-jalview.release=Release_2_9_0b1_Branch
-jalview.version=2.9.0b2
+jalview.release=Release_2_10_Branch
+jalview.version=2.10.0
</testng>
</target>
- <target name="buildindices" depends="init, prepare,linkcheck" unless="help.uptodate">
+ <target name="buildindices" depends="init, prepare" unless="help.uptodate">
<java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
<arg line="html" />
</java>
</axis-wsdl2java>
</target>
-<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
<!-- make the package jar if not already existing -->
<mkdir dir="${packageDir}" />
<!-- clean dir if it already existed -->
<target name="compileApplet" depends="init,clean">
<mkdir dir="${outputDir}" />
- <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so" />
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
</target>
<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
</packageset>
</javadoc>
</target>
-<target name="linkcheck">
- <!-- finally, publish the help files -->
+<target name="linkcheck" depends="init,prepare">
<javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
<java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
<arg file="${helpDir}"/>
Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html> FER_BRANA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html> FER2_ARATH -1 60 135 Pfam
-Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html> FER1_ARATH -1 60 135 Pfam
+Ferredoxin_fold Status: True Positive FER1_ARATH -1 50 145 Cath
<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_11</a></html> Q93Z60_ARATH -1 60 118 Pfam
Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (S) 112_11</a></html> FER1_SPIOL -1 112 112 PHOSPHORYLATION (S)
<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (T) 139_13</a></html> FER1_SPIOL -1 139 139 PHOSPHORYLATION (T)
<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (Y) 73_7</a></html> FER1_SPIOL -1 73 73 PHOSPHORYLATION (Y)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html> FER1_ARATH -1 19 19 PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html> FER1_ARATH -1 24 24 PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_ARATH -1 90 90 PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_ARATH -1 107 107 PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_ARATH -1 114 114 PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_ARATH -1 141 141 PHOSPHORYLATION (T)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html> FER1_ARATH -1 75 75 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html> FER2_ARATH -1 19 19 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html> FER2_ARATH -1 24 24 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER2_ARATH -1 90 90 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER2_ARATH -1 107 107 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER2_ARATH -1 114 114 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER2_ARATH -1 141 141 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html> FER2_ARATH -1 75 75 PHOSPHORYLATION (Y)
<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> FER_BRANA -1 38 38 PHOSPHORYLATION (S)
<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (S) 62_6</a></html> FER_BRANA -1 62 62 PHOSPHORYLATION (S)
<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html> FER_BRANA -1 89 89 PHOSPHORYLATION (T)
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
import jalview.workers.FeatureCounterI;
import jalview.workers.AlignmentAnnotationFactory;
EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT
IETHREEDMV--
>FER1_ARATH/1-148
-----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
-EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
-IETHKEEDIV--
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
+IETHKEEAIM--
>FER_BRANA/1-96
----------------------------------------------------------ATYKVKFITPEGEQ
EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
IETHKEEELV--
>FER2_ARATH/1-148
-----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
-EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
-IETHKEEAIM--
+----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
+IETHKEEDIV--
>Q93Z60_ARATH/1-118
----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------
R -> K FER3_RAPSA -1 91 91 VARIANT
M -> V FER3_RAPSA -1 95 95 VARIANT
<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html> FER3_RAPSA -1 8 83 Pfam
-Chloroplast FER1_ARATH -1 1 52 TRANSIT
-Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html> FER1_ARATH -1 60 135 Pfam
-Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html> FER_BRANA -1 8 83 Pfam
Chloroplast FER2_ARATH -1 1 52 TRANSIT
Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html> FER2_ARATH -1 60 135 Pfam
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html> FER_BRANA -1 8 83 Pfam
+Chloroplast FER1_ARATH -1 1 52 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html> FER1_ARATH -1 60 135 Pfam
<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_118</a></html> Q93Z60_ARATH -1 60 118 Pfam
Chloroplast FER1_MAIZE -1 1 52 TRANSIT
STRAND FER1_MAIZE -1 57 59 STRAND
--- /dev/null
+>a
+QQQ
+>b
+QQQ
+>c
+QQQ
+>d
+QQQ
+>e
+QQQ
+>f
+QQQ
+>g
+QQQ
+>h
+QQQ
--- /dev/null
+feature_1 8c25cd
+
+STARTGROUP Jalview
+feature_1 a -1 1 1 feature_1 0.4
+feature_1 a -1 2 2 feature_1 0.6
+feature_1 b -1 1 1 feature_1 0.8
+feature_1 b -1 2 2 feature_1 1.0
+feature_1 c -1 1 1 feature_1 1.5
+feature_1 d -1 1 1 feature_1 2.0
+feature_1 e -1 1 1 feature_1 3.0
+ENDGROUP Jalview
QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV
TIETHREEDMV--
>FER1_ARATH Ferredoxin-1, chloroplast precursor
-MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
-LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
-TIETHKEEDIV--
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
+VIETHKEEAIM--
>FER_BRANA Ferredoxin
-----------------------------------------------------------ATYKVKFITPEGE
QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
TIETHKEEELV--
>FER2_ARATH Ferredoxin-2, chloroplast precursor
-MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
-QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
-VIETHKEEAIM--
+MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
+LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
+TIETHKEEDIV--
>Q93Z60_ARATH At1g10960/T19D16_12
MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------
<mapID target="memory" url="html/memory.html" />
<mapID target="groovy" url="html/features/groovy.html" />
+ <mapID target="groovy.featurecounter" url="html/groovy/featureCounter.html" />
<mapID target="privacy" url="html/privacy.html" />
<mapID target="vamsas" url="html/vamsas/index.html"/>
<mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
<mapID target="biojson" url="html/features/bioJsonFormat.html" />
<mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
+ <mapID target="siftsmapping" url="html/features/siftsmapping.html" />
<mapID target="pdbchooser" url="html/features/structurechooser.html" />
<mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
<mapID target="biojsmsa" url="html/features/biojsmsa.html" />
+ <mapID target="ensemblfetch" url="html/features/ensemblsequencefetcher.html" />
+
+ <mapID target="uniprotfetcher" url="html/features/uniprotsequencefetcher.html" />
+
<mapID target="backIcon" url="icons/back.png" />
<mapID target="forwardIcon" url="icons/forward.png" />
<mapID target="homeIcon" url="icons/Home.png" />
<!-- 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="Split Frame View" target="splitframe" />
- <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
- <tocitem text="PDB Structure Chooser" target="pdbchooser" />
- <tocitem text="Chimera Viewer" target="chimera" />
- <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
+ <tocitem text="Retrieval from ENSEMBL" target="ensemblfetch" />
+ <tocitem text="UniProt Free Text Search" target="uniprotfetcher" />
+ <tocitem text="SIFTS for mapping PDB structures to UniProt" target="siftsmapping" />
<tocitem text="Latest Release Notes" target="release"/>
</tocitem>
</tocitem>
<tocitem text="Preferences" target="preferences" />
<tocitem text="Memory Settings" target="memory" expand="false"/>
+ <tocitem text="Scripting with Groovy" target="groovy">
+ <tocitem text="Groovy Feature Counter example" target="groovy.featurecounter"/>
+ </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>
entry from the consensus annotation label to copy the alignment's
consensus sequence to the clipboard.
<p>
- <strong>Sequence logo</strong>
+ <a name="logo"><strong>Sequence logo</strong></a>
</p>
By clicking on the label you can also activate the sequence logo. It
indicates the relative amount of residues per column which can be
<p>
<strong>Reference Sequence Alignment Views</strong>
</p>
+ <p>Many alignment analysis tasks concern a query, or reference
+ sequence. For instance, when searching for sequences from other
+ organisms that are similar to a newly sequenced gene, or when
+ searching for structurally similar sequences for use in homology
+ modelling.</p>
+<p>
+ <strong>What happens when a reference sequence is defined ?</strong>
+ </p>
<p>
The reference sequence for an alignment is indicated by its ID being
- shown in bold. When a reference sequence has been defined, the <strong>Format→Show
- unconserved</strong> option highlights mutations with respect to the
- reference sequence, rather than the alignment's consensus sequence.
- </p>
+ shown in bold. In addition:</p>
+ <ul>
+ <li><strong>Reference sequence numbering</strong>. Instead of
+ column numbers, the alignment ruler shows the reference sequence
+ positions at each column. At each tick mark, either the reference
+ sequence symbol and position is given, or the column number when a
+ gap is present at that position in the reference sequence.</li>
+ <li><strong>Format→Show unconserved</strong> highlights
+ mutations with respect to the reference sequence, rather than the
+ alignment's consensus sequence.</li>
+ </ul>
<p>
+ <strong>Defining the reference sequence</strong>
+ </p>
+ <p>Each alignment view can have its own reference sequence.</p>
<ul>
- <li>Jalview automatically assigns a reference sequence when <a
- href="../webServices/jnet.html"
- >JPred4</a> predictions are imported.
- </li>
- <li><strong>Assigning a reference sequence</strong><br /> A
- sequence can be marked as the reference sequence by right-clicking
- on it's ID to open the popup menu, and selecting the "<strong>(Sequence
- ID)→Mark as Reference</strong>" entry."</li>
+ <li><strong>Manually assigning a reference sequence</strong><br />
+ A sequence can be marked as the reference sequence by
+ right-clicking on its ID to open the popup menu, and selecting the
+ "<strong>(Sequence ID)→Mark as Reference</strong>" entry.</li>
+ <li><strong>Defining a reference when importing
+ annotation</strong><br />Jalview automatically assigns a reference
+ sequence when importing analysis results, such as those returned
+ from <a href="../webServices/jnet.html">JPred4</a> . A reference
+ sequence can also be assigned via the <a
+ href="../features/annotationsFormat.html#refsandviews">SET_REF</a> command in
+ an alignment annotation file.</li>
</ul>
<p>
<em>Reference sequence based alignment visualisation was
- introduced in Jalview 2.9.</em>
+ introduced in Jalview 2.9, and support for storage and retrieval
+ of reference sequence views in 2.10.</em>
</p>
</html>
sorting.
</p>
</ul>
- <p>
+ <p><strong>Sorting according to sequence features</strong><br/>
+ Additional sort operations for
+ alignments containing sequence features are provided in the
+ <strong><a href="../features/featuresettings.html#sortbyfeature">Feature
+ Settings</a></strong> dialog, opened via <strong>View→Feature
+ Settings...</strong><p>
<strong>Reversing the Order</strong>
</p>
<p>Selecting any item from the Sort menu will sort sequences in an
ascending order according to the property defining the sort. If the
same sort is re-applied, the sequences will be sorted in the inverse
- order. In the case of trees and alignment orderings, Jalview will
- remember your last choice for sorting the alignment and only apply
- the inverse ordering if you select the same tree or alignment
- ordering item again.</p>
+ order. In both cases, for sequences which are equivalent under the sort
+ operation, their order will be preserved (since version 2.10). In
+ the case of trees and alignment orderings, Jalview will remember
+ your last choice for sorting the alignment and only apply the
+ inverse ordering if you select the same tree or alignment ordering
+ item again.</p>
</body>
</html>
<strong>Alignment RNA Structure Consensus Annotation</strong>
</p>
+ <p>The RNA structure consensus displayed below the alignment gives the
+ percentage of valid base pairs per column for the first secondary
+ structure annotation shown on the annotation panel. These values are
+ shown as a histogram labeled "StrucConsensus", where a
+ symbol below each bar indicates whether the majority of base pairs
+ are:<ul>
+ <li>'(' - Watson-Crick (C:G, A:U/T)</li>
+ <li>'[' - Non-canonical (a.ka. wobble) (G:U/T)</li>
+ <li>'{' - Invalid (a.k.a. tertiary) (the rest)</li>
+ </ul>
+ <p>Mousing over the column gives the fraction of pairs classified
+ as Watson-Crick, Canonical or Invalid.</p>
+
+ <p>By default
+ this calculation includes gaps in columns. You can choose to ignore
+ gaps in the calculation by right clicking on the label
+ "StrucConsensus" to the left of the structure consensus bar
+ chart.<br>
+
<p>
- The RNA structure consensus displayed below the alignment is the
- percentage of valid base pairs per column. It is calculated in
- relation to a secondary structure and just paired columns are
- calculated. The canonical Watson-Crick base pairings (A-T/U, G-C)
- and the wobble base pair (G-T/U) are regarded as valid pairings.<br>
- The amount of valid base pairs is indicated by the profile in the
- Alignment Annotation row.<br> By default this calculation
- includes gaps in columns. You can choose to ignore gaps in the
- calculation by right clicking on the label "StrConsensus"
- to the left of the structure consensus bar chart.<br>
- <p>
- <strong>Structure logo</strong>
- </p>
- By clicking on the label you can also activate the structure logo. It
- is very similar to a sequence logo but counts the numbers of base
- pairs. There are two residues per column, the actual column and the
- interacting base. The opening bracket is always the one on the left
- side.
- <br> Like sequence logos the relative amount of a specific base
- pair can be estimated by its size in the logo. The tool tip of a
- column gives the exact numbers for all occurring valid base pairs.
+ <strong>RNA Structure logo</strong><br /> Right-clicking on the
+ label allows you to enable the structure logo. It is very similar to
+ a sequence logo but instead shows the distribution of base pairs.
+ There are two residues per column, the actual column and the
+ interacting base. The opening bracket is always the one on the left
+ side. <br> Like <a href="consensus.html#logo">sequence
+ logos</a>, the relative amount of a specific base pair can be
+ estimated by its size in the logo, and this can be made more obvious
+ by <em>normalising</em> the logo (enabled via the popup menu). When
+ the logo is displayed, the tool tip for a column gives the exact
+ percentages for all base pairs at that position.
</p>
</body>
</html>
</div>
<ul>
<li>Select which annotation to base the colouring scheme on
- using the top left selection box.<br />If the <strong>Per-sequence
- only</strong> tick box is not greyed out, then ticking it will limit the
- available annotation rows to just those that are sequence
- associated (e.g. T-COFFEE scores and <a
- href="../webServices/proteinDisorder.html"
- >protein disorder predictions</a>), which will colour each sequence
- according to its own per-residue scores.<br /> <em>Per-sequence
- associated annotation colouring was introduced in Jalview 2.8</em>
+ using the top left selection box. Sequence associated alignment
+ annotation are shown with the seuqence's name appended.<br />If
+ the <strong>Per-sequence only</strong> tick box is not greyed out,
+ then ticking it will limit the list of available annotation rows
+ to just the labels for those that are sequence associated.
+ Annotation rows on each sequence with the same label (e.g.
+ T-COFFEE scores and <a href="../webServices/proteinDisorder.html">protein
+ disorder predictions</a>) will then be used to colour its
+ corresponding positions in the alignment.<br /> <em>Per-sequence
+ associated annotation colouring is currently only available in
+ the Desktop.</em>
</li>
<li>If the "Use Original Colours" box is selected,
the colouring scheme will use the colouring scheme present on the
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Alignment Annotation</title></head>
+<head>
+<title>Alignment Annotation</title>
+</head>
<body>
-<p><strong>Alignment Annotation</strong></p>
+ <p>
+ <strong>Alignment Annotation</strong>
+ </p>
-<p>In addition to the definition of groups and sequence features,
- Jalview can display symbols and graphs under the columns of an
- alignment, and allow you to mark particular columns of an alignment and add symbols and text
- in the annotation area shown below the alignment (which may be hidden if <strong>View→Show
- Annotation</strong> is not ticked). Any displayed annotation row can be hidden (using the pop-up
- menu obtained by right-clicking the label), or re-ordered by dragging the label to a new
- position with the left mouse button.</p>
-<p>
-Web services can also add annotation to an alignment (see the <a
-href="../webServices/jnet.html">JNet</a> and <a
-href="../webServices/proteinDisorder.html">Disorder</a> protein
-structure prediction services), and as of Jalview 2.08 quantitative
-and symbolic annotations can be added to an alignment via an <a
-href="annotationsFormat.html">Annotations File</a> dragged into the
-alignment window or loaded from the alignment's file menu.
-</p>
-<p><a name="seqannots"/><strong>Sequence Reference Annotation</strong>
-</p>
-<p>
- Sequence reference annotation is created from 3D structure
- data, and from the results of sequence based prediction of
- <a href="../webServices/jnet.html">secondary structure</a> and <a
- href="../webServices/proteinDisorder.html">disordered region</a>
- prediction methods.
-</p>
-<p><strong>Sequence Group Annotation</strong>
-</p>
-<p>
- If sequence groups are defined, <a href="../calculations/conservation.html">Conservation</a>
- and <a href="../calculations/consensus.html">Consensus</a> annotation can be enabled
- for each group from the <a href="../menus/alwannotation.html">Annotations menu</a>, or can
- be imported from a Jalview <a href="annotationsFormat.html">Annotations file</a>.
-</p>
-<p><strong>Sequence Selection from Annotation</strong>
-</p>
-<p>
- Sequences associated with sequence (or sequence group) annotations can be selected by
- double-clicking the annotation label with these key combinations:
- <ul>
- <li>double-click - Select associated sequences (replaces current selection)</li>
- <li>shift double-click - add sequences to selection</li>
- <li>Ctrl (Mac CMD) double-click - toggles inclusion of associated sequences in the current selection</li>
- </ul>
- Note this also works in combination with manual sequence selection in the alignment.
-<p><strong>Interactive Alignment Annotation</strong></p>
-<p>
-Annotation rows are added using the <strong>Annotation Label</strong>
-menu, which is obtained by clicking anywhere on the annotation row labels
-area (below the sequence ID area).
-</p>
-<ul>
- <li><strong>Add New Row</strong><br>
- <em>Adds a new, named annotation row (a dialog box will pop up for you to
- enter the label for the new row). </em> </li>
- <li><strong>Edit Label/Description</strong><br>
- <em>This opens a dialog where you can change the name (displayed label), or the description
- (as shown on the label tooltip) of the clicked annotation. </em> </li>
- <li><strong>Hide This Row</strong><br>
- <em>Hides the annotation row whose label was clicked in order to bring up
- the menu.</em> </li>
- <li><strong>Hide All <em><label></em></strong><br>
- <em>Hides all annotation rows whose label matches the one clicked.
- (This option is only shown for annotations that relate to individual sequences,
- not for whole alignment annotations. Since Jalview 2.8.2.)</em> </li>
- <li><strong>Delete This Row</strong><br>
- <em>Deletes the annotation row whose label was clicked in order to bring up
- the menu.</em> </li>
- <li><strong>Show All Hidden Rows</strong><br>
- <em>Shows all hidden annotation rows.</em> </li>
- <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
- <em>Annotations can be saved to file or output to a text window in either the
- Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
- <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
- <em>Opens a text box with a list of comma-separated values corresponding
- to the annotation (numerical or otherwise) at each position in the row.
- This is useful to export alignment quality measurements for further analysis.</em>
- </li>
- <li><strong>Scale Label To Column</strong><em>(introduced in 2.5)</em><br>
- <em>Selecting this toggles whether column labels will be shrunk to fit within each column, or displayed using the view's standard font size.</em></li>
-</ul>
-<p>
-<strong>Editing Label and secondary structure Annotation</strong></p>
-<p>
-Use the <strong>left mouse button</strong> to select a position along the row that are to
-be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination
-with the left-click will select more than one position, or a range of
-positions on the alignment.
-</p>
-<p>Once the desired position has been selected, use the <strong>right mouse
-button</strong> to open the <strong>annotation menu</strong>:</p>
-<ul>
-<li>Helix<br><em>Mark selected positions with a helix glyph (a red
-oval), and optional text label (see below). A
-dialog box will open for you to enter the text. Consecutive ovals
-will be rendered as an unbroken red line.</em>
-</li>
-<li>Sheet<br><em>Mark selected positions with a sheet glyph (a green
-arrow oriented from left to right), and optional text label (see
-below). A dialog box will open for you to enter the text. Consecutive
-arrows will be joined together to form a single green arrow.</em>
-</li>
-<li><a name="rna">RNA Helix</a> (only shown when working with nucleotide sequences)<br>
-<em>Mark selected positions as participating in a base pair
-either upstream or downstream. When the dialog box opens, enter a
-'(' to indicate these bases pair with columns upstream (to right),
-and ')' to indicate this region pairs with bases to the left of the
-highlighted columns.<br />If any brackets do not match up, then an
-orange square will highlight the first position where a bracket was
-found not to match.
-</em>
-</li>
-<li>Label<br><em>Set the text label at the selected positions. A
-dialog box will open for you to enter the text. If
-more than one consecutive position is marked with the same label, only
-the first position's label will be rendered.</em>
-</li>
-<li>Colour<br><em>Changes the colour of the annotation text label.</em>
-</li>
-<li>Remove Annotation<br><em>Blanks any annotation at the selected positions on
-the row. Note: <strong>This cannot be undone</strong></em>
-</li>
-</ul>
-<p>
-User defined annotation is stored and retrieved using <a
-href="../features/jalarchive.html">Jalview Archives</a>.
-</p>
-<p><em>Current Limitations</em></p>
-<p>As of version 2.5, the Jalview user interface does not support the
-creation and editing of quantitative annotation (histograms and line graphs), or
-to create annotation associated with a specific sequence. It is also incapable of
-annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an
-<a href="annotationsFormat.html">Annotation file</a>.<br>
-</p>
+ <p>
+ In addition to the definition of groups and sequence features,
+ Jalview can display symbols and graphs under the columns of an
+ alignment. These annotation tracks are displayed in the annotation
+ area below the alignment. The annotation area's visibility is
+ controlled with the <strong>View→Show Annotation</strong>
+ option.
+ </p>
+ <p>
+ <strong>Types of annotation</strong>
+ <ul>
+ <li><a name="seqannots"><strong>Sequence
+ associated annotation.</strong></a><br/>Data displayed on sequence annotation
+ rows are associated with the positions of a sequence. Often this
+ is 'Reference annotation' such as secondary structure information
+ derived from 3D structure data, or from the results of sequence
+ based prediction of <a href="../webServices/jnet.html">secondary
+ structure</a> and <a href="../webServices/proteinDisorder.html">disorder</a>.
+ If reference annotation is available for a the currently selected
+ sequences, it can be shown by selecting the <strong>Add
+ Reference Annotation</strong> option in the sequence or selection popup
+ menu.</li>
+ <li><strong>Group associated annotation.</strong><br/>Data can be associated with
+ groups defined on the alignment. If sequence groups are defined, <a
+ href="../calculations/conservation.html">Conservation</a> and <a
+ href="../calculations/consensus.html">Consensus</a> annotation can
+ be enabled for each group from the <a
+ href="../menus/alwannotation.html">Annotations menu</a>, or can be
+ imported from a Jalview <a href="annotationsFormat.html">Annotations
+ file</a>.</li>
+ <li><strong>Alignment associated annotation.</strong><br />Annotation rows
+ associated with columns on the alignment are simply 'alignment
+ annotation'. Controls allow you to <a href="#iaannot">interactively create
+ alignment annotation</a> to add labels and symbols to alignment columns.
+ Jalview's consensus, conservation and quality calculations also
+ create histogram and sequence logo annotations on the alignment.
+ </li>
+ </ul>
+ <p>
+ <strong>Importing and exporting annotation</strong><br />
+ Annotations on an alignment view are saved in Jalview project files.
+ You can also load <a href="annotationsFormat.html">Annotations
+ Files</a> in order to add any kind of quantitative and symbolic
+ annotations to an alignment. To see an example, use the <strong>Export
+ Features/Annotation</strong> option from an alignment window's File menu.
+ </p>
+ <p>
+ <strong>Layout and display controls</strong><br /> Individual and
+ groups of annotation rows can be shown or hidden using the pop-up
+ menu obtained by right-clicking the label. You can also reorder them
+ by dragging the label to a new position with the left mouse button.
+ The
+ <strong>Annotations</strong> menu provides settings controlling the
+ ordering and display of sequence, group and alignment associated
+ annotation. The
+ <strong>Colour by annotation</strong> option in the colour menu
+ allows annotation to be used to
+ <a href="../colourSchemes/annotationColouring.html">shade the
+ alignment</a>. Annotations can also be used to
+ <a href="../features/columnFilterByAnnotation.html">select or
+ hide columns</a> via the dialog opened from the
+ <strong>Selection</strong> menu.
+ </p>
+ <p>
+ <strong>Sequence Highlighting and Selection from Annotation</strong>
+ </p>
+ <p>
+ A <strong>single click</strong> on the label of an annotation row
+ associated with sequences and sequence groups will cause the
+ associated sequences to be highlighted in the alignment view. <strong>Double
+ clicking</strong> the label will select the associated sequences, replacing
+ any existing selection. Like with other kinds of selection, <strong>shift
+ double-click</strong> will add associated sequences, and <strong>Ctrl
+ (Mac CMD) double-click</strong> will toggle inclusion of associated
+ sequences in the selection.
+ <p>
+ <strong>Interactive Alignment Annotation</strong>
+ </p>
+ <p>
+ <a name="iaannot"> Annotation rows</a> are added using the <strong>Annotation
+ Label</strong> menu, which is obtained by clicking anywhere on the
+ annotation row labels area (below the sequence ID area).
+ </p>
+ <ul>
+ <li><strong>Add New Row</strong><br> <em>Adds a new,
+ named annotation row (a dialog box will pop up for you to enter
+ the label for the new row). </em></li>
+ <li><strong>Edit Label/Description</strong><br> <em>This
+ opens a dialog where you can change the name (displayed label),
+ or the description (as shown on the label tooltip) of the
+ clicked annotation. </em></li>
+ <li><strong>Hide This Row</strong><br> <em>Hides the
+ annotation row whose label was clicked in order to bring up the
+ menu.</em></li>
+ <li><strong>Hide All <em><label></em></strong><br> <em>Hides
+ all annotation rows whose label matches the one clicked. (This
+ option is only shown for annotations that relate to individual
+ sequences, not for whole alignment annotations. Since Jalview
+ 2.8.2.)</em></li>
+ <li><strong>Delete This Row</strong><br> <em>Deletes
+ the annotation row whose label was clicked in order to bring up
+ the menu.</em></li>
+ <li><strong>Show All Hidden Rows</strong><br> <em>Shows
+ all hidden annotation rows.</em></li>
+ <li><strong>Export Annotation</strong> <em>(Application
+ only)</em><br> <em>Annotations can be saved to file or
+ output to a text window in either the Jalview annotations format
+ or as a spreadsheet style set of comma separated values (CSV). </em>
+ </li>
+ <li><strong>Show Values in Text Box</strong> <em>(applet
+ only)</em><br> <em>Opens a text box with a list of
+ comma-separated values corresponding to the annotation
+ (numerical or otherwise) at each position in the row. This is
+ useful to export alignment quality measurements for further
+ analysis.</em></li>
+ <li><strong>Scale Label To Column</strong><em>(introduced
+ in 2.5)</em><br> <em>Selecting this toggles whether column
+ labels will be shrunk to fit within each column, or displayed
+ using the view's standard font size.</em></li>
+ </ul>
+ <p>
+ <strong>Editing labels and secondary structure annotation rows</strong>
+ </p>
+ <p>
+ Use the <strong>left mouse button</strong> to select a position
+ along the row that are to be annotated - these regions will be
+ coloured red. Press <strong>Control</strong> or <strong>shift</strong> in
+ combination with the left-click to either select an additional position,
+ or a range of positions on the alignment.
+ </p>
+ <p>
+ Once positions have been selected, use the <strong>right
+ mouse button</strong> and select one of the following from the <strong>annotation menu</strong>:
+ </p>
+ <ul>
+ <li>Helix<br>
+ <em>Marks selected positions with a helix glyph (a red oval),
+ and optional text label (see below). A dialog box will open for
+ you to enter the text. Consecutive ovals will be rendered as an
+ unbroken red line.</em>
+ </li>
+ <li>Sheet<br>
+ <em>Marks selected positions with a sheet glyph (a green arrow
+ oriented from left to right), and optional text label (see
+ below). A dialog box will open for you to enter the text.
+ Consecutive arrows will be joined together to form a single
+ green arrow.</em>
+ </li>
+ <li><a name="rna">RNA Helix</a> (only shown when working with
+ nucleotide sequences)<br> <em>Marks selected positions
+ as participating in a base pair either upstream or downstream.
+ When the dialog box opens, enter a '(' to indicate these bases
+ pair with columns upstream (to right), and ')' to indicate this
+ region pairs with bases to the left of the highlighted columns.
+ Other kinds of base-pair annotation are also supported (e.g. 'A'
+ and 'a', or '<' and '>'), and Jalview will suggest an
+ appropriate symbol based on the closest unmatched
+ parenthesis to the left.<br />If any brackets do not match up, then an
+ orange square will highlight the first position where a bracket
+ was found not to match.
+ </em></li>
+ <li>Label<br>
+ <em>Set the text label at the selected positions. A dialog box
+ will open for you to enter the text. If more than one
+ consecutive position is marked with the same label, only the
+ first position's label will be rendered.</em>
+ </li>
+ <li>Colour<br>
+ <em>Changes the colour of the annotation text label.</em>
+ </li>
+ <li>Remove Annotation<br>
+ <em>Blanks any annotation at the selected positions on the row.
+ Note: <strong>This cannot be undone</strong>
+ </em>
+ </li>
+ </ul>
+ <p>
+ User defined annotation is stored and retrieved using <a
+ href="../features/jalarchive.html">Jalview Archives</a>.
+ </p>
+ <p>
+ <em>Current Limitations</em>
+ </p>
+ <p>
+ The Jalview user interface does not support interactive
+ creation and editing of quantitative annotation (histograms and line
+ graphs), or to create annotation associated with a specific
+ sequence or group. It is also incapable of annotation grouping or changing
+ the style of existing annotation (e.g. to change between line or bar
+ charts, or to make multiple line graphs). These annotation
+ capabilities are only possible by the import of an <a
+ href="annotationsFormat.html">Annotation file</a>.<br>
+ </p>
</body>
</html>
or hidden according to annotation rows on the alignment. The dialog
box is opened <em>via</em> "<strong>Select→Select/Hide
Columns by Annotation...</strong>", and different filters are
- presented dependent upon the data shown in the selected annotation
+ then presented for filtering data according to the selected annotation
row.
</p>
<table>
<td><img src="AnnotationColumnSelectionWithoutSM.gif"></td>
</tr>
</table>
-
- <p>If an annotation with numeric values is selected, the threshold
+ <p>The drop down menu lists the annotation available on the
+ alignment. Sequence associated annotation rows will be shown with
+ the sequence ID appended to the annotation label. It is only
+ possible to select one row at a time.</p>
+ <p>
+ If an annotation with numeric values is selected, the threshold
filter option is activated. For other types of annotation, use the
text box and secondary structure check boxes (right). The radio
buttons at the bottom of the dialog specify the action applied to
- columns matching the query.</p>
+ columns matching the query.<br /> <em>Note: annotation
+ containing only numeric labels (e.g. T-COFFEE column confidence
+ scores) will not be treated as quantitative data. You will need to
+ enter search expressions to select columns in this case.</em>
+ </p>
<ul>
<li><strong>Search Filter</strong>
<ul>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Fetching ENSEMBL Data in Jalview</title>
+</head>
+<body>
+
+ <strong>Fetching ENSEMBL Data in Jalview</strong>
+ <br /> Jalview Version 2.10 (October 2016) introduced support to
+ retrieve annotated transcripts, peptides and genomic contigs from
+ <a href="http://www.ensembl.org">ENSEMBL</a>.
+ <br />
+ <img src="selectfetchdb.gif" align="left" width="480" height="204"
+ alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+
+ <p>
+ Two types of ENSEMBL source are provided. ENSEMBL queries the main
+ ENSEMBL warehouse containing data for higher eukaryotes, and
+ EnsemblGenomes, which queries Ensembl Pathogens, and other
+ warehouses.<br />
+ <em>Ensembl support is new in Jalview, and we expect to merge
+ these sources in a future release.</em>
+ </p>
+ <p>
+ <strong>General Use</strong><br /> If you have a set of Ensembl gene
+ or transcript IDs, then you can retrieve them <em>via</em> the
+ sequence fetcher dialog opened after selecting the most appropriate
+ source (either 'ENSEMBL', or Ensembl Genomes). However, Jalview's
+ Ensembl client has a couple of additional capabilities:
+ </p>
+ <p>
+ <strong>Retrieving aligned transcripts for a genomic ID</strong>
+ </p>
+ <p>If a single genomic identifier is entered in the Ensembl
+ fetcher, Jalview will return all transcripts and products for the
+ locus, and display them in a split view - complete with sequence
+ variant annotation.</p>
+ <p>
+ <strong>Retrieving orthologs for a gene ID</strong>
+ </p>
+ <p>
+ If a gene ID is entered (e.g. fox1), Jalview will resolve Ensembl
+ genomic identifiers for a predefined set of taxa (Mouse, Rat, Human,
+ Yeast in Jalview 2.10).<br />
+ </p>
+ <p>
+ <strong><a name="ensemblannotation">Ensembl Sequence
+ Features</a></strong><br /> Jalview 2.10 includes support for the
+ visualisation and transfer genomic and transcriptomic sequence
+ features onto protein product sequences. Retrieval of a genomic
+ locus results in a set of transcripts that are annotated with
+ nucleotide variant information and exonic regions. By default,
+ intronic regions will be hidden.
+ </p>
+ <p>
+ <strong><a name="variantvis">Variant information on
+ Protein Products</a></strong><br />Jalview can translate genomic variant
+ annotation into protein sequence variant codes for variants
+ intersecting coding regions of a gene. To see this in action, use
+ the <strong>Calculate→Show cross-references</strong> menu to
+ view protein product sequences for the currently displayed (or
+ selected) sequences. The same menu allows you to recover Ensembl
+ exon, transcript and variant information when viewing UniProt
+ sequences.
+ </p>
+ <p>
+ <strong>Viewing more information about variant annotation</strong><br />
+ Variants are highlighted as red sequence features on the protein
+ sequence, with each one reporting all protein sequence variants
+ observed at that position as a result of the genomic variants.
+ Right-clicking a variant allows you to open the Ensembl Variants web
+ page for each variant, via the <strong>Link</strong> submenu.
+ </p>
+ <p>
+ <strong>Work in Progress !</strong><br />In the next few releases,
+ we hope to improve and extend Jalview's support for working with
+ Ensembl. If you have any problems, questions or suggestions then
+ please get in contact with us via the Jalview discussion list.
+ </p>
+</body>
+</html>
\ No newline at end of file
</p>
<p>
<strong><em>Feature settings pop-up menu</em></strong><br> <strong>Right-click</strong>
- on a feature to open a pop-up menu that allows you to sort the
- alignment or current selection using that feature type (see below),
- or toggle the type of colouring used for the feature. Features may
- be highlighted with either a single colour or a <a
- href="featureschemes.html"
- >feature colourscheme</a> based on either the scores associated with
- that feature or from the feature's description (e.g. to distinguish
+ on a feature to open a pop-up menu that allows you to<ul><li>Hide, show and
+ select columns containing that feature</li><li>Sort the alignment or
+ current selection using that feature type (see below)</li><li>Toggle the
+ type of colouring used for the feature</li></ul><p>Features may be highlighted
+ with either a single colour or a <a href="featureschemes.html">feature
+ colourscheme</a> based on either the scores associated with that
+ feature or from the feature's description (e.g. to distinguish
different names associated with a DOMAIN feature).
</p>
<p>
- <strong>Ordering alignment by features</strong><br> The 'Seq
+ <strong><a name="sortbyfeature">Ordering alignment by features</a></strong><br> The 'Seq
Sort by Score' and 'Seq Sort by Density' buttons will sort the
alignment based on the average score or total number of currently
active features and groups on each sequence. To order the alignment
<strong>The Groovy Shell</strong>
</p>
<p>
- <a href="http://www.groovy-lang.org/">Groovy</a> is an "<em>agile
- and dynamic language for the Java platform</em>". The groovy
- scripting language makes it extremely easy to programmatically
- interact with Java programs, in much the same way that Javascript is
- used to generate and interact with applets and other objects on the
- page.
+ Groovy (<a href="http://www.groovy-lang.org/">www.groovy-lang.org</a>)
+ is an "<em>agile and dynamic language for the Java
+ platform</em>". The groovy scripting language makes it extremely
+ easy to programmatically interact with Java programs, in much the
+ same way that Javascript is used to generate and interact with
+ applets and other objects on the page.
</p>
<p>
- <strong><em>Getting Groovy...</em> </strong><br> Jalview comes with
- an embedded installation of Groovy. All you need is to select <strong>Tools→Groovy
- Console...</strong> menu option from the Jalview Desktop's
- drop-down menu. After a short pause, you should then see the <a
- href="http://groovy-lang.org/groovyconsole.html"
- >Groovy Console</a> appear. This allows you to interactively execute Groovy
- scripts within the Jalview run-time environment.
