<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
<classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
<classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
- <classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
<classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
<classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
<classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
<classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
<classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
<classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
+ <classpathentry kind="lib" path="lib/groovy-all-2.4.6-indy.jar"/>
<classpathentry kind="output" path="classes"/>
</classpath>
<echo message="build - compiles all necessary files for Application" />
<echo message="makedist - compiles and places all necessary jar files into directory dist" />
<echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
- <echo message=" this needs a keystore and key. Add -Dtimestamp to timestamp signed jars"/>
+ <echo message=" this needs a keystore and key."/>
+ <echo message=" Add -Dtimestamp to timestamp signed jars"/>
+ <echo message=" -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
<echo message=" See docs/building.html for more information." />
<echo message="compileApplet - compiles all necessary files for Applet" />
<echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
<!-- locally valid proxy for signing with external time server -->
<property name="proxyPort" value="80"/>
<property name="proxyHost" value="sqid"/>
+ <!-- key sign/digest algorithms -->
+ <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
+ <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
<!-- default TestNG groups to run -->
<property name="testng-groups" value="Functional" />
</target>
<target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA"
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
<fileset dir="${packageDir}">
<include name="*.jar" />
</signjar>
</target>
<target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
<fileset dir="${packageDir}">
<include name="*.jar" />
</fileset>
<p>Here are some scripts to get you started:</p>
<ul><li>Getting the title, alignment and first sequence from the current alignFrame<br>
<pre>
-def alf = Jalview.getAlignframes();
+def alf = Jalview.getAlignFrames();
print alf[0].getTitle();
def alignment = alf[0].viewport.alignment;
def seq = alignment.getSequenceAt(0);
<p>
You will need the following (hopefully):<br>
<ul>
-<li>Java development kit (JDK1.6 is the recommended platform for developing with Jalview, although JDK1.7 seems to work too!).</li>
-<li>Ant (we think 1.5.4 is quite sufficient to use the simple build
-file supplied, and it seems to work with later versions e.g. 1.7).</li>
+<li>Java development kit (JDK1.8 is now the recommended platform for developing with Jalview.</li>
+<li>Ant (1.7 or later will be needed for some of the jarsigning tools).</li>
</ul>
With any luck, after setting your paths and JAVA_HOME correctly, you
just need to change to the Jalview directory and run ant (this works
-from JBuilder and eclipse too, but NetBeans is a bit trickier).
+from eclipse too, but NetBeans is a bit trickier).
<pre>
ant
</pre>
dist. But first you need to make your own key:
<p><strong>Making your own key</strong></p>
-<p>The ant 'makefulldist' target assumes that a keystore exists in a
-directory 'keys'. To make a key accessible using the default settings
-in the build.xml file then make the keys directory and add the
-jarsigner key with the following :
-</p>
-<pre>
-mkdir keys
-keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
--storepass alignmentisfun -alias jalview
- (you will have to answer some personal questions here)
-ant makedist
- (should eventually generate a Jalview.jnlp file
- in ./dist along with a set of signed jars using the jalview
- key)
-</pre>
-
- <p>
+ <p>The ant 'makefulldist' target assumes that a keystore exists in
+ a directory 'keys'. To make a key accessible using the default
+ settings in the build.xml file then make the keys directory and add
+ the jarsigner key with the following :</p>
+ <pre>mkdir keys</pre>
+ <pre>keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
+ -storepass alignmentisfun -sigalg SHA1withRSA -keyalg RSA -alias jalview</pre>
+ <em>(you will have to answer some personal questions here)</em>
+ <pre>ant makedist -DWebStartLocation="file://.pathtojalviewsource./dist" -Dapplication.codebase="*"</pre>
+ <p>This should eventually generate a jalview.jnlp file in ./dist
+ along with a set of signed jars using the jalview key). In order to
+ test locally via webstart you'll now need to add 'file:/' to your
+ java webstart security exception list. Then:</p>
+ <pre>javaws file://.pathtojalviewsource./dist/jalview.jnlp</pre>
+ <p>Please remember to remove that entry afterwards, since it will leave
+ your system vulnerable to malicious code.
+ </p>
+ <p>
<strong>Building the JalviewLite applet<br>
</strong> The JalviewLite applet is compiled using a subset of the packages in
the src directory (specifically: MCView, and jalview.{datamodel,
-->
-<div id="view_decorated" name="view_decorated" style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#appletDeployment"> here</a> to view decorated page</b></div>
+<div id="view_decorated" name="view_decorated" style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#appletDeployment"> here </a> to view decorated page</b></div>
<!-- content start -->
-<h2><a name="appletdeploymentnotes"/>Notes on applet deployment</h2>
- <ul>
- <li>Package all your data files into a single (or multiple) zip / jar
- files. This is very useful to reduce download time of large data files.
- The applet archive tag can take multiple entries separated by commas,
- eg<br>
- <pre><applet code="jalview.bin.JalviewLite"<em><strong>
- archive="jalviewApplet.jar, mydata.zip"</strong></em>>
- </pre></li>
- <li> Use Jalview for input to a HTML form. For an example of how to
- code this using Javascript, click <a href="javascript:doSubmit('formComplete')">here</a>.
- <br>
- </li>
- <li>Embed Jalview into the web page, without the "Start Jalview"
- button by setting the embed parameter to true;<br>
- <param name="embedded"
- value="true"> </li>
- <li><a href="javascript:doSubmit('appletParameters')">View full list of supported parameters here.</a> </li>
- </ul>
-
- <p><strong>**NEW FEATURES** in Jalview 2.9</strong></p>
+<h2 name="appletDeployment"> Notes on applet deployment</h2>
+<table width=80% border="1">
+ <tr><th colspan="2" align="center">Required Dependency Downloads</th></tr>
+ <tr>
+ <th>Dependency</th>
+ <th>Description</th>
+ </tr>
+ <tr>
+ <td><a href="http://www.jalview.org/builds/develop/examples/jalviewApplet.jar">JalviewApplet.jar</a> </td>
+ <td>Main Jalview Applet Jar</td>
+ </tr>
+ <tr>
+ <td><a href="http://www.jalview.org/builds/develop/examples/JmolApplet-14.2.14_2015.06.11.jar">JmolApplet-14.2.14_2015.06.11.jar</a> </td>
+ <td>Jmol Applet Jar</td>
+ </tr>
+ <tr>
+ <td><a href="http://www.jalview.org/builds/develop/examples/java-json.jar">java-json.jar</a></td>
+ <td>Required for BioJSON Generation</td>
+ </tr>
+ <tr>
+ <td><a href="http://www.jalview.org/builds/develop/examples/json_simple-1.1.jar">json_simple-1.1.jar</a></td>
+ <td>Required for BioJSON Generation</td>
+ </tr>
+</table>
+
+<p>To run Jalview applet in your web page download the Jars listed above. The snippet below shows a minimal code for embedding Jalview applet into a web page.
+<pre><code>
+<applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+ <param name="permissions" value="sandbox" />
+ <param name="file" value="plantfdx.fa" />
+ <param name="features" value="plantfdx.features" />
+ <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF" />
+ <param name="showFullId" value="false" />
+ <param name="embedded" value="true" />
+ <param name="linkLabel_1" value="Uniprot" />
+ <param name="linkUrl_1" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$" />
+ <param name="linkLabel_2" value="EMBL-EBI Search" />
+ <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$" />
+ <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp" />
+</applet>
+</code></pre>
+
+
+
+
+<ul>
+ <li>View full list of <a href="javascript:doSubmit('appletParameters')"> supported applet parameters here.</a></li>
+ <li>Package all your data files into a single (or multiple) zip /
+ jar files. This is very useful to reduce download time of large data
+ files. The applet archive tag can take multiple entries separated by
+ commas, eg<br> <pre><applet code="jalview.bin.JalviewLite"<em><strong> archive="jalviewApplet.jar, mydata.zip"</strong></em>>
+ </pre>
+ </li>
+ <li>Use Jalview for input to a HTML form. For an example of how to
+ code this using Javascript, click <a
+ href="javascript:doSubmit('formComplete')">here</a>. <br>
+ </li>
+ <li>Embed Jalview into the web page, without the "Start
+ Jalview" button by setting the embed parameter to true;<br>
+ <param name="embedded" value="true">
+ </li>
+ <li>For more examples, see the links to the left.</li>
+</ul>
+
+<table border="1" width=80%>
+ <tr><th colspan="2">Applet Release History</th>
+ <tr>
+ <th>Release</th>
+
+ <th>New Features / required changes</th>
+ </tr>
+ <tr>
+ <td><strong>2.9<br>(Latest)</strong></td>
+ <td>
<ul>
<li>Split Views for cDNA and Protein alignments<br/>Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna
</li>
<pre>archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,<font color="red">java-json.jar,json_simple-1.1.jar</font>"</pre>
</li>
</ul>
- </p>
- <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
- <ul>
+ </td>
+ </tr>
+ <tr>
+ <td><strong>2.8</strong></td>
+ <td><ul>
<li>Normalised sequence logo display
</li>
<li>RNA secondary structure annotation row
original Jalview structure viewer will still be available. <br>
</li>
- </ul>
- <p><strong>**NEW FEATURES** in Jalview 2.7</strong></p>
- <ul>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><strong>2.7</strong></td>
+ <td><ul>
<li>Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>
<li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul>
</li>
the Jmol binary distribution available at the Jmol Sourceforge site,
or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
<li>Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</li>
- </ul>
- <br><strong>**NEW FEATURES** in Jalview 2.5</strong></p>
- <ul>
- <li>New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</li>
- </ul>
- <br><strong>**NEW FEATURES** in Jalview 2.4</strong></p>
- <ul>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><strong>2.5</strong></td>
+ <td><ul>
+ <li>New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</li> </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><strong>2.4</strong></td>
+ <td><ul>
<li>New applet API methods for feature display control, views, and obtaining current selection via javascript.</li>
<li>Group show and hide parameters:
"showfeaturegroups" and
<li>"debug" parameter to control verbosity of the applet's console output.</li>
<li>"showbutton" parameter to disable launch button and open JalviewLite immediatly.</li>
<li>"nojmol" parameter to disable check for Jmol classes.</li>
- </ul><br>
- <strong>**NEW FEATURES** in Jalview 2.3</strong></p>
- <ul>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><strong>2.3</strong></td>
+ <td><ul>
<li>Note that Parameter "PDBFile" now takes
the PDB file followed by a space separated list of alignment sequence
ids to associate the structure to. It is also possible to associate
<li>Note parameter "PDBSeq" is no longer required.<br>
</li>
<li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="/development">versions archive if you want to download the old Jmol applet</a>.</li>
- <p> </p>
- </li>
- </ul>
- <strong>**NEW FEATURES** in Jalview 2.1</strong>
- <ul>
+
+ </ul></td>
+ </tr>
+ <tr>
+ <td><strong>2.1</strong></td>
+ <td><ul>
<li>Jalview Applet can read and display JNet secondary structure annotation
directly via the <strong>jnetfile</strong> parameter. <br>
</li>
<param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT"><br>
</pre>(All the usual Jalview File formats are valid, however each
new line in an alignment file must be entered as a parameter)</li>
- </ul>
+ </ul></td>
+ </tr>
+</table>
+
+
<!-- content end -->
the applet can be interacted with <em>via</em> its
<a href="javascript:doSubmit('jalviewLiteJs')">Javascript API</a>.
</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java may not be compatible with these settings. </p>
- <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
+ <p>For additional deployment notes, <a href="javascript:doSubmit('appletDeployment')">see Applet Deployment</a>.</p>
<p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
<a name="parameters"></a> <table width="97%" class="borderTable" align="center" >
<tr>
<!-- boiler plate link to alternate demopage -->
<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
</div>
-</div>
-
<!-- content template start -->
<p align="left">
<h2>JalviewLite Button Examples</h2>
-Try out JalviewLite by pressing one of the buttons below.<br/>
- For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+Try out JalviewLite by pressing one of the buttons below.
+ <a href="view-source:http://www.jalview.org/builds/develop/examples/applets.html" target="_blank">View the source for the examples below here</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/applets.html">this page</a> and viewing the page source manually).<br/>
+ For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletDeployment')"><strong>applet deployment,</strong></a> <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters,</strong></a> and other documentation in the links to the left.</p>
<p> </p><div align="center">
<p align="center">
<h2>Ferredoxins, chloroplast precursor related UniRef50
<!-- boiler plate link to alternate demopage -->
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
</div>
</div>
<li><a href="plantfdx.annotations">plantfdx.annotations</a> -
Jalview Alignment Annotations File</li>
</ul>
+ <a href="view-source:http://www.jalview.org/builds/develop/examples/embedded.html" target="_blank">View the source code for this example here</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/embedded.html">this page</a> and viewing the page source manually).<p>
<applet
code="jalview.bin.JalviewLite" width="756" height="560"
archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
modeltofiles+="1gaq.txt";
</script>
<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
-</div>
+
</div>
<!-- content template start -->
ST-TURN-IIL blue|255,0,255|absolute|20.0|95.0|below|66.0
-GAMMA-TURN-CLASSIC red|0,255,255|20.0|95.0|below|66.0
+GAMMA-TURN-CLASSIC red|0,255,255|20.0|95.0|below|66.0
BETA-TURN-IR 9a6a94
BETA-TURN-IL d6a6ca
BETA-BULGE 1dc451
ST-MOTIF ac25a1
STARTGROUP uniprot
+<html><a href="http://pfam.xfam.org/family/PF00111">Pfam family</a></html> FER_CAPAA -1 0 0 Pfam
Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_CAPAA -1 8 83 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html> FER_CAPAA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath
Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER_CAPAN -1 55 130 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_13</a></html> FER_CAPAN -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER1_SOLLC -1 55 130 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_13</a></html> FER1_SOLLC -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_13</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath
Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_PEA -1 60 135 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html> FER1_PEA -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 63_13</a></html> Q7XA98_TRIPR -1 63 138 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 63_13</a></html> Q7XA98_TRIPR -1 63 138 Pfam
Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath
Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 59_13</a></html> FER1_MESCR -1 59 134 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 59_13</a></html> FER1_MESCR -1 59 134 Pfam
Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 58_13</a></html> FER1_SPIOL -1 58 133 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 58_13</a></html> FER1_SPIOL -1 58 133 Pfam
Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER3_RAPSA -1 8 83 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html> FER3_RAPSA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath
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>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_BRANA -1 8 83 Pfam
+<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.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER2_ARATH -1 60 135 Pfam
+<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
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_11</a></html> Q93Z60_ARATH -1 60 118 Pfam
+<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
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_MAIZE -1 60 135 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html> FER1_MAIZE -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath
-<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 52_12</a></html> O80429_MAIZE -1 52 127 Pfam
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 52_12</a></html> O80429_MAIZE -1 52 127 Pfam
Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath
ENDGROUP uniprot
<!-- boiler plate link to alternate demopage -->
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
+
</div>
</div>
<p>Using the Javascript API to fill out forms using data from JalviewLite
<br/>Click the Javascript buttons below to interact with the Applet
instance on the page.</p>
-View the source in your browser to see how it has been done. <br/>
+ <a href="view-source:http://www.jalview.org/builds/develop/examples/formComplete.html" target="_blank">View the source here to see how it has been done</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/formComplete.html">this page</a> and viewing the page source manually).<br/>
<a name="api">View the full <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite API documentation</a>.</a>
<applet code="jalview.bin.JalviewLite" width="0" height="0"
archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar" name="Jalview">
* Example script that registers two alignment annotation calculators
* - one that counts residues in a column with Pfam annotation
* - one that counts only charged residues with Pfam annotation
+ * To try this, first load uniref50.fa from the examples folder, then load features
+ * from examples/exampleFeatures.txt, before running this script from the Groovy console.
+
* Modify this example as required to count by column any desired value that can be
* derived from the residue and sequence features at each position of an alignment.
*/
* - a closure (groovy function) that tests whether to include a residue
* - a closure that tests whether to increment count based on sequence features
*/
-def getColumnCounter = { name, desc, residueTester, featureCounter ->
+def getColumnCounter = { name, desc, acceptResidue, acceptFeatures ->
[
getName: { name },
getDescription: { desc },
count:
{ res, feats ->
def c = 0
- if (residueTester.call(res))
+ if (acceptResidue.call(res))
{
- if (featureCounter.call(feats))
+ if (acceptFeatures.call(feats))
{
c++
}
}
/*
- * Define annotation that counts any residue with Pfam domain annotation
+ * Define an annotation that counts any residue with Pfam domain annotation
*/
def pfamAnnotation = getColumnCounter("Pfam", "Count of residues with Pfam domain annotation", {true}, hasPfam)
/*
- * Define annotation that counts charged residues with Pfam domain annotation
+ * Define an annotation that counts charged residues with Pfam domain annotation
*/
def chargedPfamAnnotation = getColumnCounter("Pfam charged", "Count of charged residues with Pfam domain annotation", isCharged, hasPfam)
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
// do something groovy in jalview
-print "Hello World.\n";
-def alf = Jalview.getAlignFrames();
+println "Hello World.\n"
+println "First sequence is " + currentAlFrame.viewport.alignment.getSequenceAt(0).getDisplayId(true)
+
+def alf = Jalview.getAlignFrames()
for (ala in alf)
{
// ala is an jalview.gui.AlignFrame object
- print ala.getTitle()+"\n";
+ println ala.getTitle()
// get the parent jalview.datamodel.Alignment from the alignment viewport
- def alignment = ala.viewport.alignment;
+ def alignment = ala.viewport.alignment
// get the first sequence from the jalview.datamodel.Alignment object
- def seq = alignment.getSequenceAt(0);
+ def seq = alignment.getSequenceAt(0)
}
+Jalview.quit()
<!-- boiler plate link to alternate demopage -->
<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
-</div>
</div>
<!-- content template start -->
<param name="showbutton" value="false"/>
</applet>
-<h2>Javascript Launch Button</h2><p>The button below demonstrates how JalviewLite can be launched via a javascript action.</p>
+<h2>Javascript Launch Button</h2><p>The button below demonstrates how JalviewLite can be launched via a javascript action. <a href="view-source:http://www.jalview.org/builds/develop/examples/javascriptLaunch.html" target="_blank">View the source here to see how it has been done</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/javascriptLaunch.html">this page</a> and viewing the page source manually). </p>
<input type="button" name="Button1" value="Start"
onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
<!-- boiler plate link to alternate demopage -->
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
+
</div>
</div>
<h2>JalviewLite Linked Applets Demo</h2>
<p>The two applets below use <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
- </p>
+ <a href="view-source:http://www.jalview.org/builds/develop/examples/linkedapplets_ng.html" target="_blank">View the source here to see how it has been done</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/linkedapplets_ng.html">this page</a> and viewing the page source manually).</p>
<applet
Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_83</a></html> FER_CAPAA -1 8 83 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html> FER_CAPAA -1 8 83 Pfam
Chloroplast FER_CAPAN -1 1 47 TRANSIT
Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
Phosphothreonine FER_CAPAN -1 136 136 MOD_RES
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_130</a></html> FER_CAPAN -1 55 130 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_130</a></html> FER_CAPAN -1 55 130 Pfam
Chloroplast FER1_SOLLC -1 1 47 TRANSIT
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_130</a></html> FER1_SOLLC -1 55 130 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_130</a></html> FER1_SOLLC -1 55 130 Pfam
Evidence: EI4 Q93XJ9_SOLTU -1 1 48 SIGNAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_130</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_130</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
Chloroplast FER1_PEA -1 1 52 TRANSIT
L -> I (in strain: cv. Onward) FER1_PEA -1 59 59 VARIANT
I -> L (in strain: cv. Onward) FER1_PEA -1 85 85 VARIANT
Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
YPTS -> PPPA (in Ref. 2) FER1_PEA -1 132 135 CONFLICT
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER1_PEA -1 60 135 Pfam
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 63_138</a></html> Q7XA98_TRIPR -1 63 138 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html> FER1_PEA -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 63_138</a></html> Q7XA98_TRIPR -1 63 138 Pfam
Chloroplast FER1_MESCR -1 1 51 TRANSIT
Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 59_134</a></html> FER1_MESCR -1 59 134 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 59_134</a></html> FER1_MESCR -1 59 134 Pfam
Chloroplast FER1_SPIOL -1 1 50 TRANSIT
STRAND FER1_SPIOL -1 52 59 STRAND
TURN FER1_SPIOL -1 60 61 TURN
STRAND FER1_SPIOL -1 130 133 STRAND
STRAND FER1_SPIOL -1 135 138 STRAND
HELIX FER1_SPIOL -1 142 144 HELIX
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 58_133</a></html> FER1_SPIOL -1 58 133 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 58_133</a></html> FER1_SPIOL -1 58 133 Pfam
I -> V FER3_RAPSA -1 8 8 VARIANT
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
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.sanger.ac.uk/family/PF00111">Pfam 8_83</a></html> FER3_RAPSA -1 8 83 Pfam
+<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.sanger.ac.uk/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_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.sanger.ac.uk/family/PF00111">Pfam 8_83</a></html> FER_BRANA -1 8 83 Pfam
+<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.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER2_ARATH -1 60 135 Pfam
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_118</a></html> Q93Z60_ARATH -1 60 118 Pfam
+<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
+<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
STRAND FER1_MAIZE -1 72 74 STRAND
STRAND FER1_MAIZE -1 132 135 STRAND
STRAND FER1_MAIZE -1 137 141 STRAND
TURN FER1_MAIZE -1 142 142 TURN
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER1_MAIZE -1 60 135 Pfam
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 52_127</a></html> O80429_MAIZE -1 52 127 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html> FER1_MAIZE -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 52_127</a></html> O80429_MAIZE -1 52 127 Pfam
ENDGROUP uniprot
ACTACGACACGACGACGACGACG
>seq2
CDEQEATGTQDAQEQAQC
-
function() {
subCatContainer.scrollTop($(this).scrollTop());
});
-</script></hmtl>
\ No newline at end of file
+</script></html>
<strong>Normalise Consensus Logo</strong> to scale all columns of the
logo to the same height.
+ <p>
+ <strong>Group Consensus</strong><br>
+ If sequence groups have been defined, then selecting option 'Group Consensus' in the <a href="../menus/alwannotation.html">Annotations menu</a> will
+ result in Consensus being calculated for each group, as well as the alignment as a whole.
+ </p>
<p>
<strong>cDNA Consensus</strong>
</p>
(e.g. !proline).
</p>
<p>
- <em>Colouring an alignment by conservation</em><br>
+ <strong>Colouring an alignment by conservation</strong><br>
Conservation scores can be used to colour an alignment. This is
explained further in the help page for <a
href="../colourSchemes/conservation.html"
>conservation colouring</a>.
</p>
+ <p>
+ <strong>Group conservation</strong><br>
+ If sequence groups have been defined, then selecting option 'Group Conservation' in the <a href="../menus/alwannotation.html">Annotations menu</a> will
+ result in Conservation being calculated for each group, as well as the alignment as a whole.
+ </p>
</body>
</html>
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>
followed by a <em>description</em> for the row, which is shown in a
tooltip when the user mouses over the annotation row's label. Since
Jalview 2.7, the description field may also contain HTML tags (in
- the same way as a <a href="featuresFile.html">sequence feature's</a>
+ the same way as a <a href="featuresFormat.html">sequence feature's</a>
label), providing the text is enclosed in an <html/> tag.
<ul>
<em>Please note: URL links embedded in HTML descriptions are
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>BioJSON in Jalviwe</title>
+<title>BioJSON in Jalview</title>
</head>
<body>
<p>
the bottom of the list is rendered <em>below</em> a feature higher
up in the list.<br> <em><strong>You can change
the order of a feature by dragging it up and down the list with
- the mouse</strong></em>.
+ the mouse (not applet)</strong></em>.
</p>
<p>
The <strong><em>Optimise order</em></strong> button (currently only
</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
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+<meta charset="UTF-8">
+<title>mmCIF File Format</title>
+</head>
+<body>
+ <strong>mmCIF File Format</strong>
+ <p>The mmCIF file format (macromolecular Crystallographic
+ Information) was developed under the auspices of the International Union of Crystallography (IUCr) to extend the Crystallographic Information
+ File (CIF) data representation used for describing small molecule
+ structures and associated diffraction experiments.</p>
+ <strong>Merits of mmCIF file format</strong>
+ <ul>
+ <li>Large structures (containing >62 chains and/or 99999 ATOM
+ records) that cannot be fully represented in the PDB file format are
+ available in the PDB archive as single PDBx/mmCIF files.</li>
+ <li>PDBx/mmCIF file format provides richer data annotation</li>
+ <li>PDBx/mmCIF became the standard PDB archive format in 2014.
+ Since 2016 the PDB File Format is no longer being modified or
+ extended to support new content.
+ </li>
+ </ul>
+
+ <em>mmCIF file format support for importing 3D structure data from
+ flat file and EMBL-PDBe via mmCIF was added in Jalview 2.9.1</em>
+</body>
+</html>
\ No newline at end of file
retrieved by the <a href="seqfetch.html">Sequence Fetcher</a>, and
allows sequence features to be mapped directly from Uniprot das
sources to their coding region on EMBL sequence records.
+ </p>
+ <p>In Jalview 2.9.1 <a href="siftsmapping.html">SIFTS Mapping</a> was added as a better means for explicitly identifying the coordinates corresponding to a displayed sequence when viewing a PDB structure associated with a sequence </p>
</body>
</html>
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+<meta charset="UTF-8">
+<title>SIFTS Mapping</title>
+</head>
+<body>
+
+ <p><strong>SIFTS Mapping</strong></p>
+
+ <p>
+ SIFTS (Structure integration with function, taxonomy
+ and sequences) provides an up-to-date resource for residue-level
+ mapping between Uniprot and PDB entries. The information is updated and
+ released weekly simultaneously with the release of new PDB entries.
+ SIFTS Entries are published as XML files and made publicly available via an FTP
+ site hosted at the European Bioinformatics Institute.
+ </p>
+
+ <p>
+ At the point of viewing a PDB structure, Jalview downloads a SIFTS file
+ for the target entry and uses it to accurately map the sequence residues with the
+ structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch
+ Alignment algorithm to map sequence residues to structure residues, and that may not
+ always result to a correct mapping since it is computational determined.
+ </p>
+
+ <p>
+ The default method for 'Sequence ↔ Structure' mapping can be configured
+ in the Structure tab in the <strong>Tools → Preferences</strong> dialog box. When 'SIFTS'
+ is enabled as the default, all mappings between 'Sequence ↔ Structure' is
+ performed via SIFTS provided that there is a valid SIFTS entry for PDB structure. If no
+ valid SIFTS resource is available, then the 'Sequence ↔ Structure' mapping falls
+ back to Needleman and Wunsch Alignment algorithm.
+ </p>
+
+ <p>To verify the mapping method used, you can view the mapping output via the structure viewer menu <strong>File → View mapping.</strong> A sample mapping output can be seen in the screenshot below. The highlighted position shows the method used. </p>
+ <p>
+ <img src="sifts_mapping_output.png" align="left" alt="SIFTS mapping output" />
+ </p>
+
+ <p><em>SIFTS Mapping integration was added in Jalview 2.9.1</em></p>
+
+</body>
+</html>
\ No newline at end of file
<li>On selecting rows, columns or regions in one alignment, the
corresponding selection is made in the other</li>
<li>Sequence ordering in one alignment (using the cursor, or <strong><a
- href="../calculate/sorting.html"
+ href="../calculations/sorting.html"
>"Calculate→Sort")</a></strong> is also applied to the other
</li>
<li>Editing (gap insertion / deletion) in the protein alignment
panels.</li>
<li>Panel heights are adjusted dragging the divider between
them using the mouse</li>
- <li><a href="menus/alwview.html"><strong>"View→New
+ <li><a href="../menus/alwview.html"><strong>"View→New
View / Expand Views / Gather Views"</strong></a> behave as for a normal
alignment window, but always create new views as Split Frames</li>
</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>UniProtKB query fields</title>
+</head>
+
+<body>
+ <p>
+ <strong>UniProtKB query fields</strong>
+ </p>
+<p>Supported query fields for searching specific data in UniProtKB (see also <a href="text-search">query syntax</a>).</p>
+
+<table border="1" width="95%">
+ <tr>
+ <th>Field</th>
+ <th>Example</th>
+ <th>Description</th>
+ </tr>
+ <tr>
+ <td>accession</td>
+ <td>
+ <code>accession:P62988</code>
+ </td>
+ <td>
+ Lists all entries with the primary or secondary
+ accession number P62988.
+ </td>
+ </tr>
+ <tr>
+ <td>active</td>
+ <td>
+ <code>active:no </code>
+ </td>
+ <td>
+ Lists all obsolete entries.
+ </td>
+ </tr>
+ <tr>
+ <td>annotation</td>
+ <td>
+ <code>
+ annotation:(type:non-positional)
+ <br />
+ annotation:(type:positional)
+ <br />
+ annotation:(type:mod_res "Pyrrolidone carboxylic acid" evidence:experimental)
+ </code>
+ </td>
+ <td>
+ Lists all entries with:
+ <ul>
+ <li>any general annotation (comments [CC])</li>
+ <li>any sequence annotation (features [FT])</li>
+ <li>at least one amino acid modified with a Pyrrolidone carboxylic acid group</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>author</td>
+ <td>
+ <code>
+ author:ashburner
+ </code>
+ </td>
+ <td>
+ Lists all entries with at least one reference co-authored by Michael Ashburner.
+ </td>
+ </tr>
+ <tr>
+ <td>cdantigen</td>
+ <td>
+ <code>
+ cdantigen:CD233
+ </code>
+ </td>
+ <td>
+ Lists all entries whose cluster of differentiation number is CD233.
+ </td>
+ </tr>
+ <tr>
+ <td>citation</td>
+ <td>
+ <code>
+ citation:("intracellular structural proteins")
+ <br />
+ citation:(author:ashburner journal:nature)
+ citation:9169874
+ </code>
+ </td>
+ <td>
+ Lists all entries with a literature citation:
+ <ul>
+ <li>containing the phrase "intracellular structural proteins" in either title or abstract</li>
+ <li>co-authored by Michael Ashburner and published in Nature</li>
+ <li>with the PubMed identifier 9169874</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>cluster</td>
+ <td>
+ <code>
+ cluster:UniRef90_A5YMT3
+ </code>
+ </td>
+ <td>
+ Lists all entries in the UniRef 90% identity cluster whose
+ representative sequence is UniProtKB entry A5YMT3.
+ </td>
+ </tr>
+ <tr>
+ <td>count</td>
+ <td>
+ <code>
+ annotation:(type:transmem count:5)<br />
+ annotation:(type:transmem count:[5 TO *])<br />
+ annotation:(type:cofactor count:[3 TO *])
+ </code>
+ </td>
+ <td>Lists all entries with:
+ <ul>
+ <li>exactly 5 transmembrane regions</li>
+ <li>5 or more transmembrane regions</li>
+ <li>3 or more Cofactor comments</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>created</td>
+ <td>
+ <code>
+ created:[20121001 TO *]<br />
+ reviewed:yes AND created:[current TO *]
+ </code>
+ </td>
+ <td>
+ Lists all entries created since October 1st 2012.<br />
+ Lists all new UniProtKB/Swiss-Prot entries in the last release.
+ </td>
+ </tr>
+ <tr>
+ <td>database</td>
+ <td>
+ <code>
+ database:(type:pfam)
+ <br />
+ database:(type:pdb 1aut)
+ </code>
+ </td>
+ <td>
+ Lists all entries with:
+ <ul>
+ <li>a cross-reference to the Pfam database</li>
+ <li>a cross-reference to the PDB database entry 1aut</li>
+ </ul>
+
+ </td>
+ </tr>
+ <tr>
+ <td>domain</td>
+ <td>
+ <code>
+ domain:VWFA
+ </code>
+ </td>
+ <td>
+ Lists all entries with a Von Willebrand factor type A domain described
+ in the 'Family and Domains' section.
+ </td>
+ </tr>
+ <tr>
+ <td>ec</td>
+ <td>
+ <code>
+ ec:3.2.1.23
+ </code>
+ </td>
+ <td>
+ Lists all beta-galactosidases.
+ </td>
+ </tr>
+ <tr>
+ <td>evidence</td>
+ <td>
+ <code>
+ annotation:(type:signal evidence:ECO_0000269)<br />
+ (type:mod_res phosphoserine evidence:ECO_0000269)<br />
+ annotation:(type:function AND evidence:ECO_0000255)
+ </code>
+ </td>
+ <td>Lists all entries with:
+ <ul>
+ <li>a signal sequence whose positions have been experimentally proven</li>
+ <li>experimentally proven phosphoserine sites</li>
+ <li>a function manually asserted according to rules</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>family</td>
+ <td>
+ <code>
+ family:serpin
+ </code>
+ </td>
+ <td>
+ Lists all entries belonging to the Serpin family of proteins.
+ </td>
+ </tr>
+ <tr>
+ <td>fragment</td>
+ <td>
+ <code>
+ fragment:yes
+ </code>
+ </td>
+ <td>
+ Lists all entries with an incomplete sequence.
+ </td>
+ </tr>
+
+ <tr>
+ <td>gene</td>
+ <td>
+ <code>
+ gene:HSPC233
+ </code>
+ </td>
+ <td>
+ Lists all entries for proteins encoded by gene HSPC233.
+ </td>
+ </tr>
+ <tr>
+ <td>go</td>
+ <td>
+ <code>
+ go:cytoskeleton
+ <br />
+ go:0015629
+ </code>
+ </td>
+ <td>
+ Lists all entries associated with:
+ <ul>
+ <li>a GO term containing the word "cytoskeleton"</li>
+ <li>the GO term Actin cytoskeleton and any subclasses</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>host</td>
+ <td>
+ <code>
+ host:mouse
+ <br />
+ host:10090
+ <br />
+ host:40674
+ </code>
+ </td>
+ <td>
+ Lists all entries for viruses infecting:
+ <ul>
+ <li>organisms with a name containing the word "mouse"</li>
+ <li>Mus musculus (Mouse)</li>
+ <li>all mammals (all taxa classified under the taxonomy node for Mammalia)</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>id</td>
+ <td>
+ <code>id:P00750</code>
+ </td>
+ <td>
+ Returns the entry with the primary
+ accession number P00750.
+ </td>
+ </tr>
+ <tr>
+ <td>inn</td>
+ <td>
+ <code>
+ inn:Anakinra
+ </code>
+ </td>
+ <td>
+ Lists all entries whose "International Nonproprietary Name" is Anakinra.
+ </td>
+ </tr>
+ <tr>
+ <td>interactor</td>
+ <td>
+ <code>
+ interactor:P00520
+ </code>
+ </td>
+ <td>
+ Lists all entries describing interactions with the protein described by
+ entry P00520.
+ </td>
+ </tr>
+ <tr>
+ <td>keyword</td>
+ <td>
+ <code>
+ keyword:toxin
+ </code>
+ </td>
+ <td>
+ Lists all entries associated with the keyword Toxin.
+ </td>
+ </tr>
+ <tr>
+ <td>length</td>
+ <td>
+ <code>
+ length:[500 TO 700]
+ </code>
+ </td>
+ <td>
+ Lists all entries describing sequences of length between 500 and 700 residues.
+ </td>
+ </tr>
+ <tr>
+ <td>lineage</td>
+ <td />
+ <td>
+ This field is a synonym for the field <code>taxonomy</code>.
+ </td>
+ </tr>
+ <tr>
+ <td>mass</td>
+ <td>
+ <code>
+ mass:[500000 TO *]
+ </code>
+ </td>
+ <td>
+ Lists all entries describing sequences with a mass of at least 500,000 Da.
+ </td>
+ </tr>
+ <tr>
+ <td>method</td>
+ <td>
+ <code>
+ method:maldi
+ <br />
+ method:xray
+ </code>
+ </td>
+ <td>
+ Lists all entries for proteins identified by: matrix-assisted laser
+ desorption/ionization (MALDI), crystallography (X-Ray). The
+ <code>method</code> field searches names of physico-chemical
+ identification methods in the 'Biophysicochemical properties' subsection of the 'Function' section, the 'Publications' and
+ 'Cross-references' sections.
+ </td>
+ </tr>
+ <tr>
+ <td>mnemonic</td>
+ <td>
+ <code>
+ mnemonic:ATP6_HUMAN
+ </code>
+ </td>
+ <td>
+ Lists all entries with entry name (ID) ATP6_HUMAN. Searches also
+ obsolete entry names.
+ </td>
+ </tr>
+ <tr>
+ <td>modified</td>
+ <td>
+ <code>
+ modified:[20120101 TO 20120301]<br />
+ reviewed:yes AND modified:[current TO *]
+ </code>
+ </td>
+ <td>
+ Lists all entries that were last modified between January and March 2012.<br />
+ Lists all UniProtKB/Swiss-Prot entries modified in the last release.
