preferences.html"/>
+ <mapID target="strucprefs" url="html/features/preferences.html#structure"/>
<mapID target="commandline" url="html/features/commandline.html"/>
<mapID target="clarguments" url="html/features/clarguments.html"/>
<mapID target="io" url="html/io/index.html"/>
<mapID target="wsMenu" url="html/menus/wsmenu.html"/>
<mapID target="popMenu" url="html/menus/popupMenu.html"/>
+ <mapID target="popMenuAddref" url="html/menus/popupMenu.html#addrefannot"/>
<mapID target="annotPanelMenu" url="html/menus/alwannotationpanel.html"/>
<mapID target="memory" url="html/memory.html" />
- <mapID target="jalviewjnlp" url="html/jalviewjnlp.html" />
<mapID target="groovy" url="html/features/groovy.html" />
<mapID target="privacy" url="html/privacy.html" />
<mapID target="vamsas" url="html/vamsas/index.html"/>
<?xml version="1.0" encoding="ISO-8859-1" ?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) *
+ Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview.
+ * * Jalview is free software: you can redistribute it and/or * modify it
+ under the terms of the GNU General Public License * as published by the Free
+ Software Foundation, either version 3 * of the License, or (at your option)
+ any later version. * * Jalview is distributed in the hope that it will be
+ useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General
+ Public License for more details. * * You should have received a copy of the
+ GNU General Public License * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file. -->
<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
<toc version="1.0">
-<tocitem text="Jalview Documentation" target="home" expand="true" >
- <tocitem text="What's new" target="new" expand="true">
- <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
- <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
- <tocitem text="View all representative PDB structures" target="viewingpdbs.reps"/>
- <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
- </tocitem>
- <tocitem text="Editing Alignments" target ="edit"/>
- <tocitem text="Cursor Mode" target="cursor"/>
- <tocitem text="Key Strokes" target="keys"/>
- <tocitem text="Input / Output" target="io"/>
- <tocitem text="Making Figures" target="export"/>
- <tocitem text="Hidden Regions" target="hiddenRegions"/>
- <tocitem text="Multiple Views" target="multipleviews"/>
- <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
- <tocitem text="Fetching Sequences" target="seqfetch"/>
- <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
- <tocitem text="Viewing RNA structure" target="varna" />
- <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
- <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
- </tocitem>
- <tocitem text="Sequence Features" target="seqfeatures" expand="false">
- <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
- <tocitem text="Sequence Features File" target="features.fileformat"/>
- <tocitem text="Feature Colourschemes" target="features.featureschemes"/>
- <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
- <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
- <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
- <tocitem text="DAS Feature Settings" target="das.settings"/>
- <tocitem text="HTML annotation report" target="io.seqreport"/>
- </tocitem>
- <tocitem text="Web Services" target="webservice" expand="false">
- <tocitem text="JABAWS" target="jabaws"/>
- <tocitem text="Web Service Preferences" target="wsprefs"/>
- <tocitem text="Web Service Parameters" target="wsparams"/>
- <tocitem text="Sequence Alignment" target="msaservice" expand="false">
- <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"/>
- <tocitem text="Sequence Retrieval" target="seqfetch"/>
- <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
- <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
- </tocitem>
- <tocitem text="Colour Schemes" target="colours" expand="false">
- <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
- <tocitem text="ClustalX" target="colours.clustal"/>
- <tocitem text="Zappo" target="colours.zappo"/>
- <tocitem text="Taylor" target="colours.taylor"/>
- <tocitem text="Hydrophobicity" target="colours.hydro"/>
- <tocitem text="Helix propensity" target="colours.helix"/>
- <tocitem text="Strand propensity" target="colours.strand"/>
- <tocitem text="Turn propensity" target="colours.turn"/>
- <tocitem text="Buried index" target="colours.buried"/>
- <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
- <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine"/>
- <tocitem text="Blosum62" target="colours.blosum"/>
- <tocitem text="by Percentage Identity" target="colours.pid"/>
- <tocitem text="User Defined" target="colours.user"/>
- <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
- <tocitem text="By conservation" target="colours.conservation"/>
- <tocitem text="T-COFFEE Scores" target="io.tcoffeescores"/>
- <tocitem text="By Annotation" target="colours.annotation"/>
- <tocitem text="By RNA Helices" target="colours.rnahelices"/>
- </tocitem>
- <tocitem text="Calculations" target="calculations" expand="false">
- <tocitem text="Sorting alignments" target="sorting"/>
- <tocitem text="Calculating trees" target="trees"/>
- <tocitem text="Principal Component Analysis" target="pca"/>
- <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
- <tocitem text="Pairwise Alignments" target="pairwise"/>
- <tocitem text="Remove Redundancy" target="redundancy"/>
- </tocitem>
- <tocitem text="Sequence Annotations" target="seqannots" expand="true">
- <tocitem text="Annotation from Structure" target="xsspannotation" expand="false"/>
- </tocitem>
- <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
- <tocitem text="Conservation" target="calcs.alconserv"/>
- <tocitem text="Quality" target="calcs.alquality"/>
- <tocitem text="Consensus" target="calcs.consensus"/>
- <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
- <tocitem text="Annotations File Format" target="annotations.fileformat"/>
- </tocitem>
- <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
- <tocitem text="Jmol Viewer" target="pdbjmol"/>
- <tocitem text="Chimera Viewer" target="chimera"/>
- <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
- </tocitem>
- <tocitem text="Viewing RNA structures" target="varna" expand="false"> </tocitem>