+ <em>Getting Groovy...</em><br> Jalview comes with an embedded
+ installation of Groovy. Just select <strong>Tools→Groovy
+ Console...</strong> from the Jalview Desktop's drop-down menu. After a
+ short pause, you should then see the <a
+ href="http://groovy-lang.org/groovyconsole.html">Groovy
+ Console</a> appear. This allows you to interactively execute Groovy
+ scripts whilst Jalview is running. We've also provided a <strong>Calculations→Execute
+ Groovy Script</strong> button so you can execute the currently loaded
+ groovy script whilst viewing an alignment.
</p>
<p>
<strong>Executing groovy scripts on Jalview startup</strong><br>
</em>
</p>
<p>
- <strong>Executing a groovy script on a particular alignment</strong><br/>
-
- <p>
<strong>Access to Jalview's functions from Groovy Scripts</strong><br>
- There is as yet no properly defined scripting interface to Jalview,
- but all the public methods of the jalview class hierarchy can be
- called from Groovy scripts. The access point for this is the <strong>Jalview</strong>
- object defined in the groovy environment which corresponds to the
- <pre>jalview.gui.Desktop</pre>
- object which manages all the Jalview windows. Here's an example to get
- you started:
- <br>
+ The scripting interface to Jalview is still a work in progress, so
+ we recommend you also take a look at Jalview's source, since all the
+ public methods of the jalview class hierarchy can be called from
+ Groovy scripts. In addition, the following objects are also defined:
+
+
+ <ul>
+ <li><strong>Jalview</strong> - this is bound to <code>jalview.bin.Jalview</code>.<br />Useful
+ methods include:
+ <ul>
+ <li>Jalview.getAlignFrames() - returns a list of
+ jalview.gui.AlignFrame objects</li>
+ <li>Jalview.getCurrentAlignFrame() - returns the alignment
+ window which is currently being looked at by the user</li>
+ </ul></li>
+ <li><strong>currentAlFrame</strong> - this is only defined when
+ running a Groovy script via the -groovy command line argument. It
+ returns the first alignment window created after acting on the
+ other arguments passed on the command line.</li>
+ </ul>
+ <p>
+ <em>A simple script</em><br />
<ul>
<li>Getting the title, alignment and first sequence from the
current alignFrame<br> <pre>
def seq = alignment.getSequenceAt(0);
</pre>
</li>
- <li>When running a groovy script from the command line, the
- alignment that was just loaded can be referred to like so:<br>
- <pre>
+ <li>If you wanted to do the same thing from the command line, you can refer to
+ alignment that was just loaded with currentAlFrame:<br>
+ <pre>
print currentAlFrame.getTitle();</pre>
</ul>
- If you have downloaded the InstallAnywhere version of Jalview, you can
- find additional groovy scripts in the examples/groovy subfolder of the
- installation directory.
+ <p>
+ <em>Example scripts</em><br />If you have downloaded the
+ InstallAnywhere version of Jalview, you can find additional groovy
+ scripts in the examples/groovy subfolder of the installation
+ directory. The examples are also available at <a
+ href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+ </p>
+ <p>
+ <em>Using Groovy to add new Alignment Calculations</em><br />We've
+ simplified the alignment analysis programming interface in Jalview
+ 2.10 to make it easy for you to add your own dynamic annotation
+ tracks with Groovy. Have a look at the <a
+ href="../groovy/featureCounter.html">featureCounter.groovy</a>
+ example for more information.
+ </p>
+
</body>
</html>
Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em>
command (configured in <a href="dassettings.html">DAS settings</a>).
</p>
- <img src="seqfetcher.gif" align="center"
- alt="The Jalview Sequence Fetcher Dialog Box"
- >
- <p>The Sequence Fetcher dialog box can be opened via the
+ <p>The Sequence Fetcher can be opened via the
"File" menu on the main desktop in order to retrieve
sequences as a new alignment, or opened via the "File"
menu of an existing alignment to import additional sequences. There
whilst Jalview compiles the list of available sequence datasources
from the currently defined DAS server registry.</p>
<p>
- First, <strong>select the database you want to retrieve
- sequences from</strong> by clicking the button labeled 'Select database
- retrieval source'. If a database source is already selected, then
- the button's label will change to show the currently selected
- database.
+ Every time a new fetcher is opened, you will need to <strong>select the database you want to retrieve
+ sequences</strong> from the database chooser.
</p>
- <img src="selectfetchdb.gif" align="left"
+ <img src="selectfetchdb.gif" align="left" width="480" height="204"
alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)"
>
- <p>Since Jalview 2.8, the available databases are shown as a tree
- in a popup dialog box. The databases are ordered alphabetically, and
- if there are many sources for the same type of sequence identifier,
- they will be grouped together in a sub-branch branch labeled with
- the identifier.</p>
- <p>
- Once you have selected the sequence database using the popup dialog
- box, <strong>enter one or more accession ids</strong> (as a
- semi-colon separated list), or press the "Example" button
- to paste the example accession for the currently selected database
- into the retrieval box. Finally, press "OK" to initiate
- the retrieval.
- </p>
- <p>
- <strong>Fetching from The PDB with the EMBL-EBI PDBe Search
- Interface</strong>
- </p>
- <p>
- Since Jalview 2.9, selecting PDB as the sequence database will open
- the <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> for
- discovering and retrieving structures.
- </p>
+ <p>The databases are shown as a tree, and ordered alphabetically;
+ tooltips are shown if you mouse over some sources, explaining what
+ the database will retrieve. You can select one by using the up/down
+ arrow keys and hitting return, or by double clicking with the mouse.
+ <br/><em>If you have DAS sources enabled, then you may have several sources
+ for the same type of sequence identifier, and these will be grouped
+ together in a sub-branch branch labeled with the identifier.</em></p>
+ <p>Once you have selected a sequence database, its fetcher dialog
+ will open. Jalview provides two types of dialog:</p>
+ <ol><li><strong>The Free-text Search Interface</strong>
+
+ <br/>Free-text search clients are provided for PDB (Since 2.9), and
+ UniProt (Since 2.10). They provide access to each database's own
+ query system, enabling you to retrieve data by accession, free text
+ description, or any other type of supported field. For full details,
+ see each client's help page:
+ <ul>
+ <li><a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a></li>
+ <li><a href="uniprotsequencefetcher.html">UniProt Sequence
+ Fetcher</a></li>
+ </ul>
+ </li>
+ <li><strong>Accession based sequence retrieval</strong>
+ <br/>
+
+ <img src="seqfetcher.gif" align="center"
+ alt="The Jalview Sequence Fetcher Dialog Box"><br/>
+ To retrieve sequences, simply <strong>enter one or more accession ids</strong> (as a semi-colon
+ separated list), or press the "Example" button to paste the
+ example accession for the currently selected database into the
+ retrieval box. Finally, press "OK" to initiate the
+ retrieval.
+ </li>
+ </ol>
<p>
<strong>Only retrieving part of a sequence</strong>
</p>
<p>
- DAS sources (indicated by a "<em>(DAS)</em>") allow a
- range to be specified in addition to a sequence ID. To retrieve 50
- residues starting at position 35 in UNIPROT sequence P73137 using
- the UNIPROT DAS server, you would enter "'P73137:35,84'.<br />
- <em>Full support for DAS range queries was introduced in
- Jalview 2.8</em>
+ When using DAS sources (indicated by a "<em>(DAS)</em>"),
+ you can append a range in addition to a sequence ID. For example, to
+ retrieve 50 residues starting at position 35 in UNIPROT sequence
+ P73137 using the UNIPROT DAS server, you would enter
+ "'P73137:35,84'.<br /> <em>Full support for DAS range
+ queries was introduced in Jalview 2.8</em>
</p>
<p>If you use the WSDBFetch sequence fetcher services (EMBL,
record and use that information to construct a mapping between the
sequence and downloaded structure.</p>
<p>If, for some reason, no SIFTS mapping data exists, then Jalview
- will generate a mapping using its built-in Needleman and Wunsch
- global alignment algorithm. This method of mapping was used for all
- structures prior to version 2.10.
- <p>
- <strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
+ will generate a mapping using the built-in Needleman and Wunsch
+ global alignment algorithm. This is how sequence-structure mappings
+ were created before version 2.10.</p>
+ <p><strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
Configuration options controlling whether SIFTS mappings are used
can be found in the <strong>Tools → Preferences →
Structure tab</strong>, under 'Sequence ↔ Structure method'.<br /> <em>Note:</em>
<strong>Multi-Chain Mappings</strong> <br />SIFTS gives Jalview the
ability to display multi-chain mappings between UniProt sequences
and PDB structure data. This is important when working with
- multimeric proteins, since the biological unit will contain several
+ multimeric proteins, when the biological assembly can contain several
structures for the same protein sequence. Multi-chain mapping allows
all residues in a structure to be located in the alignment, and
also, when shading the structure by sequence colours, enables
conservation patterns between oligomer interfaces to be explored.
</p>
- <p>To see this in action, load uniprot sequence for FER1_MAIZE
- then veiw PDB structure for 3B2F, you will notice that mousing over
+ <p>To see this in action, Retrieve the UniProt sequence
+ FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over
the sequence results to two positions being highlighted in the
- structure, also colouring the sequence transfers the color to all
+ structure, and colouring the alignment transfers the color to all
the mapped chains in the structure.</p>
<p>
<Strong>Viewing Mapping Output</Strong> <br /> The mapping provided
by the SIFTS record is accessible via <strong>File →
View mapping</strong> menu of the structure viewers. The screenshot below
- is the mapping output for the <Strong>{FER1_MAIZE ↔
- 3B2F}</Strong> example described above, and confirms that all two chains
- were mapped. The mapping method used can be seen within the area
- highlighted with red boarder.
+ shows the mapping created between UniProt sequence FER1_MAIZE and proteins in PDB 3B2F, which reports thattwo chains
+ were mapped. The mapping method is also reported (highlighted with red border).
<p>
 <img src="sifts_mapping_output.png" align="left"
alt="SIFTS mapping output" />
+ <br/>
<p>
<em>SIFTS Mapping integration was added in Jalview 2.10</em>
</p>
<strong>Structure Chooser</strong>
</p>
- The Structure Chooser interface provides a smart technique for
- selecting PDB structures to view in Jalview by querying readily
- available meta-data of structures. The Interface can be invoked by
- selecting the
- <strong>"3D Structure Data.."</strong> option from a sequence's
- <a href="../menus/popupMenu.html">pop-up menu</a>. Some of the main
- features it provides are listed below:
+ <p>
+ The Structure Chooser interface allows you to interactively select
+ which PDB structures to view for the currently selected set of
+ sequences. It's opened by selecting the <strong>"3D
+ Structure Data.."</strong> option from the Sequence ID panel's <a
+ href="../menus/popupMenu.html">pop-up menu</a>. The dialog
+ provides:
+ </p>
<ul>
<li>Automatic discovery, retrieval and association of PDB
- entries for an alignment's sequences</li>
- <li>Visualisation of discovered structures' meta-data</li>
- <li>Ability to configure the meta-data entries to visualise</li>
- <li>Auto-selection of the best structure via filtering by the
- available metric parameters in the meta-data (i.e. resolution,
- quality etc).</li>
- <li>Selection of multiple structures in a single operation</li>
+ entries for sequences</li>
+ <li>Exploration of meta-data for available 3D structures</li>
+ <li>Automatic selection of the 'best structure' to display for
+ each sequence</li>
+ <li>Manual association of PDB entries by entering a PDB Id</li>
+ <li>Association of structure data from a local file (in mmCIF
+ or PDB format)</li>
</ul>
- Additionally, the Structure Chooser retains the following contemporary
- features of Jalview:
- <ul>
- <li>Manual association of PDB entries via entering the PDB Id
- or From File</li>
- <li>Ability to view cached PDB entries</li>
- </ul>
-
- <strong>Associating PDB files with Sequences</strong>
- <br> Discovery/Association of PDB entries to a sequence now
- happens automatically during the initialisation of the Structure
- Chooser Interface. Jalview uses the sequence's ID to query the PDB
- Rest API provided by the EBI to discover PDB Ids associated with the
- sequence.
-
- <br>
- <br>
- <strong>Configuring displayed meta-data for Structures</strong>
- <br> To configure the visible meta-data displayed for the
- discovered structures, click the 'Configure Displayed Columns' tab,
- then tick the options which you intend to make visible.
-
- <br>
- <br>
- <strong>Auto-selection of best Structures</strong>
- <br> Jalview can automatically filter and select the best
- structures using various metric categories avaialble from the
- meta-data of the structures. To perform this simply select any of the
- following options from the drop-down menu in the Structure Chooser
- interface: Best UniProt coverage, Higest Resolution, Best Quality,
- Highest Protein Chain etc. When the 'Invert' option is selected,
- Jalview returns an inverse result for the current selected option in
- the drop-down menu.
+ <p>
+ <strong>Automated discovery of structure data</strong>
+ </p>
+ <p>After selecting "3D Structure Data ..", Jalview queries the PDB
+ via the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB ids
+ associated with the sequence. It does this based on the sequence's
+ ID string, and any other associated database IDs.</p>
+ <p>
+ <strong>Exploration of meta-data for available structures</strong>
+ </p>
+ <p>Information on each structure available is displayed in columns
+ in the dialog box. By default, only the title, resolution and PDB
+ identifier are shown, but many more are provided by the PDBe. To
+ configure which ones are displayed, select the 'Configure Displayed
+ Columns' tab and tick the columns which you want to see.</p>
+ <p>
+ <strong>Selection of the best structure for each sequence</strong>
+ </p>
+ <p>Jalview can automatically select the best structures according
+ to meta-data provided by the PDB. By default, the 'Best Quality'
+ structure for each sequence will be selected, but clicking on the
+ drop down menu allows other criteria to be chosen, including
+ Resolution (only defined for X-Ray structures), Highest Protein
+ Chain etc. When 'Invert' is selected, structures are selected in
+ reverse order for the current criteria (e.g. worst quality rather
+ than best).</p>
<p>
<img src="schooser_main.png" style="width: 464px; height: 369px;">
sample alignment. Note however that if no structures were
auto-discovered, a different interface for manual association will
be invoked as seen in the screenshot below.
+
<p>
<img src="schooser_enter-id.png"
- style="width: 464px; height: 369px;"
- >
+ style="width: 464px; height: 369px;">
+
<p>
<strong>Manual selection/association of PDB files with
Sequences</strong>
</p>
- <p>To manually associate PDB files with a sequence, select any of
- the follwing options listed below from the drop-down menu in the
- interface:
+ <p>To manually associate PDB files with a sequence, select 'From
+ File', or 'Enter PDB Id' from the drop-down menu:
+
<ul>
- <li><strong>From File</strong> - You can load a PDB file from
- the local machine or network and associate it with the selected
- sequence. PDB files associated in this way will also be saved in
- the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
- <li><strong>Enter PDB Id</strong> - Jalview will use the PDB
- Rest API, provided by the EBI, to fetch the PDB file with the
- entered Id.<br></li>
- <li><strong>Cached PDB Entries</strong> - You can view PDB
- structures which have previously been downloaded/viewed using this
- option. Jalview caches previously downloaded PDB entries in the
- computer memory. However, if the project is saved before exiting
- Jalview, Jalview will serialize the cached entries to the file
- system.</li>
+ <li><strong>From File</strong> - allows you to load a PDB file
+ from the local machine or network and associate it with the
+ selected sequence. PDB files associated in this way will also be
+ saved in the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
+ <li><strong>Enter PDB Id</strong> - allows you specify a PDB ID
+ for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
+ to validate and fetch structure data.<br></li>
</ul>
+ <p>
+ <strong>Viewing existing structures for your sequences</strong>
+ </p>
+ <p>
+ If you have previously associated structure data on the alignment,
+ selecting <strong>Cached PDB Entries</strong> from the drop down
+ menu allows you to select these structures for display.
+ </p>
<p>
<em>The Structure Chooser interface was introduced in Jalview
</p>
<p>
To search UniProt, simply begin typing in the text box. After a
- short delay (uabout 1.5 seconds), results will be shown in the table
+ short delay (about 1.5 seconds), results will be shown in the table
below. You can sort results by clicking on the displayed columns,
and select entries with the mouse or keyboard. Once you have
selected one or more entries, hit the <strong>OK</strong> button to
Entries</strong> option from the drop down menu at the top of the
dialog box.</li>
</ul></li>
- <li>To view selected structures, click the <strong>"View"</strong>
- button.
- </li>
+ <li><strong>To view selected structures, click the <strong>"View"</strong>
+ button.</strong><br />
+ <ul>
+ <li>Additional structure data will be downloaded with the
+ EMBL-EBI's dbfetch service</li>
+ <li><a href="siftsmapping.html">SIFTS</a> records will also
+ be downloaded for mapping UniProt protein sequence data to PDB
+ coordinates.</li>
+ </ul></li>
</ol>
The
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Extending Jalview with Groovy - Feature Counter Example</title>
+</head>
+<body>
+ <p>
+ <strong>Extending Jalview with Groovy - A customisable
+ feature counter</strong><br />
+ <br />The groovy script below shows how to add a new calculation
+ track to a Jalview alignment window.</p><p>As currently written, it will
+ add two tracks to a protein alignment view which count Pfam features
+ in each column, and ones where a charge residue also occur.</p><p>To try
+ it for yourself:</p><ol><li>Copy and paste it into the groovy script
+ console</li><li>Load the example Feredoxin project (the one that opens
+ by default when you first launched Jalview)</li><li>Select <strong>Calculations→Execute
+ Groovy Script</strong> from the alignment window's menu bar to run the script on
+ the current view.</li></ol>
+ <em><a
+ href="http://www.jalview.org/examples/groovy/featureCounter.groovy">http://www.jalview.org/examples/groovy/featureCounter.groovy</a> - rendered with <a href="http://hilite.me">hilite.me</a></em>
+ <!-- HTML generated using hilite.me -->
+ <div
+ style="background: #ffffff; overflow: auto; width: auto; border: solid gray; border-width: .1em .1em .1em .8em; padding: .2em .6em;">
+ <pre style="margin: 0; line-height: 125%">
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Jalview - A Sequence Alignment Editor and Viewer (Version 2.10)</span>
+<span style="color: #888888"> * Copyright (C) 2016 The Jalview Authors</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * This file is part of Jalview.</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * Jalview is free software: you can redistribute it and/or</span>
+<span style="color: #888888"> * modify it under the terms of the GNU General Public License </span>
+<span style="color: #888888"> * as published by the Free Software Foundation, either version 3</span>
+<span style="color: #888888"> * of the License, or (at your option) any later version.</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * Jalview is distributed in the hope that it will be useful, but </span>
+<span style="color: #888888"> * WITHOUT ANY WARRANTY; without even the implied warranty </span>
+<span style="color: #888888"> * of MERCHANTABILITY or FITNESS FOR A PARTICULAR </span>
+<span style="color: #888888"> * PURPOSE. See the GNU General Public License for more details.</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * You should have received a copy of the GNU General Public License</span>
+<span style="color: #888888"> * along with Jalview. If not, see <http://www.gnu.org/licenses/>.</span>
+<span style="color: #888888"> * The Jalview Authors are detailed in the 'AUTHORS' file.</span>
+<span style="color: #888888"> */</span>
+
+<span style="color: #008800; font-weight: bold">import</span> <span
+ style="color: #0e84b5; font-weight: bold">jalview.workers.FeatureCounterI</span><span
+ style="color: #333333">;</span>
+<span style="color: #008800; font-weight: bold">import</span> <span
+ style="color: #0e84b5; font-weight: bold">jalview.workers.AlignmentAnnotationFactory</span><span
+ style="color: #333333">;</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Example script that registers two alignment annotation calculators</span>
+<span style="color: #888888"> * - one that counts residues in a column with Pfam annotation</span>
+<span style="color: #888888"> * - one that counts only charged residues with Pfam annotation</span>
+<span style="color: #888888"> *</span>
+<span style="color: #888888"> * To try:</span>
+<span style="color: #888888"> * 1. load uniref50.fa from the examples folder</span>
+<span style="color: #888888"> * 2. load features onto it from from examples/exampleFeatures.txt</span>
+<span style="color: #888888"> * 3. Open this script in the Groovy console.</span>
+<span style="color: #888888"> * 4. Either execute this script from the console, or via Calculate->Run Groovy Script</span>
+<span style="color: #888888"> </span>
+<span style="color: #888888"> * To explore further, try changing this script to count other kinds of occurrences of </span>
+<span style="color: #888888"> * residue and sequence features at columns in an alignment.</span>
+<span style="color: #888888"> */</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * A closure that returns true for any Charged residue</span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> isCharged <span
+ style="color: #333333">=</span> <span style="color: #333333">{</span> residue <span
+ style="color: #333333">-></span>
+ <span style="color: #008800; font-weight: bold">switch</span><span
+ style="color: #333333">(</span>residue<span
+ style="color: #333333">)</span> <span style="color: #333333">{</span>
+ <span style="color: #008800; font-weight: bold">case</span> <span
+ style="color: #333333">[</span><span
+ style="background-color: #fff0f0">'D'</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">'d'</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">'E'</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">'e'</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">'H'</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">'h'</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">'K'</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">'k'</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">'R'</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">'r'</span><span
+ style="color: #333333">]:</span>
+ <span style="color: #008800; font-weight: bold">return</span> <span
+ style="color: #008800; font-weight: bold">true</span>
+ <span style="color: #333333">}</span>
+ <span style="color: #008800; font-weight: bold">false</span>
+<span style="color: #333333">}</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * A closure that returns 1 if sequence features include type 'Pfam', else 0</span>
+<span style="color: #888888"> * Argument should be a list of SequenceFeature </span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> hasPfam <span
+ style="color: #333333">=</span> <span style="color: #333333">{</span> features <span
+ style="color: #333333">-></span>
+ <span style="color: #008800; font-weight: bold">for</span> <span
+ style="color: #333333">(</span>sf <span
+ style="color: #008800; font-weight: bold">in</span> features<span
+ style="color: #333333">)</span>
+ <span style="color: #333333">{</span>
+ <span style="color: #888888">/*</span>
+<span style="color: #888888"> * Here we inspect the type of the sequence feature.</span>
+<span style="color: #888888"> * You can also test sf.description, sf.score, sf.featureGroup,</span>
+<span style="color: #888888"> * sf.strand, sf.phase, sf.begin, sf.end</span>
+<span style="color: #888888"> * or sf.getValue(attributeName) for GFF 'column 9' properties</span>
+<span style="color: #888888"> */</span>
+ <span style="color: #008800; font-weight: bold">if</span> <span
+ style="color: #333333">(</span><span
+ style="background-color: #fff0f0">"Pfam"</span><span
+ style="color: #333333">.</span><span style="color: #0000CC">equals</span><span
+ style="color: #333333">(</span>sf<span style="color: #333333">.</span><span
+ style="color: #0000CC">type</span><span style="color: #333333">))</span>
+ <span style="color: #333333">{</span>
+ <span style="color: #008800; font-weight: bold">return</span> <span
+ style="color: #008800; font-weight: bold">true</span>
+ <span style="color: #333333">}</span>
+ <span style="color: #333333">}</span>
+ <span style="color: #008800; font-weight: bold">false</span>
+<span style="color: #333333">}</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Closure that computes an annotation based on </span>
+<span style="color: #888888"> * presence of particular residues and features</span>
+<span style="color: #888888"> * Parameters are</span>
+<span style="color: #888888"> * - the name (label) for the alignment annotation</span>
+<span style="color: #888888"> * - the description (tooltip) for the annotation</span>
+<span style="color: #888888"> * - a closure (groovy function) that tests whether to include a residue</span>
+<span style="color: #888888"> * - a closure that tests whether to increment count based on sequence features </span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> getColumnCounter <span
+ style="color: #333333">=</span> <span style="color: #333333">{</span> name<span
+ style="color: #333333">,</span> desc<span style="color: #333333">,</span> acceptResidue<span
+ style="color: #333333">,</span> acceptFeatures <span
+ style="color: #333333">-></span>
+ <span style="color: #333333">[</span>
+ <span style="color: #997700; font-weight: bold">getName:</span> <span
+ style="color: #333333">{</span> name <span
+ style="color: #333333">},</span>
+ <span style="color: #997700; font-weight: bold">getDescription:</span> <span
+ style="color: #333333">{</span> desc <span
+ style="color: #333333">},</span>
+ <span style="color: #997700; font-weight: bold">getMinColour:</span> <span
+ style="color: #333333">{</span> <span style="color: #333333">[</span><span
+ style="color: #0000DD; font-weight: bold">0</span><span
+ style="color: #333333">,</span> <span
+ style="color: #0000DD; font-weight: bold">255</span><span
+ style="color: #333333">,</span> <span
+ style="color: #0000DD; font-weight: bold">255</span><span
+ style="color: #333333">]</span> <span style="color: #333333">},</span> <span
+ style="color: #888888">// cyan</span>
+ <span style="color: #997700; font-weight: bold">getMaxColour:</span> <span
+ style="color: #333333">{</span> <span style="color: #333333">[</span><span
+ style="color: #0000DD; font-weight: bold">0</span><span
+ style="color: #333333">,</span> <span
+ style="color: #0000DD; font-weight: bold">0</span><span
+ style="color: #333333">,</span> <span
+ style="color: #0000DD; font-weight: bold">255</span><span
+ style="color: #333333">]</span> <span style="color: #333333">},</span> <span
+ style="color: #888888">// blue</span>
+ <span style="color: #997700; font-weight: bold">count:</span>
+ <span style="color: #333333">{</span> res<span
+ style="color: #333333">,</span> feats <span
+ style="color: #333333">-></span>
+ <span style="color: #333399; font-weight: bold">def</span> c <span
+ style="color: #333333">=</span> <span
+ style="color: #0000DD; font-weight: bold">0</span>
+ <span style="color: #008800; font-weight: bold">if</span> <span
+ style="color: #333333">(</span>acceptResidue<span
+ style="color: #333333">.</span><span style="color: #0000CC">call</span><span
+ style="color: #333333">(</span>res<span style="color: #333333">))</span>
+ <span style="color: #333333">{</span>
+ <span style="color: #008800; font-weight: bold">if</span> <span
+ style="color: #333333">(</span>acceptFeatures<span
+ style="color: #333333">.</span><span style="color: #0000CC">call</span><span
+ style="color: #333333">(</span>feats<span style="color: #333333">))</span>
+ <span style="color: #333333">{</span>
+ c<span style="color: #333333">++</span>
+ <span style="color: #333333">}</span>
+ <span style="color: #333333">}</span>
+ c
+ <span style="color: #333333">}</span>
+ <span style="color: #333333">]</span> <span
+ style="color: #008800; font-weight: bold">as</span> FeatureCounterI
+<span style="color: #333333">}</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Define an annotation row that counts any residue with Pfam domain annotation</span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> pfamAnnotation <span
+ style="color: #333333">=</span> getColumnCounter<span
+ style="color: #333333">(</span><span
+ style="background-color: #fff0f0">"Pfam"</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">"Count of residues with Pfam domain annotation"</span><span
+ style="color: #333333">,</span> <span style="color: #333333">{</span><span
+ style="color: #008800; font-weight: bold">true</span><span
+ style="color: #333333">},</span> hasPfam<span
+ style="color: #333333">)</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Define an annotation row that counts charged residues with Pfam domain annotation</span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> chargedPfamAnnotation <span
+ style="color: #333333">=</span> getColumnCounter<span
+ style="color: #333333">(</span><span
+ style="background-color: #fff0f0">"Pfam charged"</span><span
+ style="color: #333333">,</span> <span
+ style="background-color: #fff0f0">"Count of charged residues with Pfam domain annotation"</span><span
+ style="color: #333333">,</span> isCharged<span
+ style="color: #333333">,</span> hasPfam<span
+ style="color: #333333">)</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Register the annotations</span>
+<span style="color: #888888"> */</span>
+AlignmentAnnotationFactory<span style="color: #333333">.</span><span
+ style="color: #0000CC">newCalculator</span><span
+ style="color: #333333">(</span>pfamAnnotation<span
+ style="color: #333333">)</span>
+AlignmentAnnotationFactory<span style="color: #333333">.</span><span
+ style="color: #0000CC">newCalculator</span><span
+ style="color: #333333">(</span>chargedPfamAnnotation<span
+ style="color: #333333">)</span>
+</pre>
+ </div>
+</body>
+</html>
<body>
<p>
- <strong>Alignment Window Annotations Menu</strong> (Since Jalview
- 2.8.2)
+ <strong>Alignment Window Annotations Menu</strong> <em>Since Jalview
+ 2.8.2</em>
</p>
<ul>
<li><strong>Show Alignment Related</strong><em><br>
<li><strong>Annotation Label Popup Menu</strong><br> <em>This
menu is opened by clicking anywhere on the annotation row labels
area (below the sequence ID area).</em>
+ <br/><em><strong>Mac Users:</strong> pressing CTRL whilst clicking
+ the mouse/track pad is the same as a right-click. See your
+ system's settings to configure your track-pad's corners to
+ generate right-clicks.</em>
<ul>
<li><strong>Add New Row</strong><br> <em>Adds a
new, named annotation row (a dialog box will pop up for you
<p>
The <a href="popupMenu.html">Popup Menus</a> are opened by clicking
with the right mouse button in the alignment display area or on a
- sequence label in the alignment window.
+ sequence label in the alignment window.<br />
+ <em><strong>Mac Users:</strong> pressing CTRL whilst clicking
+ the mouse/track pad is the same as a right-click. See your
+ system's settings to configure your track-pad's corners to
+ generate right-clicks.</em>
</p>
<p>
The <a href="alwannotationpanel.html">Annotations Menu</a> is opened
<body>
<p>
- <strong>Popup Menu</strong><br> <em>This menu is visible
- when right clicking either within a selected region on the
- alignment or on a selected sequence name. It may not be accessible
- when in 'Cursor Mode' (toggled with the F2 key).</em>
+ <strong>Popup Menu</strong><br> <em>This menu is visible when
+ right clicking either within a selected region on the alignment or
+ on a selected sequence name. It may not be accessible when in
+ 'Cursor Mode' (toggled with the F2 key).</em><br /> <em><strong>Mac Users:</strong> pressing CTRL whilst clicking
+ the mouse/track pad is the same as a right-click. See your
+ system's settings to configure your track-pad's corners to
+ generate right-clicks.</em>
</p>
<ul>
<li><strong>Selection</strong>
</ul></li>
<li><strong>3D Structure Data...</strong> </strong><em>This menu is
visible when you right-click on a sequence name. When this
- option is clicked, Jalview will open a <a
- href="../features/structurechooser.html"
- >'Structure Chooser' </a> dialogue with options to select the
- structure which will eventually be opened in a 3D interactive
- view.<br> These entries will only be present if the
- sequence has <a href="../features/viewingpdbs.html">associated
- PDB structures</a>.
+ option is clicked, Jalview will open the <a
+ href="../features/structurechooser.html">'Structure
+ Chooser' </a>, which allows you to discover and view 3D structures
+ for the current selection. For more info, see <a
+ href="../features/viewingpdbs.html">viewing PDB structures</a>.
</em></li>
<li><strong>VARNA 2D Structure</strong><br />
<em> If the sequence or alignment has RNA structure, then <strong>VARNA
the alignment will have a secondary structure line shown below it,
and a number of additional options become available:
<ul>
- <li><a href="../colourschemes/rnahelicesColouring.html">RNA
+ <li><a href="../colourSchemes/rnahelicesColouring.html">RNA
Helix colouring</a> - highlights columns of alignment involved in
particular RNA helices, Uses the first displayed secondary
structure annotation.</li>
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>13/9/2016</em></strong>
+ <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>04/10/2016</em></strong>
</div>
</td>
<td><em>General</em>
<ul>
- <li><!-- JAL---></li>
+ <li><!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
<li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
+ <li><!-- JAL-2202 -->Position/residue shown in status bar when mousing over sequence associated annotation</li>
+ <li><!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket' for manual entry</li>
+ <li><!-- JAL-2214 -->RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
+ <li><!-- JAL-2092 -->Feature settings popup menu options for showing or hiding columns containing a feature</li>
+ <li><!-- JAL-1557 -->Edit selected group by double clicking on group and sequence associated annotation labels</li>
+ <li><!-- JAL-2236 -->Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs</li>
+
</ul> <em>Application</em>
<ul>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
+ <li><!-- JAL-2050-->Automatically hide introns when opening a gene/transcript view</li>
+ <li><!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search dialog</li>
+ <li><!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database</li>
+ <li><!-- JAL-2079 -->Updated download sites used for Rfam and Pfam sources to xfam.org</li>
+ <li><!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher</li>
<li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
<li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
- <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
- <li><!-- JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
- <li><!-- JAL 1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
+ <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API</li>
+ <li><!-- JAL-2027 -->Support for ENA CDS records with reverse complement operator</li>
+ <li><!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster groovy script execution</li>
+ <li><!-- JAL-1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
+ <li><!-- JAL-1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
+ <li><!-- JAL-2068 -->Support for creating new alignment calculation workers from groovy scripts</li>
<li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
+ <li><!-- JAL-1803 -->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
+ <li><!-- JAL-1993 -->Database selection dialog always shown before sequence fetcher is opened</li>
+ <li><!-- JAL-2183 -->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
+ <li><!-- JAL-1563 -->Free-text search client for UniProt using the UniProt REST API</li>
+ <li><!-- JAL-2168 -->-nonews command line parameter to prevent the news reader opening</li>
+ <li><!-- JAL-2028 -->Displayed columns for PDBe and Uniprot querying stored in preferences</li>
+ <li><!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot search results</li>
+ <li><!-- JAL-1977-->Tooltips shown on database chooser</li>
+ <li><!-- JAL-391 -->Reverse complement function in calculate menu for nucleotide sequences</li>
+ <li>
+ <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
+ </li>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+
</ul> <em>Applet</em>
<ul>
<li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
<li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
<li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
- <li><!-- JAL-2053-->hidden column markers not always rendered at right of alignment window</li>
- <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
+ <li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
+ <li><!-- JAL-2067 -->Tidied up links in help file table of contents</li>
<li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
<li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
<li><!-- JAL-2065 -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
<li><!-- JAL-2086 -->Cannot insert gaps into sequence when set as reference</li>
-
+ <li><!-- JAL-2146 -->Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation</li>
+ <li><!-- JAL-2099 -->Incorrect column numbers in ruler when hidden columns present</li>
+ <li><!-- JAL-1577 -->Colour by RNA Helices not enabled when user created annotation added to alignment</li>
+ <li><!-- JAL-1841 -->RNA Structure consensus only computed for '()' base pair annotation</li>
+ <li><!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus</li>
+ <li><!-- JAL-2174-->Extend selection with columns containing feature not working</li>
+ <li><!-- JAL-2275 -->Pfam format writer puts extra space at beginning of sequence</li>
+ <li><!-- JAL-1827 -->Incomplete sequence extracted from pdb entry 3a6s </li>
+ <li><!-- JAL-2238 -->Cannot create groups on an alignment from from a tree when t-coffee scores are shown</li>
+ <li><!-- JAL-1836,1967 -->Cannot import and view PDB structures with chains containing negative resnums (4q4h)</li>
+ <li><!-- JAL-1998 -->ArithmeticExceptions raised when parsing some structures</li>
+ <li><!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added to Clustal, PIR and PileUp output</li>
+ <li><!-- JAL-2008 -->Reordering sequence features that are not visible causes alignment window to repaint</li>
+ <li>
+ <!-- JAL-2006 -->Threshold sliders don't work in
+ graduated colour and colour by annotation row for e-value
+ scores associated with features and annotation rows
+ </li>
+ <li>
+ <!-- JAL-1797 -->amino acid physicochemical conservation
+ calculation should be case independent
+ </li>
+ <li>
+ <!-- JAL-2173 -->Remove annotation also updates hidden
+ columns
+ </li>
+ <li>
+ <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
+ </li>
+ <li>
+ <!-- JAL-2065 -->Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
+ </li>
+ <li><!-- JAL-1306 -->Quality and Conservation are now shown on load even when Consensus calculation is disabled</li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
</ul>
<em>Application</em>
<ul>
<li><!-- JAL-1011 -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
<li><!-- JAL-1989 -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
<li><!-- JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
+ <li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
+ <li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
+ <li><!-- JAL-1962 -->View mapping in structure view shows mappings between sequence and all chains in a PDB file</li>
+ <li><!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type</li>
+ <li><!-- JAL-1975 -->Export complete shown after destination file chooser is cancelled during an image export </li>
+ <li><!-- JAL-2025 -->Error when querying PDB Service with sequence name containing special characters</li>
+ <li><!-- JAL-2024 -->Manual PDB structure querying should be case insensitive</li>
+ <li><!-- JAL-2104 -->Large tooltips with broken HTML formatting don't wrap</li>
+ <li><!-- JAL-1128 -->Figures exported from wrapped view are truncated so L looks like I in consensus annotation</li>
+ <li><!-- JAL-2003 -->Export features should only export the currently displayed features for the current selection or view</li>
+ <li><!-- JAL-2036 -->Enable 'Get Cross-References' in menu after fetching cross-references</li>
+ <li><!-- JAL-2032 -->Mouseover of a copy of a sequence is not followed in the structure viewer</li>
+ <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>
+ <li>
+ <!-- JAL-2145 -->missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
+ </li>
+ <li>
+ <!-- JAL-1797 -->amino acid physicochemical conservation is case dependent
+ </li>
+ <li>
+ <!-- JAL-1448 -->RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
+ </li>
+ <li><!-- JAL-1960 -->Only offer PDB structures in structure viewer based on sequence name, PDB and Uniprot cross-references</li>
+
+ <li>
+ <!-- JAL-1976 -->No progress bar shown during export of alignment as HTML
+ </li>
+ <li>
+ <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
+ </li>
+ <li>
+ <!-- JAL-2213 -->Structures not always superimposed after multiple structures are shown for one or more sequences.