+ </td>
+ </tr>
+ <tr>
+ <td>name</td>
+ <td>
+ <code>
+ name:"prion protein"
+ </code>
+ </td>
+ <td>
+ Lists all entries for prion proteins.
+ </td>
+ </tr>
+ <tr>
+ <td>organelle</td>
+ <td>
+ <code>
+ organelle:Mitochondrion
+ </code>
+ </td>
+ <td>
+ Lists all entries for proteins encoded by a gene of the mitochondrial
+ chromosome.
+ </td>
+ </tr>
+ <tr>
+ <td>organism</td>
+ <td>
+ <code>
+ organism:"Ovis aries"
+ <br />
+ organism:9940
+ <br />
+ organism:sheep
+ <br />
+ </code>
+ </td>
+ <td>
+ Lists all entries for proteins expressed in sheep (first 2 examples) and
+ organisms whose name contains the term "sheep".
+ </td>
+ </tr>
+
+ <tr>
+ <td>plasmid</td>
+ <td>
+ <code>
+ plasmid:ColE1
+ </code>
+ </td>
+ <td>
+ Lists all entries for proteins encoded by a gene of plasmid ColE1.
+ </td>
+ </tr>
+ <tr>
+ <td>proteome</td>
+ <td>
+ <code>
+ proteome:UP000005640
+ </code>
+ </td>
+ <td>
+ Lists all entries from the human proteome.
+ </td>
+ </tr>
+ <tr>
+ <td>proteomecomponent</td>
+ <td>
+ <code>
+ proteomecomponent:"chromosome 1" and organism:9606
+ </code>
+ </td>
+ <td>
+ Lists all entries from the human chromosome 1.
+ </td>
+ </tr>
+ <tr>
+ <td>replaces</td>
+ <td>
+ <code>
+ replaces:P02023
+ </code>
+ </td>
+ <td>
+ Lists all entries that were created from a merge with entry P02023.
+ </td>
+ </tr>
+ <tr>
+ <td>reviewed</td>
+ <td>
+ <code>
+ reviewed:yes
+ </code>
+ </td>
+ <td>
+ Lists all UniProtKB/Swiss-Prot entries.
+ </td>
+ </tr>
+ <tr>
+ <td>scope</td>
+ <td>
+ <code>
+ scope:mutagenesis
+ </code>
+ </td>
+ <td>
+ Lists all entries containing a reference that was used to gather
+ information about mutagenesis.
+ </td>
+ </tr>
+ <tr>
+ <td>sequence</td>
+ <td>
+ <code>
+ sequence:P05067-9
+ </code>
+ </td>
+ <td>
+ Lists all entries containing a link to isoform 9 of the sequence
+ described in entry P05067. Allows searching by specific sequence
+ identifier.
+ </td>
+ </tr>
+ <tr>
+ <td>sequence_modified</td>
+ <td>
+ <code>
+ sequence_modified:[20120101 TO 20120301]<br />
+ reviewed:yes AND sequence_modified:[current TO *]
+ </code>
+ </td>
+ <td>
+ Lists all entries whose sequences were last modified between January and March 2012.<br />
+ Lists all UniProtKB/Swiss-Prot entries whose sequences were modified in the last release.
+ </td>
+ </tr>
+ <tr>
+ <td>source</td>
+ <td>
+ <code>
+ source:intact
+ </code>
+ </td>
+ <td>
+ Lists all entries containing a GO term whose annotation source is the
+ IntAct database.
+ </td>
+ </tr>
+ <tr>
+ <td>strain</td>
+ <td>
+ <code>
+ strain:wistar
+ </code>
+ </td>
+ <td>
+ Lists all entries containing a reference relevant to strain wistar.
+ </td>
+ </tr>
+ <tr>
+ <td>taxonomy</td>
+ <td>
+ <code>
+ taxonomy:40674
+ </code>
+ </td>
+ <td>
+ Lists all entries for proteins expressed in Mammals. This field is used to retrieve
+ entries for all organisms classified below a given taxonomic node taxonomy classification).
+ </td>
+ </tr>
+ <tr>
+ <td>tissue</td>
+ <td>
+ <code>
+ tissue:liver
+ </code>
+ </td>
+ <td>
+ Lists all entries containing a reference describing the protein sequence
+ obtained from a clone isolated from liver.
+ </td>
+ </tr>
+ <tr>
+ <td>web</td>
+ <td>
+ <code>
+ web:wikipedia
+ </code>
+ </td>
+ <td>
+ Lists all entries for proteins that are described in Wikipedia.
+ </td>
+ </tr>
+</table>
+
+</body>
+</html>
\ No newline at end of file
--- /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>The Uniprot Free Text Search Interface</title>
+</head>
+<body>
+
+ <strong>The Uniprot Free Text Search Interface</strong>
+ <p>
+ Jalview provides a specialised interface that allows fast and
+ efficient discovery and retrieval of data from the Uniprot database.
+ It allows
+ interactive querying of Uniprot metadata with free text and structured
+ queries, so sequences can be located without prior knowledge of
+ their database accessions, or <em>via</em> manual cross-referencing
+ from Uniprot or other bioinformatics websites.
+ </p>
+ <p>
+ To open the UniProt Sequence Fetcher, select UniProt as the database from
+ any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em>
+ <strong>"File →Fetch Sequences"</strong>).
+ </p>
+ <p>
+ <img src="uniprotseqfetcher.png" align="left"
+ alt="Uniprot sequence fetcher (introduced in Jalview 2.9.1)"
+ />
+ </p>
+
+ <p>
+ <strong>Searching the Uniprot Database</strong>
+ </p>
+ <p>
+ To search the Uniprot, begin typing in the text box. The results of your
+ query are shown in the search results tab, which queries Uniprot after 1.5secs every time
+ you type in the search text box. You can sort results according to
+ 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 retrieve and visualise the sequences in Jalview Alignment interface.
+ </p>
+ <ul>
+ <li><strong>Searching a specific Uniprot field </strong> If you
+ want to find sequences based on a specific Uniprot metadata field,
+ you can select it from the drop-down menu.</li>
+
+
+ <li><strong>Bulk Uniprot retrieval</strong><br>
+ Firstly, switch the search target to Uniprot Id, then enter multiple IDs by separating them with a semi-colon.
+ e.g. fila_human; mnt_human; mnt_mouse.<br />Hitting Return or OK will automatically
+ fetch those IDs, like the default Sequence Fetcher interface.</li>
+
+ <li><strong>Advanced / Custom querying</strong>
+ The table below provides a brief overview of the supported Uniprot query syntax (see <a href="uniprotqueryfields.html">query fields for UniProtKB</a>):
+ <table border="1" width="95%">
+ <tr>
+ <td><code>human antigen</code></td>
+ <td rowspan="3">All entries containing both terms.</td>
+ </tr>
+ <tr>
+ <td><code>human AND antigen</code></td>
+ </tr>
+ <tr>
+ <td><code>human && antigen</code></td>
+ </tr>
+ <tr>
+ <td><code>"human antigen"</code></td>
+ <td>All entries containing both terms in the exact order.</td>
+ </tr>
+ <tr>
+ <td><code>human -antigen</code></td>
+ <td rowspan="3">All entries containing the term <code>human</code>
+ but not <code>antigen</code>.
+ </td>
+ </tr>
+ <tr>
+ <td><code>human NOT antigen</code></td>
+ </tr>
+ <tr>
+ <td><code>human ! antigen</code></td>
+ </tr>
+ <tr>
+ <td><code>human OR mouse</code></td>
+ <td rowspan="2">All entries containing either term.</td>
+ </tr>
+ <tr>
+ <td><code>human || mouse</code></td>
+ </tr>
+ <tr>
+ <td><code>antigen AND (human OR mouse)</code></td>
+ <td>Using parentheses to override boolean precedence rules.</td>
+ </tr>
+ <tr>
+ <td><code>anti*</code></td>
+ <td>All entries containing terms starting with <code>anti</code>.
+ Asterisks can also be used at the beginning and within terms. <strong>Note:</strong>
+ Terms starting with an asterisk or a single letter followed by an
+ asterisk can slow down queries considerably.
+ </td>
+ </tr>
+ <tr>
+ <td><code> author:Tiger*</code></td>
+ <td>Citations that have an author whose name starts with <code>Tiger</code>.
+ To search in a specific field of a dataset, you must prefix your
+ search term with the field name and a colon. To discover what
+ fields can be queried explicitly, observe the query hints that are
+ shown after submitting a query or use the query builder (see
+ below).
+ </td>
+ </tr>
+ <tr>
+ <td><code>length:[100 TO *]</code></td>
+ <td>All entries with a sequence of at least 100 amino acids.</td>
+ </tr>
+ <tr>
+ <td><code>citation:(author:Arai author:Chung)</code></td>
+ <td>All entries with a publication that was coauthored by two
+ specific authors.</td>
+ </tr>
+ </table>
+ </li>
+</ul>
+ <p>
+ <strong>Result pagination</strong>
+ </p>
+ The query results returned from the Uniprot server are paginated for performance optimisation.
+ The button labelled <strong>' << '</strong> and <strong>' >> '</strong> can be used to navigate to the next or previous result page respectively.
+ The page range is shown on the title bar of the Free Text Search interface. Jalview's pagination implementation supports multiple selection of entries across multiple pages.
+
+
+ <p>
+ <strong>Customising The Uniprot Sequence Fetcher</strong>
+ </p>
+ <p>
+ To change the displayed meta-data in the search result, click the
+ 'Customise Displayed Options' tab, and select the fields you'd like
+ to displayed or remove.
+ </p>
+ <p>
+ <em>The Uniprot Free Test Search Interface was introduced in
+ Jalview 2.9.1</em>
+ </p>
+</body>
+</html>
\ No newline at end of file
</p>
<p>
+ <strong>Importing PDB Entries or files in mmCIF format</strong><br>
+ <a href="mmcif.html">mmCIF file format</a> provides an alternative means for
+ importing 3D structure data from flat file and EMBL-PDBe
+ web-service. To enable mmCIF as the default format for
+ importing PBD sequences from the PDB sequence fetcher, add or modify the
+ property
+ <code>DEFAULT_STRUCTURE_FORMAT=mmCIF</code> in Jalview properties file.
+ Once this is done, the steps followed in retrieving PDB format files above can
+ be followed to obtain the same data with mmCIF. <em>mmCIF format file support was added in Jalview 2.9.1.</em></p>
+
+
+
+ <p>
<strong>Associating a large number of PDB files to
sequences in an alignment</strong><br /> It is often the case when working
with structure alignments that you will have a directory of PDB
<td>Both</td>
<td>Cuts the (fully) selected sequences from the alignment. <!-- not yet in this version
This will not happen if only some
-columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->
+columns are selected, you should use the <a href="features/hiddenRegions.html">Hide Regions feature</a> instead.-->
</td>
</tr>
<tr>
<a href="../webServices/newsreader.html">Jalview News</a>
dialog box.
</em></li>
- <li><strong>Groovy Console...<em> (only
- available if groovy is on the classpath)</em><br></strong> <em>Opens
+ <li><strong>Groovy Console...<br></strong> <em>Opens
the <a href="../features/groovy.html">Groovy Console</a> for
interactive scripting.
</em><strong><br></strong></li>
and sequence description to be entered. Press OK to accept
your edit. To save sequence descriptions, you must save in
Fasta, PIR or Jalview File format.</em></li>
- <li><a href="sqaddrefannot"><strong>Add
- Reference Annotations<br>
- </strong><em>When enabled, copies any available alignment
+ <li><strong>Add <a href="../features/annotation.html#seqannots">Reference Annotations</a></strong><br>
+ <em>When enabled, copies any available alignment
annotation for this sequence to the current view.</em></li>
<li><strong>Set as Reference</strong> or <strong>Unmark
as Reference</strong><br /> Sets or unsets the reference sequence for
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>1/6/2016</em></strong>
+ <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>21/6/2016</em></strong>
</div>
</td>
<td><em>General</em>
<ul>
- <li></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
</ul> <em>Application</em>
<ul>
- <li></li>
+ <li><!-- JAL---></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-1369 --->Store/restore reference sequence in Jalview projects</li>
+
</ul> <em>Applet</em>
<ul>
- <li></li>
+ <li><!-- JAL---></li>
</ul></td>
<td>
<div align="left">
<em>General</em>
<ul>
- <li></li>
+ <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-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>
+
</ul>
<em>Application</em>
<ul>
- <li></li>
+ <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
+ <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
+ <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
+ <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
+ <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
+ <li><!-- JAL-2085 -->Cannot save project when view has a reference sequence defined</li>
+ <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>
+ <!-- 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><!-- --></li>
</ul>
</div>
</td>
between different screens.</li>
<li>New preference items for sequence ID tooltip and
consensus annotation</li>
- <li>Client to submit sequences and IDs to <a
- href="webServices/index.html#envision2">Envision2</a>
- Workflows
- </li>
+ <li>Client to submit sequences and IDs to Envision2 Workflows</li>
<li><em>Vamsas Capabilities</em>
<ul>
<li>Improved VAMSAS synchronization (Jalview archive
Function, and Genetics</em> 43(2): 227-241. <a
href="http://www.ncbi.nlm.nih.gov/pubmed/12112692"
>PubMed</a> or available on the <a
- href="http://www.well.ox.ac.uk/~valdar/publications.html"
+ href="http://valdarlab.unc.edu/publications.html"
>Valdar Group publications page</a>), but the SMERFs score was
developed later and described by Manning et al. in 2008 (<a
href="http://www.biomedcentral.com/1471-2105/9/51"
>REST</a> web services exposing sequence alignment, analysis, and
secondary structure prediction programs. Originally, Jalview 2's
services were maintained by the Barton group at the University of
- Dundee, and ran programs on the Life Sciences High-performace
+ Dundee, and ran programs on the Life Sciences High-performance
Computing Cluster. With the advent of <a
href="http://www.compbio.dundee.ac.uk/JABAWS"
>JABAWS</a>, however, it is possible for anyone to host Jalview web
from the input</li>
<li><em>realignment</em> - where any aligned sequences will be
used by the service to construct a profile based alignment of the
- remaining unaligned sequences.</li>
+ remaining unaligned sequences</li>
</ul>
<strong>JABAWS Alignment services</strong>
<br> Most alignment services are provided by the
<a href="JABAWS.html">JABAWS framework</a>, which allows you to
customise the precise parameters used when running each alignment
- prgoram. In addition to the 'Default settings', you may choose from a
+ program. In addition to the 'Default settings', you may choose from a
range of alignment preset settings, or create your own using the
<a href="webServicesParams.html">'Edit Settings And Run ..' dialog
box</a>.
<ul>
<li><a href="http://www.clustal.org/">Clustal Omega and
Clustal W</a> (version 2.0.12)</li>
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a>
+ <li><a href="http://mafft.cbrc.jp/alignment/software/">Mafft</a>
(version 6.8.57b)</li>
<li><a href="http://www.drive5.com/muscle">Muscle</a> (version
3.8.31)</li>
<em>Please Note:
<ul>
<li>The regular expressions supported by Jalview are those
- provided by the <a href="www.javaregex.com">Stevesoft
+ provided by the <a href="http://www.javaregex.com">Stevesoft
javaregex package</a>.
</li>
<li>Some characters must be escaped when specifying them as
<strong>What's new ?</strong>
</p>
<p>
- Jalview 2.9.0b2 is a bug fix release for Jalview 2.9.
- The release of Jalview 2.9 in September 2015 included
- a multitude of bug fixes and minor improvements (both small, and
- rather big!), it also brings major new capabilities for codon-level
- analysis of protein alignments and the retrieval and manipulation of
- structural data.</p><p>For the patches since version 2.9 was released, see the
- <a href="releases.html#Jalview.2.9.0b2">Jalview 2.9.0b2 Release Notes</a>.
+ Jalview 2.9.1 is the next major release in the Jalview 2.9 series. Full details are in the
+ <a href="releases.html#Jalview.2.9.1">Jalview 2.9.1 Release Notes</a>.
</p>
<p>
- <strong>Highlights in Jalview 2.9</strong>
+ <strong>Highlights in Jalview 2.9.1</strong>
<ul>
- <li><strong>Visualisation, editing and analysis of
- cDNA and Protein alignments</strong><br />A new <a
- href="features/splitView.html">Split View</a> window allows linked
- protein and nucleotide sequence alignments to be viewed, edited,
- and analysed as one. <br />cDNA alignments can also be
- reconstructed from protein alignments calculated by Jalview's web
- services, and update in response to edits in the amino acid view.<br />To
- start experimenting with cDNA/Protein analysis, jut drop a file
- containing cDNA sequences which code for proteins in an existing
- alignment, and Jalview will do the rest.</li>
- <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
- 2.9 provides full support for the use of Chimera to view 3D
- structures linked to alignment views in the Jalview Desktop. We've
- also included support for saving Chimera sessions in Jalview
- project files.<br />Jalview and Chimera communicate using local
- web server connections, which may cause firewall alerts on some
- systems, but has the advantage of allowing bidirectional
- communication. Communication between Jalview and Chimera is now
- much more responsive, and selected regions in Chimera are now
- shown as highlighted regions in the Jalview desktop.</li>
- <li><strong>Interactive querying of the PDBe</strong><br />Jalview
- users can now <a href="features/pdbsequencefetcher.html">browse</a> and <a href="features/viewingpdbs.html">retrieve 3D structure</a> data from the PDB
- via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
- Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
- et al 2014</a>). Developed in collaboration with the PDBe group at
- EMBL-EBI, the interface allows both structured and free-text
- queries to be performed, and allows automatic selection of the
- most relevant structures for an alignment acording to a variety of
- criteria.</li>
- <li><strong>Improved support for RNA visualisation</strong><br />Jalview
- 2.9 integrates the latest version of the <a
- href="features/varna.html">VARNA RNA Viewer</a>, and VARNA views
- can also now be stored in Jalview projects. We've also dealt with
- a number of lingering bugs in the VARNA/Jalview interface,
- including the loss of pseudoknots when RNA secondary structure is
- shown VARNA.</li>
- <li><strong>Protein Secondary Structure predictions
- with JPred4</strong><br />Jalview includes a number of new features for
- working with secondary structure predictions from the JPred4
- server. These include new <a href="menus/popupMenu.html#hideinserts">popup menu actions</a> to automatically hide insertions and highlight
- mutations in an alignment with respect to a <a href="calculations/referenceseq.html">Reference
- Sequence</a>. Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable
- SVG HTML export</a> was also developed specifically for the JPred4
- server.</li>
</ul>
</body>
<!--
History: Originally created from EMBL_common_V1.0
Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd
+ Updated May 2016 for EMBL XML 1.2 JAL-2113 JAL-2114
+ 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="EMBL_Services"/>
+ <map-to xml="ROOT"/>
<field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
<bind-xml name="entry"/>
</field>
-
<field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
<bind-xml name="Error"/>
</field>
</class>
<class name="jalview.datamodel.xdb.embl.EmblEntry">
<field name="accession" type="string">
- <bind-xml location="accession" node="attribute"/>
+ <bind-xml name="accession" node="attribute"/>
</field>
- <!-- May 2015 changed from last-updated to match xml -->
- <field name="lastUpdated" type="string">
- <bind-xml location="lastUpdated" node="attribute"/>
+ <!--
+ in EMBL XML 1.2 sequence/@version became entry/version
+ entry/@version became entry/@entryVersion
+ -->
+ <field name="sequenceVersion" type="string">
+ <bind-xml name="version" node="attribute"/>
</field>
- <field name="version" type="string">
- <bind-xml location="version" node="attribute"/>
+ <field name="entryVersion" type="string">
+ <bind-xml name="entryVersion" node="attribute"/>
+ </field>
+ <field name="dataClass" type="string">
+ <bind-xml name="dataClass" node="attribute"/>
+ </field>
+ <field name="taxonomicDivision" type="string">
+ <bind-xml name="taxonomicDivision" node="attribute"/>
+ </field>
+ <field name="moleculeType" type="string">
+ <bind-xml name="moleculeType" node="attribute"/>
+ </field>
+ <field name="sequenceLength" type="string">
+ <bind-xml name="sequenceLength" node="attribute"/>
+ </field>
+ <field name="topology" type="string">
+ <bind-xml name="topology" node="attribute" location="type"/>
+ </field>
+ <field name="firstPublicDate" type="string">
+ <bind-xml name="firstPublic" node="attribute"/>
</field>
- <field name="rCreated" type="string">
- <bind-xml location="releaseCreated" node="attribute"/>
+ <field name="firstPublicRelease" type="string">
+ <bind-xml name="firstPublicRelease" node="attribute"/>
</field>
- <field name="rLastUpdated" type="string">
- <bind-xml location="releaseLastUpdated" node="attribute"/>
+ <field name="lastUpdatedDate" type="string">
+ <bind-xml name="lastUpdated" node="attribute"/>
</field>
- <field name="desc" type="string">
+ <field name="lastUpdatedRelease" type="string">
+ <bind-xml name="lastUpdatedRelease" node="attribute"/>
+ </field>
+ <field name="description" type="string">
<bind-xml name="description" node="element"/>
</field>
<field name="keywords" type="string" collection="vector">
<bind-xml name="feature"/>
</field>
<field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
- <bind-xml name="dbreference" />
+ <bind-xml name="xref" />
</field>
<field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
<bind-xml name="sequence"/>
</field>
</class>
<class name="jalview.datamodel.xdb.embl.EmblSequence">
- <field name="type" type="string">
- <bind-xml name="type" node="attribute" location="type"/>
- </field>
- <field name="version" type="string">
- <bind-xml name="version" node="attribute" location="version"/>
- </field>
<field name="sequence" type="string">
<bind-xml node="text"/>
</field>
<field name="name" type="string">
<bind-xml name="name" node="attribute"/>
</field>
+ <field name="location" type="string">
+ <bind-xml name="location" node="attribute"/>
+ </field>
<field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
- <bind-xml name="dbreference" node="element"/>
+ <bind-xml name="xref" node="element"/>
</field>
<field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
<bind-xml name="qualifier"/>
</field>
- <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">
- <bind-xml name="location"/>
- </field>
</class>
<class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
<field name="accessionId" type="java.lang.String">
- <bind-xml name="primary" node="attribute"/>
+ <bind-xml name="id" node="attribute"/>
</field>
<field name="source" type="java.lang.String">
<bind-xml name="db" node="attribute"/>
</field>
<field name="version" type="string">
- <bind-xml name="secondary" node="attribute"/>
+ <bind-xml name="secondaryId" node="attribute"/>
</field>
</class>
<class name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
<bind-xml name="value" node="element"/>
</field>
</class>
- <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">
- <field name="locationType" type="string">
- <bind-xml name="type" node="attribute"/>
- </field>
- <field name="locationComplement" type="boolean">
- <bind-xml name="complement" node="attribute"/>
- </field>
- <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">
- <bind-xml name="locationElement"/>
- </field>
- </class>
- <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">
- <field name="type" type="string">
- <bind-xml name="type" node="attribute"/>
- </field>
- <field name="accession" type="string">
- <bind-xml name="accession" node="attribute"/>
- </field>
- <field name="version" type="string">
- <bind-xml name="version" node="attribute"/>
- </field>
- <field name="complement" type="boolean">
- <bind-xml name="complement"/>
- </field>
- <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">
- <bind-xml name="basePosition" node="element"/>
- </field>
- </class>
- <class name="jalview.datamodel.xdb.embl.BasePosition">
- <field name="type">
- <bind-xml name="type" node="attribute"/>
- </field>
- <field name="pos">
- <bind-xml node="text"/>
- </field>
- </class>
</mapping>
+/*
+ * 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.
+ */
+
pdb_data_columns
#
_group.id
g1;Quality Measures;1
g2;Cross References;2
g3;Names & Taxonomy;3
-g4;Procedures & Softwares;4
+g4;Procedures & Software;4
g5;Date Of;5
-g6;Miscellenous;6
+g6;Miscellaneous;6
#
_data_column.primary_key;pdb_id
_data_column.default_response_page_size;100
_data_column.name
_data_column.code
_data_column.group_id
-_data_column.data_type
+_data_column.data_type | _data_column.isFormated | _data_column.significantDigit
_data_column.min_col_width
_data_column.max_col_width
_data_column.preferred_col_width
UniProt Accession;uniprot_accession;String;g2;50;400;95;false;false
UniProt Coverage;uniprot_coverage;String;g6;50;400;95;false;false
Uniprot Features;uniprot_features;String;g6;50;400;95;false;false
-R Factor;r_factor;Double;g1;50;150;85;false;false
-Resolution;resolution;Double;g1;50;150;85;true;false
-Data Quality;data_quality;Double;g1;50;150;85;false;false
-Overall Quality;overall_quality;Double;g1;50;150;85;false;false
+R Factor;r_factor;Double|T|3;g1;50;150;85;false;false
+Experimental Method;experimental_method;String;g4;50;400;105;true;false
+Resolution;resolution;Double|T|3;g1;50;150;85;true;false
+Data Quality;data_quality;Double|T|2;g1;50;150;85;false;false
+Overall Quality;overall_quality;Double|T|1;g1;50;150;85;false;false
Number of Polymers;number_of_polymers;int;g6;50;400;95;false;false
Number of Protein Chains;number_of_protein_chains;int;g6;50;400;95;false;false
Number of Bound Molecule;number_of_bound_molecules;int;g6;50;400;95;false;false
Number of Polymer Residue;number_of_polymer_residues;int;g6;50;400;95;false;false
GENUS;genus;String;g3;50;400;95;false;true
Gene Name;gene_name;String;g3;50;400;95;false;true
-Experimental Method;experimental_method;String;g4;50;400;95;false;false
GO Id;go_id;String;g2;50;400;95;false;false
Assembly Id;assembly_id;String;g2;50;400;95;false;false
Assembly Form;assembly_form;String;g6;50;400;95;false;false
Interacting Molecules;interacting_molecules;String;g6;50;400;95;false;false
Pubmed Id;pubmed_id;int;g2;50;400;95;false;false
Status;status;String;g6;50;400;95;false;false
-Model Quality;model_quality;Double;g1;50;150;85;false;false
-Pivot Resolution;pivot_resolution;Double;g1;50;150;85;false;false
+Model Quality;model_quality;Double|T|2;g1;50;150;85;false;false
+Pivot Resolution;pivot_resolution;Double|T|3;g1;50;150;85;false;false
Data reduction software;data_reduction_software;String;g4;50;400;95;false;false
-Max observed residues;max_observed_residues;String;g6;50;400;95;false;false
+Max observed residues;max_observed_residues;Integer|F;g6;50;400;95;false;false
Organism scientific name;organism_scientific_name;String;g3;50;400;95;false;false
Super kingdom;superkingdom;String;g3;50;400;95;false;false
Rank;rank;String;g3;50;400;95;false;false
Citation Title;citation_title;String;g6;50;400;95;false;false
Structure Solution Software;structure_solution_software;String;g4;50;400;95;false;false
Entry Entity;entry_entity;String;g6;50;400;95;false;false
-R Free;r_free;Double;g1;50;150;85;false;false
+R Free;r_free;Double|T|3;g1;50;150;85;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
Entity Id; entity_id;String;g2;50;400;95;false;false
Beam Source Name;beam_source_name;String;g3;50;400;95;false;false
Processing Site;processing_site;String;g6;50;400;95;false;false
-Entity Weight;entity_weight;Double;g6;50;400;95;false;false
-Version;_version_;String;g6;50;400;95;false;false
+Entity Weight;entity_weight;Double|T|0;g6;50;400;95;false;false
+Version;_version_;Double|F|0;g6;50;400;95;false;false
ALL;text;String;g6;50;400;95;false;true
#
+/*
+ * 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.
+ */
+
uniprot_data_columns
#
_group.id
g3;Names & Taxonomy;1
g4;Procedures & Softwares;4
g5;Date Of;5
-g6;Miscellenous;6
+g6;Miscellaneous;6
g7;Sequences;7
g8;Function;8
g9;Interaction;9
_data_column.is_shown_by_default
_data_column.is_searchable
Uniprot Id;id;String;g3;80;150;85;true;true
-Entry Name;entry name|name;String;g3;100;150;105;true;true
-Protein names;protein names|protein name;String;g3;300;1500;500;true;true
+Entry Name;entry name|mnemonic;String;g3;100;150;105;true;true
+Protein names;protein names|name;String;g3;300;1500;500;true;true
Gene Names;genes|gene;String;g3;100;1000;145;true;true
Organism;organism;String;g3;100;1000;200;true;true
-Organism ID;organism-id;int;g3;60;100;80;false;true
-Proteomes;proteome;String;g3;50;1000;95;false;true
-Taxonomic lineage (ALL);lineage(ALL);String;g3;50;400;95;false;false
-Virus hosts;virus hosts;String;g3;50;1000;95;false;true
-Fragment;fragment;String;g7;50;1000;95;false;true
-Gene encoded by;encodedon;String;g7;50;1000;95;false;true
+Organism ID;organism-id;int;g3;60;100;80;false;false
+Proteomes;proteome;String;g3;50;1000;95;false;false
+Taxonomic lineage (ALL);lineage(ALL)|taxonomy;String;g3;50;400;95;false;false
+Virus hosts;virus hosts|host;String;g3;50;1000;95;false;true
+Fragment;fragment;String;g7;50;1000;95;false;false
+Gene encoded by;encodedon;String;g7;50;1000;95;false;false
Alternative products (isoforms);comment(ALTERNATIVE PRODUCTS);String;g7;50;1000;95;false;false
Erroneous gene model prediction;comment(ERRONEOUS GENE MODEL PREDICTION);String;g7;50;1000;95;false;false
Erroneous initiation;comment(ERRONEOUS INITIATION);String;g7;50;1000;95;false;false
RNA editing;comment(RNA EDITING);String;g7;50;1000;95;false;false
Sequence caution;comment(SEQUENCE CAUTION);String;g7;50;1000;95;false;false
Status;reviewed;String;g6;50;100;95;true;true
-Length;length;int;g7;50;100;65;true;true
-Mass;mass;String;g7;50;100;80;false;true
-Sequence;sequence;String;g7;50;1000;95;false;true
+Length;length;int|T|0;g7;50;100;65;true;true
+Mass;mass;int|T|0;g7;50;100;80;false;true
+Sequence;sequence;String;g7;50;1000;95;false;false
Alternative sequence;feature(ALTERNATIVE SEQUENCE);String;g7;50;1000;95;false;false
Natural variant;feature(NATURAL VARIANT);String;g7;50;1000;95;false;false
Non-adjacent residues;feature(NON ADJACENT RESIDUES);String;g7;50;1000;95;false;false
Metal binding;feature(METAL BINDING);String;g8;50;1000;95;false;false
Nucleotide binding;feature(NP BIND);String;g8;50;1000;95;false;false
Site;feature(SITE);String;g8;50;1000;95;false;false
-Annotation;annotation score;String;g6;50;1000;95;false;true
-Features;features;String;g6;50;1000;95;false;true
+Annotation;annotation score;String;g6;50;1000;95;false;false
+Features;features;String;g6;50;1000;95;false;false
Caution;comment(CAUTION);String;g6;50;1000;95;false;false
Miscellaneous [CC];comment(GENERAL);String;g6;50;1000;95;false;false
-Keywords;keywords;String;g6;50;1000;95;false;true
+Keywords;keywords|keyword;String;g6;50;1000;95;false;true
Protein existence;existence;String;g6;50;1000;95;false;true
-ALL;Search All;String;g7;50;1000;95;false;true;
+ALL;Search All;String;g7;50;1000;95;false;true
Subunit structure [CC];comment(SUBUNIT);String;g9;50;1000;95;false;false
-Interacts with;interactor;String;g9;50;1000;95;false;true
+Interacts with;interactor;String;g9;50;1000;95;false;false
Developmental stage;comment(DEVELOPMENTAL STAGE);String;g10;50;1000;95;false;false
Induction;comment(INDUCTION);String;g10;50;1000;95;false;false
Tissue specificity;comment(TISSUE SPECIFICITY);String;g10;50;1000;95;false;false
Date of last modification;last-modified;String;g17;80;150;100;false;true
Date of last sequence modification;sequence-modified;String;g17;80;150;100;false;true
Version (entry);version(entry);int;g17;80;100;80;false;false
-Domain;comment(DOMAIN)|domain;String;g18;80;1000;95;false;true
+Domain [cc];comment(DOMAIN)|domain;String;g18;80;1000;95;false;true
Sequence similarities;comment(SIMILARITY);String;g18;50;1000;95;false;false
Protein families;families|family;String;g18;50;1000;95;false;true
Coiled coil;feature(COILED COIL);String;g18;50;1000;95;false;false
label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new structure viewer with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.
label.associate_structure_with_sequence = Associate Structure with Sequence
label.from_file = From File
-label.enter_pdb_id = Enter PDB Id
+label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode)
label.discover_pdb_ids = Discover PDB IDs
label.text_colour = Text Colour
action.set_text_colour = Text Colour...
label.blasting_for_unidentified_sequence = BLASTing for unidentified sequences
label.select_columns_containing = Select columns containing
label.select_columns_not_containing = Select columns that do not contain
+label.hide_columns_containing = Hide columns containing
+label.hide_columns_not_containing = Hide columns that do not contain
option.trim_retrieved_seqs = Trim retrieved sequences
label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.
label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$
error.png_generation_not_implemented = PNG Generation not yet implemented
error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected
error.invalid_vamsas_session_id = Invalid vamsas session id
-error.implementation_error_cannot_create_groovyshell = Implementation Error. Cannot create groovyShell without Groovy on the classpath!
label.groovy_support_failed = Jalview Groovy Support Failed
label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong.
error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0}
error.dbrefsource_implementation_exception =DBRefSource Implementation Exception
error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0})
error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources
-label.view_controller_toggled_marked = {0} {1} columns {2} containing features of type {3} across {4} sequence(s)
+label.view_controller_toggled_marked = {0} {1} columns containing features of type {2} across {3} sequence(s)
label.toggled = Toggled
label.marked = Marked
label.not = not
label.nw_mapping = Needleman & Wunsch Alignment
label.sifts_mapping = SIFTs Mapping
label.mapping_method = Sequence \u27f7 Structure mapping method
-label.mapping_method = Sequence \u27f7 Structure mapping method
-status.waiting_for_user_to_select_output_file = Waiting for user to select {0} file.
-status.cancelled_image_export_operation = Cancelled {0} export operation.
-info.error_creating_file = Error creating {0} file.
+status.waiting_for_user_to_select_output_file = Waiting for user to select {0} file
+status.cancelled_image_export_operation = Cancelled {0} export operation
+info.error_creating_file = Error creating {0} file
exception.outofmemory_loading_mmcif_file = Out of memory loading mmCIF File
-info.error_creating_file = Error creating {0} file.
label.run_groovy = Run Groovy console script
label.run_groovy_tip = Run the script in the Groovy console over this alignment
label.couldnt_run_groovy_script = Failed to run Groovy script
label.uniprot_sequence_fetcher = UniProt Sequence Fetcher
action.next_page= >>
action.prev_page= <<
-label.next_page_tooltop=Next Page
-label.prev_page_tooltop=Previous Page
+label.next_page_tooltip=Next Page
+label.prev_page_tooltip=Previous Page
exception.bad_request=Bad request. There is a problem with your input.
exception.service_not_available=Service not available. The server is being updated, try again later.
+status.launching_3d_structure_viewer = Launching 3D Structure viewer...
+status.fetching_3d_structures_for_selected_entries = Fetching 3D Structures for selected entries...
+status.fetching_dbrefs_for_sequences_without_valid_refs = Fetching db refs for {0} sequence(s) without valid db ref required for SIFTS mapping
+status.fetching_3d_structures_for = Fetching 3D Structure for {0}
+status.obtaining_mapping_with_sifts = Obtaining mapping with SIFTS
+status.obtaining_mapping_with_nw_alignment = Obtaining mapping with NW alignment
+status.exporting_alignment_as_x_file = Exporting alignment as {0} file
label.html_content = <html>{0}</html>
label.paste_pdb_file= Pegar tu fichero PDB aquÃ.
label.paste_pdb_file_for_sequence = Pegar fichero PDB para la secuencia {0}
-label.could_not_parse_newick_file = No se pudo analizar el fichero Newick\\\!\\n {0}
+label.could_not_parse_newick_file = No se pudo analizar el fichero Newick\!\n {0}
label.successfully_pasted_tcoffee_scores_to_alignment= Pegada exitosamente la puntuación T-Coffee al alineamiento.
label.failed_add_tcoffee_scores = Fallo al añadir las puntuaciones T-Coffee:
label.successfully_pasted_annotation_to_alignment = Anotación pegada exitosamente al alineamiento.
label.select_vamsas_session_opened_as_new_vamsas_session= Selecciones una sesión vamsas para abrirla como una nueva sesión.
label.open_saved_vamsas_session = Abrir una sesión VAMSAS guardada
label.groovy_console = Consola Groovy
-label.lineart = lineart
+label.lineart = Lineart
label.dont_ask_me_again = No volver a preguntar
label.select_eps_character_rendering_style = Seleccionar el carácter EPS como estilo de visualización
label.invert_selection = Invertir selección
label.example_param = Ejemplo: {0}
label.select_file_format_before_saving = Debe seleccionar un formato de fichero antes de guardar!
label.file_format_not_specified = Formato de fichero no especificado
-label.alignment_contains_hidden_columns = El alineamiento contiene columnas ocultas.\\nQuieres guardar s\u00F3lo el alineamiento visible?