- <tocitem text="VAMSAS Data Exchange" target="vamsas">
- <!-- what can Jalview share with other apps -->
- <!-- what other apps exist -->
+<!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
+ <tocitem text="Jalview Documentation" target="home" expand="true">
+ <tocitem text="What's new" target="new" expand="true">
+ <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
+ <tocitem text="Annotation Panel Menu" target="alwAnnotations" />
+ <tocitem text="Add reference annotation" target="popMenuAddref" />
+ <tocitem text="Colour By Annotation" target="colours.annotation" />
+ <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Structure Preferences" target="strucprefs" />
+ </tocitem>
+ <tocitem text="Editing Alignments" target="edit" />
+ <tocitem text="Cursor Mode" target="cursor" />
+ <tocitem text="Key Strokes" target="keys" />
+ <tocitem text="Input / Output" target="io" />
+ <tocitem text="Making Figures" target="export" />
+ <tocitem text="Hidden Regions" target="hiddenRegions" />
+ <tocitem text="Multiple Views" target="multipleviews" />
+ <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
+ <tocitem text="Fetching Sequences" target="seqfetch" />
+ <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+ <tocitem text="Viewing RNA structure" target="varna" />
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
+ <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
+ </tocitem>
+ <tocitem text="Sequence Features" target="seqfeatures" expand="false">
+ <tocitem text="Sequence Feature Settings" target="seqfeatures.settings" />
+ <tocitem text="Sequence Features File" target="features.fileformat" />
+ <tocitem text="Feature Colourschemes" target="features.featureschemes" />
+ <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
+ <tocitem text="Editing Sequence Features" target="seqfeatedit" />
+ <tocitem text="DAS Feature Retrieval" target="das.viewing" />
+ <tocitem text="DAS Feature Settings" target="das.settings" />
+ <tocitem text="HTML annotation report" target="io.seqreport" />
+ </tocitem>
+ <tocitem text="Web Services" target="webservice" expand="false">
+ <tocitem text="JABAWS" target="jabaws" />
+ <tocitem text="Web Service Preferences" target="wsprefs" />
+ <tocitem text="Web Service Parameters" target="wsparams" />
+ <tocitem text="Sequence Alignment" target="msaservice" expand="false">
+ <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" />
+ <tocitem text="Sequence Retrieval" target="seqfetch" />
+ <tocitem text="Database Reference Retrieval" target="dbreffetcher" />
+ <tocitem text="DAS Feature Retrieval" target="das.viewing" />
</tocitem>
- <tocitem text="Window Menus" target="menus" expand="false">
- <tocitem text="Desktop Window" target="desktopMenu"/>
- <tocitem text="Alignment Window" target="alMenu">
- <tocitem text="File Menu" target="alwFile"/>
- <tocitem text="Edit Menu" target="alwEdit"/>
- <tocitem text="Select Menu" target="alwSelect"/>
- <tocitem text="View Menu" target="alwView"/>
- <tocitem text="Annotations Menu" target="alwAnnotations"/>
- <tocitem text="Format Menu" target="alwFormat"/>
- <tocitem text="Colour Menu" target="alwColour"/>
- <tocitem text="Calculation Menu" target="alwCalc"/>
- <tocitem text="Web Service Menu" target="wsMenu"/>
- <tocitem text="Annotation Panel Menu" target="annotPanelMenu"/>
- <tocitem text="Popup Menu" target="popMenu"/>
- </tocitem>
+ <tocitem text="Colour Schemes" target="colours" expand="false">
+ <tocitem text="Background Dependent Text Colour" target="backdeptextcol" />
+ <tocitem text="ClustalX" target="colours.clustal" />
+ <tocitem text="Zappo" target="colours.zappo" />
+ <tocitem text="Taylor" target="colours.taylor" />
+ <tocitem text="Hydrophobicity" target="colours.hydro" />
+ <tocitem text="Helix propensity" target="colours.helix" />
+ <tocitem text="Strand propensity" target="colours.strand" />
+ <tocitem text="Turn propensity" target="colours.turn" />
+ <tocitem text="Buried index" target="colours.buried" />
+ <tocitem text="Nucleotide colours" target="colours.nucleotide" />
+ <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
+ <tocitem text="Blosum62" target="colours.blosum" />
+ <tocitem text="by Percentage Identity" target="colours.pid" />
+ <tocitem text="User Defined" target="colours.user" />
+ <tocitem text="Above Percentage Identity" target="colours.abovepid" />
+ <tocitem text="By conservation" target="colours.conservation" />
+ <tocitem text="T-COFFEE Scores" target="io.tcoffeescores" />
+ <tocitem text="By Annotation" target="colours.annotation" />
+ <tocitem text="By RNA Helices" target="colours.rnahelices" />
+ </tocitem>
+ <tocitem text="Calculations" target="calculations" expand="false">
+ <tocitem text="Sorting alignments" target="sorting" />
+ <tocitem text="Calculating trees" target="trees" />
+ <tocitem text="Principal Component Analysis" target="pca" />
+ <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
+ <tocitem text="Pairwise Alignments" target="pairwise" />
+ <tocitem text="Remove Redundancy" target="redundancy" />
+ </tocitem>
+ <tocitem text="Sequence Annotations" target="seqannots" expand="true">
+ <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
+ </tocitem>
+ <tocitem text="Alignment Annotations" target="alannotation" expand="false">
+ <tocitem text="Conservation" target="calcs.alconserv" />
+ <tocitem text="Quality" target="calcs.alquality" />
+ <tocitem text="Consensus" target="calcs.consensus" />
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
+ <tocitem text="Annotations File Format" target="annotations.fileformat" />
+ </tocitem>
+ <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+ <tocitem text="Jmol Viewer" target="pdbjmol" />
+ <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
+ </tocitem>
+ <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+ <tocitem text="VAMSAS Data Exchange" target="vamsas">
+ <!-- what can Jalview share with other apps -->
+ <!-- what other apps exist -->
+ </tocitem>
+ <tocitem text="Window Menus" target="menus" expand="false">
+ <tocitem text="Desktop Window" target="desktopMenu" />
+ <tocitem text="Alignment Window" target="alMenu">
+ <tocitem text="File Menu" target="alwFile" />
+ <tocitem text="Edit Menu" target="alwEdit" />