+ </li>
+ <li>
+ <!-- JAL-1370 -->Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
+ </li>
+ <li>
+ <!-- JAL-1823 -->Cannot specify chain code when entering specific PDB id for sequence
+ </li>
+ <li>
+ <!-- JAL-1944 -->File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
+ </li>
+ <li><!--JAL-2026-->Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence</li>
+ <li>
+ <!-- JAL-1887 -->Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+
<!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
</ul>
<em>Applet</em>
<ul>
- <li><!-- --></li>
+ <li><!-- JAL-2151 -->Incorrect columns are selected when hidden columns present before start of sequence</li>
+ <li><!-- JAL-1986 -->Missing dependencies on applet pages (JSON jars)</li>
+ <li>
+ <!-- JAL-1947 -->Overview pixel size changes when sequences are hidden in applet
+ </li>
+ <li><!-- JAL-1996 -->Updated instructions for applet deployment on examples pages.
+ </li>
</ul>
</div>
</td>
href="http://jswingreader.sourceforge.net/"
>JSwingReader</a>.
</p>
- <br/><em>From Jalview 2.10.0, check for news on startup can be disabled with <a href="../features/clarguments.html">command-line parameter</a> '-nonews'.
- This is not recommended for normal use, but may be useful to avoid interruptions when teaching, demonstrating, recording etc.</em>
+ <br />
+ <em>If you need to prevent the news-reader opening, then add the
+ <a href="../features/clarguments.html">command-line parameter</a>
+ '-nonews' to Jalview's command-line launch.
+ </em>
</body>
</html>
<p>
<strong>Highlights in Jalview 2.10</strong>
<ul>
- <li><strong>Ensembl sequence fetcher.</strong> Annotated Genes, transcripts and
- proteins can be retrieved via Jalview's new Ensembl REST client.</li>
- <li><strong>Improved sequence/structure mappings.</strong>
- Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) to
- match PDB data positions in UniProt sequences.</li>
+ <li><strong>Ensembl sequence fetcher.</strong> Annotated Genes,
+ transcripts and proteins can be retrieved via Jalview's new <a
+ href="features/ensemblsequencefetcher.html">Ensembl REST
+ client</a>. Support for import of Ensembl data allows:
+ <ul>
+ <li><strong>Sequence variant data.</strong> Jalview
+ propagates variant annotation on genomic regions onto transcripts and
+ protein products, complete with associated metadata such as
+ clinical significance.</li>
+ <li><strong>Aligned locus view.</strong> Transcripts
+ retrieved for a gene identifier via the Ensembl or
+ EnsemblGenomes sequence databases are automatically aligned to
+ their reference genome, and introns hidden from the view.</li>
+ </ul></li>
+ <li><strong>Working with structures.</strong>
+ <ul>
+ <li><strong>More accurate structure mappings.</strong>
+ Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
+ to <a href="features/siftsmapping.html">match structures
+ to UniProt sequences</a>, even for structures containing
+ multiple copies of a sequence.</li>
+ <li><strong>Import structures as mmCIF</strong>. Jalview
+ now downloads data from the EMBL-EBI's PDBe site as <a href="features/mmcif.html">mmCIF</a>.
+ This allows very large structures to be imported, such as the HIV virus capsid assembly.</li>
+ </ul></li>
+ <li><strong>UniProt Free Text Search.</strong> The new search
+ dialog for UniProt allows you to browse and retrieve sequences
+ from UniProt with free-text search and more structured queries</li>
+ <li><strong>Reference sequence alignment view.</strong>.
+ Jalview 2.9 introduced support for reference sequences. In 2.10,
+ when a reference sequence is defined for the alignment, the
+ alignment column ruler is now numbered according to the reference
+ sequence. The reference sequence for alignment views can also be
+ saved and restored from Jalview projects.</li>
+ <li><strong>Ensembl and ENA 'show cross-references'
+ support.</strong>The Calculations menu's 'Show cross-references' will now
+ offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein
+ mapping data is available for download or display.</li>
</ul>
</body>
see ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd
see http://www.ebi.ac.uk/ena/submit/data-formats
-->
+ <!--
<class name="jalview.datamodel.xdb.embl.EmblFile">
<map-to xml="ROOT"/>
<field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
<bind-xml name="Error"/>
</field>
</class>
+ -->
<class name="jalview.datamodel.xdb.embl.EmblEntry">
+ <map-to xml="entry"/>
<field name="accession" type="string">
<bind-xml name="accession" node="attribute"/>
</field>
_data_column.is_shown_by_default
_data_column.is_searchable
PDB Id;pdb_id;String;g2;40;60;45;true;true
-Title;title;String;g6;300;1500;400;true;false
+Title;title;String;g6;50;1500;400;true;false
Molecule;molecule_name;String;g3;50;400;95;false;true
Molecule Type;molecule_type;String;g3;50;400;95;false;true
Sequence;molecule_sequence;String;g6;50;400;95;false;false
Number of Polymer Entities;number_of_polymer_entities;int;g6;50;400;95;false;false
Number of Bound Entities;number_of_bound_entities;int;g6;50;400;95;false;false
Crystallisation Reservoir;crystallisation_reservoir;String;g6;50;400;95;false;false
-Data Scalling Software;data_scaling_software;String;g4;50;400;95;false;false
+Data Scaling Software;data_scaling_software;String;g4;50;400;95;false;false
Detector;detector;String;g6;50;400;95;false;false
Detector Type;detector_type;String;g6;50;400;95;false;false
Modified Residue Flag;modified_residue_flag;String;g6;50;400;95;false;false
label.add_sbrs_definition = Add a SBRS Definition
label.edit_sbrs_definition = Edit SBRS Definition
label.delete_sbrs_definition = Delete SBRS Definition
-label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases. Some of the ids have been\n altered, most likely the start/end residue will have been updated.\n Save your alignment to maintain the updated id.\n\n
-label.sequence_names_updated = Sequence names updated
+label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases.\n(Use Calculate | Show flanking regions to show enclosing sequence.)\nTo preserve data changes, save your alignment.\n\n
+label.sequences_updated = Sequences updated
label.dbref_search_completed = DBRef search completed
label.show_all_chains = Show all chains
label.fetch_all_param = Fetch all {0}
label.invalid_font = Invalid Font
label.separate_multiple_accession_ids = Enter one or more accession IDs separated by a semi-colon ";"
label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";"
-label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This Searches the entire database)
+label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This searches the entire database)
label.replace_commas_semicolons = Replace commas with semi-colons
label.parsing_failed_syntax_errors_shown_below_param = Parsing failed. Syntax errors shown below {0}
label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown\:\n {0}
label.add_sbrs_definition = Añadir una definición SBRS
label.edit_sbrs_definition = Editar una definición SBRS
label.delete_sbrs_definition = Borrar una definición SBRS
-label.your_sequences_have_been_verified = Sus secuencias has sido verificadas en una base de datos de secuencias conocidas. Algunos de sus ID se han alterado y\n, probablemente, el residuo de inicio/fin se haya actualizado.\nGuarde su alineamiento para mantener el ID actualizado.\n\n
-label.sequence_names_updated = Nombres de secuencia actualizados
+label.your_sequences_have_been_verified = Sus secuencias has sido verificadas en una base de datos de secuencias conocidas.\n(Usar Calcular | Mostrar flancos para ver ampliación.)\nPara mantener los datos actualizados, guarde su alineamiento.\n\n
+label.sequences_updated = Secuencias actualizadas
label.dbref_search_completed = Búsqueda de DBRef terminada
label.show_all_chains = Mostrar todas las cadenas
label.fetch_all_param = Recuperar todas {0}
*/
public class ChimeraManager
{
+ private static final int REST_REPLY_TIMEOUT_MS = 15000;
+
+ private static final int CONNECTION_TIMEOUT_MS = 100;
+
private static final boolean debug = false;
private int chimeraRestPort;
BufferedReader response = null;
try
{
- response = HttpClientUtils
- .doHttpUrlPost(restUrl, commands, 100, 5000);
+ response = HttpClientUtils.doHttpUrlPost(restUrl, commands, CONNECTION_TIMEOUT_MS,
+ REST_REPLY_TIMEOUT_MS);
String line = "";
while ((line = response.readLine()) != null)
{
*/
AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame();
MapList dnaToCdsMap = new MapList(mapList.getFromRanges(),
- cdsRange, 1,
- 1);
+ cdsRange, 1, 1);
dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss,
dnaToCdsMap);
if (!mappings.contains(dnaToCdsMapping))
/*
* transfer any features on dna that overlap the CDS
*/
- transferFeatures(dnaSeq, cdsSeq, cdsToProteinMap, null,
+ transferFeatures(dnaSeq, cdsSeq, dnaToCdsMap, null,
SequenceOntologyI.CDS);
}
}
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
import java.awt.Color;
-import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.Vector;
/**
int end;
- Vector seqNums; // vector of int vectors where first is sequence checksum
+ Vector<int[]> seqNums; // vector of int vectors where first is sequence
+ // checksum
int maxLength = 0; // used by quality calcs
boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
- Hashtable[] total;
+ Map<String, Integer>[] total;
boolean canonicaliseAa = true; // if true then conservation calculation will
// symbol
/** Stores calculated quality values */
- public Vector quality;
+ private Vector<Double> quality;
/** Stores maximum and minimum values of quality values */
- public Double[] qualityRange = new Double[2];
+ private double[] qualityRange = new double[2];
- String consString = "";
+ private Sequence consSequence;
- Sequence consSequence;
+ private int threshold;
- Hashtable propHash;
+ private String name = "";
- int threshold;
-
- String name = "";
-
- int[][] cons2;
+ private int[][] cons2;
private String[] consSymbs;
*
* @param name
* Name of conservation
- * @param propHash
- * hash of properties for each symbol
* @param threshold
* to count the residues in residueHash(). commonly used value is 3
* @param sequences
* @param end
* end residue position
*/
- public Conservation(String name, Hashtable propHash, int threshold,
+ public Conservation(String name, int threshold,
List<SequenceI> sequences, int start, int end)
{
this.name = name;
- this.propHash = propHash;
this.threshold = threshold;
this.start = start;
this.end = end;
seqNums.addElement(new int[sq.length() + 1]);
}
- if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
+ if (sq.hashCode() != seqNums.elementAt(i)[0])
{
int j;
int len;
*/
public void calculate()
{
- Hashtable resultHash, ht;
int thresh, j, jSize = sequences.length;
int[] values; // Replaces residueHash
- String type, res = null;
char c;
- Enumeration enumeration2;
total = new Hashtable[maxLength];
if (canonicaliseAa)
{ // lookup the base aa code symbol
- c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
- .getCharAt(i)];
+ c = (char) ResidueProperties.aaIndex[sequences[j].getCharAt(i)];
if (c > 20)
{
c = '-';
else
{
// recover canonical aa symbol
- c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
+ c = ResidueProperties.aa[c].charAt(0);
}
}
else
thresh = (threshold * (jSize)) / 100;
// loop over all the found residues
- resultHash = new Hashtable();
+ Hashtable<String, Integer> resultHash = new Hashtable<String, Integer>();
for (char v = '-'; v < 'Z'; v++)
{
if (values[v] > thresh)
{
- res = String.valueOf(v);
+ String res = String.valueOf(v);
// Now loop over the properties
- enumeration2 = propHash.keys();
-
- while (enumeration2.hasMoreElements())
+ for (String type : ResidueProperties.propHash.keySet())
{
- type = (String) enumeration2.nextElement();
- ht = (Hashtable) propHash.get(type);
+ Map<String, Integer> ht = ResidueProperties.propHash.get(type);
// Have we ticked this before?
if (!resultHash.containsKey(type))
resultHash.put(type, ht.get("-"));
}
}
- else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
+ else if (!resultHash.get(type).equals(ht.get(res)))
{
resultHash.put(type, new Integer(-1));
}
* Calculates the conservation sequence
*
* @param consflag
- * if true, poitiveve conservation; false calculates negative
+ * if true, positive conservation; false calculates negative
* conservation
* @param percentageGaps
* commonly used value is 25
public void verdict(boolean consflag, float percentageGaps)
{
StringBuffer consString = new StringBuffer();
- String type;
- Integer result;
- int[] gapcons;
- int totGaps, count;
- float pgaps;
- Hashtable resultHash;
- Enumeration enumeration;
// NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
// EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
consSymbs = new String[end - start + 1];
for (int i = start; i <= end; i++)
{
- gapcons = countConsNGaps(i);
- totGaps = gapcons[1];
- pgaps = ((float) totGaps * 100) / sequences.length;
+ int[] gapcons = countConsNGaps(i);
+ int totGaps = gapcons[1];
+ float pgaps = ((float) totGaps * 100) / sequences.length;
consSymbs[i - start] = new String();
if (percentageGaps > pgaps)
{
- resultHash = total[i - start];
+ Map<String, Integer> resultHash = total[i - start];
// Now find the verdict
- count = 0;
- enumeration = resultHash.keys();
-
- while (enumeration.hasMoreElements())
+ int count = 0;
+ for (String type : resultHash.keySet())
{
- type = (String) enumeration.nextElement();
- result = (Integer) resultHash.get(type);
+ int result = resultHash.get(type).intValue();
// Do we want to count +ve conservation or +ve and -ve cons.?
if (consflag)
{
- if (result.intValue() == 1)
+ if (result == 1)
{
consSymbs[i - start] = type + " " + consSymbs[i - start];
count++;
}
else
{
- if (result.intValue() != -1)
+ if (result != -1)
{
+ if (result == 0)
{
- if (result.intValue() == 0)
- {
- consSymbs[i - start] = consSymbs[i - start] + " !" + type;
- }
- else
- {
- consSymbs[i - start] = type + " " + consSymbs[i - start];
- }
+ consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+ }
+ else
+ {
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
}
-
count++;
}
}
*/
private void percentIdentity2()
{
- seqNums = new Vector();
+ seqNums = new Vector<int[]>();
// calcSeqNum(s);
int i = 0, iSize = sequences.length;
// Do we need to calculate this again?
while (j < sequences.length)
{
- sqnum = (int[]) seqNums.elementAt(j);
+ sqnum = seqNums.elementAt(j);
for (i = 1; i < sqnum.length; i++)
{
/**
* Calculates the quality of the set of sequences
*
- * @param start
+ * @param startRes
* Start residue
- * @param end
+ * @param endRes
* End residue
*/
- public void findQuality(int start, int end)
+ public void findQuality(int startRes, int endRes)
{
- quality = new Vector();
+ quality = new Vector<Double>();
double max = -10000;
- int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+ int[][] BLOSUM62 = ResidueProperties.getBLOSUM62();
// Loop over columns // JBPNote Profiling info
// long ts = System.currentTimeMillis();
for (l = 0; l < size; l++)
{
- lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
+ lengths[l] = seqNums.elementAt(l).length - 1;
}
- for (j = start; j <= end; j++)
+ for (j = startRes; j <= endRes; j++)
{
bigtot = 0;
{
tot = 0;
xx = new double[24];
- seqNum = (j < lengths[k]) ? ((int[]) seqNums.elementAt(k))[j + 1]
+ seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1]
: 23; // Sequence, or gap at the end
// This is a loop over r
double newmax = -10000;
- for (j = start; j <= end; j++)
+ for (j = startRes; j <= endRes; j++)
{
- tmp = ((Double) quality.elementAt(j)).doubleValue();
+ tmp = quality.elementAt(j).doubleValue();
tmp = ((max - tmp) * (size - cons2[j][23])) / size;
// System.out.println(tmp+ " " + j);
}
// System.out.println("Quality " + s);
- qualityRange[0] = new Double(0);
- qualityRange[1] = new Double(newmax);
+ qualityRange[0] = 0D;
+ qualityRange[1] = newmax;
}
/**
- * complete the given consensus and quuality annotation rows. Note: currently
+ * Complete the given consensus and quuality annotation rows. Note: currently
* this method will enlarge the given annotation row if it is too small,
* otherwise will leave its length unchanged.
*
char c;
- if (conservation.annotations != null
+ if (conservation != null && conservation.annotations != null
&& conservation.annotations.length < alWidth)
{
conservation.annotations = new Annotation[alWidth];
if (quality2 != null)
{
- quality2.graphMax = qualityRange[1].floatValue();
+ quality2.graphMax = (float) qualityRange[1];
if (quality2.annotations != null
&& quality2.annotations.length < alWidth)
{
quality2.annotations = new Annotation[alWidth];
}
- qmin = qualityRange[0].floatValue();
- qmax = qualityRange[1].floatValue();
+ qmin = (float) qualityRange[0];
+ qmax = (float) qualityRange[1];
}
for (int i = istart; i < alWidth; i++)
value = 10;
}
- float vprop = value - min;
- vprop /= max;
- int consp = i - start;
- String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
- : "";
- conservation.annotations[i] = new Annotation(String.valueOf(c),
- conssym, ' ', value, new Color(minR + (maxR * vprop), minG
- + (maxG * vprop), minB + (maxB * vprop)));
+ if (conservation != null)
+ {
+ float vprop = value - min;
+ vprop /= max;
+ int consp = i - start;
+ String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ : "";
+ conservation.annotations[i] = new Annotation(String.valueOf(c),
+ conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+ + (maxG * vprop), minB + (maxB * vprop)));
+ }
// Quality calc
if (quality2 != null)
{
- value = ((Double) quality.elementAt(i)).floatValue();
- vprop = value - qmin;
+ value = quality.elementAt(i).floatValue();
+ float vprop = value - qmin;
vprop /= qmax;
quality2.annotations[i] = new Annotation(" ",
String.valueOf(value), ' ', value, new Color(minR
*
* @param name
* - name of conservation
- * @param consHash
- * - hash table of properties for each amino acid (normally
- * ResidueProperties.propHash)
* @param threshold
* - minimum number of conserved residues needed to indicate
* conservation (typically 3)
* @return Conservation object ready for use in visualization
*/
public static Conservation calculateConservation(String name,
- Hashtable consHash, int threshold, List<SequenceI> seqs,
- int start, int end, boolean posOrNeg, int consPercGaps,
- boolean calcQuality)
- {
- Conservation cons = new Conservation(name, consHash, threshold, seqs,
- start, end);
- return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality);
- }
-
- /**
- * @param b
- * positive (true) or negative (false) conservation
- * @param consPercGaps
- * percentage of gaps tolerated in column
- * @param calcQuality
- * flag indicating if alignment quality should be calculated
- * @return Conservation object ready for use in visualization
- */
- public static Conservation calculateConservation(Conservation cons,
- boolean b, int consPercGaps, boolean calcQuality)
+ int threshold, List<SequenceI> seqs, int start, int end,
+ boolean posOrNeg, int consPercGaps, boolean calcQuality)
{
+ Conservation cons = new Conservation(name, threshold, seqs, start, end);
cons.calculate();
- cons.verdict(b, consPercGaps);
-
+ cons.verdict(posOrNeg, consPercGaps);
+
if (calcQuality)
{
cons.findQuality();
}
-
+
return cons;
}
}
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
findXrefSourcesForSequence(seq, dna, sources);
}
}
+ sources.remove(DBRefSource.EMBL); // hack to prevent EMBL xrefs resulting in
+ // redundant datasets
+ if (dna)
+ {
+ sources.remove(DBRefSource.ENSEMBL); // hack to prevent Ensembl and
+ // EnsemblGenomes xref option shown
+ // from cdna panel
+ sources.remove(DBRefSource.ENSEMBLGENOMES);
+ }
+ // redundant datasets
return sources;
}
if (!rseqs.contains(matchInDataset))
{
rseqs.add(matchInDataset);
- // need to try harder to only add unique mappings
- if (xref.getMap().getMap().isTripletMap()
- && dataset.getMapping(seq, matchInDataset) == null
- && cf.getMappingBetween(seq, matchInDataset) == null)
+ }
+ // even if rseqs contained matchInDataset - check mappings between
+ // these seqs are added
+ // need to try harder to only add unique mappings
+ if (xref.getMap().getMap().isTripletMap()
+ && dataset.getMapping(seq, matchInDataset) == null
+ && cf.getMappingBetween(seq, matchInDataset) == null)
+ {
+ // materialise a mapping for highlighting between these
+ // sequences
+ if (fromDna)
{
- // materialise a mapping for highlighting between these sequences
- if (fromDna)
- {
- cf.addMap(dss, matchInDataset, xref.getMap().getMap(), xref.getMap().getMappedFromId());
- } else {
- cf.addMap(matchInDataset, dss, xref.getMap().getMap().getInverse(), xref.getMap().getMappedFromId());
- }
+ cf.addMap(dss, matchInDataset, xref.getMap().getMap(),
+ xref.getMap().getMappedFromId());
+ }
+ else
+ {
+ cf.addMap(matchInDataset, dss, xref.getMap().getMap()
+ .getInverse(), xref.getMap().getMappedFromId());
}
}
+
refIterator.remove();
continue;
}
// first filter in case we are retrieving crossrefs that have already been
// retrieved. this happens for cases where a database record doesn't yield
// protein products for CDS
- DBRefEntry[] dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
- for (SequenceI sq : dataset.getSequences())
- {
- boolean dupeFound = false;
- // !fromDna means we are looking only for nucleotide sequences, not
- // protein
- if (sq.isProtein() == fromDna)
- {
- for (DBRefEntry dbr : sq.getPrimaryDBRefs())
- {
- for (DBRefEntry found : DBRefUtils.searchRefs(dbrSourceSet, dbr))
- {
- sourceRefs.remove(found);
- dupeFound = true;
- }
- }
- }
- if (dupeFound)
- {
- dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
- }
- }
+ removeAlreadyRetrievedSeqs(sourceRefs, fromDna);
if (sourceRefs.size() == 0)
{
// no more work to do! We already had all requested sequence records in
if (retrieved != null)
{
- updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna);
+ boolean addedXref = false;
+ List<SequenceI> newDsSeqs = new ArrayList<SequenceI>(), doNotAdd = new ArrayList<SequenceI>();
+
for (SequenceI retrievedSequence : retrieved)
{
// dataset gets contaminated ccwith non-ds sequences. why ??!
// try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL->
SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
: retrievedSequence.getDatasetSequence();
- DBRefEntry[] dbr = retrievedSequence.getDBRefs();
- if (dbr != null)
+ addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
+ retrievedDss);
+ }
+ if (!addedXref)
+ {
+ // try again, after looking for matching IDs
+ // shouldn't need to do this unless the dbref mechanism has broken.
+ updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna);
+ for (SequenceI retrievedSequence : retrieved)
+ {
+ // dataset gets contaminated ccwith non-ds sequences. why ??!
+ // try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL->
+ SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
+ : retrievedSequence.getDatasetSequence();
+ addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
+ retrievedDss);
+ }
+ }
+ for (SequenceI newToSeq : newDsSeqs)
+ {
+ if (!doNotAdd.contains(newToSeq)
+ && dataset.findIndex(newToSeq) == -1)
{
- for (DBRefEntry dbref : dbr)
+ dataset.addSequence(newToSeq);
+ matcher.add(newToSeq);
+ }
+ }
+ }
+ }
+
+ /**
+ * Search dataset for sequences with a primary reference contained in
+ * sourceRefs.
+ *
+ * @param sourceRefs
+ * - list of references to filter.
+ * @param fromDna
+ * - type of sequence to search for matching primary reference.
+ */
+ private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
+ boolean fromDna)
+ {
+ DBRefEntry[] dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
+ for (SequenceI sq : dataset.getSequences())
+ {
+ boolean dupeFound = false;
+ // !fromDna means we are looking only for nucleotide sequences, not
+ // protein
+ if (sq.isProtein() == fromDna)
+ {
+ for (DBRefEntry dbr : sq.getPrimaryDBRefs())
+ {
+ for (DBRefEntry found : DBRefUtils.searchRefs(dbrSourceSet, dbr))
{
- // find any entry where we should put in the sequence being
- // cross-referenced into the map
- Mapping map = dbref.getMap();
- if (map != null)
+ sourceRefs.remove(found);
+ dupeFound = true;
+ }
+ }
+ }
+ if (dupeFound)
+ {
+ // rebuild the search array from the filtered sourceRefs list
+ dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
+ }
+ }
+ }
+
+ /**
+ * process sequence retrieved via a dbref on source sequence to resolve and
+ * transfer data
+ *
+ * @param cf
+ * @param sourceSequence
+ * @param retrievedSequence
+ * @return true if retrieveSequence was imported
+ */
+ private boolean importCrossRefSeq(AlignedCodonFrame cf,
+ List<SequenceI> newDsSeqs, List<SequenceI> doNotAdd,
+ SequenceI sourceSequence, SequenceI retrievedSequence)
+ {
+ /**
+ * set when retrievedSequence has been verified as a crossreference for
+ * sourceSequence
+ */
+ boolean imported = false;
+ DBRefEntry[] dbr = retrievedSequence.getDBRefs();
+ if (dbr != null)
+ {
+ for (DBRefEntry dbref : dbr)
+ {
+ SequenceI matched = findInDataset(dbref);
+ if (matched == sourceSequence)
+ {
+ // verified retrieved and source sequence cross-reference each other
+ imported = true;
+ }
+ // find any entry where we should put in the sequence being
+ // cross-referenced into the map
+ Mapping map = dbref.getMap();
+ if (map != null)
+ {
+ if (map.getTo() != null && map.getMap() != null)
+ {
+ if (map.getTo() == sourceSequence)
+ {
+ // already called to import once, and most likely this sequence
+ // already imported !
+ continue;
+ }
+ if (matched == null)
{
- if (map.getTo() != null && map.getMap() != null)
+ /*
+ * sequence is new to dataset, so save a reference so it can be added.
+ */
+ newDsSeqs.add(map.getTo());
+ continue;
+ }
+
+ /*
+ * there was a matching sequence in dataset, so now, check to see if we can update the map.getTo() sequence to the existing one.
+ */
+
+ try
+ {
+ // compare ms with dss and replace with dss in mapping
+ // if map is congruent
+ SequenceI ms = map.getTo();
+ // TODO findInDataset requires exact sequence match but
+ // 'congruent' test is only for the mapped part
+ // maybe not a problem in practice since only ENA provide a
+ // mapping and it is to the full protein translation of CDS
+ // matcher.findIdMatch(map.getTo());
+ // TODO addendum: if matched is shorter than getTo, this will fail
+ // - when it should really succeed.
+ int sf = map.getMap().getToLowest();
+ int st = map.getMap().getToHighest();
+ SequenceI mappedrg = ms.getSubSequence(sf, st);
+ if (mappedrg.getLength() > 0
+ && ms.getSequenceAsString().equals(
+ matched.getSequenceAsString()))
{
- // TODO findInDataset requires exact sequence match but
- // 'congruent' test is only for the mapped part
- // maybe not a problem in practice since only ENA provide a
- // mapping and it is to the full protein translation of CDS
- SequenceI matched = findInDataset(dbref);
- // matcher.findIdMatch(map.getTo());
- if (matched != null)
+ /*
+ * sequences were a match,
+ */
+ String msg = "Mapping updated from " + ms.getName()
+ + " to retrieved crossreference "
+ + matched.getName();
+ System.out.println(msg);
+
+ DBRefEntry[] toRefs = map.getTo().getDBRefs();
+ if (toRefs != null)
{
/*
- * already got an xref to this sequence; update this
- * map to point to the same sequence, and add
- * any new dbrefs to it
+ * transfer database refs
*/
- DBRefEntry[] toRefs = map.getTo().getDBRefs();
- if (toRefs != null)
+ for (DBRefEntry ref : toRefs)
{
- for (DBRefEntry ref : toRefs)
+ if (dbref.getSrcAccString().equals(
+ ref.getSrcAccString()))
{
- matched.addDBRef(ref); // add or update mapping
+ continue; // avoid overwriting the ref on source sequence
}
- }
- map.setTo(matched);
- }
- else
- {
- if (dataset.findIndex(map.getTo()) == -1)
- {
- dataset.addSequence(map.getTo());
- matcher.add(map.getTo());
+ matched.addDBRef(ref); // add or update mapping
}
}
- try
- {
- // compare ms with dss and replace with dss in mapping
- // if map is congruent
- SequenceI ms = map.getTo();
- int sf = map.getMap().getToLowest();
- int st = map.getMap().getToHighest();
- SequenceI mappedrg = ms.getSubSequence(sf, st);
- // SequenceI loc = dss.getSubSequence(sf, st);
- if (mappedrg.getLength() > 0
- && ms.getSequenceAsString().equals(
- dss.getSequenceAsString()))
- // && mappedrg.getSequenceAsString().equals(
- // loc.getSequenceAsString()))
- {
- String msg = "Mapping updated from " + ms.getName()
- + " to retrieved crossreference "
- + dss.getName();
- System.out.println(msg);
- map.setTo(dss);
+ doNotAdd.add(map.getTo());
+ map.setTo(matched);
- /*
- * give the reverse reference the inverse mapping
- * (if it doesn't have one already)
- */
- setReverseMapping(dss, dbref, cf);
+ /*
+ * give the reverse reference the inverse mapping
+ * (if it doesn't have one already)
+ */
+ setReverseMapping(matched, dbref, cf);
+ /*
+ * copy sequence features as well, avoiding
+ * duplication (e.g. same variation from two
+ * transcripts)
+ */
+ SequenceFeature[] sfs = ms.getSequenceFeatures();
+ if (sfs != null)
+ {
+ for (SequenceFeature feat : sfs)
+ {
/*
- * copy sequence features as well, avoiding
- * duplication (e.g. same variation from two
- * transcripts)
+ * make a flyweight feature object which ignores Parent
+ * attribute in equality test; this avoids creating many
+ * otherwise duplicate exon features on genomic sequence
*/
- SequenceFeature[] sfs = ms.getSequenceFeatures();
- if (sfs != null)
+ SequenceFeature newFeature = new SequenceFeature(
+ feat)
{
- for (SequenceFeature feat : sfs)
+ @Override
+ public boolean equals(Object o)
{
- /*
- * make a flyweight feature object which ignores Parent
- * attribute in equality test; this avoids creating many
- * otherwise duplicate exon features on genomic sequence
- */
- SequenceFeature newFeature = new SequenceFeature(
- feat)
- {
- @Override
- public boolean equals(Object o)
- {
- return super.equals(o, true);
- }
- };
- dss.addSequenceFeature(newFeature);
+ return super.equals(o, true);
}
- }
+ };
+ matched.addSequenceFeature(newFeature);
}
- cf.addMap(retrievedDss, map.getTo(), map.getMap());
- } catch (Exception e)
- {
- System.err
- .println("Exception when consolidating Mapped sequence set...");
- e.printStackTrace(System.err);
}
+
}
+ cf.addMap(retrievedSequence, map.getTo(), map.getMap());
+ } catch (Exception e)
+ {
+ System.err
+ .println("Exception when consolidating Mapped sequence set...");
+ e.printStackTrace(System.err);
}
}
}
- retrievedSequence.updatePDBIds();
- rseqs.add(retrievedDss);
- if (dataset.findIndex(retrievedDss) == -1)
- {
- dataset.addSequence(retrievedDss);
- matcher.add(retrievedDss);
- }
}
}
+ if (imported)
+ {
+ retrievedSequence.updatePDBIds();
+ rseqs.add(retrievedSequence);
+ if (dataset.findIndex(retrievedSequence) == -1)
+ {
+ dataset.addSequence(retrievedSequence);
+ matcher.add(retrievedSequence);
+ }
+ }
+ return imported;
}
/**
* Sets the inverse sequence mapping in the corresponding dbref of the mapped
}
/**
- * Returns the first identical sequence in the dataset if any, else null
+ * Returns null or the first sequence in the dataset which is identical to
+ * xref.mapTo, and has a) a primary dbref matching xref, or if none found, the
+ * first one with an ID source|xrefacc
*
* @param xref
+ * with map and mapped-to sequence
* @return
*/
SequenceI findInDataset(DBRefEntry xref)
String name2 = xref.getSource() + "|" + name;
SequenceI dss = mapsTo.getDatasetSequence() == null ? mapsTo : mapsTo
.getDatasetSequence();
+ // first check ds if ds is directly referenced
+ if (dataset.findIndex(dss) > -1)
+ {
+ return dss;
+ }
+ DBRefEntry template = new DBRefEntry(xref.getSource(), null,
+ xref.getAccessionId());
+ /**
+ * remember the first ID match - in case we don't find a match to template
+ */
+ SequenceI firstIdMatch = null;
for (SequenceI seq : dataset.getSequences())
{
+ // first check primary refs.
+ List<DBRefEntry> match = DBRefUtils.searchRefs(seq.getPrimaryDBRefs()
+ .toArray(new DBRefEntry[0]), template);
+ if (match != null && match.size() == 1 && sameSequence(seq, dss))
+ {
+ return seq;
+ }
/*
* clumsy alternative to using SequenceIdMatcher which currently
* returns sequences with a dbref to the matched accession id
* which we don't want
*/
- if (name.equals(seq.getName()) || seq.getName().startsWith(name2))
+ if (firstIdMatch == null
+ && (name.equals(seq.getName()) || seq.getName().startsWith(
+ name2)))
{
if (sameSequence(seq, dss))
{
- return seq;
+ firstIdMatch = seq;
}
}
}
- return null;
+ return firstIdMatch;
}
/**
}
/**
- * Answers true if the base-pair is either a canonical (A-T/U, C-G) or a
- * wobble (G-T/U) pair (either way round), else false
+ * Answers true if the base-pair is either a Watson-Crick (A:T/U, C:G) or a
+ * wobble (G:T/U) pair (either way round), else false
*
* @param first
* @param second
}
/**
+ * Answers true if the base-pair is Watson-Crick - (A:T/U or C:G, either way
+ * round), else false
+ *
+ * @param first
+ * @param second
+ * @return
+ */
+ public static boolean isCanonicalPair(char first, char second)
+ {
+
+ if (first > 'Z')
+ {
+ first -= 32;
+ }
+ if (second > 'Z')
+ {
+ second -= 32;
+ }
+
+ switch (first)
+ {
+ case 'A':
+ switch (second)
+ {
+ case 'T':
+ case 'U':
+ return true;
+ }
+ break;
+ case 'G':
+ switch (second)
+ {
+ case 'C':
+ return true;
+ }
+ break;
+ case 'C':
+ switch (second)
+ {
+ case 'G':
+ return true;
+ }
+ break;
+ case 'T':
+ case 'U':
+ switch (second)
+ {
+ case 'A':
+ return true;
+ }
+ break;
+ }
+ return false;
+ }
+
+ /**
* Returns the matching close pair symbol for the given opening symbol.
* Currently returns a-z for A-Z, or )]}> for ([{<, or the input symbol if it
* is not a valid opening symbol.
for (int i = start; i < end; i++) // foreach column
{
- int canonicalOrWobblePairCount = 0;
+ int canonicalOrWobblePairCount = 0, canonical = 0;
int otherPairCount = 0;
+ int nongap = 0;
maxResidue = "-";
values = new int[255];
pairs = new int[255][255];
values['-']++;
continue;
}
-
+ nongap++;
/*
* ensure upper-case for counting purposes
*/
}
if (Rna.isCanonicalOrWobblePair(c, cEnd))
{
- values['(']++;
- maxResidue = "(";
canonicalOrWobblePairCount++;
+ if (Rna.isCanonicalPair(c, cEnd))
+ {
+ canonical++;
+ }
}
else
{
- values['[']++;
- maxResidue = "[";
otherPairCount++;
}
pairs[c][cEnd]++;
}
}
- // nonGap++;
}
residueHash = new Hashtable();
residueHash.put(PAIRPROFILE, pairs);
}
-
+ values['('] = canonicalOrWobblePairCount;
+ values['['] = canonical;
+ values['{'] = otherPairCount;
/*
* the count is the number of valid pairs (as a percentage, determines
* the relative size of the profile logo)
int count = canonicalOrWobblePairCount;
/*
- * currently displaying as '(' if most pairs are valid, or as
- * '[' if there are more invalid than valid pairs
+ * display '(' if most pairs are canonical, or as
+ * '[' if there are more wobble pairs.