+label.alignment_contains_hidden_columns = El alineamiento contiene columnas ocultas.\nQuieres guardar s\u00F3lo el alineamiento visible?
label.couldnt_save_file = No se pudo guardar el fichero: {0}
label.error_saving_file = Error guardando el fichero
label.remove_from_default_list = eliminar de la lista de defectuosos?
label.remove_user_defined_colour = Eliminar el color definido por el usuario
label.you_must_select_least_two_sequences = Debes seleccionar al menos 2 secuencias.
label.invalid_selection = Selección inválida
-label.principal_component_analysis_must_take_least_four_input_sequences = El an\u00E1lisis de la componente principal debe tomar\\nal menos 4 secuencias de entrada.
+label.principal_component_analysis_must_take_least_four_input_sequences = El an\u00E1lisis de la componente principal debe tomar\nal menos 4 secuencias de entrada.
label.sequence_selection_insufficient = Selección de secuencias insuficiente
label.you_need_more_two_sequences_selected_build_tree = necesitas seleccionar más de dos secuencias para construir un árbol!
label.not_enough_sequences = No suficientes secuencias
-label.selected_region_to_tree_may_only_contain_residues_or_gaps = La regi\u00F3n seleccionada para construir un \u00E1rbol puede\\ncontener s\u00F3lo residuos o espacios.\\nPrueba usando la funci\u00F3n Pad en el men\u00FA de edici\u00F3n,\\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias.
+label.selected_region_to_tree_may_only_contain_residues_or_gaps = La regi\u00F3n seleccionada para construir un \u00E1rbol puede\ncontener s\u00F3lo residuos o espacios.\nPrueba usando la funci\u00F3n Pad en el men\u00FA de edici\u00F3n,\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias.
label.sequences_selection_not_aligned = Las secuencias seleccionadas no están alineadas
-label.sequences_must_be_aligned_before_creating_tree = Las secuencias deben estar alineadas antes de crear el \u00E1rbol.\\nPrueba usando la funci\u00F3n Pad en el men\u00FA de editar,\\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias.
+label.sequences_must_be_aligned_before_creating_tree = Las secuencias deben estar alineadas antes de crear el \u00E1rbol.\nPrueba usando la funci\u00F3n Pad en el men\u00FA de editar,\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias.
label.sequences_not_aligned = Secuencias no alineadas
label.problem_reading_tree_file = Problema al leer el fichero del árbol
label.possible_problem_with_tree_file = Posible problema con el fichero del árbol
label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Por favor seleccionar al menos tres bases de al menos una secuencia para poder realizar la traducción de cDNA.
label.translation_failed = Translation Failed
-label.error_when_translating_sequences_submit_bug_report = Desafortunadamente, algo fue mal a la hora de traducir tus secuencias.\\nPor favor, revisa la consola Jalview java \\ny presenta un informe de error que incluya el seguimiento.
+label.error_when_translating_sequences_submit_bug_report = Desafortunadamente, algo fue mal a la hora de traducir tus secuencias.\nPor favor, revisa la consola Jalview java \ny presenta un informe de error que incluya el seguimiento.
label.implementation_error = Error de implementación:
label.automatically_associate_pdb_files_with_sequences_same_name = Quieres asociar automáticamente los {0} ficheros PDB con las secuencias del alineamiento que tengan el mismo nombre?
label.automatically_associate_pdb_files_by_name = Asociar los ficheros PDB por nombre automáticamente
label.enter_view_name = Introducir nombre visible (¿?)
label.enter_label = Introducir etiqueta
label.enter_label_for_the_structure = Introducir una etiqueta para la estructura?
-label.pdb_entry_is_already_displayed = {0} Ya est\u00E1 mostrado.\\nQuieres volver a usar este visor?
+label.pdb_entry_is_already_displayed = {0} Ya est\u00E1 mostrado.\nQuieres volver a usar este visor?
label.map_sequences_to_visible_window = Mapa de secuencias en ventana visible: {0}
-label.add_pdbentry_to_view = Quieres a\u00F1adir {0} a la vista llamada\\n{1}\\n
+label.add_pdbentry_to_view = Quieres a\u00F1adir {0} a la vista llamada\n{1}\n
label.align_to_existing_structure_view = Alinear a una estructura ya existente
-label.pdb_entries_couldnt_be_retrieved = Las siguientes entradas pdb no pueden ser extra\u00EDdas del PDB\\\:\\n{0}\\nPor favor, prueba descarg\u00E1ndolas manualmente.
+label.pdb_entries_couldnt_be_retrieved = Las siguientes entradas pdb no pueden ser extra\u00EDdas del PDB\:\n{0}\nPor favor, prueba descarg\u00E1ndolas manualmente.
label.couldnt_load_file = No se pudo cargar el fichero
label.couldnt_find_pdb_id_in_file = No se pudo encontrar un Id PDB en el fichero suministrado. Por favor, introduzca un Id para identificar esta estructura.
label.no_pdb_id_in_file = No hay un Id PDB en el fichero
label.error_loading_file = Error al cargar el fichero
label.problems_opening_file = Encontrados problemas al abrir el fichero {0}!!
label.file_open_error = Error al abrir el fichero
-label.no_das_sources_selected_warn = No han sido seleccionadas fuentes DAS.\\nPor favor, seleccione algunas fuentes y\\npruebe de nuevo.
+label.no_das_sources_selected_warn = No han sido seleccionadas fuentes DAS.\nPor favor, seleccione algunas fuentes y\npruebe de nuevo.
label.no_das_sources_selected_title = No han sido seleccionadas fuentes DAS
-label.colour_scheme_exists_overwrite = El esquema de colores {0} ya existe.\\nContinuar guardando el esquema de colores como {1}?
+label.colour_scheme_exists_overwrite = El esquema de colores {0} ya existe.\nContinuar guardando el esquema de colores como {1}?
label.duplicate_scheme_name = Duplicar nombre de esquema
-label.jalview_new_questionnaire = Hay un nuevo cuestionario disponible. Querr\u00EDa completarlo ahora ?\\n
+label.jalview_new_questionnaire = Hay un nuevo cuestionario disponible. Querr\u00EDa completarlo ahora ?\n
label.jalview_user_survey = Encuesta de usuario Jalview
label.alignment_properties = Propiedades del alineamiento: {0}
label.alignment_props = Propiedades del alineamiento
error.png_generation_not_implemented = La generación de PNG no se ha implementado todavÃa
error.try_join_vamsas_session_another = Tratando de establecer una sesión VAMSAS cuando ya habÃa otra conectada
error.invalid_vamsas_session_id = Identificador de sesión VAMSAS no válido
-error.implementation_error_cannot_create_groovyshell = Error de implementación:no se puede crear groovyShell sin Groovy en el classpath
label.groovy_support_failed = El soporte Groovy de Jalview ha fallado
label.couldnt_create_groovy_shell = No es posible crear el shell de Groovy. Compruebe el fichero de log para conocer los detalles.
error.unsupported_version_calcIdparam = Versión no soportada de {0}
error.dbrefsource_implementation_exception = Excepción de implementación DBRefSource
error.implementation_error_dbinstance_must_implement_interface = Error de Implementación- getDbInstances debe recibir una clase que implemente jalview.ws.seqfetcher.DbSourceProxy (recibió {0})
error.implementation_error_must_init_dbsources =Error de implementación. Debe inicializar dbSources
-label.view_controller_toggled_marked = {0} {1} columnas {2} conteniendo caracterÃsticas del tipo {3} en {4} secuencia(s)
+label.view_controller_toggled_marked = {0} {1} columnas conteniendo caracterÃsticas del tipo {2} en {3} secuencia(s)
label.toggled = Invertida
label.marked = Marcada
label.not = no
error.implementation_error_cannot_find_service_url_in_given_set_param_store = Error de implementación: la URL del servicio en el conjunto de URL para este almacén de parámetros del servicio({0})
exception.jobsubmission_invalid_params_set = Conjunto de parámetros no válido. Comprueba la implementación de Jalview
exception.notvaliddata_group_contains_less_than_min_seqs = El grupo contiene menos de {0} secuencias.
-exception.outofmemory_loading_pdb_file = Sin menoria al cargar el fichero PDB
+exception.outofmemory_loading_pdb_file = Sin memoria al cargar el fichero PDB
exception.eps_coudnt_write_output_file = No es posible escribir el fichero de salida: {0}
exception.eps_method_not_supported = Método actualmente no suportado por la versión {0} de EpsGraphics2D
exception.eps_unable_to_get_inverse_matrix = Imposible obtener la inversa de la matrix: {0}
status.refreshing_news = Refrescando noticias
status.importing_vamsas_session_from = Importando sesión VAMSAS de {0}
status.opening_params = Abriendo {0}
-status.waiting_sequence_database_fetchers_init = Esperando la inicialización de los recuperadores de bases de datos de secuencias
+status.waiting_sequence_database_fetchers_init = Esperando inicialización de los recuperadores de bases de datos de secuencias
status.init_sequence_database_fetchers = Inicializando recuperadores de bases de datos de secuencias
status.fetching_sequence_queries_from = Recuperando {0} consultas de secuencias de {1}
status.finshed_querying = Consulta finalizada
label.chimera_missing=Visualizador de estructura Chimera no encontrado.<br/>Por favor, introduzca la ruta de Chimera,<br/>o descargar e instalar la UCSF Chimera.
label.save_as_biojs_html=Guardar como HTML BioJs
exception.pdb_rest_service_no_longer_available=Servicios Rest PDB ya no están disponibles!
+exception.fts_server_unreachable=Jalview no puede conectar con el servidor {0}. \nPor favor asegúrese de que está conectado a Internet y vuelva a intentarlo.
+exception.outofmemory_loading_mmcif_file=Sin memoria al cargar el fichero mmCIF
+label.hide_columns_not_containing=Ocultar las columnas que no contengan
+label.pdb_sequence_fetcher=Recuperador de secuencias PDB
+exception.fts_server_error=Parece que hay un error desde el servidor {0}
+exception.service_not_available=Servicio no disponible. El servidor se está actualizando, vuelva a intentarlo más tarde.
+status.waiting_for_user_to_select_output_file=Esperando que el usuario seleccione el fichero {0}
+action.prev_page=<<
+status.cancelled_image_export_operation=Operación de exportación {0} cancelada
+label.couldnt_run_groovy_script=No se ha podido ejecutar el script Groovy
+exception.bad_request=Solicitud incorrecta. Hay un problema con su entrada.
+label.run_groovy=Ejecutar script Groovy desde la consola
+action.next_page=>>
+label.uniprot_sequence_fetcher=Recuperador de secuencias UniProt
+label.prev_page_tooltip=Página anterior
+label.reverse=Invertir
+label.hide_columns_containing=Ocultar las columnas que contengan
+label.nucleotides=Nucleótidos
+label.run_groovy_tip = Ejecutar script Groovy desde la consola sobre este alineamiento
+label.nw_mapping=Alineamiento Needleman y Wunsch
+label.proteins=ProteÃna
+label.reverse_complement=Invertir y complementar
+label.next_page_tooltip=Página siguiente
+label.sifts_mapping=Mapeado SIFTs
+label.mapping_method=Método de mapeo de secuencia \u27F7 estructura
+info.error_creating_file=Error al crear fichero {0}
+exception.fts_rest_service_no_longer_available= Servicios Rest {0} ya no están disponibles!
+status.launching_3d_structure_viewer=Lanzando visualizador de estructura 3D...
+status.obtaining_mapping_with_sifts=Obteniendo mapeo por SIFTS
+status.fetching_3d_structures_for=Buscando la estructura 3D para {0}
+status.fetching_3d_structures_for_selected_entries=Buscando las estructuras 3D para entradas seleccionadas...
+status.fetching_dbrefs_for_sequences_without_valid_refs=Buscando referencias para {0} secuencia(s) sin referencia válida necesaria para mapeado SIFTS
+status.obtaining_mapping_with_nw_alignment=Obteniendo mapeo por alineamiento Needleman y Wunsch
\ No newline at end of file
<xs:attribute name="end" type="xs:int" use="required" />
<xs:attribute name="id" type="xs:string" use="required" />
<xs:attribute name="hidden" type="xs:boolean" />
+ <xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
</xs:complexType>
</xs:element>
<xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
{
EBIFetchClient ebi = new EBIFetchClient();
String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw", ".xml")
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml")
.getAbsolutePath());
if (pdbentry.getFile() != null)
return null;
}
- List<ChimeraModel> newModelList = getModelList();
- for (ChimeraModel newModel : newModelList)
+ // patch for Jalview - set model name in Chimera
+ // TODO: find a variant that works for sub-models
+ for (ChimeraModel newModel : getModelList())
{
if (!modelList.contains(newModel))
{
"setattr M name " + modelName + " #"
+ newModel.getModelNumber(), false);
modelList.add(newModel);
-
}
}
// assign color and residues to open models
for (ChimeraModel chimeraModel : modelList)
{
- // // patch for Jalview - set model name in Chimera
- // // TODO: find a variant that works for sub-models
// get model color
Color modelColor = getModelColor(chimeraModel);
if (modelColor != null)
*/
public List<String> sendChimeraCommand(String command, boolean reply)
{
- // System.out.println("chimeradebug>> " + command);
+ // System.out.println("chimeradebug>> " + command);
if (!isChimeraLaunched() || command == null
|| "".equals(command.trim()))
{
import jalview.util.Comparison;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import jalview.util.StringUtils;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
Collection<String> types, List<SequenceI> forSequences,
boolean anyType, boolean doShow)
{
- for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
+ AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
+ if (anns != null)
{
- if (anyType || types.contains(aa.label))
+ for (AlignmentAnnotation aa : anns)
{
- if ((aa.sequenceRef != null)
- && (forSequences == null || forSequences
- .contains(aa.sequenceRef)))
+ if (anyType || types.contains(aa.label))
{
- aa.visible = doShow;
+ if ((aa.sequenceRef != null)
+ && (forSequences == null || forSequences
+ .contains(aa.sequenceRef)))
+ {
+ aa.visible = doShow;
+ }
}
}
}
.codonTranslate(codon));
if (trans != null && !trans.equals(residue))
{
- String desc = residue + "->" + trans;
+ String residue3Char = StringUtils
+ .toSentenceCase(ResidueProperties.aa2Triplet.get(residue));
+ String trans3Char = StringUtils
+ .toSentenceCase(ResidueProperties.aa2Triplet.get(trans));
+ String desc = "p." + residue3Char + peptidePos + trans3Char;
// set score to 0f so 'graduated colour' option is offered! JAL-2060
SequenceFeature sf = new SequenceFeature(
SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos,
- peptidePos, 0f, null);
+ peptidePos, 0f, "Jalview");
StringBuilder attributes = new StringBuilder(32);
String id = (String) var.variant.getValue(ID);
if (id != null)
{
AlignmentI copy = new Alignment(new Alignment(seqs));
+ /*
+ * add mappings between sequences to the new alignment
+ */
+ AlignedCodonFrame mappings = new AlignedCodonFrame();
+ copy.addCodonFrame(mappings);
+ for (int i = 0; i < copy.getHeight(); i++)
+ {
+ SequenceI from = seqs[i];
+ SequenceI to = copy.getSequenceAt(i);
+ if (to.getDatasetSequence() != null)
+ {
+ to = to.getDatasetSequence();
+ }
+ int start = from.getStart();
+ int end = from.getEnd();
+ MapList map = new MapList(new int[] { start, end }, new int[] {
+ start, end }, 1, 1);
+ mappings.addMap(to, from, map);
+ }
+
SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
if (xrefs != null)
{
c = '-';
}
- if (!canonicaliseAa && 'a' <= c && c <= 'z')
- {
- c -= (32); // 32 = 'a' - 'A'
- }
+ c = toUpperCase(c);
}
values[c]++;
}
}
else
{
+ c = toUpperCase(c);
nres++;
if (nres == 1)
}
/**
+ * Returns the upper-cased character if between 'a' and 'z', else the
+ * unchanged value
+ *
+ * @param c
+ * @return
+ */
+ char toUpperCase(char c)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= (32); // 32 = 'a' - 'A'
+ }
+ return c;
+ }
+
+ /**
* Calculates the conservation sequence
*
* @param consflag
{
if (s != null)
{
- id = new String(s);
+ id = new String(s.toLowerCase());
}
else
{
}
if (s instanceof SeqIdName)
{
- return this.equals(((SeqIdName) s).id);
+ return this.stringequals(((SeqIdName) s).id);
}
else
{
if (s instanceof String)
{
- return this.equals((String) s);
+ return this.stringequals(((String) s).toLowerCase());
}
}
* @param s
* @return boolean
*/
- public boolean equals(String s)
+ private boolean stringequals(String s)
{
if (id.length() > s.length())
{
* @return true if operation affected state
*/
boolean markColumnsContainingFeatures(boolean invert,
- boolean extendCurrent, boolean clearColumns, String featureType);
+ boolean extendCurrent, boolean toggle, String featureType);
/**
* sort the alignment or current selection by average score over the given set
* This method returns the visible alignment as text, as seen on the GUI, ie
* if columns are hidden they will not be returned in the result. Use this for
* calculating trees, PCA, redundancy etc on views which contain hidden
+ * columns. This method doesn't exclude hidden sequences from the output.
+ *
+ * @param selectedRegionOnly
+ * - determines if only the selected region or entire alignment is
+ * exported
+ * @return String[]
+ */
+ String[] getViewAsString(boolean selectedRegionOnly);
+
+ /**
+ * This method returns the visible alignment as text, as seen on the GUI, ie
+ * if columns are hidden they will not be returned in the result. Use this for
+ * calculating trees, PCA, redundancy etc on views which contain hidden
* columns.
*
+ * @param selectedRegionOnly
+ * - determines if only the selected region or entire alignment is
+ * exported
+ * @param isExportHiddenSeqs
+ * - determines if hidden sequences would be exported or not.
+ *
* @return String[]
*/
- String[] getViewAsString(boolean selectedRegionOnly);
+ String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
void setSelectionGroup(SequenceGroup sg);
*/
void setFollowHighlight(boolean b);
+
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
}
import jalview.datamodel.Mapping;
+//JBPComment: this is a datamodel API - so it should be in datamodel (it's a peer of SequenceI)
public interface DBRefEntryI
{
*/
public int getEndRes();
+ /**
+ * access a mapping, if present that can be used to map positions from the
+ * associated dataset sequence to the DBRef's sequence frame.
+ *
+ * @return null or a valid mapping.
+ */
public Mapping getMap();
+
+ /**
+ * Answers true if this object is either equivalent to, or can be 'improved'
+ * by, the given entry. Specifically, answers true if
+ * <ul>
+ * <li>source and accession are identical</li>
+ * <li>version is identical, or this version is of the format "someSource:0",
+ * in which case the version for the other entry replaces it</li>
+ * <li>mappings are not compared but if this entry has no mapping, replace
+ * with that for the other entry</li>
+ * </ul>
+ *
+ * @param otherEntry
+ * @return
+ */
+ public boolean updateFrom(DBRefEntryI otherEntry);
}
package jalview.api;
+import jalview.datamodel.SequenceFeature;
+
import java.awt.Color;
public interface FeatureColourI
{
/**
- * Answers true when either isColourByLabel, isAboveThreshold or
- * isBelowThreshold answers true
+ * Answers true when the feature colour varies across the score range
*
* @return
*/
Color getMaxColour();
/**
- * Answers true if the feature is coloured by label (description); only
- * applicable when isGraduatedColour answers true
+ * Answers true if the feature has a single colour, i.e. if isColourByLabel()
+ * and isGraduatedColour() both answer false
+ *
+ * @return
+ */
+ boolean isSimpleColour();
+
+ /**
+ * Answers true if the feature is coloured by label (description)
*
* @return
*/
boolean isColourByLabel();
+ void setColourByLabel(boolean b);
+
/**
* Answers true if the feature is coloured below a threshold value; only
* applicable when isGraduatedColour answers true
*/
boolean isBelowThreshold();
+ void setBelowThreshold(boolean b);
+
/**
* Answers true if the feature is coloured above a threshold value; only
* applicable when isGraduatedColour answers true
*/
boolean isAboveThreshold();
+ void setAboveThreshold(boolean b);
+
/**
- * Answers true if the threshold is the min (or max) of the colour range; only
- * applicable when isGraduatedColour answers true
+ * Answers true if the threshold is the minimum value (when
+ * isAboveThreshold()) or maximum value (when isBelowThreshold()) of the
+ * colour range; only applicable when isGraduatedColour and either
+ * isAboveThreshold() or isBelowThreshold() answers true
*
* @return
*/
boolean isThresholdMinMax();
+ void setThresholdMinMax(boolean b);
+
/**
* Returns the threshold value (if any), else zero
*
*/
float getThreshold();
+ void setThreshold(float f);
+
+ /**
+ * Answers true if the colour varies between the actual minimum and maximum
+ * score values of the feature, or false if between absolute minimum and
+ * maximum values (or if not a graduated colour).
+ *
+ * @return
+ */
+ boolean isAutoScaled();
+
+ void setAutoScaled(boolean b);
+
+ /**
+ * Returns the maximum score of the graduated colour range
+ *
+ * @return
+ */
+ float getMax();
+
+ /**
+ * Returns the minimum score of the graduated colour range
+ *
+ * @return
+ */
+ float getMin();
+
+ /**
+ * Answers true if either isAboveThreshold or isBelowThreshold answers true
+ *
+ * @return
+ */
+ boolean hasThreshold();
+
+ /**
+ * Returns the computed colour for the given sequence feature
+ *
+ * @param feature
+ * @return
+ */
+ Color getColor(SequenceFeature feature);
+
+ /**
+ * Answers true if the feature has a simple colour, or is coloured by label,
+ * or has a graduated colour and the score of this feature instance is within
+ * the range to render (if any), i.e. does not lie below or above any
+ * threshold set.
+ *
+ * @param feature
+ * @return
+ */
+ boolean isColored(SequenceFeature feature);
+
+ /**
+ * Update the min-max range for a graduated colour scheme
+ *
+ * @param min
+ * @param max
+ */
+ void updateBounds(float min, float max);
+
/**
- * Answers true if ?
+ * Returns the colour in Jalview features file format
*
* @return
*/
- boolean isLowToHigh();
+ String toJalviewFormat(String featureType);
}
* @param ft
* @return display style for a feature
*/
- Object getFeatureStyle(String ft);
+ FeatureColourI getFeatureStyle(String ft);
/**
* update the feature style for a particular feature
*
* @param ft
* @param ggc
- * - currently allows java.awt.Color and
- * jalview.schemes.GraduatedColor
*/
- void setColour(String ft, Object ggc);
+ void setColour(String ft, FeatureColourI ggc);
AlignViewportI getViewport();
*
* @return
*/
- Map<String, Object> getFeatureColours();
+ Map<String, FeatureColourI> getFeatureColours();
/**
* query the alignment view to find all features
*
* @return
*/
- Map<String, Object> getDisplayedFeatureCols();
+ Map<String, FeatureColourI> getDisplayedFeatureCols();
/**
* get all registered groups
List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
/**
- *
- * @return true if the rendering platform supports transparency
- */
- boolean isTransparencyAvailable();
-
- /**
* get current displayed types, in ordering of rendering (on top last)
*
* @return a (possibly empty) list of feature types
import java.util.HashMap;
import java.util.HashSet;
+// JBPComment: this isn't a top-level Jalview API - should be in its own package api
+
public interface SiftsClientI
{
/**
*/
public String getDbCoordSys();
- /**
- * Get DB Evidence for the SIFTs Entry
- *
- * @return
- */
- public String getDbEvidence();
/**
* Get DB Source for the SIFTs Entry
public boolean isAccessionMatched(String accessionId);
/**
- * Get the standard DB referenced by the SIFTs Entry
- *
- * @return
- */
- public String[] getEntryDBs();
-
- /**
*
* @param mop
* MappingOutputPojo
MenuItem item = new MenuItem(label);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.alignFrame.showURL(url, target);
linkMenu.add(item);
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == abovePIDColour)
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
Object source = evt.getSource();
void hideSequences(boolean representGroup)
{
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null || sg.getSize() < 1)
- {
- ap.av.hideSequence(new SequenceI[] { seq });
- return;
- }
-
- ap.av.setSelectionGroup(null);
-
- if (representGroup)
- {
- ap.av.hideRepSequences(seq, sg);
-
- return;
- }
-
- int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
-
- ap.av.hideSequence(hseqs);
- ap.av.sendSelection();
+ ap.av.hideSequences(seq, representGroup);
}
/**
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.SequenceStructureBinding;
boolean featuresFile = false;
try
{
- Map<String, Object> colours = alignPanel.seqPanel.seqCanvas
+ Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
.getFeatureRenderer().getFeatureColours();
boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
"relaxedidmatch", false);
return annotation;
}
- private Map<String, Object> getDisplayedFeatureCols()
+ private Map<String, FeatureColourI> getDisplayedFeatureCols()
{
if (alignPanel.getFeatureRenderer() != null
&& viewport.getFeaturesDisplayed() != null)
return row;
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
boolean resizePanel = false;
+ @Override
public void mouseMoved(MouseEvent evt)
{
resizePanel = evt.getY() < 10 && evt.getX() < 14;
dragCancelled = true;
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (dragCancelled)
}
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
if (!resizePanel && !dragCancelled)
ap.annotationPanel.repaint();
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
if (evt.getY() < 10 && evt.getX() < 14)
}
}
+ @Override
public void mouseExited(MouseEvent evt)
{
dragCancelled = false;
repaint();
}
+ @Override
public void mousePressed(MouseEvent evt)
{
oldY = evt.getY();
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
if (aaa.groupRef != null)
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
av.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
av.isShowSequenceLogo());
cprof.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
av.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
// todo: make the ap scroll to the selection - not necessary, first
// click highlights/scrolls, second selects
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- ap.av.setSelectionGroup(// new SequenceGroup(
- aa[selectedRow].groupRef); // );
- ap.av.sendSelection();
+ // process modifiers
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null
+ || sg == aa[selectedRow].groupRef
+ || !(jalview.util.Platform.isControlDown(evt) || evt
+ .isShiftDown()))
+ {
+ if (jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown())
+ {
+ // clone a new selection group from the associated group
+ ap.av.setSelectionGroup(new SequenceGroup(
+ aa[selectedRow].groupRef));
+ }
+ else
+ {
+ // set selection to the associated group so it can be edited
+ ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+ }
+ }
+ else
+ {
+ // modify current selection with associated group
+ int remainToAdd = aa[selectedRow].groupRef.getSize();
+ for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+ {
+ if (jalview.util.Platform.isControlDown(evt))
+ {
+ sg.addOrRemove(sgs, --remainToAdd == 0);
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
+ sg.addSequence(sgs, --remainToAdd == 0);
+ }
+ }
+ }
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
}
else
{
// we make a copy rather than edit the current selection if no
// modifiers pressed
// see Enhancement JAL-1557
- if (!(evt.isControlDown() || evt.isShiftDown()))
+ if (!(jalview.util.Platform.isControlDown(evt) || evt
+ .isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
}
else
{
- if (evt.isControlDown())
+ if (jalview.util.Platform.isControlDown(evt))
{
sg.addOrRemove(aa[selectedRow].sequenceRef, true);
}
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
int w = getSize().width;
*/
package jalview.appletgui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.GraphLine;
import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import java.awt.Checkbox;
// AlignmentPanel ap;
- GraduatedColor cs;
+ FeatureColourI cs;
- Object oldcs;
+ FeatureColourI oldcs;
Hashtable oldgroupColours;
{
this.type = type;
fr = frenderer;
- float mm[] = ((float[][]) fr.getMinMax().get(type))[0];
+ float mm[] = fr.getMinMax().get(type)[0];
min = mm[0];
max = mm[1];
oldcs = fr.getFeatureColours().get(type);
- if (oldcs instanceof GraduatedColor)
+ if (oldcs.isGraduatedColour())
{
- cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
+ cs = new FeatureColour((FeatureColour) oldcs, min, max);
}
else
{
// promote original color to a graduated color
Color bl = Color.black;
- if (oldcs instanceof Color)
+ if (oldcs.isSimpleColour())
{
- bl = (Color) oldcs;
+ bl = oldcs.getColour();
}
// original colour becomes the maximum colour
- cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
+ cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
}
- minColour.setBackground(cs.getMinColor());
- maxColour.setBackground(cs.getMaxColor());
- minColour.setForeground(cs.getMinColor());
- maxColour.setForeground(cs.getMaxColor());
+ minColour.setBackground(cs.getMinColour());
+ maxColour.setBackground(cs.getMaxColour());
+ minColour.setForeground(cs.getMinColour());
+ maxColour.setForeground(cs.getMaxColour());
colourFromLabel.setState(cs.isColourByLabel());
adjusting = true;
} catch (Exception ex)
{
}
- threshold
- .select(cs.getThreshType() == AnnotationColourGradient.NO_THRESHOLD ? 0
- : cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
- : 2);
+ threshold.select(cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2
+ : 0));
adjusting = false;
changeColour();
private GraphLine threshline;
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == thresholdValue)
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
maxColour.setEnabled(!colourFromLabel.getState());
changeColour();
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
valueChanged();
}
}
protected void valueChanged()
{
- threshline.value = (float) slider.getValue() / 1000f;
- cs.setThresh(threshline.value);
+ threshline.value = slider.getValue() / 1000f;
+ cs.setThreshold(threshline.value);
changeColour();
PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
// ap.paintAlignment(false);
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- GraduatedColor acg = new GraduatedColor(minColour.getBackground(),
+ FeatureColour acg = new FeatureColour(minColour.getBackground(),
maxColour.getBackground(), min, max);
acg.setColourByLabel(colourFromLabel.getState());
if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
{
adjusting = true;
- acg.setThresh(threshline.value);
+ acg.setThreshold(threshline.value);
float range = max * 1000f - min * 1000f;
adjusting = false;
}
- acg.setThreshType(aboveThreshold);
+ acg.setAboveThreshold(true);
if (thresholdIsMin.getState()
&& aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
{
if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
{
- acg = new GraduatedColor(acg, threshline.value, max);
+ acg = new FeatureColour(acg, threshline.value, max);
}
else
{
- acg = new GraduatedColor(acg, min, threshline.value);
+ acg = new FeatureColour(acg, min, threshline.value);
}
}
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
if (evt.getSource() == minColour || evt.getSource() == maxColour)
// ap.paintAlignment(true);
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
*/
package jalview.appletgui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import java.awt.TextField;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
/**
* DOCUMENT ME!
public class FeatureRenderer extends
jalview.renderer.seqfeatures.FeatureRenderer
{
+
+ // Holds web links for feature groups and feature types
+ // in the form label|link
+ Hashtable featureLinks = null;
+
/**
* Creates a new FeatureRenderer object.
*
* @param av
- * DOCUMENT ME!
*/
public FeatureRenderer(AlignmentViewport av)
{
super();
this.av = av;
-
- setTransparencyAvailable(!System.getProperty("java.version")
- .startsWith("1.1"));
}
static String lastFeatureAdded;
/**
* render a feature style in the amend feature dialog box
*/
- public void updateColor(Object newcol)
+ public void updateColor(FeatureColourI newcol)
{
-
- Color bg, col = null;
- GraduatedColor gcol = null;
+ Color bg = null;
String vlabel = "";
- if (newcol instanceof Color)
- {
- isGcol = false;
- col = (Color) newcol;
- gcol = null;
- }
- else if (newcol instanceof GraduatedColor)
- {
- isGcol = true;
- gcol = (GraduatedColor) newcol;
- col = null;
- }
- else
- {
- throw new Error(
- MessageManager
- .getString("error.invalid_colour_for_mycheckbox"));
- }
- if (col != null)
+ if (newcol.isSimpleColour())
{
- setBackground(bg = col);
+ bg = newcol.getColour();
+ setBackground(bg);
}
else
{
- if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (newcol.isAboveThreshold())
+ {
+ vlabel += " (>)";
+ }
+ else if (newcol.isBelowThreshold())
{
- vlabel += " "
- + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
- : "(<)");
+ vlabel += " (<)";
}
- if (isColourByLabel = gcol.isColourByLabel())
+
+ if (isColourByLabel = newcol.isColourByLabel())
{
setBackground(bg = Color.white);
vlabel += " (by Label)";
}
else
{
- setBackground(bg = gcol.getMinColor());
- maxCol = gcol.getMaxColor();
+ setBackground(bg = newcol.getMinColour());
+ maxCol = newcol.getMaxColour();
}
}
label = vlabel;
ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
}
- Object col = getFeatureStyle(name.getText());
+ FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new jalview.schemes.UserColourScheme()
+ Color generatedColour = UserColourScheme
.createColourFromName(name.getText());
+ col = new FeatureColour(generatedColour);
}
colourPanel.updateColor(col);
start.setText(features[0].getBegin() + "");
end.setText(features[0].getEnd() + "");
description.setText(features[0].getDescription());
- Color col = getColour(name.getText());
- if (col == null)
- {
- col = new jalview.schemes.UserColourScheme()
- .createColourFromName(name.getText());
- }
- Object fcol = getFeatureStyle(name.getText());
+ // lookup (or generate) the feature colour
+ FeatureColourI fcol = getFeatureStyle(name.getText());
// simply display the feature color in a box
colourPanel.updateColor(fcol);
dialog.setResizable(true);
// TODO: render the graduated color in the box.
- colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+ colourPanel.addMouseListener(new MouseAdapter()
{
@Override
- public void mousePressed(java.awt.event.MouseEvent evt)
+ public void mousePressed(MouseEvent evt)
{
if (!colourPanel.isGcol)
{
}
else
{
- FeatureColourChooser fcc = new FeatureColourChooser(
- ap.alignFrame, name.getText());
+ new FeatureColourChooser(ap.alignFrame, name.getText());
dialog.transferFocus();
}
}
});
dialog.setVisible(true);
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+ FeaturesFile ffile = new FeaturesFile();
if (dialog.accept)
{
if (!colourPanel.isGcol)
{
// update colour - otherwise its already done.
- setColour(sf.type, colourPanel.getBackground());
+ setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
}
try
{
{
setGroupVisibility(lastFeatureGroupAdded, true);
}
- setColour(lastFeatureAdded, newColour); // was fcol
+ setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
setVisible(lastFeatureAdded);
findAllFeatures(false); // different to original applet behaviour ?