+ <tocitem text="Select Menu" target="alwSelect" />
+ <tocitem text="View Menu" target="alwView" />
+ <tocitem text="Annotations Menu" target="alwAnnotations" />
+ <tocitem text="Format Menu" target="alwFormat" />
+ <tocitem text="Colour Menu" target="alwColour" />
+ <tocitem text="Calculation Menu" target="alwCalc" />
+ <tocitem text="Web Service Menu" target="wsMenu" />
+ <tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
+ <tocitem text="Popup Menu" target="popMenu" />
+ </tocitem>
+ </tocitem>
+ <tocitem text="Preferences" target="preferences" />
+ <tocitem text="Memory Settings" target="memory" expand="false"/>
+ <tocitem text="Command Line" target="commandline" expand="false">
+ <tocitem text="Command Line Arguments" target="clarguments" />
+ <tocitem text="Groovy Shell" target="groovy" />
+ </tocitem>
+ <tocitem text="Privacy" target="privacy" />
+ </tocitem>
+ <tocitem text="Useful information" expand="true">
+ <tocitem text="Amino Acid Table" target="aminoAcids" />
+ <tocitem text="Amino Acid Properties" target="aaProperties" />
+ <tocitem text="The Genetic Code" target="geneticCode" />
+ <tocitem text="Sequence Substitution Matrices" target="subtMatrices" />
+
</tocitem>
- <tocitem text="Preferences" target="preferences"/>
- <tocitem text="Memory Settings" target="memory" expand="false">
- <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
- </tocitem>
- <tocitem text="Command Line" target="commandline" expand="false">
- <tocitem text="Command Line Arguments" target="clarguments"/>
- <tocitem text="Groovy Shell" target="groovy"/>
- </tocitem>
- <tocitem text="Privacy" target="privacy"/>
-</tocitem>
-<tocitem text="Useful information" expand="true">
- <tocitem text="Amino Acid Table" target="aminoAcids"/>
- <tocitem text="Amino Acid Properties" target="aaProperties"/>
- <tocitem text="The Genetic Code" target="geneticCode"/>
- <tocitem text="Sequence Substitution Matrices" target="subtMatrices"/>
-
-</tocitem>
</toc>
symbols and graphs, this may be black by default, so your alignment
will be coloured black.</em>
</li>
+ <li><em>Secondary structure annotation colouring</em><br />By
+ default, Jalview will employ the helix or sheet colours to shade
+ sequences and columns by available secondary structure annotation
+ tracks. In the case of RNA, each structure is processed to identify
+ distinct RNA helices and rendered in the same way as the <a
+ href="rnahelicesColouring.html">RNA Helices shading scheme</a>. <em>Structure based sequence shading was added in Jalview 2.8.2</em></li>
<li>The colour scheme can display a colour gradient from a colour
representing the minimum value in the selected annotation to a colour
representing the maximum value in the selected annotation. Use the
<p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), <br>
"Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"<br>
<em>Bioinformatics</em> <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033</p>
+ <p><strong>The Jalview Authors</strong><br/>
+ The following people have contributed to Jalview's development:
+ <ul>
+ <li>Jalview 1
+ <ul><li>Michele Clamp</li>
+ <li>James Cuff</li>
+ <li>Steve Searle</li>
+ <li>David Martin</li>
+ <li>Geoff Barton</li>
+ </ul>
+ </li><li>Jalview 2<ul>
+ <li>Jim Procter</li>
+ <li>Andrew Waterhouse</li>
+ <li>Mungo Carstairs</li>
+ <li>Tochukwu 'Charles' Ofoegbu</li>
+ <li>Jan Engelhardt</li>
+ <li>Lauren Lui</li>
+ <li>Anne Menard</li>
+ <li>Natasha Sherstnev</li>
+ <li>Daniel Barton</li>
+ <li>David Roldan-Martinez</li>
+ <li>David Martin</li>
+ <li>Geoff Barton</li>
+ </ul>
+ </li>
+ </ul>
+ </p>
</body>
</html>
+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Jalview local Jnlp File</title>
-</head>
-<body>
-<h1>Jalview local Jnlp File</h1>
-<pre>
-<jnlp spec="1.0+" codebase="http://www.jalview.org/webstart/">
- <information>
- <title>Jalview</title>
- <vendor>The Barton Group</vendor>
- <homepage href="http://www.jalview.org"/>
- <description>Jalview Multiple Alignment Editor</description>
- <description kind="short">Jalview</description>
- <icon href="http://www.jalview.org/webstart/logo_big.gif" kind="default"/>
- <association extensions="fa" mime-type="application-x/ext-file"/>
- <association extensions="fasta" mime-type="application-x/ext-file"/>
- <association extensions="fastq" mime-type="application-x/ext-file"/>
- <association extensions="blc" mime-type="application-x/ext-file"/>
- <association extensions="msf" mime-type="application-x/ext-file"/>
- <association extensions="pfam" mime-type="application-x/ext-file"/>
- <association extensions="aln" mime-type="application-x/ext-file"/>
- <association extensions="pir" mime-type="application-x/ext-file"/>
- <association extensions="stk" mime-type="application-x/ext-file"/>
- <offline-allowed/>
- </information>
- <security>
- <all-permissions/>
- </security>
- <resources>
- <!-- <em>the additional memory parameters are here</em> -->
- <j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/>
- <jar href="jalview.jar"/>
- <jar href="JGoogleAnalytics-0.2.1-SNAPSHOT.jar"/>
- <jar href="Jmol-12.1.13.jar"/>
- <jar href="activation.jar"/>
- <jar href="axis.jar"/>
- <jar href="castor-1.1-cycle-xml.jar"/>
- <jar href="commons-discovery.jar"/>
- <jar href="commons-logging.jar"/>
- <jar href="jaxrpc.jar"/>
- <jar href="jhall.jar"/>
- <jar href="log4j-1.2.8.jar"/>
- <jar href="mail.jar"/>
- <jar href="min-jaba-client.jar"/>
- <jar href="regex.jar"/>
- <jar href="saaj.jar"/>
- <jar href="vamsas-client.jar"/>
- <jar href="wsdl4j.jar"/>
- <jar href="xercesImpl.jar"/>
- <jar href="xml-apis.jar"/>
- <property name="jalview.version" value="2.6.1"/>
- </resources>
- <application-desc main-class="jalview.bin.Jalview"/>
-</jnlp>
-</pre>
-<address><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss">If
-you have problems, send an email to jalview-discuss</a></address>
-</body>
-</html>
The way you increase the memory settings for the JVM depends on which installation
of Jalview you use:</p>
<ul>
- <li><em><font size="3">Web Start Version</font></em>
- <p>JavaWS sets the JVM parameters through special tags in the JNLP file. You'll
- need to <a href="jalviewjnlp.html">make your own jnlp file</a> and add the following parameter into the
- <resources> element.