*/
- if (!maxResidue.equals("-"))
+ if (canonicalOrWobblePairCount > 0 || otherPairCount > 0)
{
- maxResidue = canonicalOrWobblePairCount >= otherPairCount ? "("
+ if (canonicalOrWobblePairCount >= otherPairCount)
+ {
+ maxResidue = (canonicalOrWobblePairCount - canonical) < canonical ? "("
: "[";
+ }
+ else
+ {
+ maxResidue = "{";
+ }
}
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
percentage = ((float) count * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
- // percentage = ((float) count * 100) / (float) nongap;
- // residueHash.put(PID_NOGAPS, new Float(percentage));
+ percentage = ((float) count * 100) / nongap;
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+
if (result[i] == null)
{
result[i] = residueHash;
{
values[')'] = values['('];
values[']'] = values['['];
+ values['}'] = values['{'];
values['('] = 0;
values['['] = 0;
- maxResidue = maxResidue.equals("(") ? ")" : "]";
+ values['{'] = 0;
+ maxResidue = maxResidue.equals("(") ? ")"
+ : maxResidue.equals("[") ? "]" : "}";
residueHash = new Hashtable();
if (profile)
percentage = ((float) count * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
+ percentage = ((float) count * 100) / nongap;
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+
result[bpEnd] = residueHash;
}
}
*/
public int calcPanelHeight();
+ /**
+ * Answers true if the viewport has at least one column selected
+ *
+ * @return
+ */
+ boolean hasSelectedColumns();
+
+ /**
+ * Answers true if the viewport has at least one hidden column
+ *
+ * @return
+ */
boolean hasHiddenColumns();
boolean isValidCharWidth();
boolean isClosed();
/**
+ * Dispose of all references or resources held by the viewport
+ */
+ void dispose();
+
+ /**
* get the associated calculation thread manager for the view
*
* @return
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
if (conservationMenuItem.getState())
{
- sg.cs.setConservation(Conservation.calculateConservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment()
- .getWidth(), false, ap.av.getConsPercGaps(), false));
+ sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+ .getAlignment().getWidth(), false, ap.av
+ .getConsPercGaps(), false));
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.getColumnSelection() != null
- && viewport.getColumnSelection().getSelected() != null && viewport
- .getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns()
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
hide = true;
viewport.hideAllSelectedSeqs();
}
- else if (!(toggleCols && viewport.getColumnSelection().getSelected()
- .size() > 0))
+ else if (!(toggleCols && viewport.hasSelectedColumns()))
{
viewport.showAllHiddenSeqs();
}
if (toggleCols)
{
- if (viewport.getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns())
{
viewport.hideSelectedColumns();
if (!toggleSeqs)
// this value is set false when selection area being dragged
boolean fastPaint = true;
- public void finalize()
+ @Override
+ public void finalize() throws Throwable
{
alignFrame = null;
av = null;
annotationPanel = null;
annotationPanelHolder = null;
annotationSpaceFillerHolder = null;
+ super.finalize();
}
public AlignmentPanel(AlignFrame af, final AlignViewport av)
addComponentListener(new ComponentAdapter()
{
+ @Override
public void componentResized(ComponentEvent evt)
{
setScrollValues(av.getStartRes(), av.getStartSeq());
final AlignmentPanel ap = this;
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(java.beans.PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
* automatically adjust annotation panel height for new annotation whilst
* ensuring the alignment is still visible.
*/
+ @Override
public void adjustAnnotationHeight()
{
// TODO: display vertical annotation scrollbar if necessary
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
int oldX = av.getStartRes();
/**
* Repaint the alignment and annotations, and, optionally, any overview window
*/
+ @Override
public void paintAlignment(boolean updateOverview)
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
invalidate();
*/
package jalview.appletgui;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
- if (av.getAlignment().getAlignmentAnnotation() == null)
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns == null)
{
return;
}
// seqAssociated.setState(acg.isSeqAssociated());
}
- Vector list = new Vector();
+ Vector<String> list = new Vector<String>();
int index = 1;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < anns.length; i++)
{
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ String label = anns[i].label;
+ if (anns[i].sequenceRef != null)
+ {
+ label = label + "_" + anns[i].sequenceRef.getName();
+ }
if (!list.contains(label))
{
list.addElement(label);
Checkbox thresholdIsMin = new Checkbox();
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == thresholdValue)
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == currentColours)
changeColour();
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (!adjusting)
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
ap.paintAlignment(true);
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
- if (av.getAlignment().getAlignmentAnnotation() == null)
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns == null)
{
return;
}
setOldColumnSelection(av.getColumnSelection());
adjusting = true;
- Vector list = new Vector();
+ Vector<String> list = new Vector<String>();
int index = 1;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < anns.length; i++)
{
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ String label = anns[i].label;
+ if (anns[i].sequenceRef != null)
+ {
+ label = label + "_" + anns[i].sequenceRef.getName();
+ }
if (!list.contains(label))
{
list.addElement(label);
this.validate();
}
+ @Override
@SuppressWarnings("unchecked")
public void reset()
{
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (!adjusting)
});
}
+ @Override
public void valueChanged(boolean updateAllAnnotation)
{
if (slider.isEnabled())
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == thresholdValue)
}
- public Vector getAnnotationItems(boolean isSeqAssociated)
- {
- Vector list = new Vector();
- int index = 1;
- int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
- {
- if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
- {
- if (isSeqAssociated)
- {
- continue;
- }
- }
- else
- {
- enableSeqAss = true;
- }
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- {
- anmap[list.size()] = i;
- list.add(label);
-
- }
- else
- {
- if (!isSeqAssociated)
- {
- anmap[list.size()] = i;
- list.add(label + "_" + (index++));
- }
- }
- }
- this.annmap = new int[list.size()];
- System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
- return list;
- }
-
protected int getSelectedThresholdItem(int indexValue)
{
int selectedThresholdItem = -1;
import java.util.List;
import java.util.Vector;
+import org.jmol.util.Logger;
+
public class AppletJmol extends EmbmenuFrame implements
// StructureListener,
KeyListener, ActionListener, ItemListener
jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
+ "_jmol_", ap.av.applet.getDocumentBase(),
ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
+ Logger.setLogLevel(Logger.LEVEL_WARN);
} catch (Exception e)
{
System.err
import jalview.datamodel.SequenceNode;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.util.Format;
import jalview.util.MappingUtils;
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
- setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+ setColor(tree.getGroups().elementAt(i), col.brighter());
- Vector<SequenceNode> l = tree.findLeaves((SequenceNode) tree
+ Vector<SequenceNode> l = tree.findLeaves(tree
.getGroups().elementAt(i));
Vector<SequenceI> sequences = new Vector<SequenceI>();
if (av.getGlobalColourScheme() != null
&& av.getGlobalColourScheme().conservationApplied())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes());
+ Conservation c = new Conservation("Group", 3,
+ sg.getSequences(null), sg.getStartRes(), sg.getEndRes());
c.calculate();
c.verdict(false, av.getConsPercGaps());
.println("Jalview Version: " + codeVersion + codeInstallation);
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
- .getDefault(
-"PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+ .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
- .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
- "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
+ .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+ // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
if (jnlpVersion == null
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
+import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.PromptUserConfig;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
}
}
+ /*
+ * configure 'full' SO model if preferences say to,
+ * else use the default (SO Lite)
+ */
+ if (Cache.getDefault("USE_FULL_SO", false))
+ {
+ SequenceOntologyFactory.setInstance(new SequenceOntology());
+ }
+
if (!headless)
{
desktop = new Desktop();
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
- List<Integer> cs = csel.getSelected();
+ List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
csel.clear();
for (Integer selectedCol : cs)
{
import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.io.FastaFile;
import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
import jalview.util.MessageManager;
import java.util.ArrayList;
}
@Override
- public void finalize()
+ public void finalize() throws Throwable
{
if (getDataset() != null)
{
getDataset().removeAlignmentRef();
}
+ nullReferences();
+ super.finalize();
+ }
+
+ /**
+ * Defensively nulls out references in case this object is not garbage
+ * collected
+ */
+ void nullReferences()
+ {
dataset = null;
sequences = null;
groups = null;
}
/**
- * decrement the alignmentRefs counter by one and call finalize if it goes to
- * zero.
+ * decrement the alignmentRefs counter by one and null references if it goes
+ * to zero.
+ *
+ * @throws Throwable
*/
- private void removeAlignmentRef()
+ private void removeAlignmentRef() throws Throwable
{
if (--alignmentRefs == 0)
{
- finalize();
+ nullReferences();
}
}
private void resolveAndAddDatasetSeq(SequenceI currentSeq,
Set<SequenceI> seqs, boolean createDatasetSequence)
{
+ SequenceI alignedSeq = currentSeq;
if (currentSeq.getDatasetSequence() != null)
{
currentSeq = currentSeq.getDatasetSequence();
{
if (dbr.getMap() != null && dbr.getMap().getTo() != null)
{
+ if (dbr.getMap().getTo() == alignedSeq)
+ {
+ /*
+ * update mapping to be to the newly created dataset sequence
+ */
+ dbr.getMap().setTo(currentSeq);
+ }
if (dbr.getMap().getTo().getDatasetSequence() != null)
{
- throw new Error("Implementation error: Map.getTo() for dbref"
- + dbr + " is not a dataset sequence.");
- // TODO: if this happens, could also rewrite the reference to
- // point to new dataset sequence
+ throw new Error(
+ "Implementation error: Map.getTo() for dbref " + dbr
+ + " from " + curDs.getName()
+ + " is not a dataset sequence.");
}
// we recurse to add all forward references to dataset sequences via
// DBRefs/etc
return;
}
// try to avoid using SequenceI.equals at this stage, it will be expensive
- Set<SequenceI> seqs = new jalview.util.LinkedIdentityHashSet<SequenceI>();
+ Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
for (int i = 0; i < getHeight(); i++)
{
/*
* list of selected columns (ordered by selection order, not column order)
*/
- private List<Integer> order = new ArrayList<Integer>();
+ private List<Integer> order;
+
+ /*
+ * an unmodifiable view of the selected columns list
+ */
+ private List<Integer> _uorder;
/**
* bitfield for column selection - allows quick lookup
*/
- private BitSet selected = new BitSet();
+ private BitSet selected;
+
+ /**
+ * Constructor
+ */
+ IntList()
+ {
+ order = new ArrayList<Integer>();
+ _uorder = Collections.unmodifiableList(order);
+ selected = new BitSet();
+ }
+
+ /**
+ * Copy constructor
+ *
+ * @param other
+ */
+ IntList(IntList other)
+ {
+ this();
+ if (other != null)
+ {
+ int j = other.size();
+ for (int i = 0; i < j; i++)
+ {
+ add(other.elementAt(i));
+ }
+ }
+ }
/**
* adds a new column i to the selection - only if i is not already selected
*
* @param i
*/
- public void add(int i)
+ void add(int i)
{
if (!selected.get(i))
{
}
}
- public void clear()
+ void clear()
{
order.clear();
selected.clear();
}
- public void remove(int col)
+ void remove(int col)
{
Integer colInt = new Integer(col);
}
}
- public boolean contains(Integer colInt)
+ boolean contains(Integer colInt)
{
return selected.get(colInt);
}
- public boolean isEmpty()
+ boolean isEmpty()
{
return order.isEmpty();
}
- public List<Integer> getList()
+ /**
+ * Returns a read-only view of the selected columns list
+ *
+ * @return
+ */
+ List<Integer> getList()
{
- return order;
+ return _uorder;
}
- public int size()
+ int size()
{
return order.size();
}
* @param i
* @return
*/
- public int elementAt(int i)
+ int elementAt(int i)
{
return order.get(i);
}
* @param change
* - delta for shift
*/
- public void compensateForEdits(int start, int change)
+ void compensateForEdits(int start, int change)
{
BitSet mask = new BitSet();
for (int i = 0; i < order.size(); i++)
selected.or(mask);
}
- public boolean isSelected(int column)
+ boolean isSelected(int column)
{
return selected.get(column);
}
- public int getMaxColumn()
+ int getMaxColumn()
{
return selected.length() - 1;
}
- public int getMinColumn()
+ int getMinColumn()
{
return selected.get(0) ? 0 : selected.nextSetBit(0);
}
/**
* @return a series of selection intervals along the range
*/
- public List<int[]> getRanges()
+ List<int[]> getRanges()
{
List<int[]> rlist = new ArrayList<int[]>();
if (selected.isEmpty())
}
/**
- * Returns a list of selected columns. The list contains no duplicates but is
- * not necessarily ordered. It also may include columns hidden from the
- * current view. This returns a copy of the actual list, and changes to the
- * copy will not affect the selection.
+ * Returns a read-only view of the (possibly empty) list of selected columns
+ * <p>
+ * The list contains no duplicates but is not necessarily ordered. It also may
+ * include columns hidden from the current view. To modify (for example sort)
+ * the list, you should first make a copy.
+ * <p>
+ * The list is not thread-safe: iterating over it could result in
+ * ConcurrentModificationException if it is modified by another thread.
*/
public List<Integer> getSelected()
{
- return new ArrayList<Integer>(selection.getList());
+ return selection.getList();
}
/**
{
if (copy != null)
{
- if (copy.selection != null)
- {
- selection = new IntList();
- for (int i = 0, j = copy.selection.size(); i < j; i++)
- {
- selection.add(copy.selection.elementAt(i));
- }
- }
+ selection = new IntList(copy.selection);
if (copy.hiddenColumns != null)
{
hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
import java.util.Collections;
import java.util.Enumeration;
import java.util.Hashtable;
-import java.util.Map.Entry;
public class PDBEntry
{
*/
private static final String CHAIN_ID = "chain_code";
- Hashtable<String, Object> properties;
+ private Hashtable<String, Object> properties;
+
+ private static final int PDB_ID_LENGTH = 4;
private String file;
}
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
+ /**
+ * Answers true if obj is a PDBEntry with the same id and chain code (both
+ * ignoring case), file, type and properties
*/
@Override
public boolean equals(Object obj)
return true;
}
PDBEntry o = (PDBEntry) obj;
- return (type == o.type || (type != null && o.type != null && o.type
- .equals(type)))
- && (id == o.id || (id != null && o.id != null && o.id
- .equalsIgnoreCase(id)))
- && (properties == o.properties || (properties != null
- && o.properties != null && properties
- .equals(o.properties)));
+ /*
+ * note that chain code is stored as a property wrapped by a
+ * CaseInsensitiveString, so we are in effect doing a
+ * case-insensitive comparison of chain codes
+ */
+ boolean idMatches = id == o.id
+ || (id != null && id.equalsIgnoreCase(o.id));
+ boolean fileMatches = file == o.file
+ || (file != null && file.equals(o.file));
+ boolean typeMatches = type == o.type
+ || (type != null && type.equals(o.type));
+ if (idMatches && fileMatches && typeMatches)
+ {
+ return properties == o.properties
+ || (properties != null && properties.equals(o.properties));
+ }
+ return false;
}
/**
public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
String filePath)
{
+ init(pdbId, chain, type, filePath);
+ }
+
+ /**
+ * @param pdbId
+ * @param chain
+ * @param entryType
+ * @param filePath
+ */
+ void init(String pdbId, String chain, PDBEntry.Type entryType, String filePath)
+ {
this.id = pdbId;
- this.type = type == null ? null : type.toString();
+ this.type = entryType == null ? null : entryType.toString();
this.file = filePath;
setChainCode(chain);
}
}
}
+ /**
+ * Make a PDBEntry from a DBRefEntry. The accession code is used for the PDB
+ * id, but if it is 5 characters in length, the last character is removed and
+ * set as the chain code instead.
+ *
+ * @param dbr
+ */
+ public PDBEntry(DBRefEntry dbr)
+ {
+ if (!DBRefSource.PDB.equals(dbr.getSource()))
+ {
+ throw new IllegalArgumentException("Invalid source: "
+ + dbr.getSource());
+ }
+
+ String pdbId = dbr.getAccessionId();
+ String chainCode = null;
+ if (pdbId.length() == PDB_ID_LENGTH + 1)
+ {
+ char chain = pdbId.charAt(PDB_ID_LENGTH);
+ if (('a' <= chain && chain <= 'z') || ('A' <= chain && chain <= 'Z'))
+ {
+ pdbId = pdbId.substring(0, PDB_ID_LENGTH);
+ chainCode = String.valueOf(chain);
+ }
+ }
+ init(pdbId, chainCode, null, null);
+ }
+
public void setFile(String f)
{
this.file = f;
}
/**
- * update entry with details from another entry concerning the same PDB
- * ID/file spec.
+ * Answers true if this object is either equivalent to, or can be 'improved'
+ * by, the given entry.
+ * <p>
+ * If newEntry has the same id (ignoring case), and doesn't have a conflicting
+ * file spec or chain code, then update this entry from its file and/or chain
+ * code.
*
* @param newEntry
* @return true if modifications were made
*/
public boolean updateFrom(PDBEntry newEntry)
{
- boolean modified = false;
+ if (this.equals(newEntry))
+ {
+ return true;
+ }
+
+ String newId = newEntry.getId();
+ if (newId == null || getId() == null)
+ {
+ return false; // shouldn't happen
+ }
+
+ /*
+ * id has to match (ignoring case)
+ */
+ if (!getId().equalsIgnoreCase(newId))
+ {
+ return false;
+ }
+
+ /*
+ * Don't update if associated with different structure files
+ */
+ String newFile = newEntry.getFile();
+ if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+ {
+ return false;
+ }
- if (getFile() == null)
+ /*
+ * Don't update if associated with different chains (ignoring case)
+ */
+ String newChain = newEntry.getChainCode();
+ if (newChain != null && newChain.length() > 0 && getChainCode() != null
+ && getChainCode().length() > 0
+ && !getChainCode().equalsIgnoreCase(newChain))
{
- // update file and type of file
- modified = newEntry.getFile() != null;
- setFile(newEntry.getFile());
+ return false;
}
- if (newEntry.getType() != null && newEntry.getFile() != null
- && newEntry.getFile().equals(getFile()))
+
+ /*
+ * set file path if not already set
+ */
+ String newType = newEntry.getType();
+ if (getFile() == null && newFile != null)
+ {
+ setFile(newFile);
+ setType(newType);
+ }
+
+ /*
+ * set file type if new entry has it and we don't
+ * (for the case where file was not updated)
+ */
+ if (getType() == null && newType != null)
{
- setType(newEntry.getType());
+ setType(newType);
}
- if (getChainCode() == null
- || (getChainCode() != null && getChainCode().length() == 0 && newEntry
- .getChainCode() != null))
+
+ /*
+ * set chain if not already set (we excluded differing
+ * chains earlier) (ignoring case change only)
+ */
+ if (newChain != null && newChain.length() > 0
+ && !newChain.equalsIgnoreCase(getChainCode()))
{
- modified |= (getChainCode() == null || !newEntry.getChainCode()
- .equals(getChainCode()));
- setChainCode(newEntry.getChainCode());
+ setChainCode(newChain);
}
- if (newEntry.properties != null)
+
+ /*
+ * copy any new or modified properties
+ */
+ Enumeration<String> newProps = newEntry.getProperties();
+ while (newProps.hasMoreElements())
{
- for (Entry<String, Object> entry : newEntry.properties.entrySet())
+ /*
+ * copy properties unless value matches; this defends against changing
+ * the case of chain_code which is wrapped in a CaseInsensitiveString
+ */
+ String key = newProps.nextElement();
+ Object value = newEntry.getProperty(key);
+ if (!value.equals(getProperty(key)))
{
- if (!entry.getValue().equals(getProperty(entry.getKey())))
- {
- modified = true;
- }
- setProperty(entry.getKey(), entry.getValue());
+ setProperty(key, value);
}
}
- return modified;
+ return true;
}
}
import jalview.analysis.AlignSeq;
import jalview.api.DBRefEntryI;
+import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
}
@Override
- public void addPDBId(PDBEntry entry)
+ public boolean addPDBId(PDBEntry entry)
{
if (pdbIds == null)
{
pdbIds = new Vector<PDBEntry>();
+ pdbIds.add(entry);
+ return true;
}
- if (!updatedPDBEntry(pdbIds, entry))
- {
- pdbIds.addElement(entry);
- }
- }
- private static boolean updatedPDBEntry(List<PDBEntry> entries,
- PDBEntry newEntry)
- {
- for (PDBEntry xtant : entries)
+ for (PDBEntry pdbe : pdbIds)
{
- if (xtant.getFile() != null && newEntry.getFile() != null
- && !xtant.getFile().equals(newEntry.getFile()))
- {
- // different structure data, so leave alone.
- continue;
- }
- // loop through to check whether we can find a matching ID
-
- // either exact
- if (!xtant.getId().equals(newEntry.getId()))
+ if (pdbe.updateFrom(entry))
{
- /* TODO: support stemming to group PDB IDs.
- // or stemming, with exactly one alphanumeric character difference
- if (xtant.getId().length() < newEntry.getId().length())
- {
- if (!newEntry.getId().startsWith(xtant.getId()))
- {
- continue;
- }
- // newEntry may be chain specific PDBEntry
- // TODO: copy/update details from newEntry to xtant
- }
- else
- {
- if (!xtant.getId().startsWith(newEntry.getId()))
- {
- continue;
- }
- // xtant may be chain specific PDBEntry
- // TODO: copy/update missing details from newEntry
- }*/
- continue;
- }
- if (xtant.getChainCode() != null && xtant.getChainCode().length() > 0
- && newEntry.getChainCode() != null
- && !newEntry.getChainCode().equals(xtant.getChainCode()))
- {
- // don't overwrite - multiple chain mappings for a sequence yield
- // multiple PDBEntries
- // each with different chaincode
- continue;
+ return false;
}
-
- xtant.updateFrom(newEntry);
-
- return true;
}
- // if we got to the end of the loop, nothing was updated.
- return false;
+ pdbIds.addElement(entry);
+ return true;
}
/**
@Override
public void setDBRefs(DBRefEntry[] dbref)
{
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
+ {
+ datasetSequence.setDBRefs(dbref);
+ return;
+ }
dbrefs = dbref;
+ if (dbrefs != null)
+ {
+ DBRefUtils.ensurePrimaries(this);
+ }
}
@Override
@Override
public void addDBRef(DBRefEntry entry)
{
- // TODO add to dataset sequence instead if there is one?
+ if (datasetSequence != null)
+ {
+ datasetSequence.addDBRef(entry);
+ return;
+ }
+
if (dbrefs == null)
{
dbrefs = new DBRefEntry[0];
temp[temp.length - 1] = entry;
dbrefs = temp;
+
+ DBRefUtils.ensurePrimaries(this);
}
@Override
public void setDatasetSequence(SequenceI seq)
{
- // TODO check for circular reference before setting?
+ if (seq == this)
+ {
+ throw new IllegalArgumentException(
+ "Implementation Error: self reference passed to SequenceI.setDatasetSequence");
+ }
+ if (seq != null && seq.getDatasetSequence() != null)
+ {
+ throw new IllegalArgumentException(
+ "Implementation error: cascading dataset sequences are not allowed.");
+ }
datasetSequence = seq;
}
private long _seqhash = 0;
+ /**
+ * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
+ * true
+ */
@Override
public boolean isProtein()
{
if (_seqhash != sequence.hashCode())
{
_seqhash = sequence.hashCode();
- _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
+ _isNa = Comparison.isNucleotide(this);
}
return !_isNa;
};
{
return false;
}
- Vector newpdb = new Vector();
- for (int i = 0; i < dbrefs.length; i++)
+ boolean added = false;
+ for (DBRefEntry dbr : dbrefs)
{
- if (DBRefSource.PDB.equals(dbrefs[i].getSource()))
+ if (DBRefSource.PDB.equals(dbr.getSource()))
{
- PDBEntry pdbe = new PDBEntry();
- pdbe.setId(dbrefs[i].getAccessionId());
- if (pdbIds == null || pdbIds.size() == 0)
- {
- newpdb.addElement(pdbe);
- }
- else
- {
- Enumeration en = pdbIds.elements();
- boolean matched = false;
- while (!matched && en.hasMoreElements())
- {
- PDBEntry anentry = (PDBEntry) en.nextElement();
- if (anentry.getId().equals(pdbe.getId()))
- {
- matched = true;
- }
- }
- if (!matched)
- {
- newpdb.addElement(pdbe);
- }
- }
- }
- }
- if (newpdb.size() > 0)
- {
- Enumeration en = newpdb.elements();
- while (en.hasMoreElements())
- {
- addPDBId((PDBEntry) en.nextElement());
+ /*
+ * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the
+ * PDB id is not already present in a 'matching' PDBEntry
+ * Constructor parses out a chain code if appended to the accession id
+ * (a fudge used to 'store' the chain code in the DBRef)
+ */
+ PDBEntry pdbe = new PDBEntry(dbr);
+ added |= addPDBId(pdbe);
}
- return true;
}
- return false;
+ return added;
}
@Override
import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
import java.awt.Color;
import java.util.ArrayList;
if ((conservation != null)
|| (cs != null && cs.conservationApplied()))
{
- Conservation c = new Conservation(groupName,
- ResidueProperties.propHash, 3, sequences, startRes,
- endRes + 1);
+ Conservation c = new Conservation(groupName, 3, sequences,
+ startRes, endRes + 1);
c.calculate();
c.verdict(false, consPercGaps);
if (conservation != null)
public int[] findPositionMap();
/**
+ * Answers true if the sequence is composed of amino acid characters. Note
+ * that implementations may use heuristic methods which are not guaranteed to
+ * give the biologically 'right' answer.
*
- * @return true if sequence is composed of amino acid characters
+ * @return
*/
public boolean isProtein();
public Vector<PDBEntry> getAllPDBEntries();
/**
- * add entry to the *normalised* vector of PDBIds.
+ * Adds the entry to the *normalised* list of PDBIds.
*
- * If a PDBEntry is passed with an entry.getID() string, as one already in the
- * list, or one is added that appears to be the same but has a chain ID
+ * If a PDBEntry is passed with the same entry.getID() string as one already
+ * in the list, or one is added that appears to be the same but has a chain ID
* appended, then the existing PDBEntry will be updated with the new
- * attributes.
+ * attributes instead, unless the entries have distinct chain codes or
+ * associated structure files.
*
* @param entry
+ * @return true if the entry was added, false if updated
*/
- public void addPDBId(PDBEntry entry);
+ public boolean addPDBId(PDBEntry entry);
/**
* update the list of PDBEntrys to include any DBRefEntrys citing structural
public void setVamsasId(String id);
+ /**
+ * set the array of Database references for the sequence.
+ *
+ * @param dbs
+ * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
+ * set are not normalised.
+ */
+ @Deprecated
public void setDBRefs(DBRefEntry[] dbs);
public DBRefEntry[] getDBRefs();
*/
package jalview.datamodel.xdb.embl;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.ws.dbsources.Uniprot;
import java.io.FileReader;
import java.io.PrintWriter;
import java.io.Reader;
+import java.net.URL;
import java.util.Vector;
import org.exolab.castor.mapping.Mapping;
}
/**
- * Parse an EmblXML file into an EmblFile object
+ * Parse an Embl XML file into an EmblEntry object
*
* @param file
* @return parsed EmblXML or null if exceptions were raised
*/
- public static EmblFile getEmblFile(File file)
+ public static EmblEntry getEmblEntry(File file)
{
if (file == null)
{
}
try
{
- return EmblFile.getEmblFile(new FileReader(file));
+ return EmblFile.getEntry(new FileReader(file));
} catch (Exception e)
{
System.err.println("Exception whilst reading EMBLfile from " + file);
return null;
}
- public static EmblFile getEmblFile(Reader file)
+ /**
+ * Reads the XML response from file and unmarshals into a Java object
+ *
+ * @param fileReader
+ * @return
+ */
+ public static EmblEntry getEntry(Reader fileReader)
{
- EmblFile record = new EmblFile();
+ EmblEntry record = new EmblEntry();
try
{
// 1. Load the mapping information from the file
Mapping map = new Mapping(record.getClass().getClassLoader());
- java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
+ URL url = record.getClass().getResource("/embl_mapping.xml");
map.loadMapping(url);
// 2. Unmarshal the data
Unmarshaller unmar = new Unmarshaller(record);
try
{
- // uncomment to DEBUG EMBLFile reading
- if (jalview.bin.Cache.getDefault(jalview.bin.Cache.CASTORLOGLEVEL,
+ if (Cache.getDefault(Cache.CASTORLOGLEVEL,
"debug").equalsIgnoreCase("DEBUG"))
{
- unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
+ unmar.setDebug(Cache.log.isDebugEnabled());
+ // unmar.setDebug(true);// uncomment to debug unmarshalling
}
} catch (Exception e)
{
unmar.setIgnoreExtraAttributes(true);
unmar.setMapping(map);
unmar.setLogWriter(new PrintWriter(System.out));
- record = (EmblFile) unmar.unmarshal(file);
+ record = (EmblEntry) unmar.unmarshal(fileReader);
canonicaliseDbRefs(record);
} catch (Exception e)
* Change blank version to "0" in any DBRefEntry, to ensure consistent
* comparison with other DBRefEntry in Jalview
*
- * @param record
+ * @param entry
* @see Uniprot#getDbVersion
*/
- static void canonicaliseDbRefs(EmblFile record)
+ static void canonicaliseDbRefs(EmblEntry entry)
{
- for (EmblEntry entry : record.getEntries())
+ if (entry == null)
{
+ return;
+ }
+// for (EmblEntry entry : record.getEntries())
+// {
if (entry.getDbRefs() != null)
{
for (DBRefEntry dbref : entry.getDbRefs())
}
}
- if (entry.getFeatures() != null)
+ if (entry.getFeatures() != null)
{
for (EmblFeature feature : entry.getFeatures())
{
}
}
}
- }
+ // }
}
}
* fetch the gene sequence(s) with features and xrefs
*/
AlignmentI geneAlignment = super.getSequenceRecords(geneId);
-
+ if (geneAlignment == null)
+ {
+ continue;
+ }
if (geneAlignment.getHeight() == 1)
{
getTranscripts(geneAlignment, geneId);
* update these constants when Jalview has been checked / updated for
* changes to Ensembl REST API
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
+ * @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.6";
- private static final String LATEST_ENSEMBL_REST_VERSION = "4.6";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "4.7";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
URL url = getUrl(ids);
BufferedReader reader = getHttpResponse(url, ids);
+ if (reader == null)
+ {
+ // request failed
+ return null;
+ }
FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
return fp;
}
writePostBody(connection, ids);
}
- InputStream response = connection.getInputStream();
int responseCode = connection.getResponseCode();
if (responseCode != 200)
* note: a GET request for an invalid id returns an error code e.g. 415
* but POST request returns 200 and an empty Fasta response
*/
- throw new IOException(
- "Response code was not 200. Detected response was "
- + responseCode);
+ System.err.println("Response code " + responseCode + " for " + url);
+ return null;
}
+ // get content
+ InputStream response = connection.getInputStream();
+
// System.out.println(getClass().getName() + " took "
// + (System.currentTimeMillis() - now) + "ms to fetch");
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Dna;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+ " chunks. Unexpected problem (" + r.getLocalizedMessage()
+ ")";
System.err.println(msg);
+ r.printStackTrace();
break;
}
}
DBRefEntry dbr = new DBRefEntry(getDbSource(),
getEnsemblDataVersion(), proteinSeq.getName(), map);
querySeq.getDatasetSequence().addDBRef(dbr);
+ DBRefEntry[] uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
+ new String[] { DBRefSource.UNIPROT });
+ DBRefEntry[] upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
+ new String[] { DBRefSource.UNIPROT });
+ if (uprots != null)
+ {
+ for (DBRefEntry up : uprots)
+ {
+ // locate local uniprot ref and map
+ List<DBRefEntry> upx = DBRefUtils.searchRefs(upxrefs, up.getAccessionId());
+ DBRefEntry upxref;
+ if (upx.size() != 0)
+ {
+ upxref = upx.get(0);
+
+ if (upx.size() > 1)
+ {
+ Cache.log
+ .warn("Implementation issue - multiple uniprot acc on product sequence.");
+ }
+ }
+ else
+ {
+ upxref = new DBRefEntry(DBRefSource.UNIPROT,
+ getEnsemblDataVersion(), up.getAccessionId());
+ }
+
+ Mapping newMap = new Mapping(ds, mapList);
+ upxref.setVersion(getEnsemblDataVersion());
+ upxref.setMap(newMap);
+ if (upx.size() == 0)
+ {
+ // add the new uniprot ref
+ querySeq.getDatasetSequence().addDBRef(upxref);
+ }
+
+ }
+ }
/*
* copy exon features to protein, compute peptide variants from dna
throw new JalviewException("ENSEMBL Rest API not available.");
}
FileParse fp = getSequenceReader(ids);
+ if (fp == null)
+ {
+ return alignment;
+ }
+
FastaFile fr = new FastaFile(fp);
if (fr.hasWarningMessage())
{
}
if (selectioncom.length() > 0)
{
- System.out.println("Select regions:\n" + selectioncom.toString());
+ // System.out.println("Select regions:\n" + selectioncom.toString());
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
// selcom.append("; ribbons; ");
String cmdString = command.toString();
- System.out.println("Superimpose command(s):\n" + cmdString);
+ // System.out.println("Superimpose command(s):\n" + cmdString);
evalStateCommand(cmdString);
}
{
selectioncom.setLength(selectioncom.length() - 1);
}
- System.out.println("Select regions:\n" + selectioncom.toString());
+ // System.out.println("Select regions:\n" + selectioncom.toString());
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
// evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
+import jalview.util.Format;
import jalview.util.MessageManager;
import java.io.IOException;
{
Viewer viewer = null;
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, String inFile, String type)
+ public JmolParser(String inFile, String type)
throws IOException
{
super(inFile, type);
}
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, FileParse fp) throws IOException
+ public JmolParser(FileParse fp) throws IOException
{
super(fp);
}
{
try
{
+ /*
+ * params -o (output to sysout) -i (no info logging, less verbose)
+ * -n (nodisplay) -x (exit when finished)
+ * see http://wiki.jmol.org/index.php/Jmol_Application
+ */
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
- null, "-x -o -n", this);
+ null, "-x -o -n -i", this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer.setBooleanProperty("defaultStructureDSSP", true);
} catch (ClassCastException x)
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
- curAtom.resNumIns = ("" + curAtom.resNumber + curAtom.insCode)
- .trim();
+ String fmt = new Format("%4i").form(curAtom.resNumber);
+ curAtom.resNumIns = (fmt + curAtom.insCode);
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
// significantAtoms.add(curAtom);
*/
protected void loadOntologyZipFile(String ontologyFile)
{
+ long now = System.currentTimeMillis();
ZipInputStream zipStream = null;
try
{
String zipFile = ontologyFile + ".zip";
- System.out.println("Loading Sequence Ontology from " + zipFile);
InputStream inStream = this.getClass().getResourceAsStream(
"/" + zipFile);
zipStream = new ZipInputStream(new BufferedInputStream(inStream));
loadOboFile(zipStream);
}
}
+ long elapsed = System.currentTimeMillis() - now;
+ System.out.println("Loaded Sequence Ontology from " + zipFile + " ("
+ + elapsed + "ms)");
} catch (Exception e)
{
e.printStackTrace();
case 502:
case 504:
case 505:
- message = MessageManager.getString("exception.fts_server_error");
+ message = MessageManager.formatMessage("exception.fts_server_error",
+ service);
break;
case 503:
message = MessageManager.getString("exception.service_not_available");
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
import java.awt.event.KeyAdapter;
protected JInternalFrame mainFrame = new JInternalFrame(
getFTSFrameTitle());
- protected IProgressIndicator progressIdicator;
+ protected IProgressIndicator progressIndicator;
protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<FTSDataColumnI>();
try
{
jbInit();
+ mainFrame.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ txt_search.requestFocusInWindow();
+ }
+ });
mainFrame.invalidate();
mainFrame.pack();
} catch (Exception e)
protected void btn_back_ActionPerformed()
{
closeAction();
- new SequenceFetcher(progressIdicator);
+ new SequenceFetcher(progressIndicator);
}
protected void disableActionButtons()
super();
pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
this.seqFetcher = seqFetcher;
- this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+ this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
.getProgressIndicator();
}
pageLimit = UniProtFTSRestClient.getInstance()
.getDefaultResponsePageSize();
this.seqFetcher = seqFetcher;
- this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+ this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
.getProgressIndicator();
}
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.getColumnSelection() != null
- && viewport.getColumnSelection().getSelected() != null && viewport
- .getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns()
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
hideSelSequences_actionPerformed(null);
hide = true;
}
- else if (!(toggleCols && viewport.getColumnSelection().getSelected()
- .size() > 0))
+ else if (!(toggleCols && viewport.hasSelectedColumns()))
{
showAllSeqs_actionPerformed(null);
}
if (toggleCols)
{
- if (viewport.getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns())
{
hideSelColumns_actionPerformed(null);
if (!toggleSeqs)
* @param align
* DOCUMENT ME!