// findAllFeatures();
*/
package jalview.appletgui;
+import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
transparency = new Scrollbar(Scrollbar.HORIZONTAL,
100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
- if (fr.isTransparencyAvailable())
- {
- transparency.addAdjustmentListener(this);
- }
- else
- {
- transparency.setEnabled(false);
- }
+ transparency.addAdjustmentListener(this);
java.net.URL url = getClass().getResource("/images/link.gif");
if (url != null)
Panel tPanel = new Panel(new BorderLayout());
- if (fr.isTransparencyAvailable())
- {
- tPanel.add(transparency, BorderLayout.CENTER);
- tPanel.add(new Label("Transparency"), BorderLayout.EAST);
- }
- else
- {
- tPanel.add(
- new Label("Transparency not available in this web browser"),
- BorderLayout.CENTER);
- }
+ tPanel.add(transparency, BorderLayout.CENTER);
+ tPanel.add(new Label("Transparency"), BorderLayout.EAST);
lowerPanel.add(tPanel, BorderLayout.SOUTH);
int x, int y)
{
final String type = check.type;
- final Object typeCol = fr.getFeatureStyle(type);
- java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
+ final FeatureColourI typeCol = fr.getFeatureStyle(type);
+ PopupMenu men = new PopupMenu(MessageManager.formatMessage(
"label.settings_for_type", new String[] { type }));
java.awt.MenuItem scr = new MenuItem(
MessageManager.getString("label.sort_by_score"));
});
men.add(dens);
+
if (minmax != null)
{
final float[][] typeMinMax = minmax.get(type);
// graduated colourschemes for those where minmax exists for the
// positional features
MenuItem mxcol = new MenuItem(
- (typeCol instanceof Color) ? "Graduated Colour"
+ (typeCol.isSimpleColour()) ? "Graduated Colour"
: "Single Colour");
men.add(mxcol);
mxcol.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- if (typeCol instanceof Color)
+ if (typeCol.isSimpleColour())
{
new FeatureColourChooser(me, type);
// write back the current colour object to update the table
}
else
{
- new UserDefinedColours(me, check.type,
- ((GraduatedColor) typeCol));
+ new UserDefinedColours(me, check.type, typeCol);
}
}
});
}
}
+
+ MenuItem selectContaining = new MenuItem(
+ MessageManager.getString("label.select_columns_containing"));
+ selectContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+ false, type);
+ }
+ });
+ men.add(selectContaining);
+
+ MenuItem selectNotContaining = new MenuItem(
+ MessageManager.getString("label.select_columns_not_containing"));
+ selectNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+ false, type);
+ }
+ });
+ men.add(selectNotContaining);
+
+ MenuItem hideContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_containing"));
+ hideContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, true);
+ }
+ });
+ men.add(hideContaining);
+
+ MenuItem hideNotContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_not_containing"));
+ hideNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, false);
+ }
+ });
+ men.add(hideNotContaining);
+
this.featurePanel.add(men);
men.show(this.featurePanel, x, y);
}
}
}
- public void setUserColour(String feature, Object originalColour)
+ public void setUserColour(String feature, FeatureColourI originalColour)
{
- if (originalColour instanceof Color
- || originalColour instanceof GraduatedColor)
- {
- fr.setColour(feature, originalColour);
- }
- else
- {
- throw new Error(
- MessageManager
- .getString("error.implementation_error_unsupported_feature_colour_object"));
- }
+ fr.setColour(feature, originalColour);
refreshTable();
}
if (evt.getClickCount() > 1)
{
- Object fcol = fr.getFeatureStyle(check.type);
- if (fcol instanceof Color)
+ FeatureColourI fcol = fr.getFeatureStyle(check.type);
+ if (fcol.isSimpleColour())
{
- new UserDefinedColours(this, check.type, (Color) fcol);
+ new UserDefinedColours(this, check.type, fcol.getColour());
}
else
{
boolean hasLink;
- GraduatedColor gcol;
+ FeatureColourI col;
- Color col;
-
- public void updateColor(Object newcol)
+ public void updateColor(FeatureColourI newcol)
{
- if (newcol instanceof Color)
+ col = newcol;
+ if (col.isSimpleColour())
{
- col = (Color) newcol;
- gcol = null;
- }
- else if (newcol instanceof GraduatedColor)
- {
- gcol = (GraduatedColor) newcol;
- col = null;
- }
- else
- {
- throw new Error(
- MessageManager
- .getString("error.invalid_colour_for_mycheckbox"));
- }
- if (col != null)
- {
- setBackground(col);
+ setBackground(col.getColour());
}
else
{
String vlabel = type;
- if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (col.isAboveThreshold())
+ {
+ vlabel += " (>)";
+ }
+ else if (col.isBelowThreshold())
{
- vlabel += " "
- + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
- : "(<)");
+ vlabel += " (<)";
}
- if (gcol.isColourByLabel())
+ if (col.isColourByLabel())
{
setBackground(Color.white);
vlabel += " (by Label)";
}
else
{
- setBackground(gcol.getMinColor());
+ setBackground(col.getMinColour());
}
this.setLabel(vlabel);
}
}
public MyCheckbox(String type, boolean selected, boolean b,
- Object featureStyle)
+ FeatureColourI featureStyle)
{
this(type, selected, b);
updateColor(featureStyle);
public void paint(Graphics g)
{
Dimension d = getSize();
- if (gcol != null)
+ if (col.isColourByLabel())
{
- if (gcol.isColourByLabel())
- {
- g.setColor(Color.white);
- g.fillRect(d.width / 2, 0, d.width / 2, d.height);
- /*
- * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
- * g.setFont(f);
- *
- * // g.setFont(g.getFont().deriveFont( //
- * AffineTransform.getScaleInstance( //
- * width/g.getFontMetrics().stringWidth("Label"), //
- * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
- * width/2, 0);
- */
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ /*
+ * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
+ * g.setFont(f);
+ *
+ * // g.setFont(g.getFont().deriveFont( //
+ * AffineTransform.getScaleInstance( //
+ * width/g.getFontMetrics().stringWidth("Label"), //
+ * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
+ * width/2, 0);
+ */
- }
- else
- {
- Color maxCol = gcol.getMaxColor();
- g.setColor(maxCol);
- g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ }
+ else if (col.isGraduatedColour())
+ {
+ Color maxCol = col.getMaxColour();
+ g.setColor(maxCol);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
- }
}
if (hasLink)
}
}
+ /**
+ * Hide columns containing (or not containing) a given feature type
+ *
+ * @param type
+ * @param columnsContaining
+ */
+ void hideFeatureColumns(final String type,
+ boolean columnsContaining)
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(
+ columnsContaining, false, false, type))
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(
+ !columnsContaining, false, false, type))
+ {
+ ap.alignFrame.viewport.hideSelectedColumns();
+ }
+ }
+ }
+
@Override
public void mousePressed(MouseEvent e)
{
+ // TODO Auto-generated method stub
+
}
}
Tooltip tooltip;
+ @Override
public void mouseMoved(MouseEvent e)
{
int seq = alignPanel.seqPanel.findSeq(e);
tooltiptext = null;
}
+ @Override
public void mouseDragged(MouseEvent e)
{
mouseDragging = true;
alignPanel.paintAlignment(false);
}
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() < 2)
}
}
+ @Override
public void mouseEntered(MouseEvent e)
{
if (scrollThread != null)
}
}
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
if (e.getClickCount() > 1)
}
if ((av.getSelectionGroup() == null)
- || ((!e.isControlDown() && !e.isShiftDown()) && av
+ || ((!jalview.util.Platform.isControlDown(e) && !e
+ .isShiftDown()) && av
.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
}
+ @Override
public void mouseReleased(MouseEvent e)
{
if (scrollThread != null)
running = false;
}
+ @Override
public void run()
{
running = true;
// do we want to thread this ? (contention with seqsel and colsel locks, I
// suspect)
- // rules are: colsel is copied if there is a real intersection between
- // sequence selection
- boolean repaint = false, copycolsel = true;
+ /*
+ * only copy colsel if there is a real intersection between
+ * sequence selection and this panel's alignment
+ */
+ boolean repaint = false;
+ boolean copycolsel = false;
if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
{
SequenceGroup sgroup = null;
}
sgroup = seqsel.intersect(av.getAlignment(),
(av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
- if ((sgroup == null || sgroup.getSize() == 0)
- && (colsel == null || colsel.isEmpty()))
+ if ((sgroup != null && sgroup.getSize() > 0))
{
- // don't copy columns if the region didn't intersect.
- copycolsel = false;
+ copycolsel = true;
}
}
if (sgroup != null && sgroup.getSize() > 0)
ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
av);
av.setColumnSelection(cs);
- av.isColSelChanged(true);
ap.scalePanelHolder.repaint();
ap.repaint();
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
+ final static int CHAR_TO_UPPER = 'A' - 'a';
+
AlignViewport av;
FontMetrics fm;
this.renderGaps = renderGaps;
}
+ @Override
public Color getResidueBoxColour(SequenceI seq, int i)
{
allGroups = av.getAlignment().findAllGroups(seq);
}
if (currentSequenceGroup.getShowNonconserved())
{
- s = getDisplayChar(srep, i, s, '.');
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
}
}
else
}
if (av.getShowUnconserved())
{
- s = getDisplayChar(srep, i, s, '.');
+ s = getDisplayChar(srep, i, s, '.', null);
}
}
}
- private char getDisplayChar(final boolean usesrep, int position, char s,
- char c)
+ /**
+ * Returns 'conservedChar' to represent the given position if the sequence
+ * character at that position is equal to the consensus (ignoring case), else
+ * returns the sequence character
+ *
+ * @param usesrep
+ * @param position
+ * @param sequenceChar
+ * @param conservedChar
+ * @return
+ */
+ private char getDisplayChar(final boolean usesrep, int position,
+ char sequenceChar, char conservedChar, SequenceGroup currentGroup)
{
// TODO - use currentSequenceGroup rather than alignment
// currentSequenceGroup.getConsensus()
- char conschar = (usesrep) ? av.getAlignment().getSeqrep()
- .getCharAt(position)
- : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
- .charAt(0);
- if (!jalview.util.Comparison.isGap(conschar) && s == conschar)
+ char conschar = (usesrep) ? (currentGroup == null
+ || position < currentGroup.getStartRes()
+ || position > currentGroup.getEndRes() ? av.getAlignment()
+ .getSeqrep().getCharAt(position)
+ : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
+ .getCharAt(position) : av.getAlignment().getSeqrep()
+ .getCharAt(position)))
+ : (currentGroup != null && currentGroup.getConsensus() != null
+ && position >= currentGroup.getStartRes()
+ && position <= currentGroup.getEndRes() && currentGroup
+ .getConsensus().annotations.length > position) ? currentGroup
+ .getConsensus().annotations[position].displayCharacter
+ .charAt(0)
+ : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
+ if (!jalview.util.Comparison.isGap(conschar)
+ && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
{
- s = c;
+ sequenceChar = conservedChar;
}
- return s;
+ return sequenceChar;
}
boolean inCurrentSequenceGroup(int res)
*/
package jalview.appletgui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
Button selectedButton;
- Vector oldColours = new Vector();
+ Vector<Color> oldColours = new Vector<Color>();
ColourSchemeI oldColourScheme;
String originalLabel;
- Object originalColour;
+ FeatureColourI originalColour;
int R = 0, G = 0, B = 0;
public UserDefinedColours(FeatureRenderer fr, Frame alignframe)
{
caller = fr;
- originalColour = fr.colourPanel.getBackground();
+ originalColour = new FeatureColour(fr.colourPanel.getBackground());
originalLabel = "Feature Colour";
setForDialog("Select Feature Colour", alignframe);
setTargetColour(fr.colourPanel.getBackground());
*
* @param caller
* - handles events
- * @param col1
+ * @param col
* - original colour
* @param alignframe
* - the parent Frame for the dialog
* @param title
* - window title
*/
- public UserDefinedColours(Component caller, Color col1, Frame alignframe,
+ public UserDefinedColours(Component caller, Color col, Frame alignframe,
String title)
{
this.caller = caller;
- originalColour = col1;
+ originalColour = new FeatureColour(col);
originalLabel = title;
setForDialog(title, alignframe);
- setTargetColour(col1);
+ setTargetColour(col);
dialog.setVisible(true);
}
*/
public UserDefinedColours(Object caller, String label, Color colour)
{
- this(caller, label, colour, colour);
+ this(caller, label, new FeatureColour(colour), colour);
}
/**
* @param graduatedColor
*/
public UserDefinedColours(FeatureSettings me, String type,
- GraduatedColor graduatedColor)
+ FeatureColourI graduatedColor)
{
- this(me, type, graduatedColor, graduatedColor.getMaxColor());
+ this(me, type, graduatedColor, graduatedColor.getMaxColour());
}
- private UserDefinedColours(Object caller, String label, Object ocolour,
- Color colour)
+ private UserDefinedColours(Object caller, String label,
+ FeatureColourI ocolour, Color colour)
{
this.caller = caller;
originalColour = ocolour;
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
final Object source = evt.getSource();
}
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (evt.getSource() == rScroller)
button.setFont(new java.awt.Font("Verdana", 1, 10));
button.addMouseListener(new java.awt.event.MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
colourButtonPressed(e);
{
if (caller instanceof FeatureSettings)
{
- ((FeatureSettings) caller).setUserColour(originalLabel, getColor());
+ ((FeatureSettings) caller).setUserColour(originalLabel,
+ new FeatureColour(getColor()));
}
else if (caller instanceof AnnotationColourChooser)
{
}
else if (caller instanceof FeatureRenderer)
{
- ((FeatureRenderer) caller).colourPanel.updateColor(getColor());
+ ((FeatureRenderer) caller).colourPanel
+ .updateColor(new FeatureColour(getColor()));
}
else if (caller instanceof FeatureColourChooser)
{
if (originalLabel.equals("Min Colour"))
{
((AnnotationColourChooser) caller)
- .minColour_actionPerformed((Color) originalColour);
+ .minColour_actionPerformed(originalColour.getColour());
}
else
{
((AnnotationColourChooser) caller)
- .maxColour_actionPerformed((Color) originalColour);
+ .maxColour_actionPerformed(originalColour.getColour());
}
}
else if (caller instanceof FeatureRenderer)
if (originalLabel.indexOf("inimum") > -1)
{
((FeatureColourChooser) caller)
- .minColour_actionPerformed((Color) originalColour);
+ .minColour_actionPerformed(originalColour.getColour());
}
else
{
((FeatureColourChooser) caller)
- .maxColour_actionPerformed((Color) originalColour);
+ .maxColour_actionPerformed(originalColour.getColour());
}
}
if (dialog != null)
Color[] newColours = new Color[24];
for (int i = 0; i < 24; i++)
{
- newColours[i] = (Color) oldColours.elementAt(i);
+ newColours[i] = oldColours.elementAt(i);
buttonPanel.getComponent(i).setBackground(newColours[i]);
}
--- /dev/null
+package jalview.bin;
+
+import java.net.URLDecoder;
+import java.util.Vector;
+
+/**
+ * Notes: this argParser does not distinguish between parameter switches,
+ * parameter values and argument text. If an argument happens to be identical to
+ * a parameter, it will be taken as such (even though it didn't have a '-'
+ * prefixing it).
+ *
+ * @author Andrew Waterhouse and JBP documented.
+ *
+ */
+public class ArgsParser
+{
+ Vector<String> vargs = null;
+
+ public ArgsParser(String[] args)
+ {
+ vargs = new Vector<String>();
+ for (int i = 0; i < args.length; i++)
+ {
+ String arg = args[i].trim();
+ if (arg.charAt(0) == '-')
+ {
+ arg = arg.substring(1);
+ }
+ vargs.addElement(arg);
+ }
+ }
+
+ /**
+ * check for and remove first occurence of arg+parameter in arglist.
+ *
+ * @param arg
+ * @return return the argument following the given arg if arg was in list.
+ */
+ public String getValue(String arg)
+ {
+ return getValue(arg, false);
+ }
+
+ public String getValue(String arg, boolean utf8decode)
+ {
+ int index = vargs.indexOf(arg);
+ String dc = null, ret = null;
+ if (index != -1)
+ {
+ ret = vargs.elementAt(index + 1).toString();
+ vargs.removeElementAt(index);
+ vargs.removeElementAt(index);
+ if (utf8decode && ret != null)
+ {
+ try
+ {
+ dc = URLDecoder.decode(ret, "UTF-8");
+ ret = dc;
+ } catch (Exception e)
+ {
+ // TODO: log failure to decode
+ }
+ }
+ }
+ return ret;
+ }
+
+ /**
+ * check for and remove first occurence of arg in arglist.
+ *
+ * @param arg
+ * @return true if arg was present in argslist.
+ */
+ public boolean contains(String arg)
+ {
+ if (vargs.contains(arg))
+ {
+ vargs.removeElement(arg);
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ public String nextValue()
+ {
+ return vargs.remove(0);
+ }
+
+ public int getSize()
+ {
+ return vargs.size();
+ }
+
+}
\ No newline at end of file
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
- Pdb.setCurrentDefaultFomart(jalview.bin.Cache.getDefault(
+ Pdb.setCurrentDefaultFormat(jalview.bin.Cache.getDefault(
"DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
*/
package jalview.bin;
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
-import java.lang.reflect.Constructor;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
-import java.net.URLDecoder;
import java.security.AllPermission;
import java.security.CodeSource;
import java.security.PermissionCollection;
*/
public class Jalview
{
+ /*
+ * singleton instance of this class
+ */
+ private static Jalview instance;
+
+ private Desktop desktop;
+
+ public static AlignFrame currentAlignFrame;
+
static
{
// grab all the rights we can the JVM
}
/**
+ * keep track of feature fetching tasks.
+ *
+ * @author JimP
+ *
+ */
+ class FeatureFetcher
+ {
+ /*
+ * TODO: generalise to track all jalview events to orchestrate batch
+ * processing events.
+ */
+
+ private int queued = 0;
+
+ private int running = 0;
+
+ public FeatureFetcher()
+ {
+
+ }
+
+ public void addFetcher(final AlignFrame af,
+ final Vector<String> dasSources)
+ {
+ final long id = System.currentTimeMillis();
+ queued++;
+ final FeatureFetcher us = this;
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ synchronized (us)
+ {
+ queued--;
+ running++;
+ }
+
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), id);
+ af.featureSettings_actionPerformed(null);
+ af.featureSettings.fetchDasFeatures(dasSources, true);
+ af.setProgressBar(null, id);
+ synchronized (us)
+ {
+ running--;
+ }
+ }
+ }).start();
+ }
+
+ public synchronized boolean allFinished()
+ {
+ return queued == 0 && running == 0;
+ }
+
+ }
+
+ public static Jalview getInstance()
+ {
+ return instance;
+ }
+
+ /**
* main class for Jalview application
*
* @param args
*/
public static void main(String[] args)
{
+ instance = new Jalview();
+ instance.doMain(args);
+ }
+
+ /**
+ * @param args
+ */
+ void doMain(String[] args)
+ {
+ System.setSecurityManager(null);
System.out.println("Java version: "
+ System.getProperty("java.version"));
System.out.println(System.getProperty("os.arch") + " "
try
{
Cache.initLogger();
- } catch (java.lang.NoClassDefFoundError error)
+ } catch (NoClassDefFoundError error)
{
error.printStackTrace();
System.out
System.exit(0);
}
- Desktop desktop = null;
+ desktop = null;
try
{
}
String file = null, protocol = null, format = null, data = null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
- Vector getFeatures = null; // vector of das source nicknames to fetch
+ FileLoader fileLoader = new FileLoader(!headless);
+ Vector<String> getFeatures = null; // vector of das source nicknames to
+ // fetch
// features from
// loading is done.
String groovyscript = null; // script to execute after all loading is
System.out.println("No files to open!");
System.exit(1);
}
- String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser
- .getValue("vsess");
+ String vamsasImport = aparser.getValue("vdoc");
+ String vamsasSession = aparser.getValue("vsess");
if (vamsasImport != null || vamsasSession != null)
{
if (desktop == null || headless)
{
try
{
- String viprotocol = jalview.io.AppletFormatAdapter
+ String viprotocol = AppletFormatAdapter
.checkProtocol(vamsasImport);
if (viprotocol == jalview.io.FormatAdapter.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
- else if (viprotocol == jalview.io.FormatAdapter.URL)
+ else if (viprotocol == FormatAdapter.URL)
{
inSession = desktop.vamsasImport(new URL(vamsasImport));
}
if (!file.startsWith("http://"))
{
- if (!(new java.io.File(file)).exists())
+ if (!(new File(file)).exists())
{
System.out.println("Can't find " + file);
if (headless)
}
}
- protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
+ protocol = AppletFormatAdapter.checkProtocol(file);
- format = new jalview.io.IdentifyFile().identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
}
else
{
- Desktop.setCurrentAlignFrame(af);
+ setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
data.replaceAll("%20", " ");
- jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
- .getColour(af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColour(af
+ .getViewport().getAlignment(), data);
if (cs == null)
{
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- "white");
+ UserColourScheme ucs = new UserColourScheme("white");
ucs.parseAppletParameter(data);
cs = ucs;
}
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
System.out.println("CMD groups[-" + data
+ "] executed successfully!");
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
System.out.println("CMD [-features " + data
+ "] executed successfully!");
{
System.out.println("CMD [-tree " + data
+ "] executed successfully!");
- fin = new jalview.io.NewickFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ fin = new NewickFile(data,
+ AppletFormatAdapter.checkProtocol(data));
if (fin != null)
{
af.getViewport().setCurrentTree(
// Execute the groovy script after we've done all the rendering stuff
// and before any images or figures are generated.
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[] { desktop, af });
+ executeGroovyScript(groovyscript, af);
System.out.println("CMD groovy[" + groovyscript
+ "] executed successfully!");
groovyscript = null;
if (format.equalsIgnoreCase("png"))
{
- af.createPNG(new java.io.File(file));
- imageName = (new java.io.File(file)).getName();
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
System.out.println("Creating PNG image: " + file);
continue;
}
else if (format.equalsIgnoreCase("svg"))
{
- File imageFile = new java.io.File(file);
+ File imageFile = new File(file);
imageName = imageFile.getName();
af.createSVG(imageFile);
System.out.println("Creating SVG image: " + file);
}
else if (format.equalsIgnoreCase("html"))
{
- File imageFile = new java.io.File(file);
+ File imageFile = new File(file);
imageName = imageFile.getName();
- new HtmlSvgOutput(new java.io.File(file), af.alignPanel);
+ new HtmlSvgOutput(new File(file), af.alignPanel);
System.out.println("Creating HTML image: " + file);
continue;
}
else if (format.equalsIgnoreCase("imgMap"))
{
- af.createImageMap(new java.io.File(file), imageName);
+ af.createImageMap(new File(file), imageName);
System.out.println("Creating image map: " + file);
continue;
}
else if (format.equalsIgnoreCase("eps"))
{
- File outputFile = new java.io.File(file);
+ File outputFile = new File(file);
System.out.println("Creating EPS file: "
+ outputFile.getAbsolutePath());
af.createEPS(outputFile);
}
else
{
- format = new jalview.io.IdentifyFile().identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
// Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
- if (jalview.bin.Cache.groovyJarsPresent())
+ if (Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[] { desktop,
- startUpAlframe });
+ executeGroovyScript(groovyscript, startUpAlframe);
}
else
{
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
- desktop.desktop,
+ PromptUserConfig prompter = new PromptUserConfig(
+ Desktop.desktop,
"USAGESTATS",
"Jalview Usage Statistics",
"Do you want to help make Jalview better by enabling "
* the Jalview Desktop object passed in to the groovy binding as the
* 'Jalview' object.
*/
- private static void executeGroovyScript(String groovyscript,
- Object[] jalviewContext)
+ private void executeGroovyScript(String groovyscript, AlignFrame af)
{
- if (jalviewContext == null)
- {
- System.err
- .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
- }
/**
* for scripts contained in files
*/
tfile = File.createTempFile("jalview", "groovy");
PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(tfile)));
- BufferedReader br = new BufferedReader(
- new java.io.InputStreamReader(System.in));
+ BufferedReader br = new BufferedReader(new InputStreamReader(
+ System.in));
String line = null;
while ((line = br.readLine()) != null)
{
}
}
}
- boolean success = false;
try
{
- /*
- * The following code performs the GroovyScriptEngine invocation using
- * reflection, and is equivalent to this fragment from the embedding
- * groovy documentation on the groovy site: <code> import
- * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
- *
- * String[] roots = new String[] { "/my/groovy/script/path" };
- * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding
- * = new Binding(); binding.setVariable("input", "world");
- * gse.run("hello.groovy", binding); </code>
- */
- Class<?>[] bspec;
- Object[] binding;
- int blen = ((jalviewContext[0] == null) ? 0 : 1)
- + ((jalviewContext[1] == null) ? 0 : 1);
- String cnames[] = new String[] { "Jalview", "currentAlFrame" };
- bspec = new Class[blen * 2];
- binding = new Object[blen * 2];
- blen = 0;
- ClassLoader cl = null;
Map<String, Object> vbinding = new HashMap<String, Object>();
- for (int jc = 0; jc < jalviewContext.length; jc++)
+ vbinding.put("Jalview", this);
+ if (af != null)
{
- if (jalviewContext[jc] != null)
- {
- if (cl == null)
- {
- cl = jalviewContext[jc].getClass().getClassLoader();
- }
- bspec[blen * 2] = String.class;
- bspec[blen * 2 + 1] = Object.class;
- binding[blen * 2] = cnames[jc];
- binding[blen * 2 + 1] = jalviewContext[jc];
- vbinding.put(cnames[jc], jalviewContext[jc]);
- blen++;
- }
+ vbinding.put("currentAlFrame", af);
}
- Class<?> gbindingc = cl.loadClass("groovy.lang.Binding");
- Constructor<?> gbcons;
- Object gbinding;
- try
- {
- gbcons = gbindingc.getConstructor(Map.class);
- gbinding = gbcons.newInstance(vbinding);
- } catch (NoSuchMethodException x)
+ Binding gbinding = new Binding(vbinding);
+ GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
+ gse.run(sfile.toString(), gbinding);
+ if ("STDIN".equals(groovyscript))
{
- // old style binding config - using series of string/object values to
- // setVariable.
- gbcons = gbindingc.getConstructor();
- gbinding = gbcons.newInstance();
- java.lang.reflect.Method setvar = gbindingc.getMethod(
- "setVariable", bspec);
- setvar.invoke(gbinding, binding);
+ // delete temp file that we made -
+ // only if it was successfully executed
+ tfile.delete();
}
-
- Class<?> gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
- Constructor<?> gseccons = gsec
- .getConstructor(new Class[] { URL[].class }); // String[].class
- // });
- Object gse = gseccons
- .newInstance(new Object[] { new URL[] { sfile } }); // .toString()
- // } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[] {
- String.class, gbindingc });
- run.invoke(gse, new Object[] { sfile.toString(), gbinding });
- success = true;
} catch (Exception e)
{
System.err.println("Exception Whilst trying to execute file " + sfile
e.printStackTrace(System.err);
}
- if (success && groovyscript.equals("STDIN"))
- {
- // delete temp file that we made - but only if it was successfully
- // executed
- tfile.delete();
- }
}
/**
*
* @return vector of DAS source nicknames to retrieve from
*/
- private static Vector checkDasArguments(ArgsParser aparser)
+ private static Vector<String> checkDasArguments(ArgsParser aparser)
{
- Vector source = null;
+ Vector<String> source = null;
String data;
String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
while ((data = aparser.getValue("dasserver", true)) != null)
{
String nickname = null;
String url = null;
- boolean seq = false, feat = true;
int pos = data.indexOf('=');
// determine capabilities
if (pos > 0)
+ nickname + "|" + url);
if (source == null)
{
- source = new Vector();
+ source = new Vector<String>();
}
source.addElement(nickname);
}
System.out.println("adding source '" + data + "'");
if (source == null)
{
- source = new Vector();
+ source = new Vector<String>();
}
source.addElement(data);
}
*
* @param dasSources
*/
- private static FeatureFetcher startFeatureFetching(final Vector dasSources)
+ private FeatureFetcher startFeatureFetching(
+ final Vector<String> dasSources)
{
FeatureFetcher ff = new FeatureFetcher();
AlignFrame afs[] = Desktop.getAlignFrames();
}
return false;
}
-}
-
-/**
- * Notes: this argParser does not distinguish between parameter switches,
- * parameter values and argument text. If an argument happens to be identical to
- * a parameter, it will be taken as such (even though it didn't have a '-'
- * prefixing it).
- *
- * @author Andrew Waterhouse and JBP documented.
- *
- */
-
-class rnabuttonlistener implements ActionListener
-{
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- System.out.println("Good idea ! ");
-
- }
-}
-
-class pbuttonlistener implements ActionListener
-{
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
-
- }
-}
-
-class ArgsParser
-{
- Vector vargs = null;
- public ArgsParser(String[] args)
- {
- vargs = new Vector();
- for (int i = 0; i < args.length; i++)
- {
- String arg = args[i].trim();
- if (arg.charAt(0) == '-')
- {
- arg = arg.substring(1);
- }
- vargs.addElement(arg);
- }
- }
-
- /**
- * check for and remove first occurence of arg+parameter in arglist.
- *
- * @param arg
- * @return return the argument following the given arg if arg was in list.
- */
- public String getValue(String arg)
+ public AlignFrame[] getAlignFrames()
{
- return getValue(arg, false);
- }
+ return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
+ : Desktop.getAlignFrames();
- public String getValue(String arg, boolean utf8decode)
- {
- int index = vargs.indexOf(arg);
- String dc = null, ret = null;
- if (index != -1)
- {
- ret = vargs.elementAt(index + 1).toString();
- vargs.removeElementAt(index);
- vargs.removeElementAt(index);
- if (utf8decode && ret != null)
- {
- try
- {
- dc = URLDecoder.decode(ret, "UTF-8");
- ret = dc;
- } catch (Exception e)
- {
- // TODO: log failure to decode
- }
- }
- }
- return ret;
}
/**
- * check for and remove first occurence of arg in arglist.
- *
- * @param arg
- * @return true if arg was present in argslist.
+ * Quit method delegates to Desktop.quit - unless running in headless mode
+ * when it just ends the JVM
*/
- public boolean contains(String arg)
+ public void quit()
{
- if (vargs.contains(arg))
+ if (desktop != null)
{
- vargs.removeElement(arg);
- return true;
+ desktop.quit();
}
else
{
- return false;
+ System.exit(0);
}
}
- public String nextValue()
+ public static AlignFrame getCurrentAlignFrame()
{
- return vargs.remove(0).toString();
+ return Jalview.currentAlignFrame;
}
- public int getSize()
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
- return vargs.size();
+ Jalview.currentAlignFrame = currentAlignFrame;
}
-
-}
-
-/**
- * keep track of feature fetching tasks.
- *
- * @author JimP
- *
- */
-class FeatureFetcher
-{
- /*
- * TODO: generalise to track all jalview events to orchestrate batch
- * processing events.
- */
-
- private int queued = 0;
-
- private int running = 0;
-
- public FeatureFetcher()
- {
-
- }
-
- public void addFetcher(final AlignFrame af, final Vector dasSources)
- {
- final long id = System.currentTimeMillis();
- queued++;
- final FeatureFetcher us = this;
- new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- synchronized (us)
- {
- queued--;
- running++;
- }
-
- af.setProgressBar(MessageManager
- .getString("status.das_features_being_retrived"), id);
- af.featureSettings_actionPerformed(null);
- af.featureSettings.fetchDasFeatures(dasSources, true);
- af.setProgressBar(null, id);
- synchronized (us)
- {
- running--;
- }
- }
- }).start();
- }
-
- public synchronized boolean allFinished()
- {
- return queued == 0 && running == 0;
- }
-
}
ColumnSelection cs = viewport.getColumnSelection();
if (bs.cardinality() > 0 || invert)
{
+ boolean changed = false;
if (cs == null)
{
cs = new ColumnSelection();
{
if (!extendCurrent)
{
+ changed = !cs.isEmpty();
cs.clear();
}
}
{
if (ibs < 0 || i < ibs)
{
+ changed = true;
if (toggle && cs.contains(i))
{
cs.removeElement(i++);
for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
.nextSetBit(i + 1))
{
+ changed = true;
if (toggle && cs.contains(i))
{
cs.removeElement(i);
}
}
}
- viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- (toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked")),
- (invert ? (Integer.valueOf((alw - alStart)
- - bs.cardinality()).toString()) : (Integer
- .valueOf(bs.cardinality()).toString())),
- featureType, Integer.valueOf(nseq).toString() }));
- return true;
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(true);
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked",
+ new String[] {
+ (toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked")),
+ (invert ? (Integer.valueOf((alw - alStart)
+ - bs.cardinality()).toString()) : (Integer
+ .valueOf(bs.cardinality()).toString())),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
+ }
}
else
{
cs.clear();
alignPanel.paintAlignment(true);
}
- return false;
}
+ return false;
}
@Override
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
}
}
+ /**
+ * adds a set of mappings (while ignoring any duplicates)
+ */
+ @Override
+ public void addCodonFrames(Iterable<AlignedCodonFrame> codons)
+ {
+ if (codons != null)
+ {
+ Iterator<AlignedCodonFrame> it = codons.iterator();
+ while (it.hasNext())
+ {
+ addCodonFrame(it.next());
+ }
+ }
+ }
+
/*
* (non-Javadoc)
*
void addCodonFrame(AlignedCodonFrame codons);
/**
+ * add a set of aligned codons mappings for this alignment, apart from any
+ * duplicates which are ignored
+ *
+ * @param codons
+ */
+ void addCodonFrames(Iterable<AlignedCodonFrame> codons);
+
+ /**
* remove a particular codon frame reference from this alignment
*
* @param codons
import java.util.Vector;
/**
- * NOTE: Columns are zero based.
+ * Data class holding the selected columns and hidden column ranges for a view.
+ * Ranges are base 1.
*/
public class ColumnSelection
{
+ /**
+ * A class to hold an efficient representation of selected columns
+ */
private class IntList
{
/*
}
return rlist;
}
+
+ @Override
+ public int hashCode()
+ {
+ // TODO Auto-generated method stub
+ return selected.hashCode();
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj instanceof IntList)
+ {
+ return ((IntList) obj).selected.equals(selected);
+ }
+ return false;
+ }
}
- IntList selected = new IntList();
+ IntList selection = new IntList();
/*
* list of hidden column [start, end] ranges; the list is maintained in
*/
public void addElement(int col)
{
- selected.add(col);
+ selection.add(col);
}
/**
*/
public void clear()
{
- selected.clear();
+ selection.clear();
}
/**
*/
public void removeElement(int col)
{
- selected.remove(col);
+ selection.remove(col);
}
/**
for (int i = start; i < end; i++)
{
colInt = new Integer(i);
- if (selected.contains(colInt))
+ if (selection.contains(colInt))
{
- selected.remove(colInt);
+ selection.remove(colInt);
}
}
}
*/
public List<Integer> getSelected()
{
- return selected.getList();
+ return selection.getList();
}
/**
*/
public List<int[]> getSelectedRanges()
{
- return selected.getRanges();
+ return selection.getRanges();
}
/**
*/
public boolean contains(int col)
{
- return (col > -1) ? selected.isSelected(col) : false;
+ return (col > -1) ? selection.isSelected(col) : false;
}
/**
*/
public boolean isEmpty()
{
- return selected == null || selected.isEmpty();
+ return selection == null || selection.isEmpty();
}
/**
*/
public int getMax()
{
- if (selected.isEmpty())
+ if (selection.isEmpty())
{
return -1;
}
- return selected.getMaxColumn();
+ return selection.getMaxColumn();
}
/**
*/
public int getMin()
{
- if (selected.isEmpty())
+ if (selection.isEmpty())
{
return 1000000000;
}
- return selected.getMinColumn();
+ return selection.getMinColumn();
}
/**
public List<int[]> compensateForEdit(int start, int change)
{
List<int[]> deletedHiddenColumns = null;
- selected.compensateForEdits(start, change);
+ selection.compensateForEdits(start, change);
if (hiddenColumns != null)
{
private void compensateForDelEdits(int start, int change)
{
- selected.compensateForEdits(start, change);
+ selection.compensateForEdits(start, change);
if (hiddenColumns != null)
{
hiddenColumns = null;
}
}
- if (selected != null && selected.size() > 0)
+ if (selection != null && selection.size() > 0)
{
- selected.pruneColumnList(shifts);
- if (selected != null && selected.size() == 0)
+ selection.pruneColumnList(shifts);
+ if (selection != null && selection.size() == 0)
{
- selected = null;
+ selection = null;
}
}
// and shift the rest.