- <pre>
-<j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/>
-</pre>
- Save the jnlp file somewhere and then - if you start Jalview through your
- web browser, point your browser at the file's url, othewise simply run javaws
- with the file location as its argument. The file's url is something like :<br>
- <pre>
+ <li><em><font size="3">Web Start Version</font></em>
+ <p>
+ JavaWS sets the JVM parameters through special tags in the JNLP
+ file. You can obtain a JNLP file with modified memory settings from
+ our service with the following link (replace 2G with desired memory
+ in G or M):<br /> <a
+ href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G">http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
+ </p>
+ <p>
+ Alternatively, if you want to create your own JNLP file then please
+ download the latest JNLP file from <a
+ href="http://www.jalview.org/webstart/jalview.jnlp">http://www.jalview.org/webstart/jalview.jnlp</a>
+ and modify the max-heap-size parameter for the j2se tag in the
+ <resources> element. e.g.
+ <pre>
+<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/>
+</pre> In both cases, you should save your new jnlp file somewhere and
+ then either point your web browser at the file's url, launch it from
+ your file browser, or from a terminal window run javaws (located in
+ your Java installation's bin directory) with the file location as its
+ argument. The file's url is something like :<br> <pre>
file://<full path to file>
-</pre>
- If jalview doesn't start up, see <a href="#memsetting">below</a>. You'll have
- to edit the above settings in the JNLP file using a text editor, save it,
- and try starting Jalview with it once more.
- <p></li>
- <li><em><font size="3">Install Anywhere version</font></em>
+</pre> If jalview doesn't start up, see <a href="#memsetting">below</a>.
+ You'll have to edit the above settings in the JNLP file using a text
+ editor, save it, and try starting Jalview with it once more.
+ </p></li>
+ <li><em><font size="3">Install Anywhere version</font></em>
<p> You need to change the InstallAnywhere configuration settings for the
application. These are found in different places depending upon which operating
system you have :
</tr>
<tr>
<td><div align="center">
- <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>18/11/2014</em></strong>
+ <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
</div></td>
<td><em>General</em>
<ul>
+ <li>Updated Java code signing certificate donated by Certum.PL.</li>
<li>Features and annotation preserved when performing pairwise
alignment</li>
<li>RNA pseudoknot annotation can be
<li>Structure viewer preferences tab</li>
<li>Disorder and Secondary Structure annotation tracks shared
between alignments</li>
- <li>UCSF launch and linked highlighting from Jalview</li>
+ <li>UCSF Chimera launch and linked highlighting from Jalview</li>
<li>Show/hide all sequence associated annotation rows for all
or current selection</li>
<li>disorder and secondary structure predictions available as
<li>Cannot open sequence feature shading/sort popup menu in
feature settings dialog</li>
<li>better tooltip placement for some areas of Jalview desktop</li>
- <li>Unable to add JABAWS Server which doesn't pass
+ <li>Allow addition of JABAWS Server which doesn't pass
validation</li>
<li>Web services parameters dialog box is too large to fit on
screen</li>
user preset</li>
<li>MSA web services warns user if they were launched with
invalid input</li>
- <li>Jalview cannot contact dasregisty (Java 8)</li>
+ <li>Jalview cannot contact DAS Registy when running on Java 8</li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
+ 'Superpose with' submenu not shown when new view created
+ </li>
- </ul> <em>Applet</em>
+ </ul> <!-- <em>Applet</em>
<ul>
</ul> <em>General</em>
- <ul>
- </ul> <em>Deployment and Documentation</em>
+ <ul>
+ </ul>--> <em>Deployment and Documentation</em>
<ul>
<li>2G and 1G options in launchApp have no effect on memory
allocation</li>
<li>launchApp service doesn't automatically open
www.jalview.org/examples/exampleFile.jar if no file is given</li>
- </ul>
- <em>Application Known issues</em>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
+ InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
+ available
+ </li>
+ </ul> <em>Application Known issues</em>
<ul>
<li>
<!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
to right
</li>
<li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
- 'Superpose with' submenu not shown when new view created
- </li>
- <li>
<!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
retrieval fails but progress bar continues for DAS retrieval with
large number of ID
structure tracks are rearranged
</li>
<li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
- InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
- available
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
+ invalid rna structure positional highlighting does not highlight
+ position of invalid base pairs
</li>
<li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
- invalid rna structure positional highlighting isn't useful
+ <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
+ out of memory errors are not raised when saving jalview project
+ from alignment window file menu
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
+ Switching to RNA Helices colouring doesn't propagate to
+ structures
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
+ colour by RNA Helices not enabled when user created annotation
+ added to alignment
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
+ Jalview icon not shown on dock in Mountain Lion/Webstart
+ </li>
+ </ul> <em>Applet Known Issues</em>
+ <ul>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
+ JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
+ Jalview and Jmol example not compatible with IE9
</li>
-</ul>
-<ul>
- <li>
- <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
- out of memory errors are not raised when saving jalview project
- from alignment window file menu
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
- Switching to RNA Helices colouring doesn't propagate to
- structures
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
- colour by RNA Helices not enabled when user created annotation
- added to alignment
- </li> TOFIX
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
- Jalview icon not shown on dock in Mountain Lion/Webstart
- </li>
- </ul>
- <em>Applet Known Issues</em>
- <ul>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
- JalviewLite needs JmolApplet and JmolData jar dependencies
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
- Jalview and Jmol example not compatible with IE9
- </li>
- <li>Sort by annotation score doesn't reverse order when
- selected</li>
- </ul>
- </td>
+ <li>Sort by annotation score doesn't reverse order when
+ selected</li>
+ </ul>
+ </td>
</tr>
<tr>
<td><div align="center">
development team.<br /> It incorporates many minor improvements and
bug-fixes, and new features for working with 3D structure data,
shading alignments by secondary structure and generation of alignment
- figures as Scalable Vector Graphics.
- <br />As ever, the highlights are detailed below, and the full list is
- given in the
- <a href="releases.html#Jalview2.8.2">Jalview 2.8.2 Release Notes</a>.