*/
+ @Override
public void setAlignment(AlignmentI align)
{
replaceMappings(align);
- this.alignment = align;
+ super.setAlignment(align);
}
/**
*/
private boolean dontScrollComplement;
+ private PropertyChangeListener propertyChangeListener;
+
/**
* Creates a new AlignmentPanel object.
*
vscroll.addAdjustmentListener(this);
final AlignmentPanel ap = this;
- av.addPropertyChangeListener(new PropertyChangeListener()
+ propertyChangeListener = new PropertyChangeListener()
{
@Override
public void propertyChange(PropertyChangeEvent evt)
alignmentChanged();
}
}
- });
+ };
+ av.addPropertyChangeListener(propertyChangeListener);
fontChanged();
adjustAnnotationHeight();
updateLayout();
PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
PaintRefresher.RemoveComponent(this);
+
+ /*
+ * try to ensure references are nulled
+ */
+ if (annotationPanel != null)
+ {
+ annotationPanel.dispose();
+ }
+
if (av != null)
{
+ av.removePropertyChangeListener(propertyChangeListener);
jalview.structure.StructureSelectionManager ssm = av
.getStructureSelectionManager();
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeCommandListener(av);
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeSelectionListener(getSeqPanel());
- av.setAlignment(null);
+ av.dispose();
av = null;
}
else
@Override
public void actionPerformed(ActionEvent e)
{
- ok_actionPerformed(e);
+ ok_actionPerformed();
}
});
cancel.setOpaque(false);
@Override
public void actionPerformed(ActionEvent e)
{
- cancel_actionPerformed(e);
+ cancel_actionPerformed();
}
});
defColours.setOpaque(false);
@Override
public void actionPerformed(ActionEvent arg0)
{
- resetColours_actionPerformed(arg0);
+ resetColours_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- annotations_actionPerformed(e);
+ annotations_actionPerformed();
}
});
getThreshold().addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- threshold_actionPerformed(e);
+ threshold_actionPerformed();
}
});
thresholdValue.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- thresholdValue_actionPerformed(e);
+ thresholdValue_actionPerformed();
}
});
slider.setPaintLabels(false);
@Override
public void actionPerformed(ActionEvent e)
{
- currentColours_actionPerformed(e);
+ currentColours_actionPerformed();
}
});
thresholdIsMin.setBackground(Color.white);
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- thresholdIsMin_actionPerformed(actionEvent);
+ thresholdIsMin_actionPerformed();
}
});
seqAssociated.setBackground(Color.white);
@Override
public void actionPerformed(ActionEvent arg0)
{
- seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
+ seqAssociated_actionPerformed(annotations);
}
});
this.validate();
}
- protected void resetColours_actionPerformed(ActionEvent arg0)
+ protected void resetColours_actionPerformed()
{
setDefaultMinMax();
updateView();
updateView();
}
+ @Override
public void reset()
{
av.setGlobalColourScheme(oldcs);
}
}
+ @Override
public void valueChanged(boolean updateAllAnnotation)
{
if (slider.isEnabled())
this.threshold = threshold;
}
- public void currentColours_actionPerformed(ActionEvent e)
+ public void currentColours_actionPerformed()
{
if (currentColours.isSelected())
{
@Override
public void actionPerformed(ActionEvent e)
{
- ok_actionPerformed(e);
+ ok_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- cancel_actionPerformed(e);
+ cancel_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- threshold_actionPerformed(e);
+ threshold_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- thresholdValue_actionPerformed(e);
+ thresholdValue_actionPerformed();
}
});
String defaultTtip = MessageManager
.getString("info.change_threshold_mode_to_enable");
- String threshold = getThreshold().getSelectedItem().toString();
- if (threshold.equalsIgnoreCase("No Threshold"))
+ String thresh = getThreshold().getSelectedItem().toString();
+ if (thresh.equalsIgnoreCase("No Threshold"))
{
thresholdValue.setToolTipText(defaultTtip);
slider.setToolTipText(defaultTtip);
}
}
+ @Override
public void reset()
{
if (this.getOldColumnSelection() != null)
}
+ @Override
public void valueChanged(boolean updateAllAnnotation)
{
if (slider.isEnabled())
AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
+ boolean fullRepaint = false;
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
ap.av.getAlignment().addAnnotation(newAnnotation);
ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+ fullRepaint = true;
}
else if (evt.getActionCommand().equals(EDITNAME))
{
+ String name = aa[selectedRow].label;
editLabelDescription(aa[selectedRow]);
- repaint();
+ if (!name.equalsIgnoreCase(aa[selectedRow].label))
+ {
+ fullRepaint = true;
+ }
}
else if (evt.getActionCommand().equals(HIDE))
{
{
ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
+ fullRepaint = true;
}
else if (evt.getActionCommand().equals(SHOWALL))
{
aa[i].visible = true;
}
}
+ fullRepaint = true;
}
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- refresh();
+ refresh(fullRepaint);
}
/**
* Redraw sensibly.
+ *
+ * @adjustHeight if true, try to recalculate panel height for visible
+ * annotations
*/
- protected void refresh()
+ protected void refresh(boolean adjustHeight)
{
- ap.validateAnnotationDimensions(false);
+ ap.validateAnnotationDimensions(adjustHeight);
ap.addNotify();
- ap.repaint();
+ if (adjustHeight)
+ {
+ // sort, repaint, update overview
+ ap.paintAlignment(true);
+ }
+ else
+ {
+ // lightweight repaint
+ ap.repaint();
+ }
}
/**
*/
boolean editLabelDescription(AlignmentAnnotation annotation)
{
+ // TODO i18n
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Name ",
"Annotation Description ", "Edit Annotation Name/Description",
// ann.visible = false;
// }
// }
- refresh();
+ refresh(true);
}
});
pop.add(hideType);
{
ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
+ ap.alignmentChanged();
}
});
pop.add(cbmi);
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.awt.image.BufferedImage;
+import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
boolean mouseDragging = false;
- boolean MAC = false;
-
// for editing cursor
int cursorX = 0;
*/
public AnnotationPanel(AlignmentPanel ap)
{
-
- MAC = jalview.util.Platform.isAMac();
-
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
- // TODO: refactor and save av.getColumnSelection for efficiency
- List<Integer> selected = viscols.getSelected();
+
+ /*
+ * the selection list (read-only view) is in selection order, not
+ * column order; make a copy so we can sort it
+ */
+ List<Integer> selected = new ArrayList<Integer>(viscols.getSelected());
Collections.sort(selected);
for (int index : selected)
{
return null;
}
}
+
+ /**
+ * Try to ensure any references held are nulled
+ */
+ public void dispose()
+ {
+ av = null;
+ ap = null;
+ image = null;
+ fadedImage = null;
+ gg = null;
+ _mwl = null;
+
+ /*
+ * I created the renderer so I will dispose of it
+ */
+ if (renderer != null)
+ {
+ renderer.dispose();
+ }
+ }
}
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
-import java.awt.event.ActionEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Vector;
protected boolean enableSeqAss = false;
- private jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ private AlignmentAnnotation currentAnnotation;
protected boolean adjusting = false;
enableSeqAss = true;
}
String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ // add associated sequence ID if available
+ if (!isSeqAssociated
+ && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+ {
+ label = label
+ + "_"
+ + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
+ .getName();
+ }
+ // make label unique
if (!list.contains(label))
{
anmap[list.size()] = i;
list.add(label);
-
}
else
{
seqAssociated.setEnabled(enableSeqAss);
}
- public void ok_actionPerformed(ActionEvent e)
+ public void ok_actionPerformed()
{
try
{
}
}
- public void cancel_actionPerformed(ActionEvent e)
+ public void cancel_actionPerformed()
{
reset();
ap.paintAlignment(true);
}
}
- public void thresholdCheck_actionPerformed(ActionEvent e)
+ public void thresholdCheck_actionPerformed()
{
updateView();
}
- public void annotations_actionPerformed(ActionEvent e)
+ public void annotations_actionPerformed()
{
updateView();
}
- public void threshold_actionPerformed(ActionEvent e)
+ public void threshold_actionPerformed()
{
updateView();
}
- public void thresholdValue_actionPerformed(ActionEvent e)
+ public void thresholdValue_actionPerformed()
{
try
{
}
}
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ public void thresholdIsMin_actionPerformed()
{
updateView();
}
.getString("label.threshold_feature_below_threshold"));
}
- protected void seqAssociated_actionPerformed(ActionEvent arg0,
- JComboBox<String> annotations, JCheckBox seqAssociated)
+ protected void seqAssociated_actionPerformed(JComboBox<String> annotations)
{
adjusting = true;
String cursel = (String) annotations.getSelectedItem();
}
protected boolean colorAlignmContaining(
- AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
+ AlignmentAnnotation currentAnn, int selectedThresholdOption)
{
AnnotationColourGradient acg = null;
if (currentColours.isSelected())
{
- acg = new AnnotationColourGradient(currentAnnotation,
- av.getGlobalColourScheme(), selectedThresholdItem);
+ acg = new AnnotationColourGradient(currentAnn,
+ av.getGlobalColourScheme(), selectedThresholdOption);
}
else
{
- acg = new AnnotationColourGradient(currentAnnotation,
+ acg = new AnnotationColourGradient(currentAnn,
minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdItem);
+ selectedThresholdOption);
}
acg.setSeqAssociated(seqAssociated.isSelected());
- if (currentAnnotation.graphMin == 0f
- && currentAnnotation.graphMax == 0f)
+ if (currentAnn.graphMin == 0f
+ && currentAnn.graphMax == 0f)
{
acg.setPredefinedColours(true);
}
if (currentColours.isSelected())
{
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- selectedThresholdItem);
+ sg.cs = new AnnotationColourGradient(currentAnn, sg.cs,
+ selectedThresholdOption);
((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
.isSelected());
}
else
{
- sg.cs = new AnnotationColourGradient(currentAnnotation,
+ sg.cs = new AnnotationColourGradient(currentAnn,
minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdItem);
+ selectedThresholdOption);
((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
.isSelected());
}
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
import java.awt.BorderLayout;
import java.awt.Color;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
import javax.swing.event.MenuEvent;
public class AppJmol extends StructureViewerBase
{
+ private static final String SPACE = " ";
+
+ private static final String BACKSLASH = "\"";
+
AppJmolBinding jmb;
JPanel scriptWindow;
scriptWindow.setVisible(false);
}
- jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
- null);
+ /*
+ * -i for no info logging (less verbose)
+ */
+ jmb.allocateViewer(renderPanel, true, "", null, null, "-i",
+ scriptWindow, null);
// jmb.newJmolPopup("Jmol");
if (command == null)
{
public void run()
{
_started = true;
+ try
+ {
+ List<String> files = fetchPdbFiles();
+ if (files.size() > 0)
+ {
+ showFilesInViewer(files);
+ }
+ } finally
+ {
+ _started = false;
+ worker = null;
+ }
+ }
+
+ /**
+ * Either adds the given files to a structure viewer or opens a new viewer to
+ * show them
+ *
+ * @param files
+ * list of absolute paths to structure files
+ */
+ void showFilesInViewer(List<String> files)
+ {
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
+ {
+ fileList.append(SPACE).append(BACKSLASH).append(Platform.escapeString(s))
+ .append(BACKSLASH);
+ }
+ String filesString = fileList.toString();
+
+ if (!addingStructures)
+ {
+ try
+ {
+ initJmol("load FILES " + filesString);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
+ }
+ else
+ {
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(filesString);
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ lastnotify = jmb.getLoadNotifiesHandled();
+
+ try
+ {
+ jmb.evalStateCommand(command);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning(
+ "When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ }
+
+ // need to wait around until script has finished
+ int waitMax = 5000; // give up after 5 seconds
+ int waitFor = 35;
+ int waitTotal = 0;
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+ .getPdbFile().length == files.size()))
+ {
+ try
+ {
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(waitFor);
+ waitTotal += waitFor;
+ } catch (Exception e)
+ {
+ }
+ if (waitTotal > waitMax)
+ {
+ System.err.println("Timed out waiting for Jmol to load files");
+ break;
+ }
+ }
+
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+ {
+ alignAddedStructures();
+ }
+ addingStructures = false;
+ }
+
+ /**
+ * Queues a thread to align structures with Jalview alignments
+ */
+ void alignAddedStructures()
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (jmb.viewer.isScriptExecuting())
+ {
+ SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ return;
+ }
+ else
+ {
+ alignStructs_withAllAlignPanels();
+ }
+ }
+ });
+ alignAddedStructures = false;
+ }
+
+ /**
+ * Retrieves and saves as file any modelled PDB entries for which we do not
+ * already have a file saved. Returns a list of absolute paths to structure
+ * files which were either retrieved, or already stored but not modelled in
+ * the structure viewer (i.e. files to add to the viewer display).
+ *
+ * @return
+ */
+ List<String> fetchPdbFiles()
+ {
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
+
+ List<String> files = new ArrayList<String>();
String pdbid = "";
- // todo - record which pdbids were successfuly imported.
- StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
try
{
- String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+ String[] filesInViewer = jmb.getPdbFile();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+ Pdb pdbclient = new Pdb();
for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
String file = jmb.getPdbEntry(pi).getFile();
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
- }
- if (progressBar != null)
+ errormsgs.append("'").append(pdbid).append("'");
+ } finally
{
- progressBar.setProgressBar(
- MessageManager.getString("label.state_completed"), hdl);
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"),
+ hdl);
+ }
}
if (pdbseq != null)
{
file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
.elementAt(0).getFile()).getAbsolutePath();
jmb.getPdbEntry(pi).setFile(file);
-
- files.append(" \"" + Platform.escapeString(file) + "\"");
+ files.add(file);
}
else
{
- errormsgs.append("'" + pdbid + "' ");
+ errormsgs.append("'").append(pdbid).append("' ");
}
}
else
{
- if (curfiles != null && curfiles.length > 0)
+ if (filesInViewer != null && filesInViewer.length > 0)
{
addingStructures = true; // already files loaded.
- for (int c = 0; c < curfiles.length; c++)
+ for (int c = 0; c < filesInViewer.length; c++)
{
- if (curfiles[c].equals(file))
+ if (filesInViewer[c].equals(file))
{
file = null;
break;
}
if (file != null)
{
- files.append(" \"" + Platform.escapeString(file) + "\"");
+ files.add(file);
}
}
}
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
- + "'");
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
}
if (errormsgs.length() > 0)
{
-
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
new String[] { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
-
- }
- long lastnotify = jmb.getLoadNotifiesHandled();
- if (files.length() > 0)
- {
- if (!addingStructures)
- {
-
- try
- {
- initJmol("load FILES " + files.toString());
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + files);
- } catch (Exception ex)
- {
- Cache.log.error("Couldn't open Jmol viewer!", ex);
- }
- }
- else
- {
- StringBuffer cmd = new StringBuffer();
- cmd.append("loadingJalviewdata=true\nload APPEND ");
- cmd.append(files.toString());
- cmd.append("\nloadingJalviewdata=null");
- final String command = cmd.toString();
- cmd = null;
- lastnotify = jmb.getLoadNotifiesHandled();
-
- try
- {
- jmb.evalStateCommand(command);
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning(
- "When trying to add structures to the Jmol viewer!",
- oomerror);
- Cache.log.debug("File locations are " + files);
- } catch (Exception ex)
- {
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);
- }
- }
-
- // need to wait around until script has finished
- while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
- .getPdbFile().length != jmb.getPdbCount()))
- {
- try
- {
- Cache.log.debug("Waiting around for jmb notify.");
- Thread.sleep(35);
- } catch (Exception e)
- {
- }
- }
-
- // refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.updateColours(ap);
- }
- // do superposition if asked to
- if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- if (jmb.viewer.isScriptExecuting())
- {
- javax.swing.SwingUtilities.invokeLater(this);
- try
- {
- Thread.sleep(5);
- } catch (InterruptedException q)
- {
- }
- ;
- return;
- }
- else
- {
- alignStructs_withAllAlignPanels();
- }
- }
- });
- alignAddedStructures = false;
- }
- addingStructures = false;
-
}
- _started = false;
- worker = null;
+ return files;
}
@Override
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
-import java.beans.PropertyVetoException;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileOutputStream;
import javax.swing.SwingUtilities;
import javax.swing.event.HyperlinkEvent;
import javax.swing.event.HyperlinkEvent.EventType;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
* ((openFrameCount - 1) % 10) + yOffset);
}
+ /*
+ * add an entry for the new frame in the Window menu
+ * (and remove it when the frame is closed)
+ */
final JMenuItem menuItem = new JMenuItem(title);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ frame.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameActivated(
- javax.swing.event.InternalFrameEvent evt)
+ public void internalFrameActivated(InternalFrameEvent evt)
{
JInternalFrame itf = desktop.getSelectedFrame();
if (itf != null)
{
itf.requestFocus();
}
-
}
@Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ public void internalFrameClosed(InternalFrameEvent evt)
{
PaintRefresher.RemoveComponent(frame);
{
openFrameCount--;
}
+
+ /*
+ * ensure no reference to alignFrame retained by menu item listener
+ */
+ if (menuItem.getActionListeners().length > 0)
+ {
+ menuItem.removeActionListener(menuItem.getActionListeners()[0]);
+ }
windowMenu.remove(menuItem);
JInternalFrame itf = desktop.getSelectedFrame();
if (itf != null)
{
itf.requestFocus();
+ if (itf instanceof AlignFrame)
+ {
+ Jalview.setCurrentAlignFrame((AlignFrame) itf);
+ }
}
System.gc();
};
}
}
});
- menuItem.addMouseListener(new MouseListener()
- {
-
- @Override
- public void mouseReleased(MouseEvent e)
- {
- }
-
- @Override
- public void mousePressed(MouseEvent e)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- try
- {
- frame.setSelected(false);
- } catch (PropertyVetoException e1)
- {
- }
- }
-
- @Override
- public void mouseEntered(MouseEvent e)
- {
- try
- {
- frame.setSelected(true);
- } catch (PropertyVetoException e1)
- {
- }
- }
-
- @Override
- public void mouseClicked(MouseEvent e)
- {
-
- }
- });
windowMenu.add(menuItem);
@Override
public void closeAll_actionPerformed(ActionEvent e)
{
+ // TODO show a progress bar while closing?
JInternalFrame[] frames = desktop.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
{
}
}
+ Jalview.setCurrentAlignFrame(null);
System.out.println("ALL CLOSED");
if (v_client != null)
{
{
ssm.resetAll();
}
+ System.gc();
}
@Override
protected void okPressed()
{
_setSelectionState();
- closeDialog();
}
@Override
*/
package jalview.gui;
+import jalview.analysis.Conservation;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
import jalview.api.structures.JalviewStructureDisplayI;
}
if (jGroup.getConsThreshold() != 0)
{
- jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All", ResidueProperties.propHash, 3,
+ Conservation c = new Conservation("All", 3,
sg.getSequences(null), 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
*/
package jalview.gui;
+import jalview.analysis.Conservation;
import jalview.binding.Annotation;
import jalview.binding.AnnotationElement;
import jalview.binding.Features;
import jalview.datamodel.PDBEntry;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
if (groups[i].getConsThreshold() != 0)
{
- jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All", ResidueProperties.propHash, 3,
+ Conservation c = new Conservation("All", 3,
sg.getSequences(null), 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
if (conservationMenuItem.isSelected())
{
// JBPNote: Conservation name shouldn't be i18n translated
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(ap.av
- .getHiddenRepSequences()), sg.getStartRes(),
+ Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
+ .getHiddenRepSequences()), sg.getStartRes(),
sg.getEndRes() + 1);
c.calculate();
public class StructureChooser extends GStructureChooser implements
IProgressIndicator
{
- private boolean structuresDiscovered = false;
-
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
+ // ensure a filter option is in force for search
+ populateFilterComboBox(true);
Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
.getString("status.searching_for_pdb_structures"),
startTime);
fetchStructuresMetaData();
- populateFilterComboBox();
+ // revise filter options if no results were found
+ populateFilterComboBox(isStructuresDiscovered());
updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(500);
pdbRequest.setFieldToSearchBy("(");
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
+ !chk_invertFilter.isSelected());
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq);
getResultTable().setModel(
FTSRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
- structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
* Populates the filter combo-box options dynamically depending on discovered
* structures
*/
- @Override
- protected void populateFilterComboBox()
+ protected void populateFilterComboBox(boolean haveData)
{
- if (isStructuresDiscovered())
+ /*
+ * temporarily suspend the change listener behaviour
+ */
+ cmb_filterOption.removeItemListener(this);
+
+ cmb_filterOption.removeAllItems();
+ if (haveData)
{
cmb_filterOption.addItem(new FilterOption("Best Quality",
"overall_quality", VIEWS_FILTER));
VIEWS_FROM_FILE));
cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
VIEWS_LOCAL_PDB));
+
+ cmb_filterOption.addItemListener(this);
}
/**
* Updates the displayed view based on the selected filter option
*/
- @Override
protected void updateCurrentView()
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
{
final long progressSessionId = System.currentTimeMillis();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ final int preferredHeight = pnl_filter.getHeight();
ssm.setProgressIndicator(this);
ssm.setProgressSessionId(progressSessionId);
new Thread(new Runnable()
@Override
public void run()
{
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER)
- {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
int pdbIdColIndex = getResultTable().getColumn("PDB Id")
.getModelIndex();
int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
- .getModelIndex();
+ .getModelIndex();
int[] selectedRows = getResultTable().getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
String pdbIdStr = getResultTable().getValueAt(row,
- pdbIdColIndex)
- .toString();
+ pdbIdColIndex).toString();
SequenceI selectedSeq = (SequenceI) getResultTable()
- .getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
+ .getValueAt(row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
pdbEntry = getFindEntry(pdbIdStr,
selectedSeq.getAllPDBEntries());
}
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
- }
- pdbEntriesToView[count++] = pdbEntry;
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
- }
- else if (currentView == VIEWS_LOCAL_PDB)
- {
- int[] selectedRows = tbl_local_pdb.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
+ }
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
- .getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
- pdbEntriesToView[count++] = pdbEntry;
- SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
+ int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+ .getModelIndex();
+ ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
+ PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+ pdbIdColIndex);
+ pdbEntriesToView[count++] = pdbEntry;
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
+ row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
- String pdbIdStr = txt_search.getText();
- PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
if (pdbIdStr.split(":").length > 1)
{
pdbEntry.setId(pdbIdStr.split(":")[0]);
{
pdbEntry.setId(pdbIdStr);
}
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
- }
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ }
- PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[] { selectedSequence });
- }
- else if (currentView == VIEWS_FROM_FILE)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- jalview.io.AppletFormatAdapter.FILE,
- selectedSequence, true, Desktop.instance);
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq(selectedPdbFileName,
+ jalview.io.AppletFormatAdapter.FILE,
+ selectedSequence, true, Desktop.instance);
launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
new SequenceI[] { selectedSequence });
- }
- closeAction();
+ }
+ closeAction(preferredHeight);
}
}).start();
}
if (SiftsSettings.isMapWithSifts())
{
- ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
int p = 0;
// TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
// real PDB ID. For moment, we can also safely do this if there is already
{
seqWithoutSrcDBRef[x++] = fSeq;
}
- new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+ dbRefFetcher.fetchDBRefs(true);
}
}
if (pdbEntriesToView.length > 1)
public boolean isStructuresDiscovered()
{
- return structuresDiscovered;
- }
-
- public void setStructuresDiscovered(boolean structuresDiscovered)
- {
- this.structuresDiscovered = structuresDiscovered;
+ return discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty();
}
public Collection<FTSData> getDiscoveredStructuresSet()
import jalview.datamodel.SequenceNode;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
import jalview.util.Format;
if (aps[a].av.getGlobalColourScheme() != null
&& aps[a].av.getGlobalColourScheme().conservationApplied())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes());
-
+ Conservation c = new Conservation("Group", 3,
+ sg.getSequences(null), sg.getStartRes(), sg.getEndRes());
c.calculate();
c.verdict(false, aps[a].av.getConsPercGaps());
sg.cs.setConservation(c);
Thread udthread = new Thread(new Runnable()
{
+ @Override
public void run()
{
Cache.log.info("Jalview updating to the Vamsas Session.");
final VamsasApplication client = this;
vclient.addDocumentUpdateHandler(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
Cache.log.debug("Dealing with document update event.");
uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE,
new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (client.promptUser)
{
String last = null;
+ @Override
public void handleMessage(Message message)
{
if (vobj2jv == null)
selecter = new SelectionListener()
{
+ @Override
public void selection(SequenceGroup seqsel,
ColumnSelection colsel, SelectionSource source)
{
{
// gather selected columns outwith the sequence positions
// too
- for (Object obj : colsel.getSelected())
+ for (Integer ival : colsel.getSelected())
{
- int ival = ((Integer) obj).intValue();
Pos p = new Pos();
- p.setI(ival + 1);
+ p.setI(ival.intValue() + 1);
range.addPos(p);
}
}
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import java.io.BufferedReader;
else if (key.equalsIgnoreCase("consThreshold"))
{
sg.cs.setConservationInc(Integer.parseInt(value));
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes() + 1);
+ Conservation c = new Conservation("Group", 3,
+ sg.getSequences(null), sg.getStartRes(),
+ sg.getEndRes() + 1);
c.calculate();
c.verdict(false, 25); // TODO: refer to conservation percent threshold
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.PDBEntry.Type;
+import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile,
- type);
+ alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
}
else
{
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+ alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
((StructureFile) alignFile).setDbRefType(format);
}
else if (format.equals("STH"))
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
}
else
{
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
((StructureFile) alignFile).setDbRefType(Type.MMCIF);
}
else if (format.equals("STH"))
public class PDBFeatureSettings extends FeatureSettingsAdapter
{
+ // TODO find one central place to define feature names
+ private static final String FEATURE_INSERTION = "INSERTION";
- public static final String FEATURE_INSERTION = "INSERTION";
-
- public static final String FEATURE_RES_NUM = "RESNUM";
+ private static final String FEATURE_RES_NUM = "RESNUM";
@Override
public boolean isFeatureDisplayed(String type)
Class cl = Class.forName("jalview.ext.jmol.JmolParser");
if (cl != null)
{
- final Constructor constructor = cl.getConstructor(new Class[] {
- boolean.class, boolean.class, boolean.class, FileParse.class });
- final Object[] args = new Object[] { visibleChainAnnotation,
- predictSecondaryStructure, externalSecondaryStructure,
- new FileParse(getDataName(), type) };
+ final Constructor constructor = cl
+ .getConstructor(new Class[] { FileParse.class });
+ final Object[] args = new Object[] { new FileParse(getDataName(),
+ type) };
StructureImportSettings.setShowSeqFeatures(false);
StructureImportSettings.setVisibleChainAnnotation(false);
package jalview.io.gff;
+
+/**
+ * A factory class that returns a model of the Sequence Ontology. By default a
+ * hard-coded subset is used (for the applet, or testing), or setInstance() can
+ * be used to set full Ontology data.
+ *
+ * @author gmcarstairs
+ *
+ */
public class SequenceOntologyFactory
{
private static SequenceOntologyI instance;
{
if (instance == null)
{
- // instance = new SequenceOntology();
instance = new SequenceOntologyLite();
}
return instance;
{ "miRNA", "transcript" },
{ "lincRNA", "transcript" },
{ "rRNA", "transcript" },
+ { "mRNA", "transcript" },
// there are many more sub-types of ncRNA...