* Return absolute column index for a visible column index
*
* @param column
- * int column index in alignment view
+ * int column index in alignment view (count from zero)
* @return alignment column index for column
*/
public int adjustForHiddenColumns(int column)
public void hideSelectedColumns()
{
- synchronized (selected)
+ synchronized (selection)
{
- for (int[] selregions : selected.getRanges())
+ for (int[] selregions : selection.getRanges())
{
hideColumns(selregions[0], selregions[1]);
}
- selected.clear();
+ selection.clear();
}
}
{
if (copy != null)
{
- if (copy.selected != null)
+ if (copy.selection != null)
{
- selected = new IntList();
- for (int i = 0, j = copy.selected.size(); i < j; i++)
+ selection = new IntList();
+ for (int i = 0, j = copy.selection.size(); i < j; i++)
{
- selected.add(copy.selected.elementAt(i));
+ selection.add(copy.selection.elementAt(i));
}
}
if (copy.hiddenColumns != null)
{
if (hiddenColumns != null && isVisible(col.intValue()))
{
- selected.add(col);
+ selection.add(col);
}
}
}
*/
public void setElementsFrom(ColumnSelection colsel)
{
- selected = new IntList();
- if (colsel.selected != null && colsel.selected.size() > 0)
+ selection = new IntList();
+ if (colsel.selection != null && colsel.selection.size() > 0)
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
*/
public boolean hasSelectedColumns()
{
- return (selected != null && selected.size() > 0);
+ return (selection != null && selection.size() > 0);
}
/**
return false;
}
+ /**
+ * Returns a hashCode built from selected columns and hidden column ranges
+ */
+ @Override
+ public int hashCode()
+ {
+ int hashCode = selection.hashCode();
+ if (hiddenColumns != null)
+ {
+ for (int[] hidden : hiddenColumns)
+ {
+ hashCode = 31 * hashCode + hidden[0];
+ hashCode = 31 * hashCode + hidden[1];
+ }
+ }
+ return hashCode;
+ }
+
+ /**
+ * Answers true if comparing to a ColumnSelection with the same selected
+ * columns and hidden columns, else false
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (!(obj instanceof ColumnSelection))
+ {
+ return false;
+ }
+ ColumnSelection that = (ColumnSelection) obj;
+
+ /*
+ * check columns selected are either both null, or match
+ */
+ if (this.selection == null)
+ {
+ if (that.selection != null)
+ {
+ return false;
+ }
+ }
+ if (!this.selection.equals(that.selection))
+ {
+ return false;
+ }
+
+ /*
+ * check hidden columns are either both null, or match
+ */
+ if (this.hiddenColumns == null)
+ {
+ return (that.hiddenColumns == null);
+ }
+ if (that.hiddenColumns == null
+ || that.hiddenColumns.size() != this.hiddenColumns.size())
+ {
+ return false;
+ }
+ int i = 0;
+ for (int[] thisRange : hiddenColumns)
+ {
+ int[] thatRange = that.hiddenColumns.get(i++);
+ if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
}
}
/**
+ * Answers true if this object is either equivalent to, or can be 'improved'
+ * by, the given entry. Specifically, answers true if
+ * <ul>
+ * <li>source and accession are identical (ignoring case)</li>
+ * <li>version is identical (ignoring case), or this version is of the format
+ * "someSource:0", in which case the version for the other entry replaces it</li>
+ * <li>mappings are not compared but if this entry has no mapping, replace
+ * with that for the other entry</li>
+ * </ul>
+ *
+ * @param other
+ * @return
+ */
+ @Override
+ public boolean updateFrom(DBRefEntryI other)
+ {
+ if (other == null)
+ {
+ return false;
+ }
+ if (other == this)
+ {
+ return true;
+ }
+
+ /*
+ * source must either match or be both null
+ */
+ String otherSource = other.getSource();
+ if ((source == null && otherSource != null)
+ || (source != null && otherSource == null)
+ || (source != null && !source.equalsIgnoreCase(otherSource)))
+ {
+ return false;
+ }
+
+ /*
+ * accession id must either match or be both null
+ */
+ String otherAccession = other.getAccessionId();
+ if ((accessionId == null && otherAccession != null)
+ || (accessionId != null && otherAccession == null)
+ || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+ {
+ return false;
+ }
+
+ /*
+ * if my version is null, "0" or "source:0" then replace with other version,
+ * otherwise the versions have to match
+ */
+ String otherVersion = other.getVersion();
+ if ((version == null || version.equals("0") || version.endsWith(":0"))
+ && otherVersion != null)
+ {
+ setVersion(otherVersion);
+ }
+ else
+ {
+ if (!version.equalsIgnoreCase(otherVersion))
+ {
+ return false;
+ }
+ }
+
+ /*
+ * if I have no mapping, take that of the other dbref
+ */
+ if (map == null)
+ {
+ setMap(other.getMap());
+ }
+ return true;
+ }
+
+ /**
* test for similar DBRef attributes, except for the map object.
*
* @param entry
@Override
public boolean equalRef(DBRefEntryI entry)
{
+ // TODO is this method and equals() not needed?
if (entry == null)
{
return false;
*/
public static final String ENSEMBL = "ENSEMBL";
+ public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
+
/**
* List of databases whose sequences might have coding regions annotated
*/
*/
public class FeatureProperties
{
-
- private static final String EMBL_CODING_FEATURE = "CDS";
+ public static final String EMBL_CODING_FEATURE = "CDS";
public static final String EXONPOS = "exon number";
AlignmentI alignment;
+ /**
+ * Constructor given a reference to an alignment (with no hidden sequences)
+ *
+ * @param al
+ */
public HiddenSequences(AlignmentI al)
{
alignment = al;
}
+ /**
+ * Answers the number of hidden sequences
+ *
+ * @return
+ */
public int getSize()
{
if (hiddenSequences == null)
return 0;
}
int count = 0;
- for (int i = 0; i < hiddenSequences.length; i++)
+ for (SequenceI seq : hiddenSequences)
{
- if (hiddenSequences[i] != null)
+ if (seq != null)
{
count++;
}
return count;
}
+ /**
+ * Answers the length of the longest hidden sequence
+ *
+ * @return
+ */
public int getWidth()
{
+ if (hiddenSequences == null)
+ {
+ return 0;
+ }
int width = 0;
- for (int i = 0; i < hiddenSequences.length; i++)
+ for (SequenceI seq : hiddenSequences)
{
- if (hiddenSequences[i] != null
- && hiddenSequences[i].getLength() > width)
+ if (seq != null && seq.getLength() > width)
{
- width = hiddenSequences[i].getLength();
+ width = seq.getLength();
}
}
}
/**
- * Call this method if sequences are removed from the main alignment
+ * Call this method after a sequence is removed from the main alignment
*/
public void adjustHeightSequenceDeleted(int seqIndex)
{
}
/**
- * Call this method if sequences are added to or removed from the main
- * alignment
+ * Call this method after a sequence is added to the main alignment
*/
public void adjustHeightSequenceAdded()
{
hiddenSequences = tmp;
}
+ /**
+ * Mark the specified sequence as hidden
+ *
+ * @param sequence
+ */
public void hideSequence(SequenceI sequence)
{
if (hiddenSequences == null)
return revealedSeqs;
}
+ /**
+ * Reveals (unhides) consecutive hidden sequences just above the given
+ * alignment index. The revealed sequences are selected (including their
+ * visible representative sequence if there was one and 'reveal' is being
+ * performed on it).
+ *
+ * @param alignmentIndex
+ * @param hiddenRepSequences
+ * a map of representative sequences to the sequences they represent
+ * @return
+ */
public List<SequenceI> showSequence(int alignmentIndex,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
+ " has been deleted whilst hidden");
}
}
-
}
}
-
return revealedSeqs;
}
public SequenceI getHiddenSequence(int alignmentIndex)
{
- return hiddenSequences[alignmentIndex];
+ return hiddenSequences == null ? null : hiddenSequences[alignmentIndex];
}
public int findIndexWithoutHiddenSeqs(int alignmentIndex)
{
+ if (hiddenSequences == null)
+ {
+ return alignmentIndex;
+ }
int index = 0;
int hiddenSeqs = 0;
if (hiddenSequences.length <= alignmentIndex)
}
index++;
}
- ;
return (alignmentIndex - hiddenSeqs);
}
public int adjustForHiddenSeqs(int alignmentIndex)
{
+ if (hiddenSequences == null)
+ {
+ return alignmentIndex;
+ }
int index = 0;
int hSize = hiddenSequences.length;
while (index <= alignmentIndex && index < hSize)
return alignmentIndex;
}
+ /**
+ * makes a copy of the alignment with hidden sequences included. Using the
+ * copy for anything other than simple output is not recommended. Note - this
+ * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR!
+ * @return
+ */
public AlignmentI getFullAlignment()
{
- int isize = hiddenSequences.length;
- SequenceI[] seq = new Sequence[isize];
-
- int index = 0;
- for (int i = 0; i < hiddenSequences.length; i++)
+ SequenceI[] seq;
+ if (hiddenSequences == null)
{
- if (hiddenSequences[i] != null)
- {
- seq[i] = hiddenSequences[i];
- }
- else
+ seq = alignment.getSequencesArray();
+ }
+ else
+ {
+ int isize = hiddenSequences.length;
+ seq = new Sequence[isize];
+
+ int index = 0;
+ for (int i = 0; i < hiddenSequences.length; i++)
{
- seq[i] = alignment.getSequenceAt(index);
- index++;
+ if (hiddenSequences[i] != null)
+ {
+ seq[i] = hiddenSequences[i];
+ }
+ else
+ {
+ seq[i] = alignment.getSequenceAt(index);
+ index++;
+ }
}
}
Alignment fAlignmt = new Alignment(seq);
fAlignmt.alignmentProperties = alignment.getProperties();
fAlignmt.groups = alignment.getGroups();
fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
+ fAlignmt.setSeqrep(alignment.getSeqrep());
return fAlignmt;
}
dbrefs = new DBRefEntry[0];
}
- int i, iSize = dbrefs.length;
-
- for (i = 0; i < iSize; i++)
+ for (DBRefEntryI dbr : dbrefs)
{
- if (dbrefs[i].equalRef(entry))
+ if (dbr.updateFrom(entry))
{
- if (entry.getMap() != null)
- {
- if (dbrefs[i].getMap() == null)
- {
- // overwrite with 'superior' entry that contains a mapping.
- dbrefs[i] = entry;
- }
- }
+ /*
+ * found a dbref that either matched, or could be
+ * updated from, the new entry - no need to add it
+ */
return;
}
}
- DBRefEntry[] temp = new DBRefEntry[iSize + 1];
- System.arraycopy(dbrefs, 0, temp, 0, iSize);
+ /*
+ * extend the array to make room for one more
+ */
+ // TODO use an ArrayList instead
+ int j = dbrefs.length;
+ DBRefEntry[] temp = new DBRefEntry[j + 1];
+ System.arraycopy(dbrefs, 0, temp, 0, j);
temp[temp.length - 1] = entry;
dbrefs = temp;
// private key for Phase designed not to conflict with real GFF data
private static final String PHASE = "!Phase";
+ // private key for ENA location designed not to conflict with real GFF data
+ private static final String LOCATION = "!Location";
+
/*
* ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
* name1=value1;name2=value2,value3;...etc
public String description;
+ /*
+ * a map of key-value pairs; may be populated from GFF 'column 9' data,
+ * other data sources (e.g. GenBank file), or programmatically
+ */
public Map<String, Object> otherDetails;
public Vector<String> links;
}
/**
+ * Sets the 'raw' ENA format location specifier e.g. join(12..45,89..121)
+ *
+ * @param loc
+ */
+ public void setEnaLocation(String loc)
+ {
+ setValue(LOCATION, loc);
+ }
+
+ /**
+ * Gets the 'raw' ENA format location specifier e.g. join(12..45,89..121)
+ *
+ * @param loc
+ */
+ public String getEnaLocation()
+ {
+ return (String) getValue(LOCATION);
+ }
+
+ /**
* Readable representation, for debug only, not guaranteed not to change
* between versions
*/
/**
* @return the representative sequence for this group
*/
+ @Override
public SequenceI getSeqrep()
{
return seqrep;
* @param seqrep
* the seqrep to set (null means no sequence representative)
*/
+ @Override
public void setSeqrep(SequenceI seqrep)
{
this.seqrep = seqrep;
*
* @return true if group has a sequence representative
*/
+ @Override
public boolean hasSeqrep()
{
return seqrep != null;
/**
*
- * @return automatically calculated consensus row
+ * @return automatically calculated consensus row note: the row is a stub if a
+ * consensus calculation has not yet been performed on the group
*/
public AlignmentAnnotation getConsensus()
{
*/
public PDBEntry getPDBEntry(String pdbId);
+ /**
+ * Set the distinct source database, and accession number from which a
+ * sequence and its start-end data were derived from. This is very important
+ * for SIFTS mappings and must be set prior to performing SIFTS mapping.
+ *
+ * @param dbRef
+ * the source dbRef for the sequence
+ */
public void setSourceDBRef(DBRefEntryI dbRef);
+ /**
+ * Get the distinct source database, and accession number from which a
+ * sequence and its start-end data were derived from.
+ *
+ * @return
+ */
public DBRefEntryI getSourceDBRef();
}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-/**
- * Data model for a feature/location/locationElement/basePosition read from an
- * EMBL query reply
- *
- * @see embl_mapping.xml
- */
-public class BasePosition
-{
- String type;
-
- String pos;
-
- /**
- * @return the pos
- */
- public String getPos()
- {
- return pos;
- }
-
- /**
- * @param pos
- * the pos to set
- */
- public void setPos(String pos)
- {
- this.pos = pos;
- }
-
- /**
- * @return the type
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- */
- public void setType(String type)
- {
- this.type = type;
- }
-}
package jalview.datamodel.xdb.embl;
import jalview.analysis.SequenceIdMatcher;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.DBRefUtils;
+import jalview.util.DnaUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.StringUtils;
+import java.text.ParseException;
import java.util.Arrays;
import java.util.Hashtable;
import java.util.List;
String accession;
- String version;
+ String entryVersion;
- String taxDivision;
+ String sequenceVersion;
- String desc;
+ String dataClass;
- String rCreated;
+ String moleculeType;
- String rLastUpdated;
+ String topology;
- String lastUpdated;
+ String sequenceLength;
+
+ String taxonomicDivision;
+
+ String description;
+
+ String firstPublicDate;
+
+ String firstPublicRelease;
+
+ String lastUpdatedDate;
+
+ String lastUpdatedRelease;
Vector<String> keywords;
}
/**
- * @return the desc
- */
- public String getDesc()
- {
- return desc;
- }
-
- /**
- * @param desc
- * the desc to set
- */
- public void setDesc(String desc)
- {
- this.desc = desc;
- }
-
- /**
* @return the features
*/
public Vector<EmblFeature> getFeatures()
}
/**
- * @return the lastUpdated
- */
- public String getLastUpdated()
- {
- return lastUpdated;
- }
-
- /**
- * @param lastUpdated
- * the lastUpdated to set
- */
- public void setLastUpdated(String lastUpdated)
- {
- this.lastUpdated = lastUpdated;
- }
-
- /**
- * @return the releaseCreated
- */
- public String getRCreated()
- {
- return rCreated;
- }
-
- /**
- * @param releaseCreated
- * the releaseCreated to set
- */
- public void setRCreated(String releaseCreated)
- {
- this.rCreated = releaseCreated;
- }
-
- /**
- * @return the releaseLastUpdated
- */
- public String getRLastUpdated()
- {
- return rLastUpdated;
- }
-
- /**
- * @param releaseLastUpdated
- * the releaseLastUpdated to set
- */
- public void setRLastUpdated(String releaseLastUpdated)
- {
- this.rLastUpdated = releaseLastUpdated;
- }
-
- /**
* @return the sequence
*/
public EmblSequence getSequence()
}
/**
- * @return the taxDivision
- */
- public String getTaxDivision()
- {
- return taxDivision;
- }
-
- /**
- * @param taxDivision
- * the taxDivision to set
- */
- public void setTaxDivision(String taxDivision)
- {
- this.taxDivision = taxDivision;
- }
-
- /**
- * @return the version
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- */
- public void setVersion(String version)
- {
- this.version = version;
- }
-
- /**
* Recover annotated sequences from EMBL file
*
* @param sourceDb
{
SequenceI dna = new Sequence(sourceDb + "|" + accession,
sequence.getSequence());
- dna.setDescription(desc);
- DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession);
+ dna.setDescription(description);
+ DBRefEntry retrievedref = new DBRefEntry(sourceDb,
+ getSequenceVersion(), accession);
dna.addDBRef(retrievedref);
// add map to indicate the sequence is a valid coordinate frame for the
// dbref
retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
new int[] { 1, dna.getLength() }, 1, 1));
- // TODO: transform EMBL Database refs to canonical form
+
if (dbRefs != null)
{
for (DBRefEntry dbref : dbRefs)
}
}
+ SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
try
{
for (EmblFeature feature : features)
}
if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
{
- parseCodingFeature(feature, sourceDb, dna, peptides);
+ parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
}
}
} catch (Exception e)
* list of protein product sequences for Embl entry
*/
void parseCodingFeature(EmblFeature feature, String sourceDb,
- SequenceI dna, List<SequenceI> peptides)
+ SequenceI dna, List<SequenceI> peptides, SequenceIdMatcher matcher)
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
String prname = "";
String prid = null;
Map<String, String> vals = new Hashtable<String, String>();
- SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
/*
* codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
}
else if (qname.equals("protein_id"))
{
- prid = q.getValues()[0];
+ prid = q.getValues()[0].trim();
}
else if (qname.equals("codon_start"))
{
try
{
- codonStart = Integer.parseInt(q.getValues()[0]);
+ codonStart = Integer.parseInt(q.getValues()[0].trim());
} catch (NumberFormatException e)
{
System.err.println("Invalid codon_start in XML for "
else if (qname.equals("product"))
{
// sometimes name is returned e.g. for V00488
- prname = q.getValues()[0];
+ prname = q.getValues()[0].trim();
}
else
{
DBRefEntry pcdnaref = new DBRefEntry();
pcdnaref.setAccessionId(prid);
pcdnaref.setSource(DBRefSource.EMBLCDS);
- pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
+ pcdnaref.setVersion(getSequenceVersion()); // same as parent EMBL
+ // version.
MapList mp = new MapList(new int[] { 1, prseq.length() },
new int[] { 1 + (codonStart - 1),
(codonStart - 1) + 3 * prseq.length() }, 1, 3);
SequenceFeature sf = makeCdsFeature(exon, xint, prname, prid, vals,
codonStart);
sf.setType(feature.getName()); // "CDS"
+ sf.setEnaLocation(feature.getLocation());
sf.setFeatureGroup(sourceDb);
dna.addSequenceFeature(sf);
}
if (map != null)
{
Mapping pmap = new Mapping(dna, map.getMap().getInverse());
- pref = new DBRefEntry(sourceDb, getVersion(),
+ pref = new DBRefEntry(sourceDb, getSequenceVersion(),
this.getAccession());
pref.setMap(pmap);
if (map.getTo() != null)
protEMBLCDS = new DBRefEntry();
protEMBLCDS.setAccessionId(prid);
protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
- protEMBLCDS.setVersion(getVersion());
+ protEMBLCDS.setVersion(getSequenceVersion());
protEMBLCDS
.setMap(new Mapping(product, map.getMap().getInverse()));
}
}
/**
- * Returns the CDS positions as a list of [start, end, start, end...]
+ * Returns the CDS positions as a single array of [start, end, start, end...]
* positions. If on the reverse strand, these will be in descending order.
*
* @param feature
*/
protected int[] getCdsRanges(EmblFeature feature)
{
- if (feature.locations == null)
+ if (feature.location == null)
{
return new int[] {};
}
- int cdsBoundaryCount = 0; // count of all start/stop locations
- int[][] cdsLocations = new int[feature.locations.size()][];
- int locationNumber = 0;
- for (EmblFeatureLocations loc : feature.locations)
+
+ try
{
- int[] locationRanges = loc.getElementRanges(accession);
- cdsLocations[locationNumber++] = locationRanges;
- cdsBoundaryCount += locationRanges.length;
- }
- int[] cdsRanges = new int[cdsBoundaryCount];
- int copyTo = 0;
- for (int[] ranges : cdsLocations)
+ List<int[]> ranges = DnaUtils.parseLocation(feature.location);
+ return listToArray(ranges);
+ } catch (ParseException e)
{
- System.arraycopy(ranges, 0, cdsRanges, copyTo, ranges.length);
- copyTo += ranges.length;
+ Cache.log.warn(String.format(
+ "Not parsing inexact CDS location %s in ENA %s",
+ feature.location, this.accession));
+ return new int[] {};
}
- return cdsRanges;
+ }
+ /**
+ * Converts a list of [start, end] ranges to a single array of [start, end,
+ * start, end ...]
+ *
+ * @param ranges
+ * @return
+ */
+ int[] listToArray(List<int[]> ranges)
+ {
+ int[] result = new int[ranges.size() * 2];
+ int i = 0;
+ for (int[] range : ranges)
+ {
+ result[i++] = range[0];
+ result[i++] = range[1];
+ }
+ return result;
}
/**
}
return exon;
}
+
+ public String getSequenceVersion()
+ {
+ return sequenceVersion;
+ }
+
+ public void setSequenceVersion(String sequenceVersion)
+ {
+ this.sequenceVersion = sequenceVersion;
+ }
+
+ public String getSequenceLength()
+ {
+ return sequenceLength;
+ }
+
+ public void setSequenceLength(String sequenceLength)
+ {
+ this.sequenceLength = sequenceLength;
+ }
+
+ public String getEntryVersion()
+ {
+ return entryVersion;
+ }
+
+ public void setEntryVersion(String entryVersion)
+ {
+ this.entryVersion = entryVersion;
+ }
+
+ public String getMoleculeType()
+ {
+ return moleculeType;
+ }
+
+ public void setMoleculeType(String moleculeType)
+ {
+ this.moleculeType = moleculeType;
+ }
+
+ public String getTopology()
+ {
+ return topology;
+ }
+
+ public void setTopology(String topology)
+ {
+ this.topology = topology;
+ }
+
+ public String getTaxonomicDivision()
+ {
+ return taxonomicDivision;
+ }
+
+ public void setTaxonomicDivision(String taxonomicDivision)
+ {
+ this.taxonomicDivision = taxonomicDivision;
+ }
+
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+ public String getFirstPublicDate()
+ {
+ return firstPublicDate;
+ }
+
+ public void setFirstPublicDate(String firstPublicDate)
+ {
+ this.firstPublicDate = firstPublicDate;
+ }
+
+ public String getFirstPublicRelease()
+ {
+ return firstPublicRelease;
+ }
+
+ public void setFirstPublicRelease(String firstPublicRelease)
+ {
+ this.firstPublicRelease = firstPublicRelease;
+ }
+
+ public String getLastUpdatedDate()
+ {
+ return lastUpdatedDate;
+ }
+
+ public void setLastUpdatedDate(String lastUpdatedDate)
+ {
+ this.lastUpdatedDate = lastUpdatedDate;
+ }
+
+ public String getLastUpdatedRelease()
+ {
+ return lastUpdatedRelease;
+ }
+
+ public void setLastUpdatedRelease(String lastUpdatedRelease)
+ {
+ this.lastUpdatedRelease = lastUpdatedRelease;
+ }
+
+ public String getDataClass()
+ {
+ return dataClass;
+ }
+
+ public void setDataClass(String dataClass)
+ {
+ this.dataClass = dataClass;
+ }
}
Vector<Qualifier> qualifiers;
- Vector<EmblFeatureLocations> locations;
+ String location;
/**
* @return the dbRefs
}
/**
- * @return the locations
+ * @return the location
*/
- public Vector<EmblFeatureLocations> getLocations()
+ public String getLocation()
{
- return locations;
+ return location;
}
/**
- * @param locations
- * the locations to set
+ * @param loc
*/
- public void setLocations(Vector<EmblFeatureLocations> locations)
+ public void setLocation(String loc)
{
- this.locations = locations;
+ this.location = loc;
}
/**
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-/**
- * Data model for a feature/location/locationElement read from an EMBL query
- * reply
- *
- * @see embl_mapping.xml
- */
-public class EmblFeatureLocElement
-{
- String type;
-
- String accession;
-
- String version;
-
- boolean complement;
-
- BasePosition basePositions[];
-
- /**
- * @return the accession
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * @param accession
- * the accession to set
- */
- public void setAccession(String accession)
- {
- this.accession = accession;
- }
-
- /**
- * @return the basePositions
- */
- public BasePosition[] getBasePositions()
- {
- return basePositions;
- }
-
- /**
- * @param basePositions
- * the basePositions to set
- */
- public void setBasePositions(BasePosition[] basePositions)
- {
- this.basePositions = basePositions;
- }
-
- /**
- * @return the complement
- */
- public boolean isComplement()
- {
- return complement;
- }
-
- /**
- * @param complement
- * the complement to set
- */
- public void setComplement(boolean complement)
- {
- this.complement = complement;
- }
-
- /**
- * @return the type
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- */
- public void setType(String type)
- {
- this.type = type;
- }
-
- /**
- * @return the version
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- */
- public void setVersion(String version)
- {
- this.version = version;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import jalview.bin.Cache;
-import jalview.util.ArrayUtils;
-
-import java.util.Arrays;
-import java.util.Vector;
-
-/**
- * Data model for a <location> child element of a <feature> read
- * from an EMBL query reply
- *
- * @see embl_mapping.xml
- * @see http://www.insdc.org/files/feature_table.html#3.4.2
- */
-public class EmblFeatureLocations
-{
- Vector<EmblFeatureLocElement> locElements;
-
- String locationType;
-
- boolean locationComplement;
-
- /**
- * @return the locationComplement
- */
- public boolean isLocationComplement()
- {
- return locationComplement;
- }
-
- /**
- * @param locationComplement
- * the locationComplement to set
- */
- public void setLocationComplement(boolean locationComplement)
- {
- this.locationComplement = locationComplement;
- }
-
- /**
- * @return the locationType
- */
- public String getLocationType()
- {
- return locationType;
- }
-
- /**
- * @param locationType
- * the locationType to set
- */
- public void setLocationType(String locationType)
- {
- this.locationType = locationType;
- }
-
- /**
- * @return the locElements
- */
- public Vector<EmblFeatureLocElement> getLocElements()
- {
- return locElements;
- }
-
- /**
- * @param locElements
- * the locElements to set
- */
- public void setLocElements(Vector<EmblFeatureLocElement> locElements)
- {
- this.locElements = locElements;
- }
-
- /**
- * Return all location elements as start-end pairs (without accessions) TODO:
- * pass back complement and 'less than or more than' range information Note:
- * do not use this since it throws away any accessionIds associated with each
- * location!
- *
- * @return int[] { start1, end1, ... }
- */
- public int[] getElementRanges()
- {
- return getElementRanges(null);
- }
-
- /**
- * Return all location elements concerning given accession as start-end pairs.
- * If the CDS feature is on the forward strand, then start <= end, if on the
- * reverse strand then start > end.
- *
- * @param accession
- * the accession string for which locations are requested, or null
- * for all locations
- * @return int[] { start1, end1, ... }
- */
- int[] getElementRanges(String accession)
- {
- int sepos = 0;
- int[] se = new int[locElements.size() * 2];
- if ("single".equalsIgnoreCase(locationType)
- || "join".equalsIgnoreCase(locationType))
- {
- for (EmblFeatureLocElement loce : locElements)
- {
- if (accession == null || loce.accession != null
- && accession.equals(loce.accession))
- {
- BasePosition bp[] = loce.getBasePositions();
- if (bp.length == 2)
- {
- try
- {
- int start = Integer.parseInt(bp[0].getPos());
- int end = Integer.parseInt(bp[1].getPos());
- se[sepos++] = start;
- se[sepos++] = end;
- } catch (NumberFormatException e)
- {
- System.err
- .println("format error in EMBL CDS location basePosition: "
- + e.getMessage());
- }
- }
- else
- {
- System.err
- .println("format error in EMBL CDS location, basePosition count = "
- + bp.length);
- }
- }
- }
- }
- else if (locationType != null)
- {
- if (Cache.log != null)
- {
- Cache.log
- .error("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
- + locationType + "'");
- }
- else
- {
- System.err
- .println("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
- + locationType + "'");
- }
- }
-
- if (sepos != se.length)
- {
- /*
- * we failed to parse something - trim off null values
- */
- se = Arrays.copyOf(se, sepos);
- }
-
- /*
- * If on the complement, reverse the ranges to [end, start, ...end1, start1].
- * For an example of a joined complement, see (tRNA feature) CAGL0B00165r on
- * http://www.ebi.ac.uk/ena/data/view/CR380948&display=xml
- * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/CR380948/emblxml
- */
- if (locationComplement)
- {
- ArrayUtils.reverseIntArray(se);
- }
- return se;
- }
-}
*/
public class EmblSequence
{
- String version;
-
String sequence;
- String type;
-
/**
* @return the sequence
*/
*/
public void setSequence(String sequence)
{
- this.sequence = sequence;
- }
-
- /**
- * @return the type
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- */
- public void setType(String type)
- {
- this.type = type;
- }
-
- /**
- * @return the version
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- */
- public void setVersion(String version)
- {
- this.version = version;
+ // remove spaces introduced by unmarshalling of newline characters
+ this.sequence = sequence.replace(" ", "");
}
}
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
-import jalview.schemes.FeatureColourAdapter;
+import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
{
if (so.isA(type, SequenceOntologyI.EXON))
{
- return new FeatureColourAdapter()
+ return new FeatureColour()
{
@Override
public boolean isColourByLabel()
}
if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
{
- return new FeatureColourAdapter()
+ return new FeatureColour()
{
@Override
--- /dev/null
+package jalview.ext.ensembl;
+
+/**
+ * A data class to model the data and rest version of one Ensembl domain,
+ * currently for rest.ensembl.org and rest.ensemblgenomes.org
+ *
+ * @author gmcarstairs
+ */
+class EnsemblInfo
+{
+ /*
+ * The http domain this object is holding data values for
+ */
+ String domain;
+
+ /*
+ * The latest version Jalview has tested for, e.g. "4.5"; a minor version change should be
+ * ok, a major version change may break stuff
+ */
+ String expectedRestVersion;
+
+ /*
+ * Major / minor / point version e.g. "4.5.1"
+ * @see http://rest.ensembl.org/info/rest/?content-type=application/json
+ */
+ String restVersion;
+
+ /*
+ * data version
+ * @see http://rest.ensembl.org/info/data/?content-type=application/json
+ */
+ String dataVersion;
+
+ /*
+ * true when http://rest.ensembl.org/info/ping/?content-type=application/json
+ * returns response code 200
+ */
+ boolean restAvailable;
+
+ /*
+ * absolute time when availability was last checked
+ */
+ long lastAvailableCheckTime;
+
+ /*
+ * absolute time when version numbers were last checked
+ */
+ long lastVersionCheckTime;
+
+ // flag set to true if REST major version is not the one expected
+ boolean restMajorVersionMismatch;
+
+ /*
+ * absolute time to wait till if we overloaded the REST service
+ */
+ long retryAfter;
+
+ /**
+ * Constructor given expected REST version number e.g 4.5 or 3.4.3
+ *
+ * @param restExpected
+ */
+ EnsemblInfo(String theDomain, String restExpected)
+ {
+ domain = theDomain;
+ expectedRestVersion = restExpected;
+ lastAvailableCheckTime = -1;
+ lastVersionCheckTime = -1;
+ }
+
+}
package jalview.ext.ensembl;
import jalview.io.FileParse;
+import jalview.util.StringUtils;
import java.io.BufferedReader;
import java.io.DataOutputStream;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import javax.ws.rs.HttpMethod;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+
import com.stevesoft.pat.Regex;
/**
*/
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
- private final static String ENSEMBL_REST = "http://rest.ensembl.org";
+ /*
+ * 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
+ */
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.4";
- protected final static String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "4.5";
+
+ private static Map<String, EnsemblInfo> domainData;
// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
- private final static long RETEST_INTERVAL = 10000L; // 10 seconds
+ private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
+
+ private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
private static final Regex TRANSCRIPT_REGEX = new Regex(
"(ENS)([A-Z]{3}|)T[0-9]{11}$");
private static final Regex GENE_REGEX = new Regex(
"(ENS)([A-Z]{3}|)G[0-9]{11}$");
- private String domain = ENSEMBL_REST;
-
- private static boolean ensemblRestAvailable = false;
-
- private static long lastCheck = -1;
-
- /*
- * absolute time to wait till if we overloaded the REST service
- */
- private static long retryAfter;
+ static
+ {
+ domainData = new HashMap<String, EnsemblInfo>();
+ domainData.put(ENSEMBL_REST, new EnsemblInfo(ENSEMBL_REST,
+ LATEST_ENSEMBL_REST_VERSION));
+ domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo(
+ ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
+ }
protected volatile boolean inProgress = false;
*/
public EnsemblRestClient(String d)
{
- domain = d;
- }
-
- /**
- * Returns the domain name to query e.g. http://rest.ensembl.org or
- * http://rest.ensemblgenomes.org
- *
- * @return
- */
- String getDomain()
- {
- return domain;
- }
-
- void setDomain(String d)
- {
- domain = d;
+ setDomain(d);
}
/**
* POST method allows multiple queries in one request; it is supported for
* sequence queries, but not for overlap
*/
- boolean multipleIds = ids.size() > 1;// useGetRequest();
+ boolean multipleIds = ids != null && ids.size() > 1;
connection.setRequestMethod(multipleIds ? HttpMethod.POST
: HttpMethod.GET);
connection.setRequestProperty("Content-Type",
// to test:
// retryDelay = "5";
+ EnsemblInfo info = domainData.get(getDomain());
if (retryDelay != null)
{
System.err.println("Ensembl REST service rate limit exceeded, wait "
+ retryDelay + " seconds before retrying");
try
{
- retryAfter = System.currentTimeMillis()
+ info.retryAfter = System.currentTimeMillis()
+ (1000 * Integer.valueOf(retryDelay));
} catch (NumberFormatException e)
{
}
else
{
- retryAfter = 0;
+ info.retryAfter = 0;
// debug:
// System.out.println(String.format(
// "%s Ensembl requests remaining of %s (reset in %ss)",
// remaining, limit, reset));
}
}
+
/**
* Rechecks if Ensembl is responding, unless the last check was successful and
* the retest interval has not yet elapsed. Returns true if Ensembl is up,
- * else false.
+ * else false. Also retrieves and saves the current version of Ensembl data
+ * and REST services at intervals.
*
* @return
*/
protected boolean isEnsemblAvailable()
{
+ EnsemblInfo info = domainData.get(getDomain());
+
long now = System.currentTimeMillis();
/*
* check if we are waiting for 'Retry-After' to expire
*/
- if (retryAfter > now)
+ if (info.retryAfter > now)
{
- System.err.println("Still " + (1 + (retryAfter - now) / 1000)
+ System.err.println("Still " + (1 + (info.retryAfter - now) / 1000)
+ " secs to wait before retrying Ensembl");
return false;
}
else
{
- retryAfter = 0;
+ info.retryAfter = 0;
+ }
+
+ /*
+ * recheck if Ensembl is up if it was down, or the recheck period has elapsed
+ */
+ boolean retestAvailability = (now - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
+ if (!info.restAvailable || retestAvailability)
+ {
+ info.restAvailable = checkEnsembl();
+ info.lastAvailableCheckTime = now;
}
- boolean retest = now - lastCheck > RETEST_INTERVAL;
- if (ensemblRestAvailable && !retest)
+ /*
+ * refetch Ensembl versions if the recheck period has elapsed
+ */
+ boolean refetchVersion = (now - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
+ if (refetchVersion)
{
- return true;
+ checkEnsemblRestVersion();
+ checkEnsemblDataVersion();
+ info.lastVersionCheckTime = now;
}
- ensemblRestAvailable = checkEnsembl();
- lastCheck = now;
- return ensemblRestAvailable;
+
+ return info.restAvailable;
}
/**
wr.close();
}
+ /**
+ * Fetches and checks Ensembl's REST version number
+ *
+ * @return
+ */
+ private void checkEnsemblRestVersion()
+ {
+ EnsemblInfo info = domainData.get(getDomain());
+
+ JSONParser jp = new JSONParser();
+ URL url = null;
+ try
+ {
+ url = new URL(getDomain()
+ + "/info/rest?content-type=application/json");
+ BufferedReader br = getHttpResponse(url, null);
+ JSONObject val = (JSONObject) jp.parse(br);
+ String version = val.get("release").toString();
+ String majorVersion = version.substring(0, version.indexOf("."));
+ String expected = info.expectedRestVersion;
+ String expectedMajorVersion = expected.substring(0,
+ expected.indexOf("."));
+ info.restMajorVersionMismatch = false;
+ try
+ {
+ /*
+ * if actual REST major version is ahead of what we expect,
+ * record this in case we want to warn the user
+ */
+ if (Float.valueOf(majorVersion) > Float
+ .valueOf(expectedMajorVersion))
+ {
+ info.restMajorVersionMismatch = true;
+ }
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Error in REST version: " + e.toString());
+ }
+
+ /*
+ * check if REST version is later than what Jalview has tested against,
+ * if so warn; we don't worry if it is earlier (this indicates Jalview has
+ * been tested in advance against the next pending REST version)
+ */
+ boolean laterVersion = StringUtils.compareVersions(version, expected) == 1;
+ if (laterVersion)
+ {
+ System.err.println(String.format(
+ "Expected %s REST version %s but found %s", getDbSource(),
+ expected,
+ version));
+ }
+ info.restVersion = version;
+ } catch (Throwable t)
+ {
+ System.err.println("Error checking Ensembl REST version: "
+ + t.getMessage());
+ }
+ }
+
+ public boolean isRestMajorVersionMismatch()
+ {
+ return domainData.get(getDomain()).restMajorVersionMismatch;
+ }
+
+ /**
+ * Fetches and checks Ensembl's data version number
+ *
+ * @return
+ */
+ private void checkEnsemblDataVersion()
+ {
+ JSONParser jp = new JSONParser();
+ URL url = null;
+ try
+ {
+ url = new URL(getDomain()
+ + "/info/data?content-type=application/json");
+ BufferedReader br = getHttpResponse(url, null);
+ JSONObject val = (JSONObject) jp.parse(br);
+ JSONArray versions = (JSONArray) val.get("releases");
+ domainData.get(getDomain()).dataVersion = versions.get(0).toString();
+ } catch (Throwable t)
+ {
+ System.err.println("Error checking Ensembl data version: "
+ + t.getMessage());
+ }
+ }
+
+ public String getEnsemblDataVersion()
+ {
+ return domainData.get(getDomain()).dataVersion;
+ }
+
+ @Override
+ public String getDbVersion()
+ {
+ return getEnsemblDataVersion();
+ }
+
}
ds.setSourceDBRef(proteinSeq.getSourceDBRef());
Mapping map = new Mapping(ds, mapList);
- DBRefEntry dbr = new DBRefEntry(getDbSource(), getDbVersion(),
- proteinSeq.getName(), map);
+ DBRefEntry dbr = new DBRefEntry(getDbSource(),
+ getEnsemblDataVersion(), proteinSeq.getName(), map);
querySeq.getDatasetSequence().addDBRef(dbr);
/*
/*
* and add a reference to itself
*/
- DBRefEntry self = new DBRefEntry(getDbSource(), "0", seq.getName());
+ DBRefEntry self = new DBRefEntry(getDbSource(),
+ getEnsemblDataVersion(), seq.getName());
seq.addDBRef(self);
}
if (ids.contains(name)
|| ids.contains(name.replace("ENSP", "ENST")))
{
- DBRefUtils.parseToDbRef(sq, DBRefSource.ENSEMBL, "0", name);
+ DBRefUtils.parseToDbRef(sq, getDbSource(),
+ getEnsemblDataVersion(), name);
}
}
if (alignment == null)
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+ protected static final String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
+
+ protected static final String ENSEMBL_REST = "http://rest.ensembl.org";
+
/*
* possible values for the 'feature' parameter of the /overlap REST service
* @see http://rest.ensembl.org/documentation/info/overlap_id
constrained, regulatory
}
+ private String domain = ENSEMBL_REST;
+
@Override
public String getDbSource()
{
// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
- return DBRefSource.ENSEMBL; // "ENSEMBL"
- }
-
- @Override
- public String getDbVersion()
- {
- return "0";
+ if (ENSEMBL_GENOMES_REST.equals(getDomain()))
+ {
+ return DBRefSource.ENSEMBLGENOMES;
+ }
+ return DBRefSource.ENSEMBL;
}
@Override
{
return true;
}
+
+ /**
+ * Returns the domain name to query e.g. http://rest.ensembl.org or
+ * http://rest.ensemblgenomes.org
+ *
+ * @return
+ */
+ protected String getDomain()
+ {
+ return domain;
+ }
+
+ protected void setDomain(String d)
+ {
+ domain = d;
+ }
}
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
import org.jmol.script.T;
-import org.jmol.viewer.JC;
import org.jmol.viewer.Viewer;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
public void closeViewer()
{
- viewer.acm.setModeMouse(JC.MOUSE_NONE);
// remove listeners for all structures in viewer
getSsm().removeStructureViewerListener(this, this.getPdbFile());
- // and shut down jmol
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
+ viewer.dispose();
lastCommand = null;
viewer = null;
releaseUIResources();
*
* @author jimp
*
- * History: v1.0 revised from original due to refactoring of
- * paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
- * http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview
+ * @version v1.0 revised from original due to refactoring of
+ * paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
+ * http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview <br/>
+ * See also testing URL from fjossinet:<br/>
+ * http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d <br/>
+ * If in doubt, check against the REST client at:
+ * https://github.com/fjossinet/RNA-Science
+ * -Toolbox/blob/master/pyrna/restclient.py
*/
public class Annotate3D
{
- private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d";
+ // also test with
+ // "http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d";
+ private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview";
private static ContentHandler createContentHandler()
{
private String lastCommand;
- private boolean loadedInline;
-
- /**
+ /*
* current set of model filenames loaded
*/
String[] modelFileNames = null;
String lastHighlightCommand;
- private List<String> lastReply;
-
/*
* incremented every time a load notification is successfully handled -
* lightweight mechanism for other threads to detect when they can start
if (lastCommand == null || !lastCommand.equals(command))
{
// trim command or it may never find a match in the replyLog!!
- lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
+ List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
+ logResponse);
if (logResponse && debug)
{
log("Response from command ('" + command + "') was:\n" + lastReply);
// End StructureListener
// //////////////////////////
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (getModelNum(pdbfile) < 0)
- {
- return null;
- }
- log("get model / residue colour attribute unimplemented");
- return null;
- }
-
/**
* returns the current featureRenderer that should be used to colour the
* structures
}
/**
- * map from string to applet
- */
- public Map getRegistryInfo()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /**
* returns the current sequenceRenderer that should be used to colour the
* structures
*
AlignmentViewPanel alignment);
/**
- * Construct and send a command to highlight zero, one or more atoms.
- *
- * <pre>
- * Done by generating a command like (to 'highlight' positions 44 and 46)
- * show #0:44,46.C
- * </pre>
+ * Construct and send a command to highlight zero, one or more atoms. We do
+ * this by sending an "rlabel" command to show the residue label at that
+ * position.
*/
@Override
public void highlightAtoms(List<AtomSpec> atoms)
{
- if (atoms == null)
+ if (atoms == null || atoms.size() == 0)
{
return;
}
+
StringBuilder cmd = new StringBuilder(128);
boolean first = true;
boolean found = false;
{
if (first)
{
- cmd.append("show #").append(cms.get(0).getModelNumber())
+ cmd.append("rlabel #").append(cms.get(0).getModelNumber())
.append(":");
}
else
cmd.append(",");
}
first = false;
- cmd.append(cms.get(0).getModelNumber()).append(":");
cmd.append(pdbResNum);
if (!chain.equals(" "))
{
String command = cmd.toString();
/*
- * Avoid repeated commands for the same residue
+ * avoid repeated commands for the same residue
*/
if (command.equals(lastHighlightCommand))
{
return;
}
- viewerCommandHistory(false);
+ /*
+ * unshow the label for the previous residue
+ */
+ if (lastHighlightCommand != null)
+ {
+ viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
+ }
if (found)
{
- viewer.sendChimeraCommand(command.toString(), false);
+ viewer.sendChimeraCommand(command, false);
}
- viewerCommandHistory(true);
this.lastHighlightCommand = command;
}
public boolean isVisibleByDefault();
/**
- * Returns the data column's data type class
+ * Returns the data column's FTS data column group
*
- * @return the Class for the data column's data type
+ * @return the FTSDataColumnGroupI for the column
*/
- public Class getDataColumnClass();
+ public FTSDataColumnGroupI getGroup();
/**
- * Returns the data colum's FTS data column group
+ * Returns the data columns data type POJO
*
- * @return the FTSDataColumnGroupI for the column
+ * @return the DataTypeI for the column
*/
- public FTSDataColumnGroupI getGroup();
+ public DataTypeI getDataType();
/**
* This interface provides a model for the dynamic data column group
*/
public int getSortOrder();
}
+
+ public interface DataTypeI
+ {
+ /**
+ * Returns the data column's data type class
+ *
+ * @return the Class for the data column's data type
+ */
+ public Class getDataTypeClass();
+
+ /**
+ * Checks if the numeric data column's data will be formated
+ *
+ * @return true means the numeric data column shall be formatted
+ */
+ public boolean isFormtted();
+
+ /**
+ * Returns the number of significant figure to be used for the numeric value
+ * formatting
+ *
+ * @return the number of significant figures
+ */
+ public int getSignificantFigures();
+ }
}
*
* @return list of columns to display by default
*/
- public Collection<FTSDataColumnI> getAllDefaulDisplayedDataColumns();
+ public Collection<FTSDataColumnI> getAllDefaultDisplayedFTSDataColumns();
/**
* Return list of FTSDataColumnI objects that can be used to perform a search
--- /dev/null
+package jalview.fts.core;
+
+import java.awt.Component;
+import java.text.DecimalFormat;
+
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.table.DefaultTableCellRenderer;
+
+/**
+ * The class to handle the formatting of the double values for JTable cells.
+ */
+public class DecimalFormatTableCellRenderer extends
+ DefaultTableCellRenderer
+{
+ private DecimalFormat formatter;
+
+ public DecimalFormatTableCellRenderer(boolean isFormated,
+ int significantFigures)
+ {
+ String integerFormater = isFormated ? "###,##0" : "0";
+ String fractionFormater = isFormated ? "###,##0." : "0.";
+ if (significantFigures > 0)
+ {
+ StringBuilder significantFigureBuilder = new StringBuilder();
+ for (int x = 1; x <= significantFigures; ++x)
+ {
+ significantFigureBuilder.append("0");
+ }
+ formatter = new DecimalFormat(fractionFormater
+ + significantFigureBuilder.toString());
+ }
+ else
+ {
+ formatter = new DecimalFormat(integerFormater);
+ }
+ super.setHorizontalAlignment(JLabel.RIGHT);
+ }
+
+ public DecimalFormatTableCellRenderer()
+ {
+ super.setHorizontalAlignment(JLabel.RIGHT);
+ }
+
+ @Override
+ public Component getTableCellRendererComponent(JTable table,
+ Object value, boolean isSelected, boolean hasFocus, int row,
+ int column)
+ {
+ if (value == null)
+ {
+ return null;
+ }
+
+ value = formatter.format(value);
+
+ return super.getTableCellRendererComponent(table, value, isSelected,
+ hasFocus, row, column);
+ }
+}
\ No newline at end of file
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.service.pdb.PDBFTSRestClient;
import java.util.ArrayList;
import java.util.Collection;
FTSRestClientI ftsRestClient)
{
this.ftsRestClient = ftsRestClient;
- Collection<FTSDataColumnI> defaultCols = ftsRestClient
- .getAllDefaulDisplayedDataColumns();
-
- structSummaryColumns.addAll(defaultCols);
-
+ if (source.equals(PreferenceSource.STRUCTURE_CHOOSER)
+ || source.equals(PreferenceSource.PREFERENCES))
+ {
+ structSummaryColumns = ((PDBFTSRestClient) ftsRestClient)
+ .getAllDefaultDisplayedStructureDataColumns();
+ }
allFTSDataColumns.addAll(ftsRestClient.getAllFTSDataColumns());
tbl_FTSDataColumnPrefs.setAutoCreateRowSorter(true);
{
case SEARCH_SUMMARY:
data[x++] = new Object[] {
- ftsRestClient.getAllDefaulDisplayedDataColumns()
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
.contains(field),
field.getName(), field.getGroup() };
break;
break;
case PREFERENCES:
data[x++] = new Object[] { field.getName(),
- ftsRestClient.getAllDefaulDisplayedDataColumns()
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
.contains(field),
structSummaryColumns.contains(field) };
break;
if (currentSource == PreferenceSource.SEARCH_SUMMARY)
{
updatePrefs(ftsRestClient
- .getAllDefaulDisplayedDataColumns(), ftsDataColumn,
+ .getAllDefaultDisplayedFTSDataColumns(), ftsDataColumn,
selected);
}
else if (currentSource == PreferenceSource.STRUCTURE_CHOOSER)
if (col == 1)
{
updatePrefs(ftsRestClient
- .getAllDefaulDisplayedDataColumns(), ftsDataColumn,
+ .getAllDefaultDisplayedFTSDataColumns(), ftsDataColumn,
selected);
}
else if (col == 2)
}
@Override
- public Class<?> getDataColumnClass()
+ public DataTypeI getDataType()
{
- String classString = lineData[2];
- classString = classString.toUpperCase();
- switch (classString)
+ final String[] dataTypeString = lineData[2].split("\\|");
+ final String classString = dataTypeString[0].toUpperCase();
+
+ return new DataTypeI()
{
- case "INT":
- case "INTEGER":
- return Integer.class;
- case "DOUBLE":
- return Double.class;
- case "STRING":
- default:
- return String.class;
- }
+
+ @Override
+ public boolean isFormtted()
+ {
+ if (dataTypeString.length > 1
+ && dataTypeString[1] != null)
+ {
+ switch (dataTypeString[1].toUpperCase())
+ {
+ case "T":
+ case "TRUE":
+ return true;
+ case "F":
+ case "False":
+ default:
+ return false;
+ }
+ }
+ return false;
+ }
+
+ @Override
+ public int getSignificantFigures()
+ {
+ if (dataTypeString.length > 2
+ && dataTypeString[2] != null)
+ {
+ return Integer.valueOf(dataTypeString[2]);
+ }
+ return 0;
+ }
+
+ @Override
+ public Class getDataTypeClass()
+ {
+ switch (classString)
+ {
+ case "INT":
+ case "INTEGER":
+ return Integer.class;
+ case "DOUBLE":
+ return Double.class;
+ case "STRING":
+ default:
+ return String.class;
+ }
+ }
+ };
+
}
@Override
&& this.getGroup().equals(that.getGroup());
}
+
};
dataColumns.add(dataCol);
}
@Override
- public Collection<FTSDataColumnI> getAllDefaulDisplayedDataColumns()
+ public Collection<FTSDataColumnI> getAllDefaultDisplayedFTSDataColumns()
{
if (defaulDisplayedDataColumns == null
|| defaulDisplayedDataColumns.isEmpty())
{
return String.class;
}
- return cols[columnIndex - colOffset].getDataColumnClass();
+ return cols[columnIndex - colOffset].getDataType()
+ .getDataTypeClass();
}
};
{
e.printStackTrace();
}
+ if (wantedField.getDataType().getDataTypeClass() == Double.class)
+ {
+ DecimalFormatTableCellRenderer dfr = new DecimalFormatTableCellRenderer(
+ wantedField.getDataType().isFormtted(),
+ wantedField.getDataType().getSignificantFigures());
+ tbl_summary.getColumn(wantedField.getName()).setCellRenderer(dfr);
+ }
+ else if (wantedField.getDataType().getDataTypeClass() == Integer.class)
+ {
+ DecimalFormatTableCellRenderer dfr = new DecimalFormatTableCellRenderer(
+ wantedField.getDataType().isFormtted(),
+ wantedField.getDataType().getSignificantFigures());
+ tbl_summary.getColumn(wantedField.getName()).setCellRenderer(dfr);
+ }
}
}
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
+import java.util.HashSet;
import java.util.List;
import javax.swing.ImageIcon;
protected int pageLimit;
+ protected HashSet<String> paginatorCart = new HashSet<String>();
+
+ protected static final DecimalFormat totalNumberformatter = new DecimalFormat(
+ "###,###");
+
private JTable tbl_summary = new JTable()
{
private boolean inLayout;
});
btn_next_page.setEnabled(false);
btn_next_page.setToolTipText(MessageManager
- .getString("label.next_page_tooltop"));
+ .getString("label.next_page_tooltip"));
btn_next_page.setFont(new java.awt.Font("Verdana", 0, 12));
btn_next_page.setText(MessageManager.getString("action.next_page"));
btn_next_page.addActionListener(new java.awt.event.ActionListener()
btn_prev_page.setEnabled(false);
btn_prev_page.setToolTipText(MessageManager
- .getString("label.prev_page_tooltop"));
+ .getString("label.prev_page_tooltip"));
btn_prev_page.setFont(new java.awt.Font("Verdana", 0, 12));
btn_prev_page.setText(MessageManager.getString("action.prev_page"));
btn_prev_page.addActionListener(new java.awt.event.ActionListener()
if (!getTypedText().equalsIgnoreCase(lastSearchTerm))
{
searchAction(true);
+ paginatorCart.clear();
lastSearchTerm = getTypedText();
}
}
txt_search.setEnabled(false);
cmb_searchTarget.setEnabled(false);
previousWantedFields = getFTSRestClient()
- .getAllDefaulDisplayedDataColumns()
+ .getAllDefaultDisplayedFTSDataColumns()
.toArray(new Object[0]);
}
if (sourceTabbedPane.getTitleAt(index).equals(searchTabTitle))
if (wantedFieldsUpdated())
{
searchAction(true);
+ paginatorCart.clear();
}
else
{
}
return Arrays.equals(getFTSRestClient()
- .getAllDefaulDisplayedDataColumns()
+ .getAllDefaultDisplayedFTSDataColumns()
.toArray(new Object[0]), previousWantedFields) ? false
: true;
public void validateSelection()
{
- if (tbl_summary.getSelectedRows().length > 0)
+ if (tbl_summary.getSelectedRows().length > 0
+ || !paginatorCart.isEmpty())
{
btn_ok.setEnabled(true);
}
@Override
public void prevPageAction()
{
+ updatePaginatorCart();
if (offSet >= pageLimit)
{
offSet = offSet - pageLimit;
@Override
public void nextPageAction()
{
+ updatePaginatorCart();
offSet = offSet + pageLimit;
searchAction(false);
+ }
+
+ public void updatePaginatorCart()
+ {
+ int primaryKeyColIndex = 0;
+ JTable resultTable = getResultTable();
+ int totalRows = resultTable.getRowCount();
+ try
+ {
+ primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
+ wantedFields, false);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ for (int row = 0; row < totalRows; row++)
+ {
+ String id = (String) resultTable.getValueAt(row, primaryKeyColIndex);
+ if (paginatorCart.contains(id))
+ {
+ paginatorCart.remove(id);
+ }
+ }
+ int[] selectedRows = resultTable.getSelectedRows();
+ for (int summaryRow : selectedRows)
+ {
+ String idStr = resultTable.getValueAt(summaryRow,
+ primaryKeyColIndex).toString();
+ paginatorCart.add(idStr);
+ }
+ // System.out.println("Paginator shopping cart size : "
+ // + paginatorCart.size());
}
+ public void updateSummaryTableSelections()
+ {
+ JTable resultTable = getResultTable();
+ if (paginatorCart.isEmpty())
+ {
+ return;
+ }
+ int primaryKeyColIndex = 0;
+ try
+ {
+ primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
+ wantedFields, false);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ // System.out.println(">>>>>> got here : 1");
+ int totalRows = resultTable.getRowCount();
+ // resultTable.clearSelection();
+ for (int row = 0; row < totalRows; row++)
+ {
+ String id = (String) resultTable.getValueAt(row, primaryKeyColIndex);
+ if (paginatorCart.contains(id))
+ {
+ resultTable.addRowSelectionInterval(row, row);
+ }
+ }
+ validateSelection();
+ }
public void refreshPaginatorState()
{
// System.out.println("resultSet count : " + resultSetCount);
String searchTarget = ((FTSDataColumnI) cmb_searchTarget
.getSelectedItem()).getCode();
wantedFields = PDBFTSRestClient.getInstance()
- .getAllDefaulDisplayedDataColumns();
+ .getAllDefaultDisplayedFTSDataColumns();
String searchTerm = decodeSearchTerm(txt_search.getText(),
searchTarget);
long endTime = System.currentTimeMillis();
totalResultSetCount = resultList.getNumberOfItemsFound();
- resultSetCount = resultList.getSearchSummary().size();
+ resultSetCount = resultList.getSearchSummary() == null ? 0
+ : resultList.getSearchSummary().size();
String result = (resultSetCount > 0) ? MessageManager
.getString("label.results") : MessageManager
.getString("label.result");
if (isPaginationEnabled() && resultSetCount > 0)
{
updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
- + " " + (offSet + 1) + " to "
- + (offSet + resultSetCount) + " of "
- + totalResultSetCount
+ + " "
+ + totalNumberformatter.format((Number) (offSet + 1))
+ + " to "
+ + totalNumberformatter
+ .format((Number) (offSet + resultSetCount))
+ + " of "
+ + totalNumberformatter
+ .format((Number) totalResultSetCount)
+ " " + " (" + (endTime - startTime) + " milli secs)");
}
else
setSearchInProgress(false);
refreshPaginatorState();
+ updateSummaryTableSelections();
}
}
}.start();
e.printStackTrace();
}
int[] selectedRows = getResultTable().getSelectedRows();
+ String searchTerm = txt_search.getText();
for (int summaryRow : selectedRows)
{
String idStr = getResultTable().getValueAt(summaryRow,
primaryKeyColIndex)
.toString();
- String searchTerm = txt_search.getText();
+ selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
+ }
+
+ for (String idStr : paginatorCart)
+ {
selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
}
{
try
{
- summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
+ summaryRowData[colCounter++] = (field.getDataType()
+ .getDataTypeClass() == Integer.class) ? Integer
.valueOf(fieldData)
- : (field.getDataColumnClass() == Double.class) ? Double
+ : (field.getDataType()
+ .getDataTypeClass() == Double.class) ? Double
.valueOf(fieldData)
- : fieldData;
+ : sanitiseData(fieldData);
} catch (Exception e)
{
e.printStackTrace();
};
}
+ private static String sanitiseData(String data)
+ {
+ String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "")
+ .replaceAll("\\[", "").replaceAll("\\]", "")
+ .replaceAll("\",\"", ", ").replaceAll("\"", "");
+ return cleanData;
+ }
+
@Override
public String getColumnDataConfigFileName()
{
}
return instance;
}
+
+ private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
+
+ public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
+ {
+ if (allDefaultDisplayedStructureDataColumns == null
+ || allDefaultDisplayedStructureDataColumns.isEmpty())
+ {
+ allDefaultDisplayedStructureDataColumns = new ArrayList<FTSDataColumnI>();
+ allDefaultDisplayedStructureDataColumns.addAll(super
+ .getAllDefaultDisplayedFTSDataColumns());
+ }
+ return allDefaultDisplayedStructureDataColumns;
+ }
}
: uniportRestRequest.getResponseSize();
int offSet = uniportRestRequest.getOffSet();
+ String query;
+ if (isAdvancedQuery(uniportRestRequest.getSearchTerm()))
+ {
+ query = uniportRestRequest.getSearchTerm();
+ }
+ else
+ {
+ query = uniportRestRequest.getFieldToSearchBy().equalsIgnoreCase(
+ "Search All") ? uniportRestRequest.getSearchTerm()
+ + " or mnemonic:" + uniportRestRequest.getSearchTerm()
+ : uniportRestRequest.getFieldToSearchBy() + ":"
+ + uniportRestRequest.getSearchTerm();
+ }
- String query = uniportRestRequest.getFieldToSearchBy()
- .equalsIgnoreCase("Search All") ? uniportRestRequest
- .getSearchTerm() : uniportRestRequest.getFieldToSearchBy()
- + ":" + uniportRestRequest.getSearchTerm();
-
- // + (uniportRestRequest.isAllowUnpublishedEntries() ? ""
- // : " AND status:REL");
- // System.out.println(">>>>> Query : " + query);
- // System.out.println(">>>>> Columns : " + wantedFields);
- // System.out.println(">>>>> Response size: " + responseSize
- // + " offset : "
- // + offSet);
WebResource webResource = null;
webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
.queryParam("format", "tab")
throw new Exception(errorMessage);
}
+ int xTotalResults = Integer.valueOf(clientResponse.getHeaders()
+ .get("X-Total-Results").get(0));
clientResponse = null;
client = null;
return parseUniprotResponse(uniProtTabDelimittedResponseString,
- uniportRestRequest);
+ uniportRestRequest, xTotalResults);
} catch (Exception e)
{
String exceptionMsg = e.getMessage();
}
}
+ public boolean isAdvancedQuery(String query)
+ {
+ if (query.contains(" AND ") || query.contains(" OR ")
+ || query.contains(" NOT ") || query.contains(" ! ")
+ || query.contains(" || ") || query.contains(" && ")
+ || query.contains(":") || query.contains("-"))
+ {
+ return true;
+ }
+ return false;
+ }
public FTSRestResponse parseUniprotResponse(
String uniProtTabDelimittedResponseString,
- FTSRestRequest uniprotRestRequest)
+ FTSRestRequest uniprotRestRequest, int xTotalResults)
{
FTSRestResponse searchResult = new FTSRestResponse();
List<FTSData> result = null;
// System.out.println(dataRow);
result.add(getFTSData(dataRow, uniprotRestRequest));
}
- searchResult.setNumberOfItemsFound(result.size());
+ searchResult.setNumberOfItemsFound(xTotalResults);
searchResult.setSearchSummary(result);
}
return searchResult;
{
try
{
- summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
- .valueOf(fieldData)
- : (field.getDataColumnClass() == Double.class) ? Double
+ summaryRowData[colCounter++] = (field.getDataType()
+ .getDataTypeClass() == Integer.class) ? Integer
+ .valueOf(fieldData.replace(",", ""))
+ : (field.getDataType()
+ .getDataTypeClass() == Double.class) ? Double
.valueOf(fieldData) : fieldData;
} catch (Exception e)
{
.getSelectedItem()).getAltCode();
wantedFields = UniProtFTSRestClient.getInstance()
- .getAllDefaulDisplayedDataColumns();
+ .getAllDefaultDisplayedFTSDataColumns();
String searchTerm = decodeSearchTerm(txt_search.getText(),
searchTarget);
}
long endTime = System.currentTimeMillis();
- resultSetCount = resultList.getNumberOfItemsFound();
+ totalResultSetCount = resultList.getNumberOfItemsFound();
+ resultSetCount = resultList.getSearchSummary() == null ? 0
+ : resultList.getSearchSummary().size();
String result = (resultSetCount > 0) ? MessageManager
.getString("label.results") : MessageManager
.getString("label.result");
if (isPaginationEnabled() && resultSetCount > 0)
{
updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
- + " " + (offSet + 1) + " to "
- + (offSet + resultSetCount)
+ + " "
+ + totalNumberformatter.format((Number) (offSet + 1))
+ + " to "
+ + totalNumberformatter
+ .format((Number) (offSet + resultSetCount))
+ + " of "
+ + totalNumberformatter
+ .format((Number) totalResultSetCount)
+ " " + " (" + (endTime - startTime) + " milli secs)");
}
else
}
setSearchInProgress(false);
refreshPaginatorState();
+ updateSummaryTableSelections();
}
}
}.start();
primaryKeyColIndex).toString();
selectedIdsSet.add(idStr);
}
-
+ selectedIdsSet.addAll(paginatorCart);
for (String selectedId : selectedIdsSet)
{
selectedIds.append(selectedId).append(";");
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.io.gff.SequenceOntologyI;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.StringSelection;
import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTargetDragEvent;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.dnd.DropTargetEvent;
@Override
public void focusGained(FocusEvent e)
{
- Desktop.setCurrentAlignFrame(AlignFrame.this);
+ Jalview.setCurrentAlignFrame(AlignFrame.this);
}
});
if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
{
- omitHidden = viewport.getViewAsString(false);
+ omitHidden = viewport.getViewAsString(false,
+ settings.isExportHiddenSequences());
}
int[] alignmentStartEnd = new int[2];
else
{
alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = viewport.getAlignment()
- .getVisibleStartAndEndIndex(
- viewport
- .getColumnSelection().getHiddenColumns());
}
+ alignmentStartEnd = alignmentToExport
+ .getVisibleStartAndEndIndex(viewport.getColumnSelection()
+ .getHiddenColumns());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
}
-
/**
* DOCUMENT ME!
*
return showp;
}
+ /**
+ * Finds and displays cross-references for the selected sequences (protein
+ * products for nucleotide sequences, dna coding sequences for peptides).
+ *
+ * @param sel
+ * the sequences to show cross-references for
+ * @param dna
+ * true if from a nucleotide alignment (so showing proteins)
+ * @param source
+ * the database to show cross-references for
+ */
protected void showProductsFor(final SequenceI[] sel, final boolean dna,
final String source)
{
AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
+ if (Cache.getDefault("HIDE_INTRONS", true))
+ {
+ newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
+ }
String newtitle = String.format("%s %s %s",
MessageManager.getString(dna ? "label.proteins"
: "label.nucleotides"), MessageManager
System.err.println("Failed to make CDS alignment");
}
al.getCodonFrames().clear();
- al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
+ al.addCodonFrames(copyAlignment.getCodonFrames());
+ al.addCodonFrames(cf);
/*
* pending getting Embl transcripts to 'align',
{
copyAlignment = AlignmentUtils.makeCopyAlignment(
sequenceSelection, xrefs.getSequencesArray());
- copyAlignment.getCodonFrames().addAll(cf);
+ copyAlignment.addCodonFrames(cf);
+ al.addCodonFrames(copyAlignment.getCodonFrames());
+ al.addCodonFrames(cf);
}
copyAlignment.setGapCharacter(AlignFrame.this.viewport
.getGapCharacter());
}
} catch (Exception e)
{
- Cache.log.error(
- "Exception when finding crossreferences", e);
+ Cache.log.error("Exception when finding crossreferences", e);
} catch (OutOfMemoryError e)
{
new OOMWarning("whilst fetching crossreferences", e);
} catch (Throwable e)
{
- Cache.log.error("Error when finding crossreferences",
- e);
+ Cache.log.error("Error when finding crossreferences", e);
} finally
{
AlignFrame.this.setProgressBar(MessageManager.formatMessage(
.getString("label.error_when_translating_sequences_submit_bug_report");
final String errorTitle = MessageManager
.getString("label.implementation_error")
- + MessageManager.getString("translation_failed");
+ + MessageManager.getString("label.translation_failed");
JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.ERROR_MESSAGE);
return;
public void drop(DropTargetDropEvent evt)
{
Transferable t = evt.getTransferable();
- java.util.List files = null;
+ java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
try
{
- DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
- {
- // Works on Windows and MacOSX
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- files = (java.util.List) t
- .getTransferData(DataFlavor.javaFileListFlavor);
- }
- else if (t.isDataFlavorSupported(uriListFlavor))
- {
- // This is used by Unix drag system
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- String data = (String) t.getTransferData(uriListFlavor);
- files = new java.util.ArrayList(1);
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data, "\r\n"); st.hasMoreTokens();)
- {
- String s = st.nextToken();
- if (s.startsWith("#"))
- {
- // the line is a comment (as per the RFC 2483)
- continue;
- }
-
- java.net.URI uri = new java.net.URI(s);
- // check to see if we can handle this kind of URI
- if (uri.getScheme().toLowerCase().startsWith("http"))
- {
- files.add(uri.toString());
- }
- else
- {
- // otherwise preserve old behaviour: catch all for file objects
- java.io.File file = new java.io.File(uri);
- files.add(file.toString());
- }
- }
- }
+ Desktop.transferFromDropTarget(files, protocols, evt, t);
} catch (Exception e)
{
e.printStackTrace();
AlignFrame.this.setMenusForViewport();
}
});
- dbRefFetcher
- .fetchDBRefs(false);
+ dbRefFetcher.fetchDBRefs(false);
}
}).start();
protected void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
{
- for (AlignmentAnnotation aa : alignPanel.getAlignment()
- .getAlignmentAnnotation())
+ AlignmentAnnotation[] anns = alignPanel.getAlignment()
+ .getAlignmentAnnotation();
+ if (anns == null)
+ {
+ return;
+ }
+ for (AlignmentAnnotation aa : anns)
{
/*
* don't display non-positional annotations on an alignment
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
-
al = dna.reverseCdna(complement);
viewport.addAlignment(al, "");
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
+ viewport.getAlignment()));
} catch (Exception ex)
{
System.err.println(ex.getMessage());
@Override
protected void runGroovy_actionPerformed()
{
- Desktop.setCurrentAlignFrame(this);
+ Jalview.setCurrentAlignFrame(this);
groovy.ui.Console console = Desktop.getGroovyConsole();
if (console != null)
{
System.err.println("Can't run Groovy script as console not found");
}
}
+
+ /**
+ * Hides columns containing (or not containing) a specified feature, provided
+ * that would not leave all columns hidden
+ *
+ * @param featureType
+ * @param columnsContaining
+ * @return
+ */
+ public boolean hideFeatureColumns(String featureType,
+ boolean columnsContaining)
+ {
+ boolean notForHiding = avc.markColumnsContainingFeatures(
+ columnsContaining, false, false, featureType);
+ if (notForHiding)
+ {
+ if (avc.markColumnsContainingFeatures(!columnsContaining, false,
+ false, featureType))
+ {
+ getViewport().hideSelectedColumns();
+ return true;
+ }
+ }
+ return false;
+ }
}
class PrintThread extends Thread
List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
for (PDBEntry pdb : pdbEntries)
{
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
for (SequenceI sq : alignment.getSequences())
{
- Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
- if (pdbs == null)
+ Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+ if (pdbRefEntries == null)
{
continue;
}
- for (PDBEntry p1 : pdbs)
+ for (PDBEntry pdbRefEntry : pdbRefEntries)
{
- if (p1.getId().equals(pdb.getId()))
+ if (pdbRefEntry.getId().equals(pdb.getId()))
{
- if (!seqs.contains(sq))
+ if (pdbRefEntry.getChainCode() != null
+ && pdb.getChainCode() != null)
{
- seqs.add(sq);
- continue;
+ if (pdbRefEntry.getChainCode().equalsIgnoreCase(
+ pdb.getChainCode())
+ && !choosenSeqs.contains(sq))
+ {
+ choosenSeqs.add(sq);
+ continue;
+ }
}
+ else
+ {
+ if (!choosenSeqs.contains(sq))
+ {
+ choosenSeqs.add(sq);
+ continue;
+ }
+ }
+
}
}
}
- seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
*
* @param featureSettings
*/
+ @Override
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
{
if (featureSettings == null)
*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
.getString("label.no_features_on_alignment");
if (features)
{
+ Map<String, FeatureColourI> displayedFeatureColours = ap
+ .getFeatureRenderer().getDisplayedFeatureCols();
FeaturesFile formatter = new FeaturesFile();
SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
- Map<String, Object> featureColours = ap.getFeatureRenderer()
+ Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
.getDisplayedFeatureCols();
boolean includeNonPositional = ap.av.isShowNPFeats();
if (GFFFormat.isSelected())
{
+ text = new FeaturesFile().printGffFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(), displayedFeatureColours,
+ true, ap.av.isShowNPFeats());
text = formatter.printGffFormat(sequences, featureColours, true,
includeNonPositional);
}
else
{
+ text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(), displayedFeatureColours, true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
text = formatter.printJalviewFormat(sequences, featureColours,
true, includeNonPositional);
}
// todo: make the ap scroll to the selection - not necessary, first
// click highlights/scrolls, second selects
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
- ap.av.setSelectionGroup(// new SequenceGroup(
- aa[selectedRow].groupRef); // );
+ // process modifiers
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null
+ || sg == aa[selectedRow].groupRef
+ || !(jalview.util.Platform.isControlDown(evt) || evt
+ .isShiftDown()))
+ {
+ if (jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown())
+ {
+ // clone a new selection group from the associated group
+ ap.av.setSelectionGroup(new SequenceGroup(
+ aa[selectedRow].groupRef));
+ }
+ else
+ {
+ // set selection to the associated group so it can be edited
+ ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+ }
+ }
+ else
+ {
+ // modify current selection with associated group
+ int remainToAdd = aa[selectedRow].groupRef.getSize();
+ for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+ {
+ if (jalview.util.Platform.isControlDown(evt))
+ {
+ sg.addOrRemove(sgs, --remainToAdd == 0);
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
+ sg.addSequence(sgs, --remainToAdd == 0);
+ }
+ }
+ }
+
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
// we make a copy rather than edit the current selection if no
// modifiers pressed
// see Enhancement JAL-1557
- if (!(evt.isControlDown() || evt.isShiftDown()))
+ if (!(jalview.util.Platform.isControlDown(evt) || evt
+ .isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
}
else
{
- if (evt.isControlDown())
+ if (jalview.util.Platform.isControlDown(evt))
{
sg.addOrRemove(aa[selectedRow].sequenceRef, true);
}
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
- ap.av.sendSelection();
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
}
}
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
+import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.util.concurrent.Executors;
import java.util.concurrent.Semaphore;
+import javax.swing.AbstractAction;
import javax.swing.DefaultDesktopManager;
import javax.swing.DesktopManager;
import javax.swing.JButton;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
+import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
import javax.swing.event.HyperlinkEvent;
import javax.swing.event.HyperlinkEvent.EventType;
static final int yOffset = 30;
- private static AlignFrame currentAlignFrame;
-
public static jalview.ws.jws1.Discoverer discoverer;
public static Object[] jalviewClipboard;
{
boolean success = true;
Transferable t = evt.getTransferable();
- java.util.List files = null;
- java.util.List protocols = null;
+ java.util.List<String> files = new ArrayList<String>();
+ java.util.List<String> protocols = new ArrayList<String>();
try
{
- DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
- {
- // Works on Windows and MacOSX
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- files = (java.util.List) t
- .getTransferData(DataFlavor.javaFileListFlavor);
- }
- else if (t.isDataFlavorSupported(uriListFlavor))
- {
- // This is used by Unix drag system
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- String data = (String) t.getTransferData(uriListFlavor);
- files = new java.util.ArrayList(1);
- protocols = new java.util.ArrayList(1);
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data, "\r\n"); st.hasMoreTokens();)
- {
- String s = st.nextToken();
- if (s.startsWith("#"))
- {
- // the line is a comment (as per the RFC 2483)
- continue;
- }
- java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase().startsWith("http"))
- {
- protocols.add(FormatAdapter.URL);
- files.add(uri.toString());
- }
- else
- {
- // otherwise preserve old behaviour: catch all for file objects
- java.io.File file = new java.io.File(uri);
- protocols.add(FormatAdapter.FILE);
- files.add(file.toString());
- }
- }
- }
+ Desktop.transferFromDropTarget(files, protocols, evt, t);
} catch (Exception e)
{
+ e.printStackTrace();
success = false;
}
dialogExecutor.shutdownNow();
}
closeAll_actionPerformed(null);
+
+ if (groovyConsole != null)
+ {
+ // suppress a possible repeat prompt to save script
+ groovyConsole.setDirty(false);
+ groovyConsole.exit();
+ }
System.exit(0);
}
if (Jalview.isHeadlessMode())
{
// Desktop.desktop is null in headless mode
- return new AlignFrame[] { currentAlignFrame };
+ return new AlignFrame[] { Jalview.currentAlignFrame };
}
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
*/
void openGroovyConsole()
{
- groovyConsole = new groovy.ui.Console();
+ if (groovyConsole == null)
+ {
+ groovyConsole = new groovy.ui.Console();
+ groovyConsole.setVariable("Jalview", this);
+ groovyConsole.run();
- /*
- * bind groovy variable 'Jalview' to the Desktop object
- */
- groovyConsole.setVariable("Jalview", this);
+ /*
+ * We allow only one console at a time, so that AlignFrame menu option
+ * 'Calculate | Run Groovy script' is unambiguous.