+ figures as Scalable Vector Graphics. <br />The majority of
+ improvements in this version of Jalview concern the desktop
+ application. As ever, the highlights are detailed below,
+ and the full list is given in the <a
+ href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
</p>
+ <p>
+ <strong>Annotation visualisation</strong> <br /> The alignment window
+ includes a new <em>Annotations</em> menu which provides controls for
+ the layout and display of sequence, group and alignment associated
+ annotation rows. It also now includes the <em>Autocalculated
+ Annotation</em> submenu (formerly located in the View menu), which
+ includes settings for the calculation and display of sequence
+ consensus, logos, and amino acid conservation for the alignment and
+ subgroups.
+ </p>
+ <p>
+ <strong>Sequence associated annotation</strong><br /> New controls
+ have also been added to the Sequence ID popup menu for the propagation
+ and display of sequence associated annotation such as secondary
+ structure assignments and disorder predictions. Annotation associated
+ with one or a group of sequence already shown on the alignment may be
+ shown or hidden, and any available annotation from 3D structure or
+ calculations performed in other Jalview windows can be copied to the
+ alignment
+ <em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
+ The <strong>Colour by annotation</strong> function has also been
+ improved, allowing secondary structure annotation to be used to shade
+ sequences and alignment columns. Protein sequences can be coloured
+ according to the presence of a helix or sheet at each position, and
+ RNA sequences can be shaded according to each structure's stem/helix
+ pattern - which enables different RNA folding topologies to be quickly
+ identified.
+ </p>
+ <p>
+ <strong>3D Structural data analysis and display</strong><br />
+ Jalview now employs Jmol's PDB data API to retrieve secondary
+ structure assignments made by the DSSP algorithm. It can also employ
+ web services to obtain secondary structure assignments from RNA
+ structures. These assignments are shown as sequence associated
+ annotation for sequences which have cross-references to the PDB, or
+ have had PDB files associated with them via the <em>Structures</em>
+ submenu of the sequence ID popup menu. The extraction and display of
+ secondary structure and B-factor column annotation is controlled <em>via</em>
+ a new <strong>Structure</strong> tab in the Jalview Desktop's
+ Preferences dialog box.
+ </p>
+ <p>
+ <Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
+ application can now be configured to employ UCSF Chimera for the
+ display of 3D structure data. UCSF Chimera is a python-based
+ high-performance molecular graphics and animation system developed by
+ the Resource for Biocomputing, Visualisation, and Informatics at the
+ University of California.<br />Jalview employs the 'StructureViz'
+ communication mechanism developed for Cytoscape by Morris et al.
+ (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
+ allows Jalview to send commands to Chimera, enabling structures to be
+ superimposed and shaded according to associated multiple aligmment
+ views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
+ would appreciate feedback ! Please send your comments to
+ jalview-discuss@jalview.org, and keep up to date with this feature's
+ development via http://issues.jalview.org/browse/JAL-1333.
+ </p>
+ <p>
+ <strong>Export of alignment figures as Scalable Vector
+ Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
+ supported by web browsers and graphics design programs, and allow
+ high-quality graphics for interactive exploration and publication.
+ Jalview now supports the generation of SVGs interactively (via the
+ Export) menu, and from the command line for server-side figure
+ generation.
+ </p>
+
</body>
</html>
YEAR=2014
-AUTHORS=J Procter, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
-AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+AUTHORS=J Procter, AM Waterhouse, M Carstairs, TC Ofoegbu, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu 'Charles' Ofoegbu, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
\ No newline at end of file
label.user_defined_colours = User defined colours
label.jalviewLite_release = JalviewLite - Release {0}
label.jaview_build_date = Build date: {0}
-label.jalview_authors_1 = Authors: : Jim Procter, Andrew Waterhouse, Lauren Lui, Jan Engelhardt, Natasha Sherstnev,
-label.jalview_authors_2 = Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
+label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu Ofoegbu, Lauren Lui, Jan Engelhardt,
+label.jalview_authors_2 = Natasha Sherstnev, Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
label.jalview_dev_managers = Development managed by The Barton Group, University of Dundee, Scotland, UK.
label.jalview_distribution_lists = For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list
label.jalview_please_cite = If you use Jalview, please cite:
label.user_defined_colours = Colores definidos del usuario
label.jalviewLite_release = JalviewLite - versión {0}
label.jaview_build_date = Fecha de creación: {0}
-label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,
-label.jalview_authors_2 = Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
+label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu Ofoegbu, Lauren Lui, Jan Engelhardt,
+label.jalview_authors_2 = Natasha Sherstnev, Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
label.jalview_dev_managers = Desarrollo gestionado por The Barton Group, University of Dundee, Scotland, UK.
label.jalview_distribution_lists = Para ayuda, ver el FAQ at www.jalview.org y/o adjuntar la lista de envío jalview-discuss@jalview.org
label.jalview_please_cite = Si usa Jalview incluya la siguiente cita, por favor:
return aa;
}
+ /**
+ * Returns an iterable collection of any annotations that match on given
+ * sequence ref, calcId and label (ignoring null values).
+ */
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation ann : getAlignmentAnnotation())
+ {
+ if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+ && ann.sequenceRef != null && ann.sequenceRef == seq
+ && ann.label != null && ann.label.equals(label))
+ {
+ aa.add(ann);
+ }
+ }
+ return aa;
+ }
+
@Override
public void moveSelectedSequencesByOne(SequenceGroup sg,
Map<SequenceI, SequenceCollectionI> map, boolean up)
Iterable<AlignmentAnnotation> findAnnotation(String calcId);
+ Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label);
+
/**
* context for this annotated collection
*
return datasetSequence;
}
+ /**
+ * Returns a new array containing this sequence's annotations, or null.
+ */
public AlignmentAnnotation[] getAnnotation()
{
- if (annotation == null)
- {
- return null;
- }
-
- AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
- for (int r = 0; r < ret.length; r++)
- {
- ret[r] = annotation.elementAt(r);
- }
+ return annotation == null ? null : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
+ }
- return ret;
+ /**
+ * Returns true if this sequence has the given annotation (by object
+ * identity).
+ */
+ @Override
+ public boolean hasAnnotation(AlignmentAnnotation ann)
+ {
+ return annotation == null ? false : annotation.contains(ann);
}
+ /**
+ * Add the given annotation, if not already added, and set its sequence ref to
+ * be this sequence. Does nothing if this sequence's annotations already
+ * include this annotation (by identical object reference).