/*
{
if (!termsNotFound.contains(term))
{
- System.out.println("SO term " + term
- + " not known - may be invalid, or model if needed in "
- + getClass().getName());
+ // suppress logging here as it reports Uniprot sequence features
+ // (which do not use SO terms) when auto-configuring feature colours
+ // System.out.println("SO term " + term
+ // + " not known - add to model if needed in "
+ // + getClass().getName());
termsNotFound.add(term);
}
}
return dsregitem;
}
- protected void finalize()
+ @Override
+ protected void finalize() throws Throwable
{
if (dsObjReg != null)
{
{
dsItemReg.clear();
}
+ super.finalize();
}
}
jvlite.setExecutor(this);
}
- public void finalize()
+ @Override
+ protected void finalize() throws Throwable
{
jvlite = null;
executor = null;
jsExecQueue.clear();
}
jsExecQueue = null;
+ super.finalize();
}
private Vector jsExecQueue;
executor = null;
}
+ @Override
public void run()
{
while (jsExecQueue != null)
final Exception[] jsex = new Exception[1];
Runnable exec = new Runnable()
{
+ @Override
public void run()
{
try
if (jex instanceof netscape.javascript.JSException
&& jvlite.jsfallbackEnabled)
{
- jsex[0] = (netscape.javascript.JSException) jex;
+ jsex[0] = jex;
if (jvlite.debug)
{
System.err.println("Falling back to javascript: url call");
return _listenerfn;
}
- public void finalise()
+ public void finalize() throws Throwable
{
jvlite = null;
super.finalize();
protected JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
- private JTabbedPane pnl_filter = new JTabbedPane();
+ protected JTabbedPane pnl_filter = new JTabbedPane();
protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
PreferenceSource.STRUCTURE_CHOOSER,
@Override
public void actionPerformed(ActionEvent e)
{
- closeAction();
+ closeAction(pnl_filter.getHeight());
}
});
btn_cancel.addKeyListener(new KeyAdapter()
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER)
{
- closeAction();
+ closeAction(pnl_filter.getHeight());
}
}
});
@Override
public void internalFrameClosing(InternalFrameEvent e)
{
- closeAction();
+ closeAction(pnl_filter.getHeight());
}
});
mainFrame.setVisible(true);
Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
}
- protected void closeAction()
+ protected void closeAction(int preferredHeight)
{
// System.out.println(">>>>>>>>>> closing internal frame!!!");
// System.out.println("width : " + mainFrame.getWidth());
// System.out.println("x : " + mainFrame.getX());
// System.out.println("y : " + mainFrame.getY());
tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
- tempUserPrefs.put("structureChooser.height", pnl_filter.getHeight());
+ tempUserPrefs.put("structureChooser.height", preferredHeight);
tempUserPrefs.put("structureChooser.x", mainFrame.getX());
tempUserPrefs.put("structureChooser.y", mainFrame.getY());
mainFrame.dispose();
}
+
public boolean wantedFieldsUpdated()
{
if (previousWantedFields == null)
protected abstract void stateChanged(ItemEvent e);
- protected abstract void updateCurrentView();
-
- protected abstract void populateFilterComboBox();
-
protected abstract void ok_ActionPerformed();
protected abstract void pdbFromFile_actionPerformed();
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
+import jalview.util.Platform;
import java.awt.BasicStroke;
import java.awt.Color;
*/
private final boolean debugRedraw;
+ private int charWidth, endRes, charHeight;
+
+ private boolean validCharWidth, hasHiddenColumns;
+
+ private FontMetrics fm;
+
+ private final boolean MAC = Platform.isAMac();
+
+ boolean av_renderHistogram = true, av_renderProfile = true,
+ av_normaliseProfile = false;
+
+ ColourSchemeI profcolour = null;
+
+ private ColumnSelection columnSelection;
+
+ private Hashtable[] hconsensus;
+
+ private Hashtable[] complementConsensus;
+
+ private Hashtable[] hStrucConsensus;
+
+ private boolean av_ignoreGapsConsensus;
+
+ /**
+ * attributes set from AwtRenderPanelI
+ */
+ /**
+ * old image used when data is currently being calculated and cannot be
+ * rendered
+ */
+ private Image fadedImage;
+
+ /**
+ * panel being rendered into
+ */
+ private ImageObserver annotationPanel;
+
+ /**
+ * width of image to render in panel
+ */
+ private int imgWidth;
+
+ /**
+ * offset to beginning of visible area
+ */
+ private int sOffset;
+
+ /**
+ * offset to end of visible area
+ */
+ private int visHeight;
+
+ /**
+ * indicate if the renderer should only render the visible portion of the
+ * annotation given the current view settings
+ */
+ private boolean useClip = true;
+
+ /**
+ * master flag indicating if renderer should ever try to clip. not enabled for
+ * jalview 2.8.1
+ */
+ private boolean canClip = false;
+
public AnnotationRenderer()
{
this(false);
this.debugRedraw = debugRedraw;
}
+ /**
+ * Remove any references and resources when this object is no longer required
+ */
+ public void dispose()
+ {
+ hconsensus = null;
+ complementConsensus = null;
+ hStrucConsensus = null;
+ fadedImage = null;
+ annotationPanel = null;
+ }
+
void drawStemAnnot(Graphics g, Annotation[] row_annotations,
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
}
- private int charWidth, endRes, charHeight;
-
- private boolean validCharWidth, hasHiddenColumns;
-
- private FontMetrics fm;
-
- private final boolean MAC = jalview.util.Platform.isAMac();
-
- boolean av_renderHistogram = true, av_renderProfile = true,
- av_normaliseProfile = false;
-
- ColourSchemeI profcolour = null;
-
- private ColumnSelection columnSelection;
-
- private Hashtable[] hconsensus;
-
- private Hashtable[] complementConsensus;
-
- private Hashtable[] hStrucConsensus;
-
- private boolean av_ignoreGapsConsensus;
-
- /**
- * attributes set from AwtRenderPanelI
- */
- /**
- * old image used when data is currently being calculated and cannot be
- * rendered
- */
- private Image fadedImage;
-
- /**
- * panel being rendered into
- */
- private ImageObserver annotationPanel;
-
- /**
- * width of image to render in panel
- */
- private int imgWidth;
-
- /**
- * offset to beginning of visible area
- */
- private int sOffset;
-
- /**
- * offset to end of visible area
- */
- private int visHeight;
-
- /**
- * indicate if the renderer should only render the visible portion of the
- * annotation given the current view settings
- */
- private boolean useClip = true;
-
- /**
- * master flag indicating if renderer should ever try to clip. not enabled for
- * jalview 2.8.1
- */
- private boolean canClip = false;
-
void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
Annotation[] row_annotations, int lastSSX, int x, int y,
int iconOffset, int startRes, int column, boolean validRes,
import java.awt.Color;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Hashtable;
static
{
- aa3Hash.put("ALA", new Integer(0));
- aa3Hash.put("ARG", new Integer(1));
- aa3Hash.put("ASN", new Integer(2));
- aa3Hash.put("ASP", new Integer(3)); // D
- aa3Hash.put("CYS", new Integer(4));
- aa3Hash.put("GLN", new Integer(5)); // Q
- aa3Hash.put("GLU", new Integer(6)); // E
- aa3Hash.put("GLY", new Integer(7));
- aa3Hash.put("HIS", new Integer(8));
- aa3Hash.put("ILE", new Integer(9));
- aa3Hash.put("LEU", new Integer(10));
- aa3Hash.put("LYS", new Integer(11));
- aa3Hash.put("MET", new Integer(12));
- aa3Hash.put("PHE", new Integer(13));
- aa3Hash.put("PRO", new Integer(14));
- aa3Hash.put("SER", new Integer(15));
- aa3Hash.put("THR", new Integer(16));
- aa3Hash.put("TRP", new Integer(17));
- aa3Hash.put("TYR", new Integer(18));
- aa3Hash.put("VAL", new Integer(19));
+ aa3Hash.put("ALA", Integer.valueOf(0));
+ aa3Hash.put("ARG", Integer.valueOf(1));
+ aa3Hash.put("ASN", Integer.valueOf(2));
+ aa3Hash.put("ASP", Integer.valueOf(3)); // D
+ aa3Hash.put("CYS", Integer.valueOf(4));
+ aa3Hash.put("GLN", Integer.valueOf(5)); // Q
+ aa3Hash.put("GLU", Integer.valueOf(6)); // E
+ aa3Hash.put("GLY", Integer.valueOf(7));
+ aa3Hash.put("HIS", Integer.valueOf(8));
+ aa3Hash.put("ILE", Integer.valueOf(9));
+ aa3Hash.put("LEU", Integer.valueOf(10));
+ aa3Hash.put("LYS", Integer.valueOf(11));
+ aa3Hash.put("MET", Integer.valueOf(12));
+ aa3Hash.put("PHE", Integer.valueOf(13));
+ aa3Hash.put("PRO", Integer.valueOf(14));
+ aa3Hash.put("SER", Integer.valueOf(15));
+ aa3Hash.put("THR", Integer.valueOf(16));
+ aa3Hash.put("TRP", Integer.valueOf(17));
+ aa3Hash.put("TYR", Integer.valueOf(18));
+ aa3Hash.put("VAL", Integer.valueOf(19));
// IUB Nomenclature for ambiguous peptides
- aa3Hash.put("ASX", new Integer(20)); // "B";
- aa3Hash.put("GLX", new Integer(21)); // Z
- aa3Hash.put("XAA", new Integer(22)); // X unknown
- aa3Hash.put("-", new Integer(23));
- aa3Hash.put("*", new Integer(23));
- aa3Hash.put(".", new Integer(23));
- aa3Hash.put(" ", new Integer(23));
- aa3Hash.put("Gap", new Integer(23));
- aa3Hash.put("UR3", new Integer(24));
+ aa3Hash.put("ASX", Integer.valueOf(20)); // "B";
+ aa3Hash.put("GLX", Integer.valueOf(21)); // Z
+ aa3Hash.put("XAA", Integer.valueOf(22)); // X unknown
+ aa3Hash.put("-", Integer.valueOf(23));
+ aa3Hash.put("*", Integer.valueOf(23));
+ aa3Hash.put(".", Integer.valueOf(23));
+ aa3Hash.put(" ", Integer.valueOf(23));
+ aa3Hash.put("Gap", Integer.valueOf(23));
+ aa3Hash.put("UR3", Integer.valueOf(24));
}
static
public static final Color midBlue = new Color(100, 100, 255);
- public static final Vector scaleColours = new Vector();
-
- static
- {
- scaleColours.addElement(new Color(114, 0, 147));
- scaleColours.addElement(new Color(156, 0, 98));
- scaleColours.addElement(new Color(190, 0, 0));
- scaleColours.addElement(Color.red);
- scaleColours.addElement(new Color(255, 125, 0));
- scaleColours.addElement(Color.orange);
- scaleColours.addElement(new Color(255, 194, 85));
- scaleColours.addElement(Color.yellow);
- scaleColours.addElement(new Color(255, 255, 181));
- scaleColours.addElement(Color.white);
- }
-
- public static final Color[] taylor = { new Color(204, 255, 0), // A
- // Greenish-yellowy-yellow
+ // not currently in use
+ // public static final Vector<Color> scaleColours = new Vector<Color>();
+ // static
+ // {
+ // scaleColours.addElement(new Color(114, 0, 147));
+ // scaleColours.addElement(new Color(156, 0, 98));
+ // scaleColours.addElement(new Color(190, 0, 0));
+ // scaleColours.addElement(Color.red);
+ // scaleColours.addElement(new Color(255, 125, 0));
+ // scaleColours.addElement(Color.orange);
+ // scaleColours.addElement(new Color(255, 194, 85));
+ // scaleColours.addElement(Color.yellow);
+ // scaleColours.addElement(new Color(255, 255, 181));
+ // scaleColours.addElement(Color.white);
+ // }
+
+ public static final Color[] taylor = { new Color(204, 255, 0),
+ // A Greenish-yellowy-yellow
new Color(0, 0, 255), // R Blueish-bluey-blue
new Color(204, 0, 255), // N Blueish-reddy-blue
new Color(255, 0, 0), // D Reddish-reddy-red
{ -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
-8, -8, -8, -8, -8, -8, 1 }, };
- public static final Hashtable ssHash = new Hashtable(); // stores the number
- // value of the aa
-
- static
- {
- ssHash.put("H", Color.magenta);
- ssHash.put("E", Color.yellow);
- ssHash.put("-", Color.white);
- ssHash.put(".", Color.white);
- ssHash.put("S", Color.cyan);
- ssHash.put("T", Color.blue);
- ssHash.put("G", Color.pink);
- ssHash.put("I", Color.pink);
- ssHash.put("B", Color.yellow);
- }
+ // not currently used
+ // public static final Map<String, Color> ssHash = new Hashtable<String,
+ // Color>();
+ // static
+ // {
+ // ssHash.put("H", Color.magenta);
+ // ssHash.put("E", Color.yellow);
+ // ssHash.put("-", Color.white);
+ // ssHash.put(".", Color.white);
+ // ssHash.put("S", Color.cyan);
+ // ssHash.put("T", Color.blue);
+ // ssHash.put("G", Color.pink);
+ // ssHash.put("I", Color.pink);
+ // ssHash.put("B", Color.yellow);
+ // }
/*
* new Color(60, 136, 238), // U Color.white, // I Color.white, // X
scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62, 0));
scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250, 0));
scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
-
}
public static final Color[] pidColours = { midBlue,
public static final float[] pidThresholds = { 80, 60, 40, };
- public static Map<String, List<String>> codonHash = new HashMap<String, List<String>>();
-
- private static List<String> Lys = new ArrayList<String>();
-
- private static List<String> Asn = new ArrayList<String>();
-
- private static List<String> Gln = new ArrayList<String>();
-
- private static List<String> His = new ArrayList<String>();
-
- private static List<String> Glu = new ArrayList<String>();
-
- private static List<String> Asp = new ArrayList<String>();
-
- private static List<String> Tyr = new ArrayList<String>();
-
- private static List<String> Thr = new ArrayList<String>();
-
- private static List<String> Pro = new ArrayList<String>();
-
- private static List<String> Ala = new ArrayList<String>();
-
- private static List<String> Ser = new ArrayList<String>();
-
- private static List<String> Arg = new ArrayList<String>();
-
- private static List<String> Gly = new ArrayList<String>();
-
- private static List<String> Trp = new ArrayList<String>();
-
- private static List<String> Cys = new ArrayList<String>();
-
- private static List<String> Ile = new ArrayList<String>();
-
- private static List<String> Met = new ArrayList<String>();
-
- private static List<String> Leu = new ArrayList<String>();
-
- private static List<String> Val = new ArrayList<String>();
-
- private static List<String> Phe = new ArrayList<String>();
-
- public static List<String> STOP = new ArrayList<String>();
+ public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
public static String START = "ATG";
- static
- {
- codonHash.put("K", Lys);
- codonHash.put("N", Asn);
- codonHash.put("Q", Gln);
- codonHash.put("H", His);
- codonHash.put("E", Glu);
- codonHash.put("D", Asp);
- codonHash.put("Y", Tyr);
- codonHash.put("T", Thr);
- codonHash.put("P", Pro);
- codonHash.put("A", Ala);
- codonHash.put("S", Ser);
- codonHash.put("R", Arg);
- codonHash.put("G", Gly);
- codonHash.put("W", Trp);
- codonHash.put("C", Cys);
- codonHash.put("I", Ile);
- codonHash.put("M", Met);
- codonHash.put("L", Leu);
- codonHash.put("V", Val);
- codonHash.put("F", Phe);
- codonHash.put("STOP", STOP);
- }
-
/**
* Nucleotide Ambiguity Codes
*/
// make all codons for this combination
char allres[][] = new char[tpos.length][];
String _acodon = "";
- char _anuc;
for (ipos = 0; ipos < tpos.length; ipos++)
{
if (acodon[ipos].length == 0 || tpos[ipos] < 0)
}
}
}
-
- }
-
- static
- {
- Lys.add("AAA");
- Lys.add("AAG");
- Asn.add("AAC");
- Asn.add("AAT");
-
- Gln.add("CAA");
- Gln.add("CAG");
- His.add("CAC");
- His.add("CAT");
-
- Glu.add("GAA");
- Glu.add("GAG");
- Asp.add("GAC");
- Asp.add("GAT");
-
- Tyr.add("TAC");
- Tyr.add("TAT");
-
- Thr.add("ACA");
- Thr.add("ACG");
- Thr.add("ACC");
- Thr.add("ACT");
-
- Pro.add("CCA");
- Pro.add("CCG");
- Pro.add("CCC");
- Pro.add("CCT");
-
- Ala.add("GCA");
- Ala.add("GCG");
- Ala.add("GCC");
- Ala.add("GCT");
-
- Ser.add("TCA");
- Ser.add("TCG");
- Ser.add("TCC");
- Ser.add("TCT");
- Ser.add("AGC");
- Ser.add("AGT");
-
- Arg.add("AGA");
- Arg.add("AGG");
- Arg.add("CGA");
- Arg.add("CGG");
- Arg.add("CGC");
- Arg.add("CGT");
-
- Gly.add("GGA");
- Gly.add("GGG");
- Gly.add("GGC");
- Gly.add("GGT");
-
- STOP.add("TGA");
- STOP.add("TAA");
- STOP.add("TAG");
-
- Trp.add("TGG");
-
- Cys.add("TGC");
- Cys.add("TGT");
-
- Ile.add("ATA");
- Ile.add("ATC");
- Ile.add("ATT");
-
- Met.add("ATG");
-
- Leu.add("CTA");
- Leu.add("CTG");
- Leu.add("CTC");
- Leu.add("CTT");
- Leu.add("TTA");
- Leu.add("TTG");
-
- Val.add("GTA");
- Val.add("GTG");
- Val.add("GTC");
- Val.add("GTT");
-
- Phe.add("TTC");
- Phe.add("TTT");
}
// Stores residue codes/names and colours and other things
- public static Hashtable propHash = new Hashtable();
+ public static Map<String, Map<String, Integer>> propHash = new Hashtable<String, Map<String, Integer>>();
- public static Hashtable hydrophobic = new Hashtable();
+ public static Map<String, Integer> hydrophobic = new Hashtable<String, Integer>();
- public static Hashtable polar = new Hashtable();
+ public static Map<String, Integer> polar = new Hashtable<String, Integer>();
- public static Hashtable small = new Hashtable();
+ public static Map<String, Integer> small = new Hashtable<String, Integer>();
- public static Hashtable positive = new Hashtable();
+ public static Map<String, Integer> positive = new Hashtable<String, Integer>();
- public static Hashtable negative = new Hashtable();
+ public static Map<String, Integer> negative = new Hashtable<String, Integer>();
- public static Hashtable charged = new Hashtable();
+ public static Map<String, Integer> charged = new Hashtable<String, Integer>();
- public static Hashtable aromatic = new Hashtable();
+ public static Map<String, Integer> aromatic = new Hashtable<String, Integer>();
- public static Hashtable aliphatic = new Hashtable();
+ public static Map<String, Integer> aliphatic = new Hashtable<String, Integer>();
- public static Hashtable tiny = new Hashtable();
+ public static Map<String, Integer> tiny = new Hashtable<String, Integer>();
- public static Hashtable proline = new Hashtable();
+ public static Map<String, Integer> proline = new Hashtable<String, Integer>();
static
{
- hydrophobic.put("I", new Integer(1));
- hydrophobic.put("L", new Integer(1));
- hydrophobic.put("V", new Integer(1));
- hydrophobic.put("C", new Integer(1));
- hydrophobic.put("A", new Integer(1));
- hydrophobic.put("G", new Integer(1));
- hydrophobic.put("M", new Integer(1));
- hydrophobic.put("F", new Integer(1));
- hydrophobic.put("Y", new Integer(1));
- hydrophobic.put("W", new Integer(1));
- hydrophobic.put("H", new Integer(1));
- hydrophobic.put("K", new Integer(1));
- hydrophobic.put("X", new Integer(1));
- hydrophobic.put("-", new Integer(1));
- hydrophobic.put("*", new Integer(1));
- hydrophobic.put("R", new Integer(0));
- hydrophobic.put("E", new Integer(0));
- hydrophobic.put("Q", new Integer(0));
- hydrophobic.put("D", new Integer(0));
- hydrophobic.put("N", new Integer(0));
- hydrophobic.put("S", new Integer(0));
- hydrophobic.put("T", new Integer(0));
- hydrophobic.put("P", new Integer(0));
+ hydrophobic.put("I", Integer.valueOf(1));
+ hydrophobic.put("L", Integer.valueOf(1));
+ hydrophobic.put("V", Integer.valueOf(1));
+ hydrophobic.put("C", Integer.valueOf(1));
+ hydrophobic.put("A", Integer.valueOf(1));
+ hydrophobic.put("G", Integer.valueOf(1));
+ hydrophobic.put("M", Integer.valueOf(1));
+ hydrophobic.put("F", Integer.valueOf(1));
+ hydrophobic.put("Y", Integer.valueOf(1));
+ hydrophobic.put("W", Integer.valueOf(1));
+ hydrophobic.put("H", Integer.valueOf(1));
+ hydrophobic.put("K", Integer.valueOf(1));
+ hydrophobic.put("X", Integer.valueOf(1));
+ hydrophobic.put("-", Integer.valueOf(1));
+ hydrophobic.put("*", Integer.valueOf(1));
+ hydrophobic.put("R", Integer.valueOf(0));
+ hydrophobic.put("E", Integer.valueOf(0));
+ hydrophobic.put("Q", Integer.valueOf(0));
+ hydrophobic.put("D", Integer.valueOf(0));
+ hydrophobic.put("N", Integer.valueOf(0));
+ hydrophobic.put("S", Integer.valueOf(0));
+ hydrophobic.put("T", Integer.valueOf(0));
+ hydrophobic.put("P", Integer.valueOf(0));
}
static
{
- polar.put("Y", new Integer(1));
- polar.put("W", new Integer(1));
- polar.put("H", new Integer(1));
- polar.put("K", new Integer(1));
- polar.put("R", new Integer(1));
- polar.put("E", new Integer(1));
- polar.put("Q", new Integer(1));
- polar.put("D", new Integer(1));
- polar.put("N", new Integer(1));
- polar.put("S", new Integer(1));
- polar.put("T", new Integer(1));
- polar.put("X", new Integer(1));
- polar.put("-", new Integer(1));
- polar.put("*", new Integer(1));
- polar.put("I", new Integer(0));
- polar.put("L", new Integer(0));
- polar.put("V", new Integer(0));
- polar.put("C", new Integer(0));
- polar.put("A", new Integer(0));
- polar.put("G", new Integer(0));
- polar.put("M", new Integer(0));
- polar.put("F", new Integer(0));
- polar.put("P", new Integer(0));
+ polar.put("Y", Integer.valueOf(1));
+ polar.put("W", Integer.valueOf(1));
+ polar.put("H", Integer.valueOf(1));
+ polar.put("K", Integer.valueOf(1));
+ polar.put("R", Integer.valueOf(1));
+ polar.put("E", Integer.valueOf(1));
+ polar.put("Q", Integer.valueOf(1));
+ polar.put("D", Integer.valueOf(1));
+ polar.put("N", Integer.valueOf(1));
+ polar.put("S", Integer.valueOf(1));
+ polar.put("T", Integer.valueOf(1));
+ polar.put("X", Integer.valueOf(1));
+ polar.put("-", Integer.valueOf(1));
+ polar.put("*", Integer.valueOf(1));
+ polar.put("I", Integer.valueOf(0));
+ polar.put("L", Integer.valueOf(0));
+ polar.put("V", Integer.valueOf(0));
+ polar.put("C", Integer.valueOf(0));
+ polar.put("A", Integer.valueOf(0));
+ polar.put("G", Integer.valueOf(0));
+ polar.put("M", Integer.valueOf(0));
+ polar.put("F", Integer.valueOf(0));
+ polar.put("P", Integer.valueOf(0));
}
static
{
- small.put("I", new Integer(0));
- small.put("L", new Integer(0));
- small.put("V", new Integer(1));
- small.put("C", new Integer(1));
- small.put("A", new Integer(1));
- small.put("G", new Integer(1));
- small.put("M", new Integer(0));
- small.put("F", new Integer(0));
- small.put("Y", new Integer(0));
- small.put("W", new Integer(0));
- small.put("H", new Integer(0));
- small.put("K", new Integer(0));
- small.put("R", new Integer(0));
- small.put("E", new Integer(0));
- small.put("Q", new Integer(0));
- small.put("D", new Integer(1));
- small.put("N", new Integer(1));
- small.put("S", new Integer(1));
- small.put("T", new Integer(1));
- small.put("P", new Integer(1));
- small.put("-", new Integer(1));
- small.put("*", new Integer(1));
+ small.put("I", Integer.valueOf(0));
+ small.put("L", Integer.valueOf(0));
+ small.put("V", Integer.valueOf(1));
+ small.put("C", Integer.valueOf(1));
+ small.put("A", Integer.valueOf(1));
+ small.put("G", Integer.valueOf(1));
+ small.put("M", Integer.valueOf(0));
+ small.put("F", Integer.valueOf(0));
+ small.put("Y", Integer.valueOf(0));
+ small.put("W", Integer.valueOf(0));
+ small.put("H", Integer.valueOf(0));
+ small.put("K", Integer.valueOf(0));
+ small.put("R", Integer.valueOf(0));
+ small.put("E", Integer.valueOf(0));
+ small.put("Q", Integer.valueOf(0));
+ small.put("D", Integer.valueOf(1));
+ small.put("N", Integer.valueOf(1));
+ small.put("S", Integer.valueOf(1));
+ small.put("T", Integer.valueOf(1));
+ small.put("P", Integer.valueOf(1));
+ small.put("-", Integer.valueOf(1));
+ small.put("*", Integer.valueOf(1));
}
static
{
- positive.put("I", new Integer(0));
- positive.put("L", new Integer(0));
- positive.put("V", new Integer(0));
- positive.put("C", new Integer(0));
- positive.put("A", new Integer(0));
- positive.put("G", new Integer(0));
- positive.put("M", new Integer(0));
- positive.put("F", new Integer(0));
- positive.put("Y", new Integer(0));
- positive.put("W", new Integer(0));
- positive.put("H", new Integer(1));
- positive.put("K", new Integer(1));
- positive.put("R", new Integer(1));
- positive.put("E", new Integer(0));
- positive.put("Q", new Integer(0));
- positive.put("D", new Integer(0));
- positive.put("N", new Integer(0));
- positive.put("S", new Integer(0));
- positive.put("T", new Integer(0));
- positive.put("P", new Integer(0));
- positive.put("-", new Integer(1));
- positive.put("*", new Integer(1));
+ positive.put("I", Integer.valueOf(0));
+ positive.put("L", Integer.valueOf(0));
+ positive.put("V", Integer.valueOf(0));
+ positive.put("C", Integer.valueOf(0));
+ positive.put("A", Integer.valueOf(0));
+ positive.put("G", Integer.valueOf(0));
+ positive.put("M", Integer.valueOf(0));
+ positive.put("F", Integer.valueOf(0));
+ positive.put("Y", Integer.valueOf(0));
+ positive.put("W", Integer.valueOf(0));
+ positive.put("H", Integer.valueOf(1));
+ positive.put("K", Integer.valueOf(1));
+ positive.put("R", Integer.valueOf(1));
+ positive.put("E", Integer.valueOf(0));
+ positive.put("Q", Integer.valueOf(0));
+ positive.put("D", Integer.valueOf(0));
+ positive.put("N", Integer.valueOf(0));
+ positive.put("S", Integer.valueOf(0));
+ positive.put("T", Integer.valueOf(0));
+ positive.put("P", Integer.valueOf(0));
+ positive.put("-", Integer.valueOf(1));
+ positive.put("*", Integer.valueOf(1));
}
static
{
- negative.put("I", new Integer(0));
- negative.put("L", new Integer(0));
- negative.put("V", new Integer(0));
- negative.put("C", new Integer(0));
- negative.put("A", new Integer(0));
- negative.put("G", new Integer(0));
- negative.put("M", new Integer(0));
- negative.put("F", new Integer(0));
- negative.put("Y", new Integer(0));
- negative.put("W", new Integer(0));
- negative.put("H", new Integer(0));
- negative.put("K", new Integer(0));
- negative.put("R", new Integer(0));
- negative.put("E", new Integer(1));
- negative.put("Q", new Integer(0));
- negative.put("D", new Integer(1));
- negative.put("N", new Integer(0));
- negative.put("S", new Integer(0));
- negative.put("T", new Integer(0));
- negative.put("P", new Integer(0));
- negative.put("-", new Integer(1));
- negative.put("*", new Integer(1));
+ negative.put("I", Integer.valueOf(0));
+ negative.put("L", Integer.valueOf(0));
+ negative.put("V", Integer.valueOf(0));
+ negative.put("C", Integer.valueOf(0));
+ negative.put("A", Integer.valueOf(0));
+ negative.put("G", Integer.valueOf(0));
+ negative.put("M", Integer.valueOf(0));
+ negative.put("F", Integer.valueOf(0));
+ negative.put("Y", Integer.valueOf(0));
+ negative.put("W", Integer.valueOf(0));
+ negative.put("H", Integer.valueOf(0));
+ negative.put("K", Integer.valueOf(0));
+ negative.put("R", Integer.valueOf(0));
+ negative.put("E", Integer.valueOf(1));
+ negative.put("Q", Integer.valueOf(0));
+ negative.put("D", Integer.valueOf(1));
+ negative.put("N", Integer.valueOf(0));
+ negative.put("S", Integer.valueOf(0));
+ negative.put("T", Integer.valueOf(0));
+ negative.put("P", Integer.valueOf(0));
+ negative.put("-", Integer.valueOf(1));
+ negative.put("*", Integer.valueOf(1));
}
static
{
- charged.put("I", new Integer(0));
- charged.put("L", new Integer(0));
- charged.put("V", new Integer(0));
- charged.put("C", new Integer(0));
- charged.put("A", new Integer(0));
- charged.put("G", new Integer(0));
- charged.put("M", new Integer(0));
- charged.put("F", new Integer(0));
- charged.put("Y", new Integer(0));
- charged.put("W", new Integer(0));
- charged.put("H", new Integer(1));
- charged.put("K", new Integer(1));
- charged.put("R", new Integer(1));
- charged.put("E", new Integer(1));
- charged.put("Q", new Integer(0));
- charged.put("D", new Integer(1));
- charged.put("N", new Integer(0)); // Asparagine is polar but not charged.
+ charged.put("I", Integer.valueOf(0));
+ charged.put("L", Integer.valueOf(0));
+ charged.put("V", Integer.valueOf(0));
+ charged.put("C", Integer.valueOf(0));
+ charged.put("A", Integer.valueOf(0));
+ charged.put("G", Integer.valueOf(0));
+ charged.put("M", Integer.valueOf(0));
+ charged.put("F", Integer.valueOf(0));
+ charged.put("Y", Integer.valueOf(0));
+ charged.put("W", Integer.valueOf(0));
+ charged.put("H", Integer.valueOf(1));
+ charged.put("K", Integer.valueOf(1));
+ charged.put("R", Integer.valueOf(1));
+ charged.put("E", Integer.valueOf(1));
+ charged.put("Q", Integer.valueOf(0));
+ charged.put("D", Integer.valueOf(1));
+ charged.put("N", Integer.valueOf(0)); // Asparagine is polar but not
+ // charged.
// Alternative would be charged and
// negative (in basic form)?
- charged.put("S", new Integer(0));
- charged.put("T", new Integer(0));
- charged.put("P", new Integer(0));
- charged.put("-", new Integer(1));
- charged.put("*", new Integer(1));
+ charged.put("S", Integer.valueOf(0));
+ charged.put("T", Integer.valueOf(0));
+ charged.put("P", Integer.valueOf(0));
+ charged.put("-", Integer.valueOf(1));
+ charged.put("*", Integer.valueOf(1));
}
static
{
- aromatic.put("I", new Integer(0));
- aromatic.put("L", new Integer(0));
- aromatic.put("V", new Integer(0));
- aromatic.put("C", new Integer(0));
- aromatic.put("A", new Integer(0));
- aromatic.put("G", new Integer(0));
- aromatic.put("M", new Integer(0));
- aromatic.put("F", new Integer(1));
- aromatic.put("Y", new Integer(1));
- aromatic.put("W", new Integer(1));
- aromatic.put("H", new Integer(1));
- aromatic.put("K", new Integer(0));
- aromatic.put("R", new Integer(0));
- aromatic.put("E", new Integer(0));
- aromatic.put("Q", new Integer(0));
- aromatic.put("D", new Integer(0));
- aromatic.put("N", new Integer(0));
- aromatic.put("S", new Integer(0));
- aromatic.put("T", new Integer(0));
- aromatic.put("P", new Integer(0));
- aromatic.put("-", new Integer(1));
- aromatic.put("*", new Integer(1));
+ aromatic.put("I", Integer.valueOf(0));
+ aromatic.put("L", Integer.valueOf(0));
+ aromatic.put("V", Integer.valueOf(0));
+ aromatic.put("C", Integer.valueOf(0));
+ aromatic.put("A", Integer.valueOf(0));
+ aromatic.put("G", Integer.valueOf(0));
+ aromatic.put("M", Integer.valueOf(0));
+ aromatic.put("F", Integer.valueOf(1));
+ aromatic.put("Y", Integer.valueOf(1));
+ aromatic.put("W", Integer.valueOf(1));
+ aromatic.put("H", Integer.valueOf(1));
+ aromatic.put("K", Integer.valueOf(0));
+ aromatic.put("R", Integer.valueOf(0));
+ aromatic.put("E", Integer.valueOf(0));
+ aromatic.put("Q", Integer.valueOf(0));
+ aromatic.put("D", Integer.valueOf(0));
+ aromatic.put("N", Integer.valueOf(0));
+ aromatic.put("S", Integer.valueOf(0));
+ aromatic.put("T", Integer.valueOf(0));
+ aromatic.put("P", Integer.valueOf(0));
+ aromatic.put("-", Integer.valueOf(1));
+ aromatic.put("*", Integer.valueOf(1));
}
static
{
- aliphatic.put("I", new Integer(1));
- aliphatic.put("L", new Integer(1));
- aliphatic.put("V", new Integer(1));
- aliphatic.put("C", new Integer(0));
- aliphatic.put("A", new Integer(0));
- aliphatic.put("G", new Integer(0));
- aliphatic.put("M", new Integer(0));
- aliphatic.put("F", new Integer(0));
- aliphatic.put("Y", new Integer(0));
- aliphatic.put("W", new Integer(0));
- aliphatic.put("H", new Integer(0));
- aliphatic.put("K", new Integer(0));
- aliphatic.put("R", new Integer(0));
- aliphatic.put("E", new Integer(0));
- aliphatic.put("Q", new Integer(0));
- aliphatic.put("D", new Integer(0));
- aliphatic.put("N", new Integer(0));
- aliphatic.put("S", new Integer(0));
- aliphatic.put("T", new Integer(0));
- aliphatic.put("P", new Integer(0));
- aliphatic.put("-", new Integer(1));
- aliphatic.put("*", new Integer(1));
+ aliphatic.put("I", Integer.valueOf(1));
+ aliphatic.put("L", Integer.valueOf(1));
+ aliphatic.put("V", Integer.valueOf(1));
+ aliphatic.put("C", Integer.valueOf(0));
+ aliphatic.put("A", Integer.valueOf(0));
+ aliphatic.put("G", Integer.valueOf(0));
+ aliphatic.put("M", Integer.valueOf(0));
+ aliphatic.put("F", Integer.valueOf(0));
+ aliphatic.put("Y", Integer.valueOf(0));
+ aliphatic.put("W", Integer.valueOf(0));
+ aliphatic.put("H", Integer.valueOf(0));
+ aliphatic.put("K", Integer.valueOf(0));
+ aliphatic.put("R", Integer.valueOf(0));
+ aliphatic.put("E", Integer.valueOf(0));
+ aliphatic.put("Q", Integer.valueOf(0));
+ aliphatic.put("D", Integer.valueOf(0));
+ aliphatic.put("N", Integer.valueOf(0));
+ aliphatic.put("S", Integer.valueOf(0));
+ aliphatic.put("T", Integer.valueOf(0));
+ aliphatic.put("P", Integer.valueOf(0));
+ aliphatic.put("-", Integer.valueOf(1));
+ aliphatic.put("*", Integer.valueOf(1));
}
static
{
- tiny.put("I", new Integer(0));
- tiny.put("L", new Integer(0));
- tiny.put("V", new Integer(0));
- tiny.put("C", new Integer(0));
- tiny.put("A", new Integer(1));
- tiny.put("G", new Integer(1));
- tiny.put("M", new Integer(0));
- tiny.put("F", new Integer(0));
- tiny.put("Y", new Integer(0));
- tiny.put("W", new Integer(0));
- tiny.put("H", new Integer(0));
- tiny.put("K", new Integer(0));
- tiny.put("R", new Integer(0));
- tiny.put("E", new Integer(0));
- tiny.put("Q", new Integer(0));
- tiny.put("D", new Integer(0));
- tiny.put("N", new Integer(0));
- tiny.put("S", new Integer(1));
- tiny.put("T", new Integer(0));
- tiny.put("P", new Integer(0));
- tiny.put("-", new Integer(1));
- tiny.put("*", new Integer(1));
+ tiny.put("I", Integer.valueOf(0));
+ tiny.put("L", Integer.valueOf(0));
+ tiny.put("V", Integer.valueOf(0));
+ tiny.put("C", Integer.valueOf(0));
+ tiny.put("A", Integer.valueOf(1));
+ tiny.put("G", Integer.valueOf(1));
+ tiny.put("M", Integer.valueOf(0));
+ tiny.put("F", Integer.valueOf(0));
+ tiny.put("Y", Integer.valueOf(0));
+ tiny.put("W", Integer.valueOf(0));
+ tiny.put("H", Integer.valueOf(0));
+ tiny.put("K", Integer.valueOf(0));
+ tiny.put("R", Integer.valueOf(0));
+ tiny.put("E", Integer.valueOf(0));
+ tiny.put("Q", Integer.valueOf(0));
+ tiny.put("D", Integer.valueOf(0));
+ tiny.put("N", Integer.valueOf(0));
+ tiny.put("S", Integer.valueOf(1));
+ tiny.put("T", Integer.valueOf(0));
+ tiny.put("P", Integer.valueOf(0));
+ tiny.put("-", Integer.valueOf(1));
+ tiny.put("*", Integer.valueOf(1));
}
static
{
- proline.put("I", new Integer(0));
- proline.put("L", new Integer(0));
- proline.put("V", new Integer(0));
- proline.put("C", new Integer(0));
- proline.put("A", new Integer(0));
- proline.put("G", new Integer(0));
- proline.put("M", new Integer(0));
- proline.put("F", new Integer(0));
- proline.put("Y", new Integer(0));
- proline.put("W", new Integer(0));
- proline.put("H", new Integer(0));
- proline.put("K", new Integer(0));
- proline.put("R", new Integer(0));
- proline.put("E", new Integer(0));
- proline.put("Q", new Integer(0));
- proline.put("D", new Integer(0));
- proline.put("N", new Integer(0));
- proline.put("S", new Integer(0));
- proline.put("T", new Integer(0));
- proline.put("P", new Integer(1));
- proline.put("-", new Integer(1));
- proline.put("*", new Integer(1));
+ proline.put("I", Integer.valueOf(0));
+ proline.put("L", Integer.valueOf(0));
+ proline.put("V", Integer.valueOf(0));
+ proline.put("C", Integer.valueOf(0));
+ proline.put("A", Integer.valueOf(0));
+ proline.put("G", Integer.valueOf(0));
+ proline.put("M", Integer.valueOf(0));
+ proline.put("F", Integer.valueOf(0));
+ proline.put("Y", Integer.valueOf(0));
+ proline.put("W", Integer.valueOf(0));
+ proline.put("H", Integer.valueOf(0));
+ proline.put("K", Integer.valueOf(0));
+ proline.put("R", Integer.valueOf(0));
+ proline.put("E", Integer.valueOf(0));
+ proline.put("Q", Integer.valueOf(0));
+ proline.put("D", Integer.valueOf(0));
+ proline.put("N", Integer.valueOf(0));
+ proline.put("S", Integer.valueOf(0));
+ proline.put("T", Integer.valueOf(0));
+ proline.put("P", Integer.valueOf(1));
+ proline.put("-", Integer.valueOf(1));
+ proline.put("*", Integer.valueOf(1));
}
static
propMatrixF[i][j] = 0;
propMatrixPos[i][j] = 0;
propMatrixEpos[i][j] = 0;
- for (Enumeration<String> en = propHash.keys(); en.hasMoreElements();)
+ for (String ph : propHash.keySet())
{
- String ph = en.nextElement();
- Map<String, Integer> pph = (Map<String, Integer>) propHash
- .get(ph);
+ Map<String, Integer> pph = propHash.get(ph);
if (pph.get(ic) != null && pph.get(jc) != null)
{
int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue();
return pog;
}
- public static Vector getCodons(String res)
- {
- if (codonHash.containsKey(res))
- {
- return (Vector) codonHash.get(res);
- }
-
- return null;
- }
-
public static String codonTranslate(String lccodon)
{
- if (false)
- {
- return _codonTranslate(lccodon);
- }
String cdn = codonHash2.get(lccodon.toUpperCase());
if ("*".equals(cdn))
{
return cdn;
}
- public static String _codonTranslate(String lccodon)
- {
- String codon = lccodon.toUpperCase();
- // all base ambiguity codes yield an 'X' amino acid residue
- if (codon.indexOf('X') > -1 || codon.indexOf('N') > -1)
- {
- return "X";
- }
- for (String key : codonHash.keySet())
- {
- if (codonHash.get(key).contains(codon))
- {
- return key;
- }
- }
-
- return null;
- }
-
public static int[][] getDefaultPeptideMatrix()
{
return ResidueProperties.getBLOSUM62();
return pog;
}
- public static Hashtable toDssp3State;
+ public static Hashtable<String, String> toDssp3State;
static
{
- toDssp3State = new Hashtable();
+ toDssp3State = new Hashtable<String, String>();
toDssp3State.put("H", "H");
toDssp3State.put("E", "E");
toDssp3State.put("C", " ");
String ssc = ssstring.substring(i, i + 1);
if (toDssp3State.containsKey(ssc))
{
- ss.append((String) toDssp3State.get(ssc));
+ ss.append(toDssp3State.get(ssc));
}
else
{
}
- public static String getCanonicalAminoAcid(String aa)
+ public static String getCanonicalAminoAcid(String aA)
{
- String canonical = modifications.get(aa);
- return canonical == null ? aa : canonical;
+ String canonical = modifications.get(aA);
+ return canonical == null ? aA : canonical;
}
// main method generates perl representation of residue property hash
// / cut here
public static void main(String[] args)
{
- Hashtable aa = new Hashtable();
+ Hashtable<String, Vector<String>> aaProps = new Hashtable<String, Vector<String>>();
System.out.println("my %aa = {");
// invert property hashes
- Enumeration prop = propHash.keys();
- while (prop.hasMoreElements())
+ for (String pname : propHash.keySet())
{
- String pname = (String) prop.nextElement();
- Hashtable phash = (Hashtable) propHash.get(pname);
- Enumeration res = phash.keys();
- while (res.hasMoreElements())
+ Map<String, Integer> phash = propHash.get(pname);
+ for (String rname : phash.keySet())
{
- String rname = (String) res.nextElement();
- Vector aprops = (Vector) aa.get(rname);
+ Vector<String> aprops = aaProps.get(rname);
if (aprops == null)
{
- aprops = new Vector();
- aa.put(rname, aprops);
+ aprops = new Vector<String>();
+ aaProps.put(rname, aprops);
}
- Integer hasprop = (Integer) phash.get(rname);
+ Integer hasprop = phash.get(rname);
if (hasprop.intValue() == 1)
{
aprops.addElement(pname);
}
}
}
- Enumeration res = aa.keys();
+ Enumeration<String> res = aaProps.keys();
while (res.hasMoreElements())
{
- String rname = (String) res.nextElement();
+ String rname = res.nextElement();
System.out.print("'" + rname + "' => [");
- Enumeration props = ((Vector) aa.get(rname)).elements();
+ Enumeration<String> props = aaProps.get(rname).elements();
while (props.hasMoreElements())
{
- System.out.print("'" + (String) props.nextElement() + "'");
+ System.out.print("'" + props.nextElement() + "'");
if (props.hasMoreElements())
{
System.out.println(", ");
/**
* Returns a list of residue characters for the specified inputs
*
- * @param nucleotide
+ * @param forNucleotide
* @param includeAmbiguous
* @return
*/
- public static List<String> getResidues(boolean nucleotide,
+ public static List<String> getResidues(boolean forNucleotide,
boolean includeAmbiguous)
{
List<String> result = new ArrayList<String>();
- if (nucleotide)
+ if (forNucleotide)
{
for (String nuc : nucleotideName.keySet())
{
seqMap = new IdentityHashMap<SequenceI, Color[]>();
AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
: alignment.getContext();
+ if (alcontext == null)
+ {
+ return;
+ }
int w = 0;
for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
import jalview.gui.IProgressIndicator;
import jalview.io.AppletFormatAdapter;
import jalview.io.StructureFile;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
-
- boolean isParseWithJMOL = StructureImportSettings
- .getDefaultPDBFileParser().equalsIgnoreCase(
- StructureImportSettings.StructureParser.JMOL_PARSER
- .toString());
- if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile)))
- {
- pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
- secStructServices, pdbFile, protocol);
- }
- else
- {
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
- }
+ pdb = new JmolParser(pdbFile, protocol);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null && refb.getSource() != null
+ if (refa.getSource() != null
+ && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null && refb.getSource() != null
+ if (refa.getSource() != null
+ && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null && refb.getSource() != null
+ if (refa.getSource() != null
+ && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null && refb.getSource() != null
+ if (refa.getSource() != null
+ && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
return matches;
}
+ /**
+ * promote direct database references to primary for nucleotide or protein
+ * sequences if they have an appropriate primary ref
+ * <table>
+ * <tr>
+ * <th>Seq Type</th>
+ * <th>Primary DB</th>
+ * <th>Direct which will be promoted</th>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>dna</td>
+ * <td>Ensembl</td>
+ * <td>ENA</td>
+ * </tr>
+ * </table>
+ *
+ * @param sequence
+ */
+ public static void ensurePrimaries(SequenceI sequence)
+ {
+ List<DBRefEntry> pr = sequence.getPrimaryDBRefs();
+ if (pr.size() == 0)
+ {
+ // nothing to do
+ return;
+ }
+ List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+ {
+ DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
+ sequence.getDBRefs());
+ if (selfArray == null || selfArray.length == 0)
+ {
+ // nothing to do
+ return;
+ }
+ selfs.addAll(Arrays.asList(selfArray));
+ }
+
+ // filter non-primary refs
+ for (DBRefEntry p : pr)
+ {
+ while (selfs.contains(p))
+ {
+ selfs.remove(p);
+ }
+ }
+ List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+
+ for (DBRefEntry p : pr)
+ {
+ List<String> promType = new ArrayList<String>();
+ if (sequence.isProtein())
+ {
+ switch (getCanonicalName(p.getSource()))
+ {
+ case DBRefSource.UNIPROT:
+ // case DBRefSource.UNIPROTKB:
+ // case DBRefSource.UP_NAME:
+ // search for and promote ensembl
+ promType.add(DBRefSource.ENSEMBL);
+ break;
+ case DBRefSource.ENSEMBL:
+ // search for and promote Uniprot
+ promType.add(DBRefSource.UNIPROT);
+ break;
+ }
+ }
+ else
+ {
+ // TODO: promote transcript refs
+ }
+
+ // collate candidates and promote them
+ DBRefEntry[] candidates = selectRefs(
+ selfs.toArray(new DBRefEntry[0]),
+ promType.toArray(new String[0]));
+ if (candidates != null)
+ {
+ for (DBRefEntry cand : candidates)
+ {
+ if (cand.hasMap())
+ {
+ if (cand.getMap().getTo() != null
+ && cand.getMap().getTo() != sequence)
+ {
+ // can't promote refs with mappings to other sequences
+ continue;
+ }
+ if (cand.getMap().getMap().getFromLowest() != sequence
+ .getStart()
+ && cand.getMap().getMap().getFromHighest() != sequence
+ .getEnd())
+ {
+ // can't promote refs with mappings from a region of this sequence
+ // - eg CDS
+ continue;
+ }
+ }
+ // and promote
+ cand.setVersion(p.getVersion() + " (promoted)");
+ selfs.remove(cand);
+ toPromote.add(cand);
+ if (!cand.isPrimaryCandidate())
+ {
+ System.out.println("Warning: Couldn't promote dbref "
+ + cand.toString() + " for sequence "
+ + sequence.toString());
+ }
+ }
+ }
+ }
+ }
+
}
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
import jalview.structure.CommandListener;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.workers.StrucConsensusThread;
import java.awt.Color;
+import java.beans.PropertyChangeSupport;
import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.BitSet;
public void updateConservation(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (alignment.isNucleotide() || conservation == null
+ if (alignment.isNucleotide()
+ || (conservation == null && quality == null)
|| !autoCalculateConsensus)
{
return;
return false;
}
+ public void setAlignment(AlignmentI align)
+ {
+ this.alignment = align;
+ }
+
+ /**
+ * Clean up references when this viewport is closed
+ */
+ @Override
+ public void dispose()
+ {
+ /*
+ * defensively null out references to large objects in case
+ * this object is not garbage collected (as if!)