+ * Disable 'Groovy Console', and enable 'Run script', when the console is
+ * opened, and the reverse when it is closed
+ */
+ Window window = (Window) groovyConsole.getFrame();
+ window.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ public void windowClosed(WindowEvent e)
+ {
+ /*
+ * rebind CMD-Q from Groovy Console to Jalview Quit
+ */
+ addQuitHandler();
+ enableExecuteGroovy(false);
+ }
+ });
+ }
/*
- * start the console
+ * show Groovy console window (after close and reopen)
*/
- groovyConsole.run();
+ ((Window) groovyConsole.getFrame()).setVisible(true);
/*
- * Allow only one console at a time, so that the AlignFrame menu option
- * 'Calculate | Run Groovy script' is unambiguous.
- * Disable 'new console', and enable 'Run script', when the console is
- * opened, and the reverse when it is closed
+ * if we got this far, enable 'Run Groovy' in AlignFrame menus
+ * and disable opening a second console
*/
- Window window = (Window) groovyConsole.getFrame();
- window.addWindowListener(new WindowAdapter()
+ enableExecuteGroovy(true);
+ }
+
+ /**
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
+ * binding when opened
+ */
+ protected void addQuitHandler()
+ {
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()),
+ "Quit");
+ getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@Override
- public void windowClosed(WindowEvent e)
+ public void actionPerformed(ActionEvent e)
{
- groovyShell.setEnabled(true);
- enableExecuteGroovy(false);
+ quit();
}
});
-
- /*
- * if we got this far, enable 'Run Groovy' in AlignFrame menus
- * and disable opening a second console
- */
- groovyShell.setEnabled(false);
- enableExecuteGroovy(true);
}
/**
* Enable or disable 'Run Groovy script' in AlignFrame calculate menus
*
* @param enabled
+ * true if Groovy console is open
*/
public void enableExecuteGroovy(boolean enabled)
{
+ /*
+ * disable opening a second Groovy console
+ * (or re-enable when the console is closed)
+ */
+ groovyShell.setEnabled(!enabled);
+
AlignFrame[] alignFrames = getAlignFrames();
if (alignFrames != null)
{
* The dust settles...give focus to the tab we did this from.
*/
myTopFrame.setDisplayedView(myTopFrame.alignPanel);
-
}
- public static AlignFrame getCurrentAlignFrame()
+ public static groovy.ui.Console getGroovyConsole()
{
- return currentAlignFrame;
+ return groovyConsole;
}
- public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+ public static void transferFromDropTarget(List<String> files,
+ List<String> protocols, DropTargetDropEvent evt, Transferable t)
+ throws Exception
{
- Desktop.currentAlignFrame = currentAlignFrame;
- }
- public static groovy.ui.Console getGroovyConsole()
- {
- return groovyConsole;
+ DataFlavor uriListFlavor = new DataFlavor(
+ "text/uri-list;class=java.lang.String");
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
+ // Works on Windows and MacOSX
+ Cache.log.debug("Drop handled as javaFileListFlavor");
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ for (Object file : (List) t
+ .getTransferData(DataFlavor.javaFileListFlavor))
+ {
+ files.add(((File)file).toString());
+ protocols.add(FormatAdapter.FILE);
+ }
+ }
+ else
+ {
+ // Unix like behaviour
+ boolean added = false;
+ String data = null;
+ if (t.isDataFlavorSupported(uriListFlavor))
+ {
+ Cache.log.debug("Drop handled as uriListFlavor");
+ // This is used by Unix drag system
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ data = (String) t.getTransferData(uriListFlavor);
+ }
+ if (data == null)
+ {
+ // fallback to text: workaround - on OSX where there's a JVM bug
+ Cache.log.debug("standard URIListFlavor failed. Trying text");
+ // try text fallback
+ data = (String) t.getTransferData(new DataFlavor(
+ "text/plain;class=java.lang.String"));
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("fallback returned " + data);
+ }
+ }
+ while (protocols.size() < files.size())
+ {
+ Cache.log.debug("Adding missing FILE protocol for "
+ + files.get(protocols.size()));
+ protocols.add(FormatAdapter.FILE);
+ }
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data, "\r\n"); st.hasMoreTokens();)
+ {
+ added = true;
+ String s = st.nextToken();
+ if (s.startsWith("#"))
+ {
+ // the line is a comment (as per the RFC 2483)
+ continue;
+ }
+ java.net.URI uri = new java.net.URI(s);
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ protocols.add(FormatAdapter.URL);
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ protocols.add(FormatAdapter.FILE);
+ files.add(file.toString());
+ }
+ }
+ if (Cache.log.isDebugEnabled())
+ {
+ if (data == null || !added)
+ {
+ Cache.log
+ .debug("Couldn't resolve drop data. Here are the supported flavors:");
+ for (DataFlavor fl : t.getTransferDataFlavors())
+ {
+ Cache.log.debug("Supported transfer dataflavor: "
+ + fl.toString());
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ Object df = t.getTransferData(fl);
+ if (df != null)
+ {
+ Cache.log.debug("Retrieves: " + df);
+ }
+ else
+ {
+ Cache.log.debug("Retrieved nothing");
+ }
+ }
+ }
+ }
+ }
}
-
}
*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.GraphLine;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
-import java.util.Hashtable;
import javax.swing.BorderFactory;
import javax.swing.JCheckBox;
// FeatureSettings fs;
FeatureRenderer fr;
- private GraduatedColor cs;
+ private FeatureColourI cs;
- private Object oldcs;
+ private FeatureColourI oldcs;
/**
*
* @return the last colour setting selected by user - either oldcs (which may
* be a java.awt.Color) or the new GraduatedColor
*/
- public Object getLastColour()
+ public FeatureColourI getLastColour()
{
if (cs == null)
{
return cs;
}
- Hashtable oldgroupColours;
-
AlignmentPanel ap;
boolean adjusting = false;
}
});
- float mm[] = ((float[][]) fr.getMinMax().get(type))[0];
+ float mm[] = fr.getMinMax().get(type)[0];
min = mm[0];
max = mm[1];
scaleFactor = (max == min) ? 1f : 100f / (max - min);
oldcs = fr.getFeatureColours().get(type);
- if (oldcs instanceof GraduatedColor)
+ if (!oldcs.isSimpleColour())
{
- if (((GraduatedColor) oldcs).isAutoScale())
+ if (oldcs.isAutoScaled())
{
// update the scale
- cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
+ cs = new FeatureColour((FeatureColour) oldcs, min, max);
}
else
{
- cs = new GraduatedColor((GraduatedColor) oldcs);
+ cs = new FeatureColour((FeatureColour) oldcs);
}
}
else
{
// promote original color to a graduated color
- Color bl = Color.black;
- if (oldcs instanceof Color)
+ Color bl = oldcs.getColour();
+ if (bl == null)
{
- bl = (Color) oldcs;
+ bl = Color.BLACK;
}
// original colour becomes the maximum colour
- cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
+ cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
cs.setColourByLabel(false);
}
- minColour.setBackground(oldminColour = cs.getMinColor());
- maxColour.setBackground(oldmaxColour = cs.getMaxColor());
+ minColour.setBackground(oldminColour = cs.getMinColour());
+ maxColour.setBackground(oldmaxColour = cs.getMaxColour());
adjusting = true;
try
{
}
// update the gui from threshold state
- thresholdIsMin.setSelected(!cs.isAutoScale());
+ thresholdIsMin.setSelected(!cs.isAutoScaled());
colourByLabel.setSelected(cs.isColourByLabel());
- if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (cs.hasThreshold())
{
// initialise threshold slider and selector
- threshold
- .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
- : 2);
+ threshold.setSelectedIndex(cs.isAboveThreshold() ? 1 : 2);
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
- "Threshold", Color.black);
+ threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
}
return;
}
- int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
+ boolean aboveThreshold = false;
+ boolean belowThreshold = false;
if (threshold.getSelectedIndex() == 1)
{
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+ aboveThreshold = true;
}
else if (threshold.getSelectedIndex() == 2)
{
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+ belowThreshold = true;
}
+ boolean hasThreshold = aboveThreshold || belowThreshold;
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- GraduatedColor acg;
+ FeatureColourI acg;
if (cs.isColourByLabel())
{
- acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
+ acg = new FeatureColour(oldminColour, oldmaxColour, min, max);
}
else
{
- acg = new GraduatedColor(oldminColour = minColour.getBackground(),
+ acg = new FeatureColour(oldminColour = minColour.getBackground(),
oldmaxColour = maxColour.getBackground(), min, max);
}
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+ if (!hasThreshold)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
thresholdIsMin.setEnabled(false);
}
- else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
- && threshline == null)
+ else if (threshline == null)
{
// todo visual indication of feature threshold
- threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
- "Threshold", Color.black);
+ threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
}
- if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ if (hasThreshold)
{
adjusting = true;
- acg.setThresh(threshline.value);
+ acg.setThreshold(threshline.value);
float range = (max - min) * scaleFactor;
adjusting = false;
}
- acg.setThreshType(aboveThreshold);
- if (thresholdIsMin.isSelected()
- && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ acg.setAboveThreshold(aboveThreshold);
+ acg.setBelowThreshold(belowThreshold);
+ if (thresholdIsMin.isSelected() && hasThreshold)
{
acg.setAutoScaled(false);
- if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
+ if (aboveThreshold)
{
- acg = new GraduatedColor(acg, threshline.value, max);
+ acg = new FeatureColour((FeatureColour) acg, threshline.value, max);
}
else
{
- acg = new GraduatedColor(acg, min, threshline.value);
+ acg = new FeatureColour((FeatureColour) acg, min, threshline.value);
}
}
else
public void valueChanged()
{
threshline.value = slider.getValue() / scaleFactor;
- cs.setThresh(threshline.value);
+ cs.setThreshold(threshline.value);
changeColour();
ap.paintAlignment(false);
}
*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
static String lastDescriptionAdded;
- Object oldcol, fcol;
+ FeatureColourI oldcol, fcol;
int featureIndex = 0;
@Override
public void mousePressed(MouseEvent evt)
{
- if (fcol instanceof Color)
+ if (fcol.isSimpleColour())
{
Color col = JColorChooser.showDialog(Desktop.desktop,
MessageManager.getString("label.select_feature_colour"),
- ((Color) fcol));
+ fcol.getColour());
if (col != null)
{
- fcol = col;
- updateColourButton(bigPanel, colour, col);
+ fcol = new FeatureColour(col);
+ updateColourButton(bigPanel, colour, new FeatureColour(col));
}
}
else
{
-
if (fcc == null)
{
final String type = features[featureIndex].getType();
ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
}
- Object col = getFeatureStyle(name.getText());
+ FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new jalview.schemes.UserColourScheme()
- .createColourFromName(name.getText());
+ col = new FeatureColour(UserColourScheme
+ .createColourFromName(name.getText()));
}
oldcol = fcol = col;
updateColourButton(bigPanel, colour, col);
*
* @param bigPanel
* @param col
- * @param col2
+ * @param col
*/
protected void updateColourButton(JPanel bigPanel, JLabel colour,
- Object col2)
+ FeatureColourI col)
{
colour.removeAll();
colour.setIcon(null);
colour.setToolTipText(null);
colour.setText("");
- if (col2 instanceof Color)
+ if (col.isSimpleColour())
{
- colour.setBackground((Color) col2);
+ colour.setBackground(col.getColour());
}
else
{
colour.setBackground(bigPanel.getBackground());
colour.setForeground(Color.black);
- FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
- // colour.setForeground(colour.getBackground());
+ FeatureSettings.renderGraduatedColor(colour, col);
}
}
*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.bin.Cache;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.schemabinding.version2.JalviewUserColours;
+import jalview.schemes.FeatureColour;
+import jalview.util.Format;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.QuickSort;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.dbsources.das.api.jalviewSourceI;
table.setDefaultEditor(Color.class, new ColorEditor(this));
- table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this));
- table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer());
+ table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
+ table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
table.addMouseListener(new MouseAdapter()
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (evt.isPopupTrigger())
+ if (SwingUtilities.isRightMouseButton(evt))
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.getMinMax(),
frame = new JInternalFrame();
frame.setContentPane(this);
- if (new jalview.util.Platform().isAMac())
+ if (Platform.isAMac())
{
Desktop.addInternalFrame(frame,
MessageManager.getString("label.sequence_feature_settings"),
final Object typeCol, final Map<String, float[][]> minmax, int x,
int y)
{
+ final FeatureColourI featureColour = (FeatureColourI) typeCol;
+
JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
"label.settings_for_param", new String[] { type }));
JMenuItem scr = new JMenuItem(
// positional features
final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
"Graduated Colour");
- mxcol.setSelected(!(typeCol instanceof Color));
+ mxcol.setSelected(!featureColour.isSimpleColour());
men.add(mxcol);
mxcol.addActionListener(new ActionListener()
{
{
if (e.getSource() == mxcol)
{
- if (typeCol instanceof Color)
+ if (featureColour.isSimpleColour())
{
FeatureColourChooser fc = new FeatureColourChooser(me.fr,
type);
"Select new Colour", true, // modal
colorChooser, this, // OK button handler
null); // no CANCEL button handler
- colorChooser.setColor(((GraduatedColor) typeCol)
- .getMaxColor());
+ colorChooser.setColor(featureColour.getMaxColour());
dialog.setVisible(true);
}
}
MessageManager.getString("label.select_columns_containing"));
selCols.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent arg0)
{
MessageManager.getString("label.select_columns_not_containing"));
clearCols.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent arg0)
{
false, type);
}
});
+ JMenuItem hideCols = new JMenuItem(
+ MessageManager.getString("label.hide_columns_containing"));
+ hideCols.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.hideFeatureColumns(type, true);
+ }
+ });
+ JMenuItem hideOtherCols = new JMenuItem(
+ MessageManager.getString("label.hide_columns_not_containing"));
+ hideOtherCols.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.hideFeatureColumns(type, false);
+ }
+ });
men.add(selCols);
men.add(clearCols);
+ men.add(hideCols);
+ men.add(hideOtherCols);
men.show(table, x, y);
}
/**
* contains a float[3] for each feature type string. created by setTableData
*/
- Hashtable typeWidth = null;
+ Map<String, float[]> typeWidth = null;
@Override
synchronized public void discoverAllFeatureData()
{
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
+ Vector<String> allFeatures = new Vector<String>();
+ Vector<String> allGroups = new Vector<String>();
SequenceFeature[] tmpfeatures;
String group;
for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
return;
}
resettingTable = true;
- typeWidth = new Hashtable();
+ typeWidth = new Hashtable<String, float[]>();
// TODO: change avWidth calculation to 'per-sequence' average and use long
// rather than float
float[] avWidth = null;
SequenceFeature[] tmpfeatures;
String group = null, type;
- Vector visibleChecks = new Vector();
+ Vector<String> visibleChecks = new Vector<String>();
// Find out which features should be visible depending on which groups
// are selected / deselected
}
else
{
- avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
+ avWidth = typeWidth.get(tmpfeatures[index].getType());
}
avWidth[0]++;
if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
InputStreamReader in = new InputStreamReader(new FileInputStream(
file), "UTF-8");
- jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
- jucs = jucs.unmarshal(in);
+ JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
Cache.log.warn("Couldn't parse out graduated feature color.",
e);
}
- GraduatedColor gcol = new GraduatedColor(mincol, maxcol,
+ FeatureColourI gcol = new FeatureColour(mincol, maxcol,
newcol.getMin(), newcol.getMax());
if (newcol.hasAutoScale())
{
}
if (newcol.hasThreshold())
{
- gcol.setThresh(newcol.getThreshold());
- gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default
+ gcol.setThreshold(newcol.getThreshold());
}
if (newcol.getThreshType().length() > 0)
{
String ttyp = newcol.getThreshType();
- if (ttyp.equalsIgnoreCase("NONE"))
- {
- gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
- }
if (ttyp.equalsIgnoreCase("ABOVE"))
{
- gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ gcol.setAboveThreshold(true);
}
if (ttyp.equalsIgnoreCase("BELOW"))
{
- gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ gcol.setBelowThreshold(true);
}
}
fr.setColour(name = newcol.getName(), gcol);
}
else
{
- fr.setColour(name = jucs.getColour(i).getName(), new Color(
- Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+ Color color = new Color(
+ Integer.parseInt(jucs.getColour(i).getRGB(), 16));
+ fr.setColour(name = jucs.getColour(i).getName(),
+ new FeatureColour(color));
}
fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
}
void save()
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ Cache.getProperty("LAST_DIRECTORY"),
new String[] { "fc" },
new String[] { "Sequence Feature Colours" },
"Sequence Feature Colours");
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(choice), "UTF-8"));
- Set fr_colours = fr.getAllFeatureColours();
- Iterator e = fr_colours.iterator();
+ Set<String> fr_colours = fr.getAllFeatureColours();
+ Iterator<String> e = fr_colours.iterator();
float[] sortOrder = new float[fr_colours.size()];
String[] sortTypes = new String[fr_colours.size()];
int i = 0;
while (e.hasNext())
{
- sortTypes[i] = e.next().toString();
+ sortTypes[i] = e.next();
sortOrder[i] = fr.getOrder(sortTypes[i]);
i++;
}
- jalview.util.QuickSort.sort(sortOrder, sortTypes);
+ QuickSort.sort(sortOrder, sortTypes);
sortOrder = null;
- Object fcol;
- GraduatedColor gcol;
for (i = 0; i < sortTypes.length; i++)
{
jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
col.setName(sortTypes[i]);
- col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
- .getName())));
- fcol = fr.getFeatureStyle(sortTypes[i]);
- if (fcol instanceof GraduatedColor)
+ FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
+ if (fcol.isSimpleColour())
{
- gcol = (GraduatedColor) fcol;
- col.setMin(gcol.getMin());
- col.setMax(gcol.getMax());
- col.setMinRGB(jalview.util.Format.getHexString(gcol
- .getMinColor()));
- col.setAutoScale(gcol.isAutoScale());
- col.setThreshold(gcol.getThresh());
- col.setColourByLabel(gcol.isColourByLabel());
- switch (gcol.getThreshType())
- {
- case AnnotationColourGradient.NO_THRESHOLD:
- col.setThreshType("NONE");
- break;
- case AnnotationColourGradient.ABOVE_THRESHOLD:
- col.setThreshType("ABOVE");
- break;
- case AnnotationColourGradient.BELOW_THRESHOLD:
- col.setThreshType("BELOW");
- break;
- }
+ col.setRGB(Format.getHexString(fcol.getColour()));
+ }
+ else
+ {
+ col.setRGB(Format.getHexString(fcol.getMaxColour()));
+ col.setMin(fcol.getMin());
+ col.setMax(fcol.getMax());
+ col.setMinRGB(jalview.util.Format.getHexString(fcol
+ .getMinColour()));
+ col.setAutoScale(fcol.isAutoScaled());
+ col.setThreshold(fcol.getThreshold());
+ col.setColourByLabel(fcol.isColourByLabel());
+ col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" : (fcol
+ .isBelowThreshold() ? "BELOW" : "NONE"));
}
ucs.addColour(col);
}
int num = 0;
for (int i = 0; i < data.length; i++)
{
- awidth = (float[]) typeWidth.get(data[i][0]);
+ awidth = typeWidth.get(data[i][0]);
if (awidth[0] > 0)
{
width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
fetchDAS.setEnabled(false);
cancelDAS.setEnabled(true);
dassourceBrowser.setGuiEnabled(false);
- Vector selectedSources = dassourceBrowser.getSelectedSources();
+ Vector<jalviewSourceI> selectedSources = dassourceBrowser
+ .getSelectedSources();
doDasFeatureFetch(selectedSources, true, true);
}
* Vector of Strings to resolve to DAS source nicknames.
* @return sources that are present in source list.
*/
- public List<jalviewSourceI> resolveSourceNicknames(Vector sources)
+ public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
{
return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
}
*
* @return vector of selected das source nicknames
*/
- public Vector getSelectedSources()
+ public Vector<jalviewSourceI> getSelectedSources()
{
return dassourceBrowser.getSelectedSources();
}
* if true then runs in same thread, otherwise passes to the Swing
* executor
*/
- public void fetchDasFeatures(Vector sources, boolean block)
+ public void fetchDasFeatures(Vector<String> sources, boolean block)
{
initDasSources();
List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
}
@Override
- public Component getTableCellRendererComponent(JTable table,
+ public Component getTableCellRendererComponent(JTable tbl,
Object color, boolean isSelected, boolean hasFocus, int row,
int column)
{
+ FeatureColourI cellColour = (FeatureColourI) color;
// JLabel comp = new JLabel();
// comp.
setOpaque(true);
// setBounds(getBounds());
Color newColor;
setToolTipText(baseTT);
- setBackground(table.getBackground());
- if (color instanceof GraduatedColor)
+ setBackground(tbl.getBackground());
+ if (!cellColour.isSimpleColour())
{
- Rectangle cr = table.getCellRect(row, column, false);
- FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color,
+ Rectangle cr = tbl.getCellRect(row, column, false);
+ FeatureSettings.renderGraduatedColor(this, cellColour,
(int) cr.getWidth(), (int) cr.getHeight());
}
{
this.setText("");
this.setIcon(null);
- newColor = (Color) color;
- // comp.
+ newColor = cellColour.getColour();
setBackground(newColor);
- // comp.setToolTipText("RGB value: " + newColor.getRed() + ", "
- // + newColor.getGreen() + ", " + newColor.getBlue());
}
if (isSelected)
{
if (selectedBorder == null)
{
selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
- table.getSelectionBackground());
+ tbl.getSelectionBackground());
}
- // comp.
setBorder(selectedBorder);
}
else
if (unselectedBorder == null)
{
unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
- table.getBackground());
+ tbl.getBackground());
}
- // comp.
setBorder(unselectedBorder);
}
* @param comp
* @param gcol
*/
- public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol)
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)
{
int w = comp.getWidth(), h = comp.getHeight();
if (w < 20)
renderGraduatedColor(comp, gcol, w, h);
}
- public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol,
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
int w, int h)
{
boolean thr = false;
String tt = "";
String tx = "";
- if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD)
+ if (gcol.isAboveThreshold())
{
thr = true;
tx += ">";
- tt += "Thresholded (Above " + gcol.getThresh() + ") ";
+ tt += "Thresholded (Above " + gcol.getThreshold() + ") ";
}
- if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
+ if (gcol.isBelowThreshold())
{
thr = true;
tx += "<";
- tt += "Thresholded (Below " + gcol.getThresh() + ") ";
+ tt += "Thresholded (Below " + gcol.getThreshold() + ") ";
}
if (gcol.isColourByLabel())
{
}
else
{
- Color newColor = gcol.getMaxColor();
+ Color newColor = gcol.getMaxColour();
comp.setBackground(newColor);
// System.err.println("Width is " + w / 2);
Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
class FeatureIcon implements Icon
{
- GraduatedColor gcol;
+ FeatureColourI gcol;
Color backg;
Color mpcolour = Color.white;
- FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace)
+ FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)
{
gcol = gfc;
backg = bg;
g.setColor(backg);
g.fillRect(0, 0, width, height);
// need an icon here.
- g.setColor(gcol.getMaxColor());
+ g.setColor(gcol.getMaxColour());
g.setFont(new Font("Verdana", Font.PLAIN, 9));
}
else
{
- Color minCol = gcol.getMinColor();
+ Color minCol = gcol.getMinColour();
g.setColor(minCol);
g.fillRect(0, 0, s1, height);
if (midspace)
g.setColor(Color.white);
g.fillRect(s1, 0, e1 - s1, height);
}
- g.setColor(gcol.getMaxColor());
+ g.setColor(gcol.getMaxColour());
g.fillRect(0, e1, width - e1, height);
}
}
{
FeatureSettings me;
- GraduatedColor currentGColor;
+ FeatureColourI currentColor;
FeatureColourChooser chooser;
String type;
- Color currentColor;
-
JButton button;
JColorChooser colorChooser;
{
// The user has clicked the cell, so
// bring up the dialog.
- if (currentColor != null)
+ if (currentColor.isSimpleColour())
{
// bring up simple color chooser
- button.setBackground(currentColor);
- colorChooser.setColor(currentColor);
+ button.setBackground(currentColor.getColour());
+ colorChooser.setColor(currentColor.getColour());
dialog.setVisible(true);
}
else
}
else
{ // User pressed dialog's "OK" button.
- if (currentColor != null)
+ if (currentColor.isSimpleColour())
{
- currentColor = colorChooser.getColor();
+ currentColor = new FeatureColour(colorChooser.getColor());
}
else
{
- // class cast exceptions may be raised if the chooser created on a
- // non-graduated color
- currentGColor = (GraduatedColor) chooser.getLastColour();
+ currentColor = chooser.getLastColour();
}
me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
fireEditingStopped();
@Override
public Object getCellEditorValue()
{
- if (currentColor == null)
- {
- return currentGColor;
- }
return currentColor;
}
public Component getTableCellEditorComponent(JTable table, Object value,
boolean isSelected, int row, int column)
{
- currentGColor = null;
- currentColor = null;
+ currentColor = (FeatureColourI) value;
this.selectedRow = row;
type = me.table.getValueAt(row, 0).toString();
button.setOpaque(true);
button.setBackground(me.getBackground());
- if (value instanceof GraduatedColor)
+ if (!currentColor.isSimpleColour())
{
- currentGColor = (GraduatedColor) value;
JLabel btn = new JLabel();
btn.setSize(button.getSize());
- FeatureSettings.renderGraduatedColor(btn, currentGColor);
+ FeatureSettings.renderGraduatedColor(btn, currentColor);
button.setBackground(btn.getBackground());
button.setIcon(btn.getIcon());
button.setText(btn.getText());
{
button.setText("");
button.setIcon(null);
- currentColor = (Color) value;
- button.setBackground(currentColor);
+ button.setBackground(currentColor.getColour());
}
return button;
}
return;
}
-
if ((av.getSelectionGroup() == null)
- || ((!e.isControlDown() && !e.isShiftDown()) && av
- .getSelectionGroup() != null))
+ || (!jalview.util.Platform.isControlDown(e)
+ && !e.isShiftDown() && av.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
import java.awt.BorderLayout;
import java.awt.Component;
-import java.awt.Container;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.GridLayout;
@Override
public void actionPerformed(ActionEvent arg0)
{
- showDialog(null);
+ showDialog();
}
});
return viewdbs;
jc.validate();
// j.setPreferredSize(new Dimension(300,50));
add(jc, BorderLayout.CENTER);
+ ok.setEnabled(false);
j.add(ok);
j.add(cancel);
add(j, BorderLayout.SOUTH);
closeDialog();
}
- private void showDialog(Container parent)
+ void showDialog()
{
oldselection = selection;
oldtsel = tsel;
{
return;
}
+ ok.setEnabled(false);
if (dbviews.getSelectionCount() == 0)
{
selection = null;
}
+
tsel = dbviews.getSelectionPaths();
boolean forcedFirstChild = false;
List<DbSourceProxy> srcs = new ArrayList<DbSourceProxy>();
.getLastPathComponent();
if (dmt.getUserObject() != null)
{
+ /*
+ * enable OK button once a selection has been made
+ */
+ ok.setEnabled(true);
if (dmt.getUserObject() instanceof DbSourceProxy)
{
srcs.add((DbSourceProxy) dmt.getUserObject());
}
}
+ dbstatex.setText(" ");
if (allowMultiSelections)
{
dbstatus.setText(MessageManager.formatMessage(
(srcs.size() == 1 ? "" : "s"),
(srcs.size() > 0 ? " with " + x + " test quer"
+ (x == 1 ? "y" : "ies") : ".") }));
- dbstatex.setText(" ");
}
else
{
dbstatex.setText(MessageManager.formatMessage(
"label.example_param", new String[] { qr }));
}
- else
- {
- dbstatex.setText(" ");
- }
}
else
{
*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.StringUtils;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
+import java.awt.Color;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.DataInputStream;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
-import java.util.StringTokenizer;
import java.util.Vector;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
object.setVersion(jalview.bin.Cache.getDefault("VERSION",
"Development Build"));
- jalview.datamodel.AlignmentI jal = av.getAlignment();
+ /**
+ * rjal is full height alignment, jal is actual alignment with full metadata
+ * but excludes hidden sequences.
+ */
+ jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
if (av.hasHiddenRows())
{
- jal = jal.getHiddenSequences().getFullAlignment();
+ rjal = jal.getHiddenSequences().getFullAlignment();
}
SequenceSet vamsasSet = new SequenceSet();
{
// switch jal and the dataset
jal = jal.getDataset();
+ rjal = jal;
}
}
if (jal.getProperties() != null)
Set<String> calcIdSet = new HashSet<String>();
// SAVE SEQUENCES
- for (int i = 0; i < jal.getHeight(); i++)
+ for (final SequenceI jds : rjal.getSequences())
{
- final SequenceI jds = jal.getSequenceAt(i);
final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
: jds.getDatasetSequence();
String id = seqHash(jds);
// Store any sequences this sequence represents
if (av.hasHiddenRows())
{
+ // use rjal, contains the full height alignment
jseq.setHidden(av.getAlignment().getHiddenSequences()
.isHidden(jds));
- if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
+ if (av.isHiddenRepSequence(jds))
{
jalview.datamodel.SequenceI[] reps = av
- .getRepresentedSequences(jal.getSequenceAt(i))
- .getSequencesInOrder(jal);
+ .getRepresentedSequences(jds)
+ .getSequencesInOrder(rjal);
for (int h = 0; h < reps.length; h++)
{
- if (reps[h] != jal.getSequenceAt(i))
+ if (reps[h] != jds)
{
- jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ jseq.addHiddenSequences(rjal.findIndex(reps[h]));
}
}
}
}
+ // mark sequence as reference - if it is the reference for this view
+ if (jal.hasSeqrep())
+ {
+ jseq.setViewreference(jds == jal.getSeqrep());
+ }
}
+ // TODO: omit sequence features from each alignment view's XML dump if we
+ // are storing dataset
if (jds.getSequenceFeatures() != null)
{
jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
alc.addAlcodMap(alcmap);
}
}
-
+ // TODO: delete this ? dead code from 2.8.3->2.9 ?
// {
// AlcodonFrame alc = new AlcodonFrame();
// vamsasSet.addAlcodonFrame(alc);
.getFeatureRenderer().getRenderOrder()
.toArray(new String[0]);
- Vector settingsAdded = new Vector();
- Object gstyle = null;
- GraduatedColor gcol = null;
+ Vector<String> settingsAdded = new Vector<String>();
if (renderOrder != null)
{
- for (int ro = 0; ro < renderOrder.length; ro++)
+ for (String featureType : renderOrder)
{
- gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getFeatureStyle(renderOrder[ro]);
+ FeatureColourI fcol = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer()
+ .getFeatureStyle(featureType);
Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- if (gstyle instanceof GraduatedColor)
+ setting.setType(featureType);
+ if (!fcol.isSimpleColour())
{
- gcol = (GraduatedColor) gstyle;
- setting.setColour(gcol.getMaxColor().getRGB());
- setting.setMincolour(gcol.getMinColor().getRGB());
- setting.setMin(gcol.getMin());
- setting.setMax(gcol.getMax());
- setting.setColourByLabel(gcol.isColourByLabel());
- setting.setAutoScale(gcol.isAutoScale());
- setting.setThreshold(gcol.getThresh());
- setting.setThreshstate(gcol.getThreshType());
+ setting.setColour(fcol.getMaxColour().getRGB());
+ setting.setMincolour(fcol.getMinColour().getRGB());
+ setting.setMin(fcol.getMin());
+ setting.setMax(fcol.getMax());
+ setting.setColourByLabel(fcol.isColourByLabel());
+ setting.setAutoScale(fcol.isAutoScaled());
+ setting.setThreshold(fcol.getThreshold());
+ // -1 = No threshold, 0 = Below, 1 = Above
+ setting.setThreshstate(fcol.isAboveThreshold() ? 1
+ : (fcol.isBelowThreshold() ? 0 : -1));
}
else
{
- setting.setColour(ap.getSeqPanel().seqCanvas
- .getFeatureRenderer().getColour(renderOrder[ro])
- .getRGB());
+ setting.setColour(fcol.getColour().getRGB());
}
setting.setDisplay(av.getFeaturesDisplayed().isVisible(
- renderOrder[ro]));
+ featureType));
float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getOrder(renderOrder[ro]);
+ .getOrder(featureType);
if (rorder > -1)
{
setting.setOrder(rorder);
}
fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
+ settingsAdded.addElement(featureType);
}
}
- // Make sure we save none displayed feature settings
- Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getFeatureColours().keySet().iterator();
- while (en.hasNext())
- {
- String key = en.next().toString();
- if (settingsAdded.contains(key))
- {
- continue;
- }
-
- Setting setting = new Setting();
- setting.setType(key);
- setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getColour(key).getRGB());
-
- setting.setDisplay(false);
- float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getOrder(key);
- if (rorder > -1)
- {
- setting.setOrder(rorder);
- }
- fs.addSetting(setting);
- settingsAdded.addElement(key);
- }
// is groups actually supposed to be a map here ?
- en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ Iterator<String> en = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer()
.getFeatureGroups().iterator();
- Vector groupsAdded = new Vector();
+ Vector<String> groupsAdded = new Vector<String>();
while (en.hasNext())
{
- String grp = en.next().toString();
+ String grp = en.next();
if (groupsAdded.contains(grp))
{
continue;
groupsAdded.addElement(grp);
}
jms.setFeatureSettings(fs);
-
}
if (av.hasHiddenColumns())
List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
boolean multipleView = false;
-
+ SequenceI referenceseqForView = null;
JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
int vi = 0; // counter in vamsasSeq array
for (int i = 0; i < jseqs.length; i++)
vi++;
}
+ if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
+ {
+ referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
+ }
+
if (jseqs[i].getHidden())
{
if (hiddenSeqs == null)
hiddenSeqs.add(seqRefIds.get(seqId));
}
-
}
// /
Alignment al = new Alignment(orderedSeqs);
+ if (referenceseqForView != null)
+ {
+ al.setSeqrep(referenceseqForView);
+ }
// / Add the alignment properties
for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
{
}
/**
+ * Answers true if 'version' is equal to or later than 'supported', where each
+ * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
+ * changes. Development and test values for 'version' are leniently treated
+ * i.e. answer true.
*
* @param supported
* - minimum version we are comparing against
* @param version
- * - version of data being processsed.