+ */
public void addAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation == null)
endRes = seqsel.endRes;
cs = seqsel.cs;
if (seqsel.description != null)
+ {
description = new String(seqsel.description);
+ }
hidecols = seqsel.hidecols;
hidereps = seqsel.hidereps;
idColour = seqsel.idColour;
}
}
if (!found)
+ {
continue;
+ }
}
AlignmentAnnotation newannot = new AlignmentAnnotation(
seq.getAnnotation()[a]);
}
/**
+ * Returns a list of annotations that match the specified sequenceRef, calcId
+ * and label, ignoring null values.
+ *
+ * @return list of AlignmentAnnotation objects
+ */
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation ann : getAlignmentAnnotation())
+ {
+ if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+ && ann.sequenceRef != null && ann.sequenceRef == seq
+ && ann.label != null && ann.label.equals(label))
+ {
+ aa.add(ann);
+ }
+ }
+ return aa;
+ }
+
+ /**
* Answer true if any annotation matches the calcId passed in (if not null).
*
* @param calcId
public AlignmentAnnotation[] getAnnotation();
+ public boolean hasAnnotation(AlignmentAnnotation ann);
+
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
/**
* Check for any annotations on the underlying dataset sequences (for the
- * current selection group) which are not on the alignment annotations for the
- * sequence. If any are found, enable the option to add them to the alignment.
- * The criteria for 'on the alignment' is finding an alignment annotation on
- * the sequence, that matches on calcId and label. A tooltip is also
- * constructed that displays the source (calcId) and type (label) of the
- * annotations that can be added.
+ * current selection group) which are not 'on the alignment'.If any are found,
+ * enable the option to add them to the alignment. The criteria for 'on the
+ * alignment' is finding an alignment annotation on the alignment, matched on
+ * calcId, label and sequenceRef.
+ *
+ * A tooltip is also constructed that displays the source (calcId) and type
+ * (label) of the annotations that can be added.
*
* @param menuItem
* @param forSequences
/*
* For each sequence selected in the alignment, make a list of any
* annotations on the underlying dataset sequence which are not already on
- * the sequence in the alignment.
+ * the alignment.
*
* Build a map of { alignmentSequence, <List of annotations to add> }
*/
+ AlignmentI al = this.ap.av.getAlignment();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
for (SequenceI seq : forSequences)
{
for (AlignmentAnnotation dsann : datasetAnnotations)
{
/*
- * If the sequence has no annotation that matches this one, then add
- * this one to the results list.
+ * Find matching annotations on the alignment.
*/
- if (seq.getAlignmentAnnotations(dsann.getCalcId(), dsann.label)
- .isEmpty())
+ final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
+ .findAnnotations(seq, dsann.getCalcId(),
+ dsann.label);
+ if (!matchedAlignmentAnnotations.iterator().hasNext())
{
result.add(dsann);
tipEntries.put(dsann.getCalcId(), dsann.label);
}
copyAnn.restrict(startRes, endRes);
- // add to the sequence (sets copyAnn.datasetSequence)
- seq.addAlignmentAnnotation(copyAnn);
+ /*
+ * Add to the sequence (sets copyAnn.datasetSequence), unless the
+ * original annotation is already on the sequence.
+ */
+ if (!seq.hasAnnotation(ann))
+ {
+ seq.addAlignmentAnnotation(copyAnn);
+ }
// adjust for gaps
copyAnn.adjustForAlignment();
// add to the alignment and set visible
}
else
{
- label = (key = type2id(aa.label.toLowerCase())) + "_cons";
+ key = type2id(aa.label.toLowerCase());
+ if (key == null)
+ {
+ label = aa.label;
+ }
+ else
+ {
+ label = key + "_cons";
+ }
}
-
if (label == null)
{
label = aa.label;
}
+ label = label.replace(" ", "_");
out.append(new Format("%-" + maxid + "s").form("#=GC " + label
+ " "));
String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
.toString(sequenceI.getCharAt(k)))
: annot.displayCharacter;
- if (key.equals("SS"))
+ if (key != null && key.equals("SS"))
{
if (annot == null)
{
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.FlowLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
-import javax.swing.*;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
/**
* DOCUMENT ME!
toolsMenu.add(showConsole);
toolsMenu.add(showNews);
toolsMenu.add(garbageCollect);
- toolsMenu.add(snapShotWindow);
+ // toolsMenu.add(snapShotWindow);
inputMenu.add(inputLocalFileMenuItem);
inputMenu.add(inputURLMenuItem);
inputMenu.add(inputTextboxMenuItem);
|| (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
: aj.value <= annotationThreshold.value)))
{
- if (predefinedColours && aj.colour != null)
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black))
{
currentColour = aj.colour;
}
jws2Discoverer.addInvalidServiceUrl(jwsserver);
}
;
- if (service != null)
+ if (service != null
+ && !Jws2InstanceFactory.ignoreService(srv.toString()))
{
noservices = false;
Jws2Instance svc = null;
*/
package jalview.ws.jws2.jabaws2;
-import java.util.HashMap;
-
-import compbio.data.msa.JABAService;
import jalview.ws.jws2.AAConClient;
import jalview.ws.jws2.JPred301Client;
import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.uimodel.AlignAnalysisUIText;
+import java.util.HashMap;
+import java.util.HashSet;
+
+import compbio.data.msa.JABAService;
+
public class Jws2InstanceFactory
{
private static HashMap<String, AlignAnalysisUIText> aaConGUI;
+ private static HashSet<String> ignoreGUI;
private static String category_rewrite(String cat_name)
{
return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction"
AAConClient.getAlignAnalysisUITest());
aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
RNAalifoldClient.getAlignAnalysisUITest());
+ // disable the JPred301 client in jalview ...