+ */
+ consensus = null;
+ complementConsensus = null;
+ strucConsensus = null;
+ conservation = null;
+ quality = null;
+ groupConsensus = null;
+ groupConservation = null;
+ hconsensus = null;
+ hcomplementConsensus = null;
+ // TODO removed listeners from changeSupport?
+ changeSupport = null;
+ setAlignment(null);
+ }
+
@Override
public boolean isClosed()
{
}
@Override
+ public boolean hasSelectedColumns()
+ {
+ ColumnSelection columnSelection = getColumnSelection();
+ return columnSelection != null && columnSelection.hasSelectedColumns();
+ }
+
+ @Override
public boolean hasHiddenColumns()
{
return colSel != null && colSel.hasHiddenColumns();
return ignoreGapsInConsensusCalculation;
}
- // / property change stuff
-
+ // property change stuff
// JBPNote Prolly only need this in the applet version.
- private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
protected boolean showConservation = true;
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
{
- cs.setConservation(Conservation.calculateConservation("All",
- ResidueProperties.propHash, 3, alignment.getSequences(), 0,
- alignment.getWidth(), false, getConsPercGaps(), false));
+ cs.setConservation(Conservation.calculateConservation("All", 3,
+ alignment.getSequences(), 0, alignment.getWidth(), false,
+ getConsPercGaps(), false));
}
}
if (sg != null
&& (sgs = sg.getStartRes()) >= 0
&& sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
+ && !this.hasSelectedColumns())
{
if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
{
}
try
{
- cons = Conservation.calculateConservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
+ cons = Conservation.calculateConservation("All", 3,
alignment.getSequences(), 0, alWidth - 1, false,
ConsPercGaps, quality != null);
} catch (IndexOutOfBoundsException x)
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.DasSourceBrowser;
import jalview.gui.Desktop;
import jalview.gui.FeatureSettings;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
+import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import uk.ac.ebi.picr.model.UPEntry;
+import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
/**
* Implements a runnable for validating a sequence against external databases
*/
public class DBRefFetcher implements Runnable
{
+ private static final String NEWLINE = System.lineSeparator();
+
public interface FetchFinishedListenerI
{
void finished();
}
- private List<FetchFinishedListenerI> listeners;
-
SequenceI[] dataset;
IProgressIndicator progressWindow;
CutAndPasteTransfer output = new CutAndPasteTransfer();
- StringBuffer sbuffer = new StringBuffer();
-
boolean running = false;
/**
*/
uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
- // /This will be a collection of Vectors of sequenceI refs.
+ // This will be a collection of Vectors of sequenceI refs.
// The key will be the seq name or accession id of the seq
- Hashtable seqRefs;
+ Hashtable<String, Vector<SequenceI>> seqRefs;
DbSourceProxy[] dbSources;
SequenceFetcher sfetcher;
+ private List<FetchFinishedListenerI> listeners;
+
private SequenceI[] alseqs;
- /**
+ /*
* when true - retrieved sequences will be trimmed to cover longest derived
* alignment sequence
*/
trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
if (sources == null)
{
- // af.featureSettings_actionPerformed(null);
- String[] defdb = null, otherdb = sfetcher
- .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
- List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
- Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
- .getSelectedSources() : new jalview.gui.DasSourceBrowser()
- .getSelectedSources();
- Enumeration<jalviewSourceI> en = dasselsrc.elements();
- while (en.hasMoreElements())
+ setDatabaseSources(featureSettings, isNucleotide);
+ }
+ else
+ {
+ // we assume the caller knows what they're doing and ensured that all the
+ // db source names are valid
+ dbSources = sources;
+ }
+ }
+
+ /**
+ * Helper method to configure the list of database sources to query
+ *
+ * @param featureSettings
+ * @param forNucleotide
+ */
+ void setDatabaseSources(FeatureSettings featureSettings,
+ boolean forNucleotide)
+ {
+ // af.featureSettings_actionPerformed(null);
+ String[] defdb = null;
+ List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
+ Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
+ .getSelectedSources() : new DasSourceBrowser()
+ .getSelectedSources();
+
+ for (jalviewSourceI src : dasselsrc)
+ {
+ List<DbSourceProxy> sp = src.getSequenceSourceProxies();
+ if (sp != null)
{
- jalviewSourceI src = en.nextElement();
- List<DbSourceProxy> sp = src.getSequenceSourceProxies();
- if (sp != null)
+ selsources.addAll(sp);
+ if (sp.size() > 1)
{
- selsources.addAll(sp);
- if (sp.size() > 1)
- {
- Cache.log.debug("Added many Db Sources for :" + src.getTitle());
- }
+ Cache.log.debug("Added many Db Sources for :" + src.getTitle());
}
}
- // select appropriate databases based on alignFrame context.
- if (isNucleotide)
- {
- defdb = DBRefSource.DNACODINGDBS;
- }
- else
- {
- defdb = DBRefSource.PROTEINDBS;
- }
- List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
- for (String ddb : defdb)
+ }
+ // select appropriate databases based on alignFrame context.
+ if (forNucleotide)
+ {
+ defdb = DBRefSource.DNACODINGDBS;
+ }
+ else
+ {
+ defdb = DBRefSource.PROTEINDBS;
+ }
+ List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+ for (String ddb : defdb)
+ {
+ List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+ if (srcesfordb != null)
{
- List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
- if (srcesfordb != null)
+ for (DbSourceProxy src : srcesfordb)
{
- srces.addAll(srcesfordb);
+ if (!srces.contains(src))
+ {
+ srces.addAll(srcesfordb);
+ }
}
}
- // append the PDB data source, since it is 'special', catering for both
- // nucleotide and protein
- srces.addAll(sfetcher.getSourceProxy(DBRefSource.PDB));
-
- // append the selected sequence sources to the default dbs
- srces.addAll(selsources);
- dbSources = srces.toArray(new DbSourceProxy[0]);
- }
- else
- {
- // we assume the caller knows what they're doing and ensured that all the
- // db source names are valid
- dbSources = sources;
}
+ // append the PDB data source, since it is 'special', catering for both
+ // nucleotide and protein
+ // srces.addAll(sfetcher.getSourceProxy(DBRefSource.PDB));
+
+ srces.addAll(selsources);
+ dbSources = srces.toArray(new DbSourceProxy[srces.size()]);
}
/**
}
// append additional sources
DbSourceProxy[] otherdb = sfetcher
- .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+ .getDbSourceProxyInstances(DasSequenceSource.class);
if (otherdb != null && otherdb.length > 0)
{
DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
*/
public void fetchDBRefs(boolean waitTillFinished)
{
+ // TODO can we not simply write
+ // if (waitTillFinished) { run(); } else { new Thread(this).start(); }
+
Thread thread = new Thread(this);
thread.start();
running = true;
{
key = key.toUpperCase();
- Vector seqs;
+ Vector<SequenceI> seqs;
if (seqRefs.containsKey(key))
{
- seqs = (Vector) seqRefs.get(key);
+ seqs = seqRefs.get(key);
if (seqs != null && !seqs.contains(seq))
{
}
else if (seqs == null)
{
- seqs = new Vector();
+ seqs = new Vector<SequenceI>();
seqs.addElement(seq);
}
}
else
{
- seqs = new Vector();
+ seqs = new Vector<SequenceI>();
seqs.addElement(seq);
}
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
{
- picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator()
+ picrClient = new AccessionMapperServiceLocator()
.getAccessionMapperPort();
}
} catch (Exception e)
System.err.println("Couldn't locate PICR service instance.\n");
e.printStackTrace();
}
+
+ Vector<SequenceI> sdataset = new Vector<SequenceI>(
+ Arrays.asList(dataset));
+ List<String> warningMessages = new ArrayList<String>();
+
int db = 0;
- Vector sdataset = new Vector();
- for (int s = 0; s < dataset.length; s++)
- {
- sdataset.addElement(dataset[s]);
- }
while (sdataset.size() > 0 && db < dbSources.length)
{
- int maxqlen = 1; // default number of queries made to at one time
- System.err.println("Verifying against " + dbSources[db].getDbName());
- boolean dn = false;
+ int maxqlen = 1; // default number of queries made at one time
+ System.out.println("Verifying against " + dbSources[db].getDbName());
// iterate through db for each remaining un-verified sequence
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
sdataset.copyInto(currSeqs);// seqs that are to be validated against
// dbSources[db]
- Vector queries = new Vector(); // generated queries curSeq
- seqRefs = new Hashtable();
+ Vector<String> queries = new Vector<String>(); // generated queries curSeq
+ seqRefs = new Hashtable<String, Vector<SequenceI>>();
int seqIndex = 0;
- jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];
+ DbSourceProxy dbsource = dbSources[db];
+ // for moment, we dumbly iterate over all retrieval sources for a
+ // particular database
+ // TODO: introduce multithread multisource queries and logic to remove a
+ // query from other sources if any source for a database returns a
+ // record
+ maxqlen = dbsource.getMaximumQueryCount();
+
+ while (queries.size() > 0 || seqIndex < currSeqs.length)
{
- // for moment, we dumbly iterate over all retrieval sources for a
- // particular database
- // TODO: introduce multithread multisource queries and logic to remove a
- // query from other sources if any source for a database returns a
- // record
- maxqlen = dbsource.getMaximumQueryCount();
-
- while (queries.size() > 0 || seqIndex < currSeqs.length)
+ if (queries.size() > 0)
{
- if (queries.size() > 0)
- {
- // Still queries to make for current seqIndex
- StringBuffer queryString = new StringBuffer("");
- int numq = 0, nqSize = (maxqlen > queries.size()) ? queries
- .size() : maxqlen;
+ // Still queries to make for current seqIndex
+ StringBuffer queryString = new StringBuffer("");
+ int numq = 0;
+ int nqSize = (maxqlen > queries.size()) ? queries
+ .size() : maxqlen;
- while (queries.size() > 0 && numq < nqSize)
- {
- String query = (String) queries.elementAt(0);
- if (dbsource.isValidReference(query))
- {
- queryString.append((numq == 0) ? "" : dbsource
- .getAccessionSeparator());
- queryString.append(query);
- numq++;
- }
- // remove the extracted query string
- queries.removeElementAt(0);
- }
- // make the queries and process the response
- AlignmentI retrieved = null;
- try
- {
- if (jalview.bin.Cache.log.isDebugEnabled())
- {
- jalview.bin.Cache.log.debug("Querying "
- + dbsource.getDbName() + " with : '"
- + queryString.toString() + "'");
- }
- retrieved = dbsource.getSequenceRecords(queryString
- .toString());
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } catch (OutOfMemoryError err)
+ while (queries.size() > 0 && numq < nqSize)
+ {
+ String query = queries.elementAt(0);
+ if (dbsource.isValidReference(query))
{
- new OOMWarning("retrieving database references ("
- + queryString.toString() + ")", err);
+ queryString.append((numq == 0) ? "" : dbsource
+ .getAccessionSeparator());
+ queryString.append(query);
+ numq++;
}
- if (retrieved != null)
+ // remove the extracted query string
+ queries.removeElementAt(0);
+ }
+ // make the queries and process the response
+ AlignmentI retrieved = null;
+ try
+ {
+ if (Cache.log.isDebugEnabled())
{
- transferReferences(sdataset, dbsource.getDbSource(),
- retrieved, trimDsSeqs);
+ Cache.log.debug("Querying " + dbsource.getDbName()
+ + " with : '" + queryString.toString() + "'");
}
+ retrieved = dbsource.getSequenceRecords(queryString.toString());
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } catch (OutOfMemoryError err)
+ {
+ new OOMWarning("retrieving database references ("
+ + queryString.toString() + ")", err);
+ }
+ if (retrieved != null)
+ {
+ transferReferences(sdataset, dbsource.getDbSource(), retrieved,
+ trimDsSeqs, warningMessages);
}
- else
+ }
+ else
+ {
+ // make some more strings for use as queries
+ for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
{
- // make some more strings for use as queries
- for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
+ SequenceI sequence = dataset[seqIndex];
+ DBRefEntry[] uprefs = DBRefUtils.selectRefs(
+ sequence.getDBRefs(),
+ new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ // });
+ // check for existing dbrefs to use
+ if (uprefs != null && uprefs.length > 0)
{
- SequenceI sequence = dataset[seqIndex];
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRefs(),
- new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
- // });
- // check for existing dbrefs to use
- if (uprefs != null && uprefs.length > 0)
+ for (int j = 0; j < uprefs.length; j++)
{
- for (int j = 0; j < uprefs.length; j++)
- {
- addSeqId(sequence, uprefs[j].getAccessionId());
- queries.addElement(uprefs[j].getAccessionId()
- .toUpperCase());
- }
+ addSeqId(sequence, uprefs[j].getAccessionId());
+ queries.addElement(uprefs[j].getAccessionId().toUpperCase());
}
- else
+ }
+ else
+ {
+ // generate queries from sequence ID string
+ StringTokenizer st = new StringTokenizer(sequence.getName(),
+ "|");
+ while (st.hasMoreTokens())
{
- // generate queries from sequence ID string
- StringTokenizer st = new StringTokenizer(
- sequence.getName(), "|");
- while (st.hasMoreTokens())
+ String token = st.nextToken();
+ UPEntry[] presp = null;
+ if (picrClient != null)
{
- String token = st.nextToken();
- UPEntry[] presp = null;
- if (picrClient != null)
+ // resolve the string against PICR to recover valid IDs
+ try
{
- // resolve the string against PICR to recover valid IDs
- try
- {
- presp = picrClient.getUPIForAccession(token, null,
- picrClient.getMappedDatabaseNames(), null,
- true);
- } catch (Exception e)
- {
- System.err.println("Exception with Picr for '"
- + token + "'\n");
- e.printStackTrace();
- }
- }
- if (presp != null && presp.length > 0)
+ presp = picrClient
+ .getUPIForAccession(token, null,
+ picrClient.getMappedDatabaseNames(),
+ null, true);
+ } catch (Exception e)
{
- for (int id = 0; id < presp.length; id++)
- {
- // construct sequences from response if sequences are
- // present, and do a transferReferences
- // otherwise transfer non sequence x-references directly.
- }
- System.out
- .println("Validated ID against PICR... (for what its worth):"
- + token);
- addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ System.err.println("Exception with Picr for '" + token
+ + "'\n");
+ e.printStackTrace();
}
- else
+ }
+ if (presp != null && presp.length > 0)
+ {
+ for (int id = 0; id < presp.length; id++)
{
- // if ()
- // System.out.println("Not querying source with token="+token+"\n");
- addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ // construct sequences from response if sequences are
+ // present, and do a transferReferences
+ // otherwise transfer non sequence x-references directly.
}
+ System.out
+ .println("Validated ID against PICR... (for what its worth):"
+ + token);
+ addSeqId(sequence, token);
+ queries.addElement(token.toUpperCase());
+ }
+ else
+ {
+ // if ()
+ // System.out.println("Not querying source with token="+token+"\n");
+ addSeqId(sequence, token);
+ queries.addElement(token.toUpperCase());
}
}
}
}
// advance to next database
db++;
- } // all databases have been queries.
- if (sbuffer.length() > 0)
+ } // all databases have been queried
+ if (!warningMessages.isEmpty())
{
- output.setText(MessageManager
- .getString("label.your_sequences_have_been_verified")
- + sbuffer.toString());
+ StringBuilder sb = new StringBuilder(warningMessages.size() * 30);
+ sb.append(MessageManager
+ .getString("label.your_sequences_have_been_verified"));
+ for (String msg : warningMessages)
+ {
+ sb.append(msg).append(NEWLINE);
+ }
+ output.setText(sb.toString());
+
Desktop.addInternalFrame(output,
- MessageManager.getString("label.sequence_names_updated"),
+ MessageManager.getString("label.sequences_updated"),
600, 300);
// The above is the dataset, we must now find out the index
// of the viewed sequence
/**
* Verify local sequences in seqRefs against the retrieved sequence database
- * records.
+ * records. Returns true if any sequence was modified as a result (start/end
+ * changed and/or sequence enlarged), else false.
*
+ * @param sdataset
+ * dataset sequences we are retrieving for
+ * @param dbSource
+ * database source we are retrieving from
+ * @param retrievedAl
+ * retrieved sequences as alignment
* @param trimDatasetSeqs
- *
+ * if true, sequences will not be enlarged to match longer retrieved
+ * sequences, only their start/end adjusted
+ * @param warningMessages
+ * a list of messages to add to
*/
- void transferReferences(Vector sdataset, String dbSource,
- AlignmentI retrievedAl, boolean trimDatasetSeqs) // File
- // file)
+ boolean transferReferences(Vector<SequenceI> sdataset,
+ String dbSource,
+ AlignmentI retrievedAl, boolean trimDatasetSeqs,
+ List<String> warningMessages)
{
- System.out.println("trimming ? " + trimDatasetSeqs);
+ // System.out.println("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
- return;
+ return false;
}
+
+ boolean modified = false;
SequenceI[] retrieved = recoverDbSequences(retrievedAl
.getSequencesArray());
SequenceI sequence = null;
- boolean transferred = false;
- StringBuffer messages = new StringBuffer();
- // Vector entries = new Uniprot().getUniprotEntries(file);
-
- int i, iSize = retrieved.length; // entries == null ? 0 : entries.size();
- // UniprotEntry entry;
- for (i = 0; i < iSize; i++)
+ for (SequenceI retrievedSeq : retrieved)
{
- SequenceI entry = retrieved[i]; // (UniprotEntry) entries.elementAt(i);
-
// Work out which sequences this sequence matches,
// taking into account all accessionIds and names in the file
- Vector sequenceMatches = new Vector();
+ Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
// look for corresponding accession ids
- DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
- entry.getDBRefs(), new String[] { dbSource });
+ DBRefEntry[] entryRefs = DBRefUtils.selectRefs(retrievedSeq.getDBRefs(),
+ new String[] { dbSource });
if (entryRefs == null)
{
System.err
.println("Dud dbSource string ? no entryrefs selected for "
- + dbSource + " on " + entry.getName());
+ + dbSource + " on " + retrievedSeq.getName());
continue;
}
for (int j = 0; j < entryRefs.length; j++)
{
- String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();
+ String accessionId = entryRefs[j].getAccessionId();
// match up on accessionId
if (seqRefs.containsKey(accessionId.toUpperCase()))
{
- Vector seqs = (Vector) seqRefs.get(accessionId);
+ Vector<SequenceI> seqs = seqRefs.get(accessionId);
for (int jj = 0; jj < seqs.size(); jj++)
{
- sequence = (SequenceI) seqs.elementAt(jj);
+ sequence = seqs.elementAt(jj);
if (!sequenceMatches.contains(sequence))
{
sequenceMatches.addElement(sequence);
}
}
}
- if (sequenceMatches.size() == 0)
+ if (sequenceMatches.isEmpty())
{
// failed to match directly on accessionId==query so just compare all
// sequences to entry
- Enumeration e = seqRefs.keys();
+ Enumeration<String> e = seqRefs.keys();
while (e.hasMoreElements())
{
- Vector sqs = (Vector) seqRefs.get(e.nextElement());
+ Vector<SequenceI> sqs = seqRefs.get(e.nextElement());
if (sqs != null && sqs.size() > 0)
{
- Enumeration sqe = sqs.elements();
+ Enumeration<SequenceI> sqe = sqs.elements();
while (sqe.hasMoreElements())
{
sequenceMatches.addElement(sqe.nextElement());
*/
// sequenceMatches now contains the set of all sequences associated with
// the returned db record
- String entrySeq = entry.getSequenceAsString().toUpperCase();
+ final String retrievedSeqString = retrievedSeq.getSequenceAsString();
+ String entrySeq = retrievedSeqString.toUpperCase();
for (int m = 0; m < sequenceMatches.size(); m++)
{
- sequence = (SequenceI) sequenceMatches.elementAt(m);
+ sequence = sequenceMatches.elementAt(m);
// only update start and end positions and shift features if there are
// no existing references
// TODO: test for legacy where uniprot or EMBL refs exist but no
// TODO:
// verify sequence against the entry sequence
+ Mapping mp;
+ final int sequenceStart = sequence.getStart();
+
+ boolean remoteEnclosesLocal = false;
String nonGapped = AlignSeq.extractGaps("-. ",
sequence.getSequenceAsString()).toUpperCase();
-
int absStart = entrySeq.indexOf(nonGapped);
- Mapping mp;
-
- final int sequenceStart = sequence.getStart();
if (absStart == -1)
{
// couldn't find local sequence in sequence from database, so check if
{
// verification failed. couldn't find any relationship between
// entrySeq and local sequence
- messages.append(sequence.getName()
- + " SEQUENCE NOT %100 MATCH \n");
+ // messages suppressed as many-to-many matches are confusing
+ // String msg = sequence.getName()
+ // + " Sequence not 100% match with "
+ // + retrievedSeq.getName();
+ // addWarningMessage(warningMessages, msg);
continue;
}
/*
- * found match for the whole of the database sequence within the local
- * sequence's reference frame.
+ * retrieved sequence is a proper subsequence of local sequence
*/
- transferred = true;
- sbuffer.append(sequence.getName() + " HAS " + absStart
- + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
+ String msg = sequence.getName() + " has " + absStart
+ + " prefixed residues compared to "
+ + retrievedSeq.getName();
+ addWarningMessage(warningMessages, msg);
/*
* So create a mapping to the external entry from the matching region of
*/
mp = new Mapping(null, new int[] { sequenceStart + absStart,
sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
- { entry.getStart(), entry.getStart() + entrySeq.length() - 1 },
+ { retrievedSeq.getStart(), retrievedSeq.getStart() + entrySeq.length() - 1 },
1, 1);
updateRefFrame = false;
}
else
{
/*
- * found a match for the local sequence within sequence from
- * the external database
+ * local sequence is a subsequence of (or matches) retrieved sequence
*/
- transferred = true;
-
- // update start and end of local sequence to place it in entry's
- // reference frame.
- // apply identity map map from whole of local sequence to matching
- // region of database
- // sequence
- mp = null; // Mapping.getIdentityMap();
- // new Mapping(null,
- // new int[] { absStart+sequence.getStart(),
- // absStart+sequence.getStart()+entrySeq.length()-1},
- // new int[] { entry.getStart(), entry.getEnd() }, 1, 1);
- // relocate local features for updated start
+ remoteEnclosesLocal = true;
+ mp = null;
if (updateRefFrame)
{
- if (sequence.getSequenceFeatures() != null)
+ SequenceFeature[] sfs = sequence.getSequenceFeatures();
+ if (sfs != null)
{
/*
* relocate existing sequence features by offset
*/
- SequenceFeature[] sf = sequence.getSequenceFeatures();
int start = sequenceStart;
int end = sequence.getEnd();
- int startShift = 1 - absStart - start; // how much the features
- // are
- // to be shifted by
- for (int sfi = 0; sfi < sf.length; sfi++)
+ int startShift = 1 - absStart - start;
+
+ if (startShift != 0)
{
- if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
+ for (SequenceFeature sf : sfs)
{
- // shift feature along by absstart
- sf[sfi].setBegin(sf[sfi].getBegin() + startShift);
- sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
+ if (sf.getBegin() >= start && sf.getEnd() <= end)
+ {
+ sf.setBegin(sf.getBegin() + startShift);
+ sf.setEnd(sf.getEnd() + startShift);
+ modified = true;
+ }
}
}
}
}
System.out.println("Adding dbrefs to " + sequence.getName()
- + " from " + dbSource + " sequence : " + entry.getName());
- sequence.transferAnnotation(entry, mp);
+ + " from " + dbSource + " sequence : " + retrievedSeq.getName());
+ sequence.transferAnnotation(retrievedSeq, mp);
- absStart += entry.getStart();
+ absStart += retrievedSeq.getStart();
int absEnd = absStart + nonGapped.length() - 1;
if (!trimDatasetSeqs)
{
- // insert full length sequence from record
- sequence.setSequence(entry.getSequenceAsString());
- sequence.setStart(entry.getStart());
+ /*
+ * update start position and/or expand to longer retrieved sequence
+ */
+ if (!retrievedSeqString.equals(sequence.getSequenceAsString())
+ && remoteEnclosesLocal)
+ {
+ sequence.setSequence(retrievedSeqString);
+ modified = true;
+ addWarningMessage(warningMessages,
+ "Sequence for " + sequence.getName()
+ + " expanded from " + retrievedSeq.getName());
+ }
+ if (sequence.getStart() != retrievedSeq.getStart())
+ {
+ sequence.setStart(retrievedSeq.getStart());
+ modified = true;
+ if (absStart != sequenceStart)
+ {
+ addWarningMessage(warningMessages, "Start/end position for "
+ + sequence.getName() + " updated from "
+ + retrievedSeq.getName());
+ }
+ }
}
if (updateRefFrame)
{
if (trimDatasetSeqs)
{
// just fix start/end
- sequence.setStart(absStart);
- sequence.setEnd(absEnd);
+ if (sequence.getStart() != absStart
+ || sequence.getEnd() != absEnd)
+ {
+ sequence.setStart(absStart);
+ sequence.setEnd(absEnd);
+ modified = true;
+ addWarningMessage(warningMessages, "Start/end for "
+ + sequence.getName() + " updated from "
+ + retrievedSeq.getName());
+ }
}
// search for alignment sequences to update coordinate frame for
for (int alsq = 0; alsq < alseqs.length; alsq++)
{
alseqs[alsq].setEnd(ngAlsq.length()
+ alseqs[alsq].getStart() - 1);
+ modified = true;
}
}
}
// ids, so we can query all enabled DAS servers for them ?
}
}
- if (!transferred)
+ return modified;
+ }
+
+ /**
+ * Adds the message to the list unless it already contains it
+ *
+ * @param messageList
+ * @param msg
+ */
+ void addWarningMessage(List<String> messageList, String msg)
+ {
+ if (!messageList.contains(msg))
{
- // report the ID/sequence mismatches
- sbuffer.append(messages);
+ messageList.add(msg);
}
}
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
- Vector nseq = new Vector();
+ Vector<SequenceI> nseq = new Vector<SequenceI>();
for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
{
nseq.addElement(sequencesArray[i]);
- DBRefEntry dbr[] = sequencesArray[i].getDBRefs();
- jalview.datamodel.Mapping map = null;
+ DBRefEntry[] dbr = sequencesArray[i].getDBRefs();
+ Mapping map = null;
for (int r = 0; (dbr != null) && r < dbr.length; r++)
{
if ((map = dbr[r].getMap()) != null)
"exception.ebiembl_retrieval_failed_on", new String[] {
emprefx.toLowerCase(), query.trim() }), e);
}
- return getEmblSequenceRecords(emprefx, query, reply);
+ return getEmblSequenceRecords(emprefx, reply);
}
/**
* @param emprefx
* either EMBL or EMBLCDS strings are allowed - anything else will
* not retrieve emblxml
- * @param query
* @param file
* the EMBL XML file containing the results of a query
* @return
* @throws Exception
*/
- public AlignmentI getEmblSequenceRecords(String emprefx, String query,
- File reply) throws Exception
+ public AlignmentI getEmblSequenceRecords(String emprefx, File reply)
+ throws Exception
{
- EmblFile efile = null;
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ EmblEntry entry = null;
if (reply != null && reply.exists())
{
file = reply.getAbsolutePath();
if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
{
- efile = EmblFile.getEmblFile(reply);
+ entry = EmblFile.getEmblEntry(reply);
}
}
+ // TODO don't need peptides any more?
List<SequenceI> peptides = new ArrayList<SequenceI>();
- if (efile != null)
+ AlignmentI al = null;
+ if (entry != null)
{
- for (EmblEntry entry : efile.getEntries())
+ SequenceI seq = entry.getSequence(emprefx, peptides);
+ if (seq != null)
{
- SequenceI seq = entry.getSequence(emprefx, peptides);
- if (seq != null)
- {
- seqs.add(seq.deriveSequence());
- // place DBReferences on dataset and refer
- }
+ seq.deriveSequence();
+ // place DBReferences on dataset and refer
+ al = new Alignment(new SequenceI[] { seq });
}
}
-
- AlignmentI al = null;
- if (!seqs.isEmpty())
- {
- al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
- }
stopQuery();
return al;
}
import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
import com.stevesoft.pat.Regex;
*/
public class Pdb extends EbiFileRetrievedProxy
{
+ private static final String SEPARATOR = "|";
+ private static final String COLON = ":";
+ private static final int PDB_ID_LENGTH = 4;
+
+
public Pdb()
{
super();
}
- public static final String FEATURE_INSERTION = "INSERTION";
-
- public static final String FEATURE_RES_NUM = "RESNUM";
-
/*
* (non-Javadoc)
*
@Override
public String getAccessionSeparator()
{
- // TODO Auto-generated method stub
return null;
}
public AlignmentI getSequenceRecords(String queries) throws Exception
{
AlignmentI pdbAlignment = null;
- Vector result = new Vector();
String chain = null;
String id = null;
- if (queries.indexOf(":") > -1)
+ if (queries.indexOf(COLON) > -1)
{
- chain = queries.substring(queries.indexOf(":") + 1);
- id = queries.substring(0, queries.indexOf(":"));
+ chain = queries.substring(queries.indexOf(COLON) + 1);
+ id = queries.substring(0, queries.indexOf(COLON));
}
else
{
id = queries;
}
- if (queries.length() > 4 && chain == null)
+
+ /*
+ * extract chain code if it is appended to the id and we
+ * don't already have one
+ */
+ if (queries.length() > PDB_ID_LENGTH && chain == null)
{
- chain = queries.substring(4, 5);
- id = queries.substring(0, 4);
+ chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
+ id = queries.substring(0, PDB_ID_LENGTH);
}
+
if (!isValidReference(id))
{
System.err.println("Ignoring invalid pdb query: '" + id + "'");
chid = pid.getChainCode();
}
- ;
-
}
if (chain == null
|| (chid != null && (chid.equals(chain)
{
// FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
// TODO: suggest simplify naming to 1qip|A as default name defined
- pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
- + "|" + pdbcs.getName());
+ pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
+ + SEPARATOR + pdbcs.getName());
// Might need to add more metadata to the PDBEntry object
// like below
/*
{
onlyPdbEntries.addElement(pdb);
}
+ if ("EMBL".equals(pdb.getType()))
+ {
+ // look for a CDS reference and add it, too.