+ ignoreGUI = new HashSet<String>();
+ ignoreGUI.add(compbio.ws.client.Services.JpredWS.toString());
aaConGUI.put(compbio.ws.client.Services.JpredWS.toString(),
JPred301Client.getAlignAnalysisUITest());
}
}
/**
+ * exclusion list to avoid creating GUI elements for services we don't fully
+ * support
+ *
+ * @param serviceType
+ * @return
+ */
+ public static boolean ignoreService(String serviceType)
+ {
+ init();
+ return (ignoreGUI.contains(serviceType.toString()));
+ }
+ /**
* construct a service instance and configure it with any additional
* properties needed so Jalview can access it correctly
*
init();
Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
category_rewrite(name), description, service);
-
svc.aaui = aaConGUI.get(serviceType.toString());
return svc;
}
/**
* Tests for addAlignmentAnnotation. Note this method has the side-effect of
- * setting the sequenceRef on the annotation.
+ * setting the sequenceRef on the annotation. Adding the same annotation twice
+ * should be ignored.
*/
@Test
public void testAddAlignmentAnnotation()
AlignmentAnnotation[] anns = seq.getAnnotation();
assertEquals(1, anns.length);
assertSame(annotation, anns[0]);
+
+ // re-adding does nothing
+ seq.addAlignmentAnnotation(annotation);
+ anns = seq.getAnnotation();
+ assertEquals(1, anns.length);
+ assertSame(annotation, anns[0]);
+
+ // an identical but different annotation can be added
+ final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
+ "b", 2d);
+ seq.addAlignmentAnnotation(annotation2);
+ anns = seq.getAnnotation();
+ assertEquals(2, anns.length);
+ assertSame(annotation, anns[0]);
+ assertSame(annotation2, anns[1]);
+
}
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
import jalview.util.MessageManager;
import java.awt.Component;
@Before
public void setUp() throws IOException
{
- alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA,
+ alignment = new FormatAdapter().readFile(TEST_DATA,
AppletFormatAdapter.PASTE, "FASTA");
AlignFrame af = new AlignFrame(alignment, 700, 500);
parentPanel = new AlignmentPanel(af, af.getViewport());
public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
{
JMenuItem menu = new JMenuItem();
- List<SequenceI> seqs = new ArrayList<SequenceI>();
/*
* Initial state is that sequences have annotations, and have dataset
* sequences, but the dataset sequences have no annotations. Hence nothing
* to add.
*/
- seqs = parentPanel.getAlignment().getSequences();
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertFalse(menu.isEnabled());
public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
{
JMenuItem menu = new JMenuItem();
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+ // make up new annotations and add to dataset sequences, sequences and
+ // alignment
+ attachReferenceAnnotations(seqs, true, true);
- seqs = parentPanel.getAlignment().getSequences();
- // copy annotation from sequence to dataset
- seqs.get(1).getDatasetSequence()
- .addAlignmentAnnotation(seqs.get(1).getAnnotation()[0]);
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertFalse(menu.isEnabled());
}
{
JMenuItem menu = new JMenuItem();
List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
// make up new annotations and add to dataset sequences
+ attachReferenceAnnotations(seqs, false, false);
+
+ testee.configureReferenceAnnotationsMenu(menu, seqs);
+ assertTrue(menu.isEnabled());
+ String expected = "<html><table width=350 border=0><tr><td>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
+ assertEquals(expected, menu.getToolTipText());
+ }
+
+ /**
+ * Test building the 'add reference annotations' menu for the case where
+ * several reference annotations are on the dataset and the sequences but not
+ * on the alignment. The menu item should be enabled, and acquire a tooltip
+ * which lists the annotation sources (calcIds) and type (labels).
+ */
+ @Test
+ public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
+ {
+ JMenuItem menu = new JMenuItem();
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+ // make up new annotations and add to dataset sequences and sequences
+ attachReferenceAnnotations(seqs, true, false);
+
+ testee.configureReferenceAnnotationsMenu(menu, seqs);
+ assertTrue(menu.isEnabled());
+ String expected = "<html><table width=350 border=0><tr><td>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
+ assertEquals(expected, menu.getToolTipText());
+ }
+ /**
+ * Generate annotations and add to dataset sequences and (optionally)
+ * sequences and/or alignment
+ *
+ * @param seqs
+ * @param addToSequence
+ * @param addToAlignment
+ */
+ private void attachReferenceAnnotations(List<SequenceI> seqs,
+ boolean addToSequence, boolean addToAlignment)
+ {
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
"secondary structure", "", 0);
annotation.setCalcId("PBD");
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
+ if (addToSequence)
+ {
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ }
+ if (addToAlignment)
+ {
+ this.alignment.addAnnotation(annotation);
+ }
// PDB.Temp on Sequence1
annotation = new AlignmentAnnotation("Temp", "", 0);
annotation.setCalcId("PBD");
seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
+ if (addToSequence)
+ {
+ seqs.get(1).addAlignmentAnnotation(annotation);
+ }
+ if (addToAlignment)
+ {
+ this.alignment.addAnnotation(annotation);
+ }
// JMOL.secondary structure on Sequence0
annotation = new AlignmentAnnotation("secondary structure", "", 0);
annotation.setCalcId("JMOL");
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
+ if (addToSequence)
+ {
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ }
+ if (addToAlignment)
+ {
+ this.alignment.addAnnotation(annotation);
+ }
+ }
- testee.configureReferenceAnnotationsMenu(menu, seqs);
- assertTrue(menu.isEnabled());
- String expected = "<html><table width=350 border=0><tr><td>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
- assertEquals(expected, menu.getToolTipText());
+ /**
+ * Test building the 'add reference annotations' menu for the case where there
+ * are two alignment views:
+ * <ul>
+ * <li>in one view, reference annotations have been added (are on the
+ * datasets, sequences and alignment)</li>
+ * <li>in the current view, reference annotations are on the dataset and
+ * sequence, but not the alignment</li>
+ * </ul>
+ * The menu item should be enabled, and acquire a tooltip which lists the
+ * annotation sources (calcIds) and type (labels).