+ String cdsId = (String) pdb.getProperty("protein sequence ID");
+ if (cdsId != null && cdsId.trim().length() > 0)
+ {
+ // remove version
+ String[] vrs = cdsId.split("\\.");
+ dbr = new DBRefEntry(DBRefSource.EMBLCDS, vrs.length > 1 ? vrs[1]
+ : DBRefSource.UNIPROT + ":" + dbVersion, vrs[0]);
+ dbRefs.add(dbr);
+ }
+ }
+ if ("Ensembl".equals(pdb.getType()))
+ {
+ /*UniprotXML
+ * <dbReference type="Ensembl" id="ENST00000321556">
+ * <molecule id="Q9BXM7-1"/>
+ * <property type="protein sequence ID" value="ENSP00000364204"/>
+ * <property type="gene ID" value="ENSG00000158828"/>
+ * </dbReference>
+ */
+ String cdsId = (String) pdb.getProperty("protein sequence ID");
+ if (cdsId != null && cdsId.trim().length() > 0)
+ {
+ dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
+ + ":" + dbVersion, cdsId.trim());
+ dbRefs.add(dbr);
+
+ }
+ }
+
}
sequence.setPDBId(onlyPdbEntries);
sequence.addSequenceFeature(sf);
}
}
- sequence.setDBRefs(dbRefs.toArray(new DBRefEntry[0]));
+ for (DBRefEntry dbr : dbRefs)
+ {
+ sequence.addDBRef(dbr);
+ }
return sequence;
}
if (outFile != null)
{
FileOutputStream fio = new FileOutputStream(outFile);
+ // fio.write("<?xml version='1.0' encoding='UTF-8'?>\n".getBytes());
byte[] bb = new byte[32 * 1024];
int l;
while ((l = is.read(bb)) > 0)
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.structure.StructureImportSettings;
import java.io.IOException;
import java.util.List;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBfileTest
pf.addAnnotations(al);
return al.getAlignmentAnnotation();
}
+
+ //@formatter:on
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Boolean.TRUE.toString());
+ StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ }
}
/*
* scenario:
* dna1 --> [4, 6] [10,12] --> pep1
- * dna2 --> [1, 3] [7, 9] [13,15] --> pep1
+ * dna2 --> [1, 3] [7, 9] [13,15] --> pep2
*/
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
dna.setDataset(null);
/*
+ * put a variant feature on dna2 base 8
+ * - should transfer to cds2 base 5
+ */
+ dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
+ 0f, null));
+
+ /*
* need a sourceDbRef if we are to construct dbrefs to the CDS
* sequence from the dna contig sequences
*/
assertSame(cds2Dss, m.getSequence());
assertEquals(7, m.getStart());
assertEquals(9, m.getEnd());
+
+ /*
+ * check cds2 acquired a variant feature in position 5
+ */
+ SequenceFeature[] sfs = cds2Dss.getSequenceFeatures();
+ assertNotNull(sfs);
+ assertEquals(1, sfs.length);
+ assertEquals("variant", sfs[0].type);
+ assertEquals(5, sfs[0].begin);
+ assertEquals(5, sfs[0].end);
}
/**
seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
sources = new CrossRef(new SequenceI[] { seq }, al)
.findXrefSourcesForSequences(false);
- assertEquals(4, sources.size());
- assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+ // method is patched to remove EMBL from the sources to match
+ assertEquals(3, sources.size());
+ assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
/*
* add a sequence to the alignment which has a dbref to UNIPROT|A1234
al.addSequence(seq2);
sources = new CrossRef(new SequenceI[] { seq, seq2 }, al)
.findXrefSourcesForSequences(false);
- assertEquals(3, sources.size());
- assertEquals("[EMBLCDS, EMBL, GENEDB]", sources.toString());
+ // method removed EMBL from sources to match
+ assertEquals(2, sources.size());
+ assertEquals("[EMBLCDS, GENEDB]", sources.toString());
}
/**
public void testFindXrefSequences_withFetch()
{
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
- dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
- dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P30419"));
- dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314"));
final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
+ pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+
final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
+ pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
/*
* argument false suppresses adding DAS sources
* 'spliced transcript' with CDS ranges
*/
SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa");
- braf002.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
+ braf002.addDBRef(new DBRefEntry("UNIPROT", "ENSEMBL|0", "H7C5K3"));
braf002.addSequenceFeature(new SequenceFeature("CDS", "", 2, 6, 0f,
null));
braf002.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, 0f,
* which happens to be true for Uniprot,PDB,EMBL but not Pfam,Rfam,Ensembl
*/
final SequenceI pep1 = new Sequence("UNIPROT|P15056", "MAAL");
+ pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
final SequenceI pep2 = new Sequence("UNIPROT|H7C5K3", "QALF");
-
+ pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
/*
* argument false suppresses adding DAS sources
* todo: define an interface type SequenceFetcherI and mock that
*/
final SequenceI x07547 = new Sequence("EMBL|X07547", "cccAAACCCTTTGGG");
DBRefEntry dbref7 = new DBRefEntry("UNIPROT", "0", "P0CE20");
- dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"),
+ dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"),
new MapList(map2)));
x07547.addDBRef(dbref7);
DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4");
}
}
+ @Test(groups = { "Functional" })
+ public void testIsCanonicalPair()
+ {
+ String bases = "acgtuACGTU";
+ for (int i = 0; i < bases.length(); i++)
+ {
+ for (int j = 0; j < bases.length(); j++)
+ {
+ char first = bases.charAt(i);
+ char second = bases.charAt(j);
+ boolean result = Rna.isCanonicalPair(first, second);
+ String pair = new String(new char[] { first, second })
+ .toUpperCase();
+ if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
+ || pair.equals("UA") || pair.equals("GC")
+ || pair.equals("CG"))
+ {
+ assertTrue(pair + " should be valid", result);
+ }
+ else
+ {
+ assertFalse(pair + " should be invalid", result);
+ }
+ }
+ }
+ }
+
/**
* Tests for isOpeningParenthesis with char or String argument
*/
public void testReplace()
{
// seem to need a dataset sequence on the edited sequence here
- seqs[1].setDatasetSequence(seqs[1]);
+ seqs[1].createDatasetSequence();
new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] { seqs[1] },
4, 8, al);
assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
assertEquals(23, startEnd[1]);
}
+ /**
+ * Tests that dbrefs with mappings to sequence get updated if the sequence
+ * acquires a dataset sequence
+ */
+ @Test(groups = "Functional")
+ public void testCreateDataset_updateDbrefMappings()
+ {
+ SequenceI pep = new Sequence("pep", "ASD");
+ SequenceI dna = new Sequence("dna", "aaaGCCTCGGATggg");
+ SequenceI cds = new Sequence("cds", "GCCTCGGAT");
+
+ // add dbref from dna to peptide
+ DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep");
+ dbr.setMap(new Mapping(pep, new MapList(new int[] { 4, 15 }, new int[] {
+ 1, 4 }, 3, 1)));
+ dna.addDBRef(dbr);
+
+ // add dbref from dna to peptide
+ DBRefEntry dbr2 = new DBRefEntry("UNIPROT", "", "pep");
+ dbr2.setMap(new Mapping(pep, new MapList(new int[] { 1, 12 }, new int[]
+ { 1, 4 }, 3, 1)));
+ cds.addDBRef(dbr2);
+
+ // add dbref from peptide to dna
+ DBRefEntry dbr3 = new DBRefEntry("EMBL", "", "dna");
+ dbr3.setMap(new Mapping(dna, new MapList(new int[] { 1, 4 }, new int[] {
+ 4, 15 }, 1, 3)));
+ pep.addDBRef(dbr3);
+
+ // add dbref from peptide to cds
+ DBRefEntry dbr4 = new DBRefEntry("EMBLCDS", "", "cds");
+ dbr4.setMap(new Mapping(cds, new MapList(new int[] { 1, 4 }, new int[] {
+ 1, 12 }, 1, 3)));
+ pep.addDBRef(dbr4);
+
+ AlignmentI protein = new Alignment(new SequenceI[] { pep });
+
+ /*
+ * create the alignment dataset
+ */
+ ((Alignment) protein).createDatasetAlignment();
+
+ AlignmentI ds = protein.getDataset();
+
+ // should be 3 sequences in dataset
+ assertEquals(3, ds.getHeight());
+ assertTrue(ds.getSequences().contains(pep.getDatasetSequence()));
+ assertTrue(ds.getSequences().contains(dna));
+ assertTrue(ds.getSequences().contains(cds));
+
+ /*
+ * verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset
+ */
+ DBRefEntry[] dbRefs = pep.getDBRefs();
+ assertEquals(2, dbRefs.length);
+ assertSame(dna, dbRefs[0].map.to);
+ assertSame(cds, dbRefs[1].map.to);
+ assertEquals(1, dna.getDBRefs().length);
+ assertSame(pep.getDatasetSequence(), dna.getDBRefs()[0].map.to);
+ assertEquals(1, cds.getDBRefs().length);
+ assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
+ }
+
}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNotSame;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
import java.util.Arrays;
import java.util.BitSet;
+import java.util.Collections;
+import java.util.ConcurrentModificationException;
import java.util.List;
import org.testng.annotations.Test;
// removing an element in the list removes it
cs.removeElement(2);
- // ...but not from the copy list!
- assertEquals(2, sel.size());
+ // ...and also from the read-only view
+ assertEquals(1, sel.size());
sel = cs.getSelected();
assertEquals(1, sel.size());
assertEquals(new Integer(5), sel.get(0));
* were added
*/
@Test(groups = { "Functional" })
- public void testGetSelection()
+ public void testGetSelected()
{
ColumnSelection cs = new ColumnSelection();
int[] sel = { 4, 3, 7, 21 };
cs.addElement(col);
}
- List<Integer> selected1 = cs.getSelected();
- assertEquals(4, selected1.size());
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertEquals("[4, 3, 7, 21]", selected.toString());
/*
- * getSelected returns a copy, verify the list
- * is externally immutable
+ * getSelected returns a read-only view of the list
+ * verify the view follows any changes in it
*/
- selected1.clear();
- List<Integer> selected2 = cs.getSelected();
- assertNotSame(selected1, selected2);
- assertEquals(4, selected2.size());
- int i = 0;
- for (int col : sel)
+ cs.removeElement(7);
+ cs.addElement(1);
+ cs.removeElement(4);
+ assertEquals("[3, 21, 1]", selected.toString());
+ }
+
+ /**
+ * Test to verify that the list returned by getSelection cannot be modified
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSelected_isReadOnly()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(3);
+
+ List<Integer> selected = cs.getSelected();
+ try
+ {
+ selected.clear();
+ fail("expected exception");
+ } catch (UnsupportedOperationException e)
+ {
+ // expected
+ }
+ try
+ {
+ selected.add(1);
+ fail("expected exception");
+ } catch (UnsupportedOperationException e)
+ {
+ // expected
+ }
+ try
+ {
+ selected.remove(3);
+ fail("expected exception");
+ } catch (UnsupportedOperationException e)
{
- assertEquals(col, selected2.get(i++).intValue());
+ // expected
}
+ try
+ {
+ Collections.sort(selected);
+ fail("expected exception");
+ } catch (UnsupportedOperationException e)
+ {
+ // expected
+ }
+ }
- cs.removeElement(7);
+ /**
+ * Test that demonstrates a ConcurrentModificationException is thrown if you
+ * change the selection while iterating over it
+ */
+ @Test(
+ groups = "Functional",
+ expectedExceptions = { ConcurrentModificationException.class })
+ public void testGetSelected_concurrentModification()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(0);
cs.addElement(1);
- cs.removeElement(4);
+ cs.addElement(2);
- List<Integer> selected3 = cs.getSelected();
- assertEquals(3, selected3.size());
- assertEquals(3, selected3.get(0).intValue());
- assertEquals(21, selected3.get(1).intValue());
- assertEquals(1, selected3.get(2).intValue());
+ /*
+ * simulate changing the list under us (e.g. in a separate
+ * thread) while iterating over it -> ConcurrentModificationException
+ */
+ List<Integer> selected = cs.getSelected();
+ for (Integer col : selected)
+ {
+ if (col.intValue() == 0)
+ {
+ cs.removeElement(1);
+ }
+ }
}
@Test(groups = "Functional")
assertTrue(selected.contains(6));
assertTrue(selected.contains(10));
}
+
+ @Test(groups = "Functional")
+ public void testCopyConstructor()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(3);
+ cs.addElement(1);
+ cs.hideColumns(10, 11);
+ cs.hideColumns(5, 7);
+ assertEquals("[5, 7]", Arrays.toString(cs.getHiddenColumns().get(0)));
+
+ ColumnSelection cs2 = new ColumnSelection(cs);
+ assertTrue(cs2.hasSelectedColumns());
+ assertTrue(cs2.hasHiddenColumns());
+ // order of column selection is preserved
+ assertEquals("[3, 1]", cs2.getSelected().toString());
+ assertEquals(2, cs2.getHiddenColumns().size());
+ // hidden columns are held in column order
+ assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenColumns().get(0)));
+ assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenColumns().get(1)));
+ }
}
/*
+ assertEquals(case7, case9);
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotEquals;
+import static org.testng.Assert.assertNotSame;
import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import jalview.datamodel.PDBEntry.Type;
//import org.testng.Assert;
import org.testng.annotations.AfterMethod;
PDBEntry pdbEntry = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB,
"x/y/z/File");
+ // id comparison is not case sensitive
PDBEntry case1 = new PDBEntry("1XYZ", "A", PDBEntry.Type.PDB,
"x/y/z/File");
+ // chain code comparison is not case sensitive
PDBEntry case2 = new PDBEntry("1xyz", "a", PDBEntry.Type.PDB,
"x/y/z/File");
+ // different type
PDBEntry case3 = new PDBEntry("1xyz", "A", PDBEntry.Type.FILE,
"x/y/z/File");
+ // different everything
PDBEntry case4 = new PDBEntry(null, null, null, null);
+ // null id
PDBEntry case5 = new PDBEntry(null, "A", PDBEntry.Type.PDB,
"x/y/z/File");
+ // null chain
PDBEntry case6 = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
"x/y/z/File");
+ // null type
PDBEntry case7 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
+ // null file
PDBEntry case8 = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB, null);
+ // identical to case7
PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
+ // different file only
+ PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
/*
- * assertions will invoke PDBEntry.equals()
+ * assertEquals will invoke PDBEntry.equals()
*/
assertFalse(pdbEntry.equals(null));
assertFalse(pdbEntry.equals("a"));
assertNotEquals(case5, pdbEntry);
assertNotEquals(case6, pdbEntry);
assertNotEquals(case7, pdbEntry);
- assertEquals(case8, pdbEntry);
+ assertNotEquals(case8, pdbEntry);
assertEquals(case7, case9);
+ assertNotEquals(case9, case10);
+
+ // add properties
+ case7.setProperty("hello", "world");
+ assertNotEquals(case7, case9);
+ case9.setProperty("hello", "world");
+ assertEquals(case7, case9);
+ case9.setProperty("hello", "WORLD");
+ assertNotEquals(case7, case9);
/*
* change string wrapper property to string...
pdbEntry.setChainCode(null);
assertNull(pdbEntry.getChainCode());
}
+
+ @Test(groups = { "Functional" })
+ public void testGetType()
+ {
+ assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("FILE"));
+ assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("File"));
+ assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file"));
+ assertNotSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file "));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testTypeMatches()
+ {
+ // TODO Type.matches() is not used - delete?
+ assertTrue(PDBEntry.Type.FILE.matches("FILE"));
+ assertTrue(PDBEntry.Type.FILE.matches("File"));
+ assertTrue(PDBEntry.Type.FILE.matches("file"));
+ assertFalse(PDBEntry.Type.FILE.matches("FILE "));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testUpdateFrom()
+ {
+ PDBEntry pdb1 = new PDBEntry("3A6S", null, null, null);
+ PDBEntry pdb2 = new PDBEntry("3A6S", null, null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+
+ /*
+ * mismatch of pdb id not allowed
+ */
+ pdb2 = new PDBEntry("1A70", "A", null, null);
+ assertFalse(pdb1.updateFrom(pdb2));
+ assertNull(pdb1.getChainCode());
+
+ /*
+ * match of pdb id is not case sensitive
+ */
+ pdb2 = new PDBEntry("3a6s", "A", null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "A");
+ assertEquals(pdb1.getId(), "3A6S");
+
+ /*
+ * add chain - with differing case for id
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, null);
+ pdb2 = new PDBEntry("3a6s", "A", null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "A");
+
+ /*
+ * change of chain is not allowed
+ */
+ pdb2 = new PDBEntry("3A6S", "B", null, null);
+ assertFalse(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "A");
+
+ /*
+ * change chain from null
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, null);
+ pdb2 = new PDBEntry("3A6S", "B", null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "B");
+
+ /*
+ * set file and type
+ */
+ pdb2 = new PDBEntry("3A6S", "B", Type.FILE, "filePath");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getFile(), "filePath");
+ assertEquals(pdb1.getType(), Type.FILE.toString());
+
+ /*
+ * change of file is not allowed
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, "file1");
+ pdb2 = new PDBEntry("3A6S", "A", null, "file2");
+ assertFalse(pdb1.updateFrom(pdb2));
+ assertNull(pdb1.getChainCode());
+ assertEquals(pdb1.getFile(), "file1");
+
+ /*
+ * set type without change of file
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, "file1");
+ pdb2 = new PDBEntry("3A6S", null, Type.PDB, "file1");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getType(), Type.PDB.toString());
+
+ /*
+ * set file with differing case of id and chain code
+ */
+ pdb1 = new PDBEntry("3A6S", "A", null, null);
+ pdb2 = new PDBEntry("3a6s", "a", Type.PDB, "file1");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getType(), Type.PDB.toString());
+ assertEquals(pdb1.getId(), "3A6S"); // unchanged
+ assertEquals(pdb1.getFile(), "file1"); // updated
+ assertEquals(pdb1.getChainCode(), "A"); // unchanged
+
+ /*
+ * changing nothing returns true
+ */
+ pdb1 = new PDBEntry("3A6S", "A", Type.PDB, "file1");
+ pdb2 = new PDBEntry("3A6S", null, null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "A");
+ assertEquals(pdb1.getType(), Type.PDB.toString());
+ assertEquals(pdb1.getFile(), "file1");
+
+ /*
+ * add and update properties only
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, null);
+ pdb2 = new PDBEntry("3A6S", null, null, null);
+ pdb1.setProperty("destination", "mars");
+ pdb1.setProperty("hello", "world");
+ pdb2.setProperty("hello", "moon");
+ pdb2.setProperty("goodbye", "world");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getProperty("destination"), "mars");
+ assertEquals(pdb1.getProperty("hello"), "moon");
+ assertEquals(pdb1.getProperty("goodbye"), "world");
+
+ /*
+ * add properties only
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, null);
+ pdb2 = new PDBEntry("3A6S", null, null, null);
+ pdb2.setProperty("hello", "moon");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getProperty("hello"), "moon");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testConstructor_fromDbref()
+ {
+ PDBEntry pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70"));
+ assertEquals(pdb.getId(), "1A70");
+ assertNull(pdb.getChainCode());
+ assertNull(pdb.getType());
+ assertNull(pdb.getFile());
+
+ /*
+ * from dbref with chain code appended
+ */
+ pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70B"));
+ assertEquals(pdb.getId(), "1A70");
+ assertEquals(pdb.getChainCode(), "B");
+
+ /*
+ * from dbref with overlong accession
+ */
+ pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70BC"));
+ assertEquals(pdb.getId(), "1A70BC");
+ assertNull(pdb.getChainCode());
+
+ /*
+ * from dbref which is not for PDB
+ */
+ try
+ {
+ pdb = new PDBEntry(new DBRefEntry("PDBe", "0", "1A70"));
+ fail("Expected exception");
+ } catch (IllegalArgumentException e)
+ {
+ // expected;
+ }
+ }
+
}
* is there a usecase for this ? setDatasetSequence should throw an error if
* this actually occurs.
*/
- sq.getDatasetSequence().setDatasetSequence(sq); // loop!
+ try
+ {
+ sq.getDatasetSequence().setDatasetSequence(sq); // loop!
+ Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
+ } catch (IllegalArgumentException e)
+ {
+ // TODO Jalview error/exception class for raising implementation errors
+ assertTrue(e.getMessage().toLowerCase()
+ .contains("implementation error"));
+ }
assertNull(sq.getSequenceFeatures());
}
sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+ // these are the same as ones already added
DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
- DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version1", "2PDB");
+ DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
pdb2pdb });
- sq.getDatasetSequence().addDBRef(pdb1pdb);
- sq.getDatasetSequence().addDBRef(pdb2pdb);
+ sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
+ sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
sq.getDatasetSequence().addDBRef(
- new DBRefEntry("PDB", "version3", "3PDB"));
+ new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
sq.getDatasetSequence().addDBRef(
- new DBRefEntry("PDB", "version4", "4PDB"));
+ new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
PDBEntry pdbe1a=new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
new AlignmentAnnotation("Test annot", "Test annot description",
annots));
Assert.assertEquals(sq.getDescription(), "Test sequence description..");
- Assert.assertEquals(sq.getDBRefs().length, 5);
+ Assert.assertEquals(sq.getDBRefs().length, 5); // DBRefs are on dataset
+ // sequence
Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
Assert.assertNotNull(sq.getAnnotation());
Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
- Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 4);
+ Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 5); // same
+ // as
+ // sq.getDBRefs()
Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
4);
Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
Assert.assertEquals(derived.getDescription(),
"Test sequence description..");
- Assert.assertEquals(derived.getDBRefs().length, 4); // come from dataset
+ Assert.assertEquals(derived.getDBRefs().length, 5); // come from dataset
Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
Assert.assertNotNull(derived.getAnnotation());
Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
- Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 4);
+ Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 5);
Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
.size(), 4);
Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
assertTrue(primaryDBRefs.contains(dbr1));
assertTrue(primaryDBRefs.contains(dbr3));
}
+
+ /**
+ * Test the method that updates the list of PDBEntry from any new DBRefEntry
+ * for PDB
+ */
+ @Test(groups = { "Functional" })
+ public void testUpdatePDBIds()
+ {
+ PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null);
+ seq.addPDBId(pdbe1);
+ seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234"));
+ seq.addDBRef(new DBRefEntry("PDB", "0", "1A70"));
+ seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa"));
+ seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
+ // 7 is not a valid chain code:
+ seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
+
+ seq.updatePDBIds();
+ List<PDBEntry> pdbIds = seq.getAllPDBEntries();
+ assertEquals(4, pdbIds.size());
+ assertSame(pdbe1, pdbIds.get(0));
+ // chain code got added to 3A6S:
+ assertEquals("B", pdbe1.getChainCode());
+ assertEquals("1A70", pdbIds.get(1).getId());
+ // 4BQGA is parsed into id + chain
+ assertEquals("4BQG", pdbIds.get(2).getId());
+ assertEquals("a", pdbIds.get(2).getChainCode());
+ assertEquals("2GIS7", pdbIds.get(3).getId());
+ assertNull(pdbIds.get(3).getChainCode());
+ }
+
+ /**
+ * Test the method that either adds a pdbid or updates an existing one
+ */
+ @Test(groups = { "Functional" })
+ public void testAddPDBId()
+ {
+ PDBEntry pdbe = new PDBEntry("3A6S", null, null, null);
+ seq.addPDBId(pdbe);
+ assertEquals(1, seq.getAllPDBEntries().size());
+ assertSame(pdbe, seq.getPDBEntry("3A6S"));
+ assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive
+
+ // add the same entry
+ seq.addPDBId(pdbe);
+ assertEquals(1, seq.getAllPDBEntries().size());
+ assertSame(pdbe, seq.getPDBEntry("3A6S"));
+
+ // add an identical entry
+ seq.addPDBId(new PDBEntry("3A6S", null, null, null));
+ assertEquals(1, seq.getAllPDBEntries().size());
+ assertSame(pdbe, seq.getPDBEntry("3A6S"));
+
+ // add a different entry
+ PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null);
+ seq.addPDBId(pdbe2);
+ assertEquals(2, seq.getAllPDBEntries().size());
+ assertSame(pdbe, seq.getAllPDBEntries().get(0));
+ assertSame(pdbe2, seq.getAllPDBEntries().get(1));
+
+ // update pdbe with chain code, file, type
+ PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath");
+ seq.addPDBId(pdbe3);
+ assertEquals(2, seq.getAllPDBEntries().size());
+ assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ
+ assertEquals("3A6S", pdbe.getId()); // unchanged
+ assertEquals("A", pdbe.getChainCode()); // updated
+ assertEquals(Type.PDB.toString(), pdbe.getType()); // updated
+ assertEquals("filepath", pdbe.getFile()); // updated
+ assertSame(pdbe2, seq.getAllPDBEntries().get(1));
+
+ // add with a different file path
+ PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2");
+ seq.addPDBId(pdbe4);
+ assertEquals(3, seq.getAllPDBEntries().size());
+ assertSame(pdbe4, seq.getAllPDBEntries().get(2));
+
+ // add with a different chain code
+ PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath");
+ seq.addPDBId(pdbe5);
+ assertEquals(4, seq.getAllPDBEntries().size());
+ assertSame(pdbe5, seq.getAllPDBEntries().get(3));
+ }
+
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testSetDatasetSequence_toSelf()
+ {
+ seq.setDatasetSequence(seq);
+ }
+
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testSetDatasetSequence_cascading()
+ {
+ SequenceI seq2 = new Sequence("Seq2", "xyz");
+ seq2.createDatasetSequence();
+ seq.setDatasetSequence(seq2);
+ }
}
package jalview.datamodel.xdb.embl;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
// not the whole sequence but enough for this test...
List<SequenceI> peptides = new ArrayList<SequenceI>();
SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
- EmblFile ef = EmblTestHelper.getEmblFile();
- assertEquals(1, ef.getEntries().size());
- EmblEntry testee = ef.getEntries().get(0);
+ EmblEntry ef = EmblTestHelper.getEmblFile();
+ assertNotNull(ef);
+ // assertEquals(1, ef.getEntries().size());
+ // EmblEntry testee = ef.getEntries().get(0);
String sourceDb = "EMBL";
- SequenceI dna = testee.makeSequence(sourceDb);
+ SequenceI dna = ef.makeSequence(sourceDb);
/*
* parse three CDS features, with two/one/no Uniprot cross-refs
*/
- for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
+ for (EmblFeature feature : ef.getFeatures())
{
if ("CDS".equals(feature.getName()))
{
- testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
+ ef.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
}
}
package jalview.datamodel.xdb.embl;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import jalview.datamodel.DBRefEntry;
-import java.util.Vector;
-
import org.testng.annotations.Test;
public class EmblFileTest
@Test(groups = { "Functional" })
public void testGetEmblFile()
{
- Vector<EmblEntry> entries = EmblTestHelper.getEmblFile().getEntries();
- assertEquals(1, entries.size());
- EmblEntry entry = entries.get(0);
+ EmblEntry entry = EmblTestHelper.getEmblFile();
+ assertNotNull(entry);
+ // assertEquals(1, entries.size());
+ // EmblEntry entry = entries.get(0);
assertEquals("X07547", entry.getAccession());
assertEquals("C. trachomatis plasmid", entry.getDescription());
// adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
// dna and translations truncated for convenience
private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
- + "<ROOT>"
+ // + "<ROOT>"
+ "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
+ " dataClass=\"STD\" taxonomicDivision=\"PRO\""
+ " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
*/
+ "<sequence>GGTATGTCCTCTAGTACAAAC\n"
+ "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
- + "</sequence></entry></ROOT>";
+ + "</sequence></entry>";
- static EmblFile getEmblFile()
+ static EmblEntry getEmblFile()
{
- return EmblFile.getEmblFile(new StringReader(TESTDATA));
+ return EmblFile.getEntry(new StringReader(TESTDATA));
}
}
@BeforeMethod(alwaysRun = true)
public void setUp()
{
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+ Boolean.FALSE.toString());
Cache.applicationProperties.setProperty("ADD_SS_ANN",
Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
{
PDBfile mctest = new PDBfile(false, false, false, pdbStr,
AppletFormatAdapter.FILE);
- JmolParser jtest = new JmolParser(false, false, false, pdbStr,
- jalview.io.AppletFormatAdapter.FILE);
+ JmolParser jtest = new JmolParser(pdbStr, AppletFormatAdapter.FILE);
Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
assertTrue(
private void checkFirstAAIsAssoc(SequenceI sq)
{
- assertTrue("No secondary structure assigned for protein sequence.",
+ assertTrue("No secondary structure assigned for protein sequence for "
+ + sq.getName(),
sq.getAnnotation() != null && sq.getAnnotation().length >= 1
&& sq.getAnnotation()[0].hasIcons);
assertTrue(
PDBfile mctest = new PDBfile(false, false, false,
pastePDBDataWithChainBreak,
AppletFormatAdapter.PASTE);
- boolean annotFromStructure = false;
- boolean localSecondaryStruct = false;
- boolean serviceSecondaryStruct = false;
- JmolParser jtest = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct,
- pastePDBDataWithChainBreak,
- jalview.io.AppletFormatAdapter.PASTE);
+ JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
+ AppletFormatAdapter.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
{
PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
AppletFormatAdapter.PASTE);
- boolean annotFromStructure = false;
- boolean localSecondaryStruct = false;
- boolean serviceSecondaryStruct = false;
- JmolParser jtest = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
- jalview.io.AppletFormatAdapter.PASTE);
+ JmolParser jtest = new JmolParser(pdbWithAltLoc,
+ AppletFormatAdapter.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
{
mctest = new PDBfile(false, false, false, testFile,
AppletFormatAdapter.FILE);
- jtest = new JmolParser(false, false, false, testFile,
- jalview.io.AppletFormatAdapter.FILE);
+ jtest = new JmolParser(testFile, AppletFormatAdapter.FILE);
} catch (IOException e)
{
System.err.println("Exception thrown while parsing : " + pdbStr);
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[] { "-props",
- "test/jalview/testProps.jvprops" });
+ Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" });
}
@BeforeMethod(alwaysRun = true)
assertTrue(ssmMappings.contains(acf2));
assertFalse(ssmMappings.contains(acf3));
}
+
+ /**
+ * Test for JAL-1306 - conservation thread should run even when only Quality
+ * (and not Conservation) is enabled in Preferences
+ */
+ @Test(groups = { "Functional" })
+ public void testUpdateConservation_qualityOnly()
+ {
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.FALSE.toString());
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.FALSE.toString());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", FormatAdapter.FILE);
+ AlignmentAnnotation[] anns = af.viewport.getAlignment().getAlignmentAnnotation();
+ assertNotNull("No annotations found", anns);
+ assertEquals("More than one annotation found", 1, anns.length);
+ assertTrue("Annotation is not Quality",
+ anns[0].description.startsWith("Alignment Quality"));
+ Annotation[] annotations = anns[0].annotations;
+ assertNotNull("Quality annotations are null", annotations);
+ assertNotNull("Quality in column 1 is null", annotations[0]);
+ assertTrue("No quality value in column 1", annotations[0].value > 10f);
+ }
}
@BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
// pin down annotation sort order for test
Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name());
import jalview.bin.Cache;
import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
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.JTextArea;
import org.testng.annotations.AfterClass;
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.setPreferredSize(new Dimension(400, 400));
+ String msg = "This is a dummy string. See the dummy string go.\n";
+ msg += msg; // 2
+ msg += msg; // 4
+ msg += msg; // 8
+ msg += msg; // 16
+ JTextArea evt = new JTextArea(
+ "Click here and drag text over this window to freeze java.\n\n"
+ + msg);
+ cont.add(evt);
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()
+ // final JMenu jm = new JMenu("Do");
+ // JMenuItem jmi = new JMenuItem("this");
+ // jm.add(jmi);
+ evt.addMouseListener(new MouseAdapter()
{
@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();
});
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;
- }
- });
+ // 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)
{
seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
26);
- seq.setDatasetSequence(seq);
+ seq.createDatasetSequence();
for (int x = 1; x < 5; x++)
{
DBRefEntry dbRef = new DBRefEntry();
}
@Test(groups = { "Functional" })
- public void populateFilterComboBoxTest()
+ public void populateFilterComboBoxTest() throws InterruptedException
{
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
- sc.populateFilterComboBox();
+ sc.populateFilterComboBox(false);
int optionsSize = sc.getCmbFilterOption().getItemCount();
assertEquals(3, optionsSize); // if structures are not discovered then don't
// populate filter options
- sc.setStructuresDiscovered(true);
- sc.populateFilterComboBox();
- try
- {
- Thread.sleep(2000);
- } catch (InterruptedException e)
- {
- e.printStackTrace();
- }
+ sc.populateFilterComboBox(true);
optionsSize = sc.getCmbFilterOption().getItemCount();
assertTrue(optionsSize > 3); // if structures are found, filter options
// should be populated
SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU:19 1gaqA", sf[0].getDescription());
+ assertEquals("GLU: 19 1gaqA", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR:314 1gaqA", sf[295].getDescription());
+ assertEquals("TYR: 314 1gaqA", sf[295].getDescription());
/*
* 1GAQ/B
sf = al.getSequenceAt(1).getSequenceFeatures();
assertEquals(98, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("ALA:1 1gaqB", sf[0].getDescription());
+ assertEquals("ALA: 1 1gaqB", sf[0].getDescription());
assertEquals("RESNUM", sf[97].getType());
- assertEquals("ALA:98 1gaqB", sf[97].getDescription());
+ assertEquals("ALA: 98 1gaqB", sf[97].getDescription());
/*
* 1GAQ/C
sf = al.getSequenceAt(2).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU:19 1gaqC", sf[0].getDescription());
+ assertEquals("GLU: 19 1gaqC", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR:314 1gaqC", sf[295].getDescription());
+ assertEquals("TYR: 314 1gaqC", sf[295].getDescription());
}
@Test(groups = { "Functional" })
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
- al.getSequenceAt(i).setDatasetSequence(
- al.getSequenceAt(i).createDatasetSequence());
+ al.getSequenceAt(i).createDatasetSequence();
}
assertNotNull("Couldn't read supplied alignment data.", al);
return al;
for (Sequence seq : seqs)
{
- seq.setDatasetSequence(seq);
+ seq.createDatasetSequence();
expectedSeqs.put(seq.getName(), seq);
}
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
- al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+ al.getSequenceAt(i).createDatasetSequence();
}
String outputfile = rf.formatSequences(ioformat, al, true);
System.out.println("Output file in '" + ioformat + "':\n"
}
assertEquals(
"Generated and imported alignment have different annotation sets",
- aa_new_size, aa_original_size);
+ aa_original_size, aa_new_size);
// check sequences, annotation and features
SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
+ codon.getKey() + "\", \"" + codon.getValue() + "\");");
}
}
-
- @Test(groups = { "Functional" })
- public void checkOldCodonagainstNewCodonTable()
- {
- // note - this test will be removed once the old codon table (including
- // Vectors) is removed
- String additional = "", failtrans = "", differentTr = "";
- for (String amacid : ResidueProperties.codonHash.keySet())
- {
- for (String codon : ResidueProperties.codonHash.get(amacid))
- {
- String trans = ResidueProperties.codonTranslate(codon);
- String oldtrans = ResidueProperties._codonTranslate(codon);
- if (trans == null)
- {
- additional += "\nOld translation table includes additional codons for "
- + amacid + " : " + codon;
- }
- if (oldtrans == null)
- {
- failtrans += ("\nold translation routine failed for old translation entry (aa was "
- + amacid + " codon was " + codon + ")");
- }
- if (!oldtrans.equals(trans))
- {
- differentTr += ("\nDifferent translation for old and new routines: "
- + amacid
- + " "
- + codon
- + " => expected "
- + oldtrans
- + " and got " + trans);
- }
- }
- }
- assertTrue("" + additional + "\n" + failtrans + "\n" + differentTr,
- additional.length() == 0 && failtrans.length() == 0
- && differentTr.length() == 0);
- }
}
SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("GLU:19 1gaqA", sf.getDescription());
+ assertEquals("GLU: 19 1gaqA", sf.getDescription());
/*
* Verify a RESNUM sequence feature in the StructureSelectionManager mapped
sf = map.sequence.getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("ALA:1 1gaqB", sf.getDescription());
+ assertEquals("ALA: 1 1gaqB", sf.getDescription());
}
}
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
// ensure 'add annotation from structure' is selected
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
@Test(groups = { "Network" }, enabled = true)
public void testRnaSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT",
"PDB");
List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
@Test(groups = { "Network" }, enabled = true)
public void testPdbSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
StructureImportSettings
.setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
@Test(groups = { "Network" }, enabled = true)
public void testmmCifSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
testRetrieveProteinSeqFromPDB();
}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.datamodel.UniprotEntry;
import java.io.Reader;
+ "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
+ "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
+ "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
+ + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
+ "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
+ "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
+ "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
* Check cross-references
*/
Vector<PDBEntry> xrefs = entry.getDbReference();
- assertEquals(2, xrefs.size());
+ assertEquals(3, xrefs.size());
PDBEntry xref = xrefs.get(0);
assertEquals("2FSQ", xref.getId());
assertEquals("2FSR", xref.getId());
assertEquals("PDBsum", xref.getType());
assertFalse(xref.getProperties().hasMoreElements());
+
+ xref = xrefs.get(2);
+ assertEquals("AE007869", xref.getId());
+ assertEquals("EMBL", xref.getType());
+ assertEquals("AAK85932.1",
+ xref.getProperty("protein sequence ID"));
+ assertEquals("Genomic_DNA",
+ xref.getProperty("molecule type"));
}
+ @Test(groups = { "Functional" })
+ public void testGetUniprotSequence()
+ {
+ UniprotEntry entry = new Uniprot().getUniprotEntries(
+ new StringReader(UNIPROT_XML)).get(0);
+ SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
+ assertNotNull(seq);
+ assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
+
+ }
/**
* Test the method that formats the sequence id
*/
sfs[0].getType()));
assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB,
- DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL });
+ new String[] { DBRefSource.UNIPROT });
assertNotNull(dr);
assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
assertEquals("Expected cross reference map to be one amino acid", dr[0]
package jalview.ws.sifts;
import jalview.api.DBRefEntryI;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
@BeforeTest(alwaysRun = true)
public void setUpSiftsClient() throws SiftsException
{
+ // read test props before manipulating config
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
// SIFTs entries are updated weekly - so use saved SIFTs file to enforce
// test reproducibility
new SiftsSettings();
git://source.jalview.org / jalview.git / commitdiff