+ */
+ @Test
+ public void testConfigureReferenceAnnotationsMenu_twoViews()
+ {
}
/**
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STATUS: Fully Functional LICENSED Edition
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</property>
<property name="withoutVmSearchOption">
<short>10</short>
</property>
<property name="withVMSearchOption">
- <short>21</short>
+ <short>20</short>
</property>
<property name="win32InstallerLauncherType">
<short>90</short>
<boolean>true</boolean>
</property>
<property name="credentialInformation">
- <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="27759feba050">
+ <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="1f4abcab8706">
<property name="hostName">
<string><![CDATA[]]></string>
</property>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.installer.options.valid.vm.list]]></string>
- <string><![CDATA[1.6,1.7,1.8+]]></string>
+ <string><![CDATA[1.7+]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.project.build.last.date]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.project.save.last.date]]></string>
- <string><![CDATA[01 November 2013 13:57:31 o'clock GMT]]></string>
+ <string><![CDATA[02 December 2014 16:16:01 o'clock GMT]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.build.options.optimization.platform.cdrom]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.installer.options.platform.macosx.vm.version]]></string>
- <string><![CDATA[1.6+]]></string>
+ <string><![CDATA[1.7+]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.build.platform.java.novm]]></string>
<int>8</int>
</property>
<property name="revision">
- <int>0</int>
+ <int>2</int>
</property>
<property name="subRevision">
<int>0</int>
</property>
</object>
</property>
+ <property name="upgradeCode">
+ <object class="com.zerog.registry.UUID">
+ <method name="update">
+ <string><![CDATA[fe7d6410-1ed5-11b2-a662-f4777f28dbfc]]></string>
+ </method>
+ </object>
+ </property>
<property name="supportURL">
<string><![CDATA[http://www.jalview.org/faq]]></string>
</property>
<string><![CDATA[jalview-discuss@jalview.org]]></string>
</property>
<property name="copyright">
- <string><![CDATA[2013]]></string>
+ <string><![CDATA[2014]]></string>
</property>
<property name="license">
<string><![CDATA[Commercial]]></string>
<property name="oldStyleInstallersEnabled">
<boolean>false</boolean>
</property>
+ <property name="upgradeSettings">
+ <object class="com.zerog.ia.installer.UpgradeSettings" objectID="1b941ce786e7">
+ <property name="enableUpgrade">
+ <boolean>false</boolean>
+ </property>
+ <property name="upgradeConfigurationsList">
+ <object class="java.util.ArrayList" list="true">
+ <method name="add">
+ <object class="com.zerog.ia.installer.UpgradeConfiguration" objectID="1b941ce886e7">
+ <property name="detectionBasedOn">
+ <string><![CDATA[PRODUCT_CODE]]></string>
+ </property>
+ <property name="requireValidationForPreviousProductCode">
+ <boolean>false</boolean>
+ </property>
+ <property name="maxVersion">
+ <object class="com.zerog.ia.installer.util.Version" objectID="1b941cea86e7">
+ <property name="major">
+ <int>1</int>
+ </property>
+ <property name="minor">
+ <int>0</int>
+ </property>
+ <property name="revision">
+ <int>0</int>
+ </property>
+ <property name="subRevision">
+ <int>0</int>
+ </property>
+ </object>
+ </property>
+ <property name="minVersion">
+ <object class="com.zerog.ia.installer.util.Version" objectID="1b941ce886e8">
+ <property name="major">
+ <int>1</int>
+ </property>
+ <property name="minor">
+ <int>0</int>
+ </property>
+ <property name="revision">
+ <int>0</int>
+ </property>
+ <property name="subRevision">
+ <int>0</int>
+ </property>
+ </object>
+ </property>
+ <property name="configurationName">
+ <string><![CDATA[Default Upgrade Configuration]]></string>
+ </property>
+ </object>
+ </method>
+ </object>
+ </property>
+ <property name="abortInstallationIfUninstallFails">
+ <boolean>true</boolean>
+ </property>
+ <property name="automaticallyRemoveAllExistingInstallations">
+ <boolean>true</boolean>
+ </property>
+ <property name="promptUserOnExistanceOfMultiplePreviousInstallations">
+ <boolean>false</boolean>
+ </property>
+ <property name="allowCustomizationOfUserInstallDirectory">
+ <boolean>false</boolean>
+ </property>
+ <property name="retainFeaturePreferences">
+ <boolean>false</boolean>
+ </property>
+ </object>
+ </property>
+ <property name="tomcatServerNamesList">
+ <object class="java.util.ArrayList" list="true"/>
+ </property>
<visualChildren>
<object class="com.zerog.ia.installer.InstallSet" objectID="fe7d6493a66a">
<property name="belongsToUninstallPhase">
<object refID="24485f8aa671"/>
<object refID="24485f89a672"/>
<object refID="24485f8aa672"/>
- <object refID="244ffffaa672"/>
- <object refID="244f00faa672"/>
+ <object refID="244ffffaa672"/>
+ <object refID="244f00faa672"/>
<object refID="24485f8ba672"/>
<object refID="24485f8aa673"/>
<object refID="24485f8ba673"/>
<object refID="f44ca391ab9f"/>
<object refID="f44ca392ab9f"/>
<object refID="f44ca393ab9f"/>
- <object refID=""1f46cffffab93"/>
+ <object refID="f46c2f42ab93"/>
+ <object refID="1f46cffffab93"/>
+ <object refID="1f46efeefab93"/>
<object class="com.zerog.ia.installer.actions.InstallFile" objectID="f44fc5b2aba1">
<property name="belongsToUninstallPhase">
<boolean>false</boolean>
<int>0</int>
</property>
</object>
- <object refID="f46c2f42ab93"/>
<object class="com.zerog.ia.installer.actions.InstallDirectory" objectID="24485f85a670">
<property name="belongsToUninstallPhase">
<boolean>false</boolean>
<object refID="24485f8aa671"/>
<object refID="24485f89a672"/>
<object refID="24485f8aa672"/>
- <object refID="244ffffaa672"/>
- <object refID="244f00faa672"/>
+ <object refID="244ffffaa672"/>
+ <object refID="244f00faa672"/>
<object refID="24485f8ba672"/>
<object refID="24485f8aa673"/>
<object refID="24485f8ba673"/>
<object refID="f44ca393ab9f"/>
<object refID="f46c2f42ab93"/>
<object refID="1f46cffffab93"/>
+ <object refID="1f46efeefab93"/>
</visualChildren>
</object>
<object class="com.zerog.ia.installer.actions.InstallDirectory" objectID="f44fc5d5aba1">
git://source.jalview.org / jalview.git / commitdiff