- * @return true if version is development/null or evaluates to the same or
- * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
+ * - version of data being processsed
+ * @return
*/
public static boolean isVersionStringLaterThan(String supported,
String version)
{
- if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
+ if (supported == null || version == null
+ || version.equalsIgnoreCase("DEVELOPMENT BUILD")
|| version.equalsIgnoreCase("Test")
|| version.equalsIgnoreCase("AUTOMATED BUILD"))
{
}
else
{
- StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
- version, ".");
- while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
- {
- // convert b to decimal to catch bugfix releases within a series
- String curT = currentV.nextToken().toLowerCase().replace('b', '.');
- String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
- try
- {
- float supportedVersionToken = Float.parseFloat(curT);
- float myVersiontoken = Float.parseFloat(fileT);
- if (supportedVersionToken > myVersiontoken)
- {
- // current version is newer than the version that wrote the file
- return false;
- }
- if (supportedVersionToken < myVersiontoken)
- {
- // current version is older than the version that wrote the file
- return true;
- }
- } catch (NumberFormatException nfe)
- {
- System.err
- .println("** WARNING: Version comparison failed for tokens ("
- + curT
- + ") and ("
- + fileT
- + ")\n** Current: '"
- + supported + "' and Version: '" + version + "'");
- }
- }
- if (currentV.hasMoreElements())
- {
- // fileV has no minor version but identical series to current
- return false;
- }
+ return StringUtils.compareVersions(version, supported, "b") >= 0;
}
- return true;
}
Vector<JalviewStructureDisplayI> newStructureViewers = null;
.getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
}
+ if (al.hasSeqrep())
+ {
+ af.getViewport().setColourByReferenceSeq(true);
+ af.getViewport().setDisplayReferenceSeq(true);
+ }
+
af.viewport.setGatherViewsHere(view.getGatheredViews());
if (view.getSequenceSetId() != null)
af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
- Hashtable featureGroups = new Hashtable();
- Hashtable featureColours = new Hashtable();
- Hashtable featureOrder = new Hashtable();
+ Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
+ Map<String, Float> featureOrder = new Hashtable<String, Float>();
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
if (setting.hasMincolour())
{
- GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
- new java.awt.Color(setting.getMincolour()),
- new java.awt.Color(setting.getColour()),
- setting.getMin(), setting.getMax()) : new GraduatedColor(
- new java.awt.Color(setting.getMincolour()),
- new java.awt.Color(setting.getColour()), 0, 1);
+ FeatureColourI gc = setting.hasMin() ? new FeatureColour(
+ new Color(setting.getMincolour()), new Color(
+ setting.getColour()), setting.getMin(),
+ setting.getMax()) : new FeatureColour(new Color(
+ setting.getMincolour()), new Color(setting.getColour()),
+ 0, 1);
if (setting.hasThreshold())
{
- gc.setThresh(setting.getThreshold());
- gc.setThreshType(setting.getThreshstate());
+ gc.setThreshold(setting.getThreshold());
+ int threshstate = setting.getThreshstate();
+ // -1 = None, 0 = Below, 1 = Above threshold
+ if (threshstate == 0)
+ {
+ gc.setBelowThreshold(true);
+ }
+ else if (threshstate == 1)
+ {
+ gc.setAboveThreshold(true);
+ }
}
gc.setAutoScaled(true); // default
if (setting.hasAutoScale())
}
else
{
- featureColours.put(setting.getType(),
- new java.awt.Color(setting.getColour()));
+ featureColours.put(setting.getType(), new FeatureColour(
+ new Color(setting.getColour())));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
fdi.setVisible(setting.getType());
}
}
- Hashtable fgtable = new Hashtable();
+ Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
.wrapTooltip(
true,
((desc == null || desc.trim().length() == 0) ? MessageManager
- .getString("label.opt_and_params_further_details ")
+ .getString("label.opt_and_params_further_details")
: desc)
+ "<br><img src=\"" + linkImageURL + "\"/>"));
enabled.addMouseListener(this);
+ linkImageURL
+ "\"/>"
+ MessageManager
- .getString("label.opt_and_params_further_detail")
+ .getString("label.opt_and_params_further_details")
: "")));
}
void hideSequences(boolean representGroup)
{
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null || sg.getSize() < 1)
- {
- ap.av.hideSequence(new SequenceI[] { sequence });
- return;
- }
-
- ap.av.setSelectionGroup(null);
-
- if (representGroup)
- {
- ap.av.hideRepSequences(sequence, sg);
-
- return;
- }
-
- int gsize = sg.getSize();
- SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
-
- ap.av.hideSequence(hseqs);
- // refresh(); TODO: ? needed ?
- ap.av.sendSelection();
+ ap.av.hideSequences(sequence, representGroup);
}
public void copy_actionPerformed()
ap, true));
}
- public void enterPDB_actionPerformed()
- {
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager.getString("label.enter_pdb_id"),
- MessageManager.getString("label.enter_pdb_id"),
- JOptionPane.QUESTION_MESSAGE);
-
- if (id != null && id.length() > 0)
- {
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- sequence.getDatasetSequence().addPDBId(entry);
- }
- }
-
- public void discoverPDB_actionPerformed()
- {
-
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
- { sequence }
- : ap.av.getSequenceSelection());
- Thread discpdb = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- boolean isNuclueotide = ap.alignFrame.getViewport().getAlignment()
- .isNucleotide();
-
- new jalview.ws.DBRefFetcher(sequences, ap.alignFrame, null,
- ap.alignFrame.featureSettings, isNuclueotide)
- .fetchDBRefs(false);
-
- }
-
- });
- discpdb.start();
- }
-
public void sequenceFeature_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
private WsPreferences wsPrefs;
+ private OptionsParam promptEachTimeOpt = new OptionsParam(
+ MessageManager.getString("label.prompt_each_time"),
+ "Prompt each time");
+
+ private OptionsParam lineArtOpt = new OptionsParam(
+ MessageManager.getString("label.lineart"), "Lineart");
+
+ private OptionsParam textOpt = new OptionsParam(
+ MessageManager.getString("action.text"), "Text");
+
/**
* Creates a new Preferences object.
*/
/*
* Set Output tab defaults
*/
- epsRendering
- .addItem(MessageManager.getString("label.prompt_each_time"));
- epsRendering.addItem(MessageManager.getString("label.lineart"));
- epsRendering.addItem(MessageManager.getString("action.text"));
- epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
- "Prompt each time"));
+ epsRendering.addItem(promptEachTimeOpt);
+ epsRendering.addItem(lineArtOpt);
+ epsRendering.addItem(textOpt);
+ String defaultEPS = Cache.getDefault("EPS_RENDERING",
+ "Prompt each time");
+ if (defaultEPS.equalsIgnoreCase("Text"))
+ {
+ epsRendering.setSelectedItem(textOpt);
+ }
+ else if (defaultEPS.equalsIgnoreCase("Lineart"))
+ {
+ epsRendering.setSelectedItem(lineArtOpt);
+ }
+ else
+ {
+ epsRendering.setSelectedItem(promptEachTimeOpt);
+ }
autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
userIdWidth.setEnabled(!autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
/*
* Save Output settings
*/
- if (epsRendering.getSelectedItem().equals("Prompt each time"))
- {
- Cache.applicationProperties.remove("EPS_RENDERING");
- }
- else
- {
- Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
- .getSelectedItem().toString());
- }
+ Cache.applicationProperties.setProperty("EPS_RENDERING",
+ ((OptionsParam) epsRendering.getSelectedItem()).getCode());
/*
* Save Connections settings
}
}
+ public class OptionsParam
+ {
+ private String name;
+
+ private String code;
+
+ public OptionsParam(String name, String code)
+ {
+ this.name = name;
+ this.code = code;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ @Override
+ public String toString()
+ {
+ return name;
+ }
+
+ @Override
+ public boolean equals(Object that)
+ {
+ if (!(that instanceof OptionsParam))
+ {
+ return false;
+ }
+ return this.code.equalsIgnoreCase(((OptionsParam) that).code);
+ }
+
+ @Override
+ public int hashCode(){
+ return name.hashCode() + code.hashCode();
+ }
+ }
}
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
+import java.util.List;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.ToolTipManager;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * The panel containing the sequence ruler (when not in wrapped mode), and
+ * supports a range of mouse operations to select, hide or reveal columns.
*/
public class ScalePanel extends JPanel implements MouseMotionListener,
MouseListener
{
protected int offy = 4;
- /** DOCUMENT ME!! */
public int width;
protected AlignViewport av;
boolean stretchingGroup = false;
- int min; // used by mouseDragged to see if user
+ /*
+ * min, max hold the extent of a mouse drag action
+ */
+ int min;
- int max; // used by mouseDragged to see if user
+ int max;
boolean mouseDragging = false;
- // wants to delete columns
+ /*
+ * holds a hidden column range when the mouse is over an adjacent column
+ */
+ int[] reveal;
+
+ /**
+ * Constructor
+ *
+ * @param av
+ * @param ap
+ */
public ScalePanel(AlignViewport av, AlignmentPanel ap)
{
this.av = av;
@Override
public void mouseMoved(MouseEvent evt)
{
+ this.setToolTipText(null);
+ reveal = null;
if (!av.hasHiddenColumns())
{
return;
res = av.getColumnSelection().adjustForHiddenColumns(res);
- reveal = null;
if (av.getColumnSelection().getHiddenColumns() != null)
{
for (int[] region : av.getColumnSelection().getHiddenColumns())
.getString("label.reveal_hidden_columns"));
break;
}
- else
- {
- this.setToolTipText(null);
- }
}
}
repaint();
}
- int[] reveal;
-
/**
* DOCUMENT ME!
*
ColumnSelection cs = av.getColumnSelection();
int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
- int s;
if (cs != null)
{
gg.setColor(new Color(220, 0, 0));
}
}
}
- // Draw the scale numbers
- gg.setColor(Color.black);
-
- int scalestartx = (startx / 10) * 10;
-
- SequenceI refSeq = av.getAlignment().getSeqrep();
- int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
- if (refSeq != null)
- {
- // find bounds and set origin appopriately
- // locate first visible position for this sequence
- int[] refbounds = av.getColumnSelection()
- .locateVisibleBoundsOfSequence(refSeq);
-
- refSp = refbounds[0];
- refEp = refbounds[1];
- refStart = refbounds[2];
- refEnd = refbounds[3];
- refStartI = refbounds[4];
- refEndI = refbounds[5];
- scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
- }
-
int widthx = 1 + endx - startx;
FontMetrics fm = gg.getFontMetrics(av.getFont());
- int y = avCharHeight - fm.getDescent();
-
- if (refSeq == null && scalestartx % 10 == 0)
- {
- scalestartx += 5;
- }
-
- String string;
- int maxX = 0, refN, iadj;
- // todo: add a 'reference origin column' to set column number relative to
- for (int i = scalestartx; i < endx; i += 5)
- {
- if (((i - refSp) % 10) == 0)
- {
- iadj = av.getColumnSelection().adjustForHiddenColumns(i) - 1;
- if (refSeq == null)
- {
- string = String.valueOf(iadj + 1);
- }
- else
- {
- refN = refSeq.findPosition(iadj);
- // TODO show bounds if position is a gap
- // - ie L--R -> "1L|2R" for
- // marker
- if (iadj < refStartI)
- {
- string = String.valueOf(iadj - refStartI);
- }
- else if (iadj > refEndI)
- {
- string = "+" + String.valueOf(iadj - refEndI);
- }
- else
- {
- string = String.valueOf(refN) + refSeq.getCharAt(iadj);
- }
- }
- if ((i - startx - 1) * avCharWidth > maxX)
- {
- gg.drawString(string, (i - startx - 1) * avCharWidth, y);
- maxX = (i - startx + 1) * avCharWidth + fm.stringWidth(string);
- }
-
- gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
- y + 2,
- ((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
- + (fm.getDescent() * 2));
- }
- else
- {
- gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
- + fm.getDescent(), ((i - startx - 1) * avCharWidth)
- + (avCharWidth / 2), y + (fm.getDescent() * 2));
- }
- }
-
+ int y = avCharHeight, yOf = fm.getDescent();
+ y -= yOf;
if (av.hasHiddenColumns())
{
+ // draw any hidden column markers
gg.setColor(Color.blue);
int res;
if (av.getShowHiddenMarkers()
continue;
}
- gg.fillPolygon(new int[] { res * avCharWidth - avCharHeight / 4,
- res * avCharWidth + avCharHeight / 4, res * avCharWidth },
- new int[] { y - avCharHeight / 2, y - avCharHeight / 2,
- y + 8 }, 3);
+ gg.fillPolygon(new int[] {
+ -1 + res * avCharWidth - avCharHeight / 4,
+ -1 + res * avCharWidth + avCharHeight / 4,
+ -1 + res * avCharWidth }, new int[] { y, y, y + 2 * yOf }, 3);
}
}
+ }
+ // Draw the scale numbers
+ gg.setColor(Color.black);
+
+ int maxX = 0;
+ List<Object[]> marks = jalview.renderer.ScaleRenderer.calculateMarks(
+ av, startx, endx);
+ for (Object[] mark : marks)
+ {
+ boolean major = Boolean.valueOf((Boolean) mark[0]);
+ int mpos = ((Integer) mark[1]).intValue(); // (i - startx - 1)
+ String mstring = (String) mark[2];
+ if (mstring != null)
+ {
+ if (mpos * avCharWidth > maxX)
+ {
+ gg.drawString(mstring, mpos * avCharWidth, y);
+ maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring);
+ }
+ }
+ if (major)
+ {
+ gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2,
+ (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
+ }
+ else
+ {
+ gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf,
+ (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
+ }
+ }
+ if (av.hasHiddenColumns())
+ {
if (reveal != null && reveal[0] > startx && reveal[0] < endx)
{
gg.drawString(MessageManager.getString("label.reveal_columns"),
}
}
+
}
private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
updateViewport();
- int scalestartx = startx - (startx % 10) + 10;
-
- g.setColor(Color.black);
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
+ for (Object[] mark : jalview.renderer.ScaleRenderer.calculateMarks(av,
+ startx, endx))
{
- int value = i;
- if (av.hasHiddenColumns())
+ int mpos = ((Integer) mark[1]).intValue(); // (i - startx - 1)
+ if (mpos < 0)
{
- value = av.getColumnSelection().adjustForHiddenColumns(value);
+ continue;
}
+ String mstring = (String) mark[2];
- g.drawString(String.valueOf(value), (i - startx - 1) * charWidth,
- ypos - (charHeight / 2));
-
- g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
- (ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
- + (charWidth / 2), ypos - 2);
+ if (Boolean.valueOf((Boolean) mark[0]))
+ {
+ if (mstring != null)
+ {
+ g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
+ }
+ g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2)
+ - (charHeight / 2), (mpos * charWidth) + (charWidth / 2),
+ ypos - 2);
+ }
}
}
// do we want to thread this ? (contention with seqsel and colsel locks, I
// suspect)
- // rules are: colsel is copied if there is a real intersection between
- // sequence selection
+ /*
+ * only copy colsel if there is a real intersection between
+ * sequence selection and this panel's alignment
+ */
boolean repaint = false;
- boolean copycolsel = true;
+ boolean copycolsel = false;
SequenceGroup sgroup = null;
if (seqsel != null && seqsel.getSize() > 0)
}
sgroup = seqsel.intersect(av.getAlignment(),
(av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
- if ((sgroup == null || sgroup.getSize() == 0)
- || (colsel == null || colsel.isEmpty()))
+ if ((sgroup != null && sgroup.getSize() > 0))
{
- // don't copy columns if the region didn't intersect.
- copycolsel = false;
+ copycolsel = true;
}
}
if (sgroup != null && sgroup.getSize() > 0)
ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
av);
av.setColumnSelection(cs);
- av.isColSelChanged(true);
PaintRefresher.Refresh(this, av.getSequenceSetId());
import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.seqfetcher.DbSourceProxy;
frame = new JInternalFrame();
frame.setContentPane(this);
- if (new jalview.util.Platform().isAMac())
+ if (Platform.isAMac())
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
+ Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 240);
}
else
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
+ Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 180);
}
}
jPanel1.add(close);
jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
jPanel2.setLayout(borderLayout3);
- databaseButt = database.getDatabaseSelectorButton();
+ databaseButt = /*database.getDatabaseSelectorButton();
+ final JButton viewdbs =*/new JButton(
+ MessageManager.getString("action.select_ddbb"));
+ databaseButt.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ hidePanel();
+ database.showDialog();
+ }
+ });
databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
{
debounceTrap++;
String currentSelection = database.getSelectedItem();
+ if (currentSelection == null)
+ {
+ close_actionPerformed(null);
+ }
+
+ showPanel();
if (currentSelection.equalsIgnoreCase("pdb")
&& (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
this.add(jPanel2, java.awt.BorderLayout.NORTH);
jScrollPane1.getViewport().add(textArea);
+ /*
+ * open the database tree
+ */
+ database.waitForInput();
}
private void pdbSourceAction()
}
if (Cache.getDefault("HIDE_INTRONS", true))
{
- hideIntronsIfPresent(af);
+ af.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
return al;
}
- /**
- * Hide columns not containing 'exon' features, provided there are exon
- * features on the alignment
- *
- * @param af
- */
- public void hideIntronsIfPresent(AlignFrame af)
- {
- boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
- false,
- SequenceOntologyI.EXON);
- if (hasExons)
- {
- af.avc.markColumnsContainingFeatures(true, false, true,
- SequenceOntologyI.EXON);
- af.getViewport().hideSelectedColumns();
- }
- }
-
void showErrorMessage(final String error)
{
resetDialog();
{
this.progressIndicator = progressIndicator;
}
+
+ /**
+ * Make this panel visible (after a selection has been made in the database
+ * chooser)
+ */
+ void showPanel()
+ {
+ frame.setVisible(true);
+ }
+
+ /**
+ * Hide this panel (on clicking the database button to open the database
+ * chooser)
+ */
+ void hidePanel()
+ {
+ frame.setVisible(false);
+ }
}
import java.awt.FontMetrics;
import java.awt.Graphics;
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
final static int CHAR_TO_UPPER = 'A' - 'a';
}
if (!isarep && av.getShowUnconserved())
{
- s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+ s = getDisplayChar(srep, i, s, '.', null);
}
{
// TODO - use currentSequenceGroup rather than alignment
// currentSequenceGroup.getConsensus()
- char conschar = (usesrep) ? (currentGroup == null ? av.getAlignment()
+ char conschar = (usesrep) ? (currentGroup == null
+ || position < currentGroup.getStartRes()
+ || position > currentGroup.getEndRes() ? av.getAlignment()
.getSeqrep().getCharAt(position)
: (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
.getCharAt(position) : av.getAlignment().getSeqrep()
.getCharAt(position)))
- : (currentGroup != null && currentGroup.getConsensus() != null) ? currentGroup
+ : (currentGroup != null && currentGroup.getConsensus() != null
+ && position >= currentGroup.getStartRes()
+ && position <= currentGroup.getEndRes() && currentGroup
+ .getConsensus().annotations.length > position) ? currentGroup
.getConsensus().annotations[position].displayCharacter
.charAt(0)
: av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
import jalview.jbgui.GStructureChooser;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.ws.DBRefFetcher;
import jalview.ws.sifts.SiftsSettings;
import java.awt.event.ItemEvent;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Objects;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBox;
{
long startTime = System.currentTimeMillis();
pdbRestCleint = PDBFTSRestClient.getInstance();
- Collection<FTSDataColumnI> wantedFields = pdbRestCleint
- .getAllDefaulDisplayedDataColumns();
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
discoveredStructuresSet = new LinkedHashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest,
+ getResultTable().setModel(
+ FTSRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
boolean isPDBRefsFound = false;
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
- HashSet<String> seqRefs = new LinkedHashSet<String>();
+ Set<String> seqRefs = new LinkedHashSet<String>();
if (seq.getAllPDBEntries() != null)
{
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append("pdb_id")
- .append(":")
-.append(entry.getId().toLowerCase())
+ queryBuilder.append("pdb_id:")
+ .append(entry.getId().toLowerCase())
.append(" OR ");
isPDBRefsFound = true;
// seqRefs.add(entry.getId());
{
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
- queryBuilder
-.append("uniprot_accession").append(":")
+ queryBuilder.append("uniprot_accession:")
.append(getDBRefId(dbRef))
.append(" OR ");
- queryBuilder
-.append("uniprot_id")
- .append(":")
- .append(getDBRefId(dbRef)).append(" OR ");
+ queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
+ .append(" OR ");
isUniProtRefsFound = true;
}
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- queryBuilder.append("pdb_id")
- .append(":").append(getDBRefId(dbRef).toLowerCase())
+ queryBuilder.append("pdb_id:")
+ .append(getDBRefId(dbRef).toLowerCase())
.append(" OR ");
isPDBRefsFound = true;
}
}
/**
- * Remove the following special characters from input string +, -, &, |, !, (,
- * ), {, }, [, ], ^, ", ~, *, ?, :, \
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
*
* @param seqName
* @return
*/
- private static String sanitizeSeqName(String seqName)
+ static String sanitizeSeqName(String seqName)
{
Objects.requireNonNull(seqName);
return seqName.replaceAll("\\[\\d*\\]", "")
- .replaceAll("[^\\dA-Za-z|]", "").replaceAll("\\s+", "+");
+ .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
}
long startTime = System.currentTimeMillis();
pdbRestCleint = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
- Collection<FTSDataColumnI> wantedFields = pdbRestCleint
- .getAllDefaulDisplayedDataColumns();
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
Collection<FTSData> filteredResponse = new HashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
FTSRestRequest pdbRequest = new FTSRestRequest();
if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
{
- System.out.println(">>>>>> Filtering with uniprot coverate");
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(");
Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- tbl_summary.setModel(FTSRestResponse.getTableModel(
+ getResultTable().setModel(
+ FTSRestResponse.getTableModel(
lastPdbRequest, reorderedStructuresSet));
- FTSRestResponse.configureTableColumn(tbl_summary, wantedFields);
- tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120);
- tbl_summary.getColumn("Ref Sequence").setMinWidth(100);
- tbl_summary.getColumn("Ref Sequence").setMaxWidth(200);
+ FTSRestResponse.configureTableColumn(getResultTable(),
+ wantedFields);
+ getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
+ getResultTable().getColumn("Ref Sequence").setMinWidth(100);
+ getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
// Update table selection model here
- tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+ getResultTable().addRowSelectionInterval(0,
+ filterResponseCount - 1);
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_filter_time", totalTime));
}
{
cmb_filterOption.addItem(new FilterOption("Best Quality",
"overall_quality", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage",
- "uniprot_coverage", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Best Resolution",
"resolution", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- if (tbl_summary.getSelectedRows().length > 0)
+ if (getResultTable().getSelectedRows().length > 0)
{
btn_view.setEnabled(true);
}
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = tbl_summary.getColumn("PDB Id")
+ int pdbIdColIndex = getResultTable().getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
+ int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
.getModelIndex();
- int[] selectedRows = tbl_summary.getSelectedRows();
+ int[] selectedRows = getResultTable().getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
for (int row : selectedRows)
{
- String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
+ String pdbIdStr = getResultTable().getValueAt(row,
+ pdbIdColIndex)
.toString();
- SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
+ SequenceI selectedSeq = (SequenceI) getResultTable()
+ .getValueAt(row,
refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
+ if (pdbIdStr.split(":").length > 1)
+ {
+ pdbEntry.setId(pdbIdStr.split(":")[0]);
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+ }
+ else
+ {
+ pdbEntry.setId(pdbIdStr);
+ }
pdbEntry.setType(PDBEntry.Type.PDB);
selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
}
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
- ssm.setProgressBar("Launching PDB structure viewer..");
+ ssm.setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"));
final StructureViewer sViewer = new StructureViewer(ssm);
if (SiftsSettings.isMapWithSifts())
{
+ ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
for (SequenceI seq : sequences)
{
- if (seq.getSourceDBRef() == null)
+ if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
{
- ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching Database refs..");
- new jalview.ws.DBRefFetcher(sequences, null, null, null, false)
- .fetchDBRefs(true);
- break;
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
+ }
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ int y = seqsWithoutSourceDBRef.size();
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_dbrefs_for_sequences_without_valid_refs",
+ y));
+ SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
+ int x = 0;
+ for (SequenceI fSeq : seqsWithoutSourceDBRef)
+ {
+ seqWithoutSrcDBRef[x++] = fSeq;
}
+ new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
}
}
- if (pdbEntriesToView.length > 1)
- {
- ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
- for (SequenceI seq : sequences)
- {
- seqsMap.add(new SequenceI[] { seq });
- }
- SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
+ if (pdbEntriesToView.length > 1)
+ {
+ ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+ for (SequenceI seq : sequences)
+ {
+ seqsMap.add(new SequenceI[] { seq });
+ }
+ SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching PDB Structures for selected entries..");
- sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
- }
- else
- {
+ ssm.setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"));
+ sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
+ }
+ else
+ {
ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching PDB Structure for "
- + pdbEntriesToView[0].getId());
- sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
+ ssm.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()));
+ sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ }
}
/**
isValidPBDEntry = false;
if (txt_search.getText().length() > 0)
{
+ String searchTerm = txt_search.getText().toLowerCase();
+ searchTerm = searchTerm.split(":")[0];
+ // System.out.println(">>>>> search term : " + searchTerm);
List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest
- .setSearchTerm(txt_search.getText().toLowerCase() + ")");
+.setSearchTerm(searchTerm + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
pdbRestCleint = PDBFTSRestClient.getInstance();
wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
final JPanel col2 = new JPanel();
col2.setPreferredSize(new Dimension(40, 20));
col2.setBorder(BorderFactory.createEtchedBorder());
- col2.setToolTipText(MessageManager.getString("label.ligth_colour"));
+ col2.setToolTipText(MessageManager.getString("label.light_colour"));
col2.setBackground(new Color(original2));
final JPanel bigpanel = new JPanel(new BorderLayout());
JPanel panel = new JPanel();
col1.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
Color col = JColorChooser.showDialog(bigpanel,
col2.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
Color col = JColorChooser.showDialog(bigpanel,
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
thresholdChanged(slider.getValue());
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
}
+ @Override
public void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = false;
itemf.setSelected(treeCanvas.applyToAllViews);
itemf.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = itemf.isSelected();
}
}
+ @Override
public void run()
{
* @param e
* DOCUMENT ME!
*/
+ @Override
public void textbox_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAsNewick_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
* @param e
* DOCUMENT ME!
*/
+ @Override
public void printMenu_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
treeCanvas.startPrinting();
}
+ @Override
public void originalSeqData_actionPerformed(ActionEvent e)
{
if (!tree.hasOriginalSequenceData())
* @param e
* DOCUMENT ME!
*/
+ @Override
public void fitToWindow_actionPerformed(ActionEvent e)
{
treeCanvas.fitToWindow = fitToWindow.isSelected();
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
if (treeCanvas == null)
* @param e
* DOCUMENT ME!
*/
+ @Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowDistances(distanceMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void epsTree_actionPerformed(ActionEvent e)
{
boolean accurateText = true;
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pngTree_actionPerformed(ActionEvent e)
{
int width = treeCanvas.getWidth();
tree.applyToNodes(new NodeTransformI()
{
+ @Override
public void transform(BinaryNode node)
{
if (node instanceof SequenceNode
*/
public String printCSVAnnotations(AlignmentAnnotation[] annotations)
{
+ if (annotations == null)
+ {
+ return "";
+ }
StringBuffer sp = new StringBuffer();
for (int i = 0; i < annotations.length; i++)
{
import jalview.analysis.AlignmentUtils;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
import jalview.api.FeaturesSourceI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.io.gff.GffHelperBase;
import jalview.io.gff.GffHelperFactory;
import jalview.io.gff.GffHelperI;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
-import jalview.util.Format;
import jalview.util.MapList;
import jalview.util.ParseHtmlBodyAndLinks;
import jalview.util.StringUtils;
-import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import java.util.StringTokenizer;
/**
* Parses and writes features files, which may be in Jalview, GFF2 or GFF3
* - process html strings into plain text
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Map<String, Object> colours,
+ public boolean parse(AlignmentI align,
+ Map<String, FeatureColourI> colours,
boolean removeHTML)
{
return parse(align, colours, removeHTML, false);
* - when true, ID matches to compound sequence IDs are allowed
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Map<String, Object> colours,
+ public boolean parse(AlignmentI align,
+ Map<String, FeatureColourI> colours,
boolean removeHTML, boolean relaxedIdmatching)
{
Map<String, String> gffProps = new HashMap<String, String>();
else if (ft.equalsIgnoreCase("endgroup"))
{
// We should check whether this is the current group,
- // but at present theres no way of showing more than 1 group
+ // but at present there's no way of showing more than 1 group
featureGroup = null;
}
else
{
- parseFeatureColour(line, ft, gffColumns, colours);
+ String colscheme = gffColumns[1];
+ FeatureColourI colour = FeatureColour
+ .parseJalviewFeatureColour(colscheme);
+ if (colour != null)
+ {
+ colours.put(ft, colour);
+ }
}
continue;
}
* @param featureGroup
*/
protected boolean parseJalviewFeature(String line, String[] gffColumns,
- AlignmentI alignment, Map<String, Object> featureColours,
+ AlignmentI alignment, Map<String, FeatureColourI> featureColours,
boolean removeHTML, boolean relaxedIdMatching, String featureGroup)
{
/*
* synthesize a colour from the feature type
*/
UserColourScheme ucs = new UserColourScheme(ft);
- featureColours.put(ft, ucs.findColour('A'));
+ featureColours.put(ft, new FeatureColour(ucs.findColour('A')));
}
SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos,
endPos, featureGroup);
}
/**
- * Process a feature type colour specification
- *
- * @param line
- * the current input line (for error messages only)
- * @param featureType
- * the first token on the line
- * @param gffColumns
- * holds tokens on the line
- * @param colours
- * map to which to add derived colour specification
- */
- protected void parseFeatureColour(String line, String featureType,
- String[] gffColumns, Map<String, Object> colours)
- {
- Object colour = null;
- String colscheme = gffColumns[1];
- if (colscheme.indexOf("|") > -1
- || colscheme.trim().equalsIgnoreCase("label"))
- {
- colour = parseGraduatedColourScheme(line, colscheme);
- }
- else
- {
- UserColourScheme ucs = new UserColourScheme(colscheme);
- colour = ucs.findColour('A');
- }
- if (colour != null)
- {
- colours.put(featureType, colour);
- }
- }
-
- /**
- * Parse a Jalview graduated colour descriptor
- *
- * @param line
- * @param colourDescriptor
- * @return
- */
- protected GraduatedColor parseGraduatedColourScheme(String line,
- String colourDescriptor)
- {
- // Parse '|' separated graduated colourscheme fields:
- // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
- // can either provide 'label' only, first is optional, next two
- // colors are required (but may be
- // left blank), next is optional, nxt two min/max are required.
- // first is either 'label'
- // first/second and third are both hexadecimal or word equivalent
- // colour.
- // next two are values parsed as floats.
- // fifth is either 'above','below', or 'none'.
- // sixth is a float value and only required when fifth is either
- // 'above' or 'below'.
- StringTokenizer gcol = new StringTokenizer(colourDescriptor, "|", true);
- // set defaults
- float min = Float.MIN_VALUE, max = Float.MAX_VALUE;
- boolean labelCol = false;
- // Parse spec line
- String mincol = gcol.nextToken();
- if (mincol == "|")
- {
- System.err
- .println("Expected either 'label' or a colour specification in the line: "
- + line);
- return null;
- }
- String maxcol = null;
- if (mincol.toLowerCase().indexOf("label") == 0)
- {
- labelCol = true;
- mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip '|'
- mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
- }
- String abso = null, minval, maxval;
- if (mincol != null)
- {
- // at least four more tokens
- if (mincol.equals("|"))
- {
- mincol = "";
- }
- else
- {
- gcol.nextToken(); // skip next '|'
- }
- // continue parsing rest of line
- maxcol = gcol.nextToken();
- if (maxcol.equals("|"))
- {
- maxcol = "";
- }
- else
- {
- gcol.nextToken(); // skip next '|'
- }
- abso = gcol.nextToken();
- gcol.nextToken(); // skip next '|'
- if (abso.toLowerCase().indexOf("abso") != 0)
- {
- minval = abso;
- abso = null;
- }
- else
- {
- minval = gcol.nextToken();
- gcol.nextToken(); // skip next '|'
- }
- maxval = gcol.nextToken();
- if (gcol.hasMoreTokens())
- {
- gcol.nextToken(); // skip next '|'
- }
- try
- {
- if (minval.length() > 0)
- {
- min = Float.valueOf(minval);
- }
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the minimum value for graduated colour for type ("
- + colourDescriptor
- + ") - did you misspell 'auto' for the optional automatic colour switch ?");
- e.printStackTrace();
- }
- try
- {
- if (maxval.length() > 0)
- {
- max = Float.valueOf(maxval);
- }
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the maximum value for graduated colour for type ("
- + colourDescriptor + ")");
- e.printStackTrace();
- }
- }
- else
- {
- // add in some dummy min/max colours for the label-only
- // colourscheme.
- mincol = "FFFFFF";
- maxcol = "000000";
- }
-
- GraduatedColor colour = null;
- try
- {
- colour = new GraduatedColor(
- new UserColourScheme(mincol).findColour('A'),
- new UserColourScheme(maxcol).findColour('A'), min, max);
- } catch (Exception e)
- {
- System.err.println("Couldn't parse the graduated colour scheme ("
- + colourDescriptor + ")");
- e.printStackTrace();
- }
- if (colour != null)
- {
- colour.setColourByLabel(labelCol);
- colour.setAutoScaled(abso == null);
- // add in any additional parameters
- String ttype = null, tval = null;
- if (gcol.hasMoreTokens())
- {
- // threshold type and possibly a threshold value
- ttype = gcol.nextToken();
- if (ttype.toLowerCase().startsWith("below"))
- {
- colour.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
- }
- else if (ttype.toLowerCase().startsWith("above"))
- {
- colour.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
- }
- else
- {
- colour.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
- if (!ttype.toLowerCase().startsWith("no"))
- {
- System.err.println("Ignoring unrecognised threshold type : "
- + ttype);
- }
- }
- }
- if (colour.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- try
- {
- gcol.nextToken();
- tval = gcol.nextToken();
- colour.setThresh(new Float(tval).floatValue());
- } catch (Exception e)
- {
- System.err.println("Couldn't parse threshold value as a float: ("
- + tval + ")");
- e.printStackTrace();
- }
- }
- // parse the thresh-is-min token ?
- if (gcol.hasMoreTokens())
- {
- System.err
- .println("Ignoring additional tokens in parameters in graduated colour specification\n");
- while (gcol.hasMoreTokens())
- {
- System.err.println("|" + gcol.nextToken());
- }
- System.err.println("\n");
- }
- }
- return colour;
- }
-
- /**
* clear any temporary handles used to speed up ID matching
*/
protected void resetMatcher()
* @return features file contents
*/
public String printJalviewFormat(SequenceI[] sequences,
- Map<String, Object> visible)
+ Map<String, FeatureColourI> visible)
{
return printJalviewFormat(sequences, visible, true, true);
}
* @return features file contents
*/
public String printJalviewFormat(SequenceI[] sequences,
- Map<String, Object> visible, boolean visOnly, boolean nonpos)
+ Map<String, FeatureColourI> visible, boolean visOnly,
+ boolean nonpos)
{
StringBuilder out = new StringBuilder(256);
boolean featuresGen = false;
// viewed features
// TODO: decide if feature links should also be written here ?
Iterator<String> en = visible.keySet().iterator();
- String featureType, color;
while (en.hasNext())
{
- featureType = en.next().toString();
-
- if (visible.get(featureType) instanceof GraduatedColor)
- {
- GraduatedColor gc = (GraduatedColor) visible.get(featureType);
- color = (gc.isColourByLabel() ? "label|" : "")
- + Format.getHexString(gc.getMinColor()) + "|"
- + Format.getHexString(gc.getMaxColor())
- + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
- + gc.getMax() + "|";
- if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
- {
- color += "below";
- }
- else
- {
- if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- System.err.println("WARNING: Unsupported threshold type ("
- + gc.getThreshType() + ") : Assuming 'above'");
- }
- color += "above";
- }
- // add the value
- color += "|" + gc.getThresh();
- }
- else
- {
- color += "none";
- }
- }
- else if (visible.get(featureType) instanceof Color)
- {
- color = Format.getHexString((Color) visible.get(featureType));
- }
- else
- {
- // legacy support for integer objects containing colour triplet values
- color = Format.getHexString(new Color(Integer.parseInt(visible
- .get(featureType).toString())));
- }
- out.append(featureType);
- out.append(TAB);
- out.append(color);
- out.append(newline);
+ String featureType = en.next().toString();
+ FeatureColourI colour = visible.get(featureType);
+ out.append(colour.toJalviewFormat(featureType)).append(newline);
}
}
+
// Work out which groups are both present and visible
List<String> groups = new ArrayList<String>();
int groupIndex = 0;
features = sequences[i].getSequenceFeatures();
if (features != null)
{
- for (int j = 0; j < features.length; j++)
+ for (SequenceFeature sequenceFeature : features)
{
- isnonpos = features[j].begin == 0 && features[j].end == 0;
+ isnonpos = sequenceFeature.begin == 0 && sequenceFeature.end == 0;
if ((!nonpos && isnonpos)
|| (!isnonpos && visOnly && !visible
- .containsKey(features[j].type)))
+ .containsKey(sequenceFeature.type)))
{
// skip if feature is nonpos and we ignore them or if we only
// output visible and it isn't non-pos and it's not visible
}
if (group != null
- && (features[j].featureGroup == null || !features[j].featureGroup
+ && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup
.equals(group)))
{
continue;
}
- if (group == null && features[j].featureGroup != null)
+ if (group == null && sequenceFeature.featureGroup != null)
{
continue;
}
// we have features to output
featuresGen = true;
- if (features[j].description == null
- || features[j].description.equals(""))
+ if (sequenceFeature.description == null
+ || sequenceFeature.description.equals(""))
{
- out.append(features[j].type).append(TAB);
+ out.append(sequenceFeature.type).append(TAB);
}
else
{
- if (features[j].links != null
- && features[j].getDescription().indexOf("<html>") == -1)
+ if (sequenceFeature.links != null
+ && sequenceFeature.getDescription().indexOf("<html>") == -1)
{
out.append("<html>");
}
- out.append(features[j].description + " ");
- if (features[j].links != null)
+ out.append(sequenceFeature.description);
+ if (sequenceFeature.links != null)
{
- for (int l = 0; l < features[j].links.size(); l++)
+ for (int l = 0; l < sequenceFeature.links.size(); l++)
{
- String label = features[j].links.elementAt(l).toString();
+ String label = sequenceFeature.links.elementAt(l);
String href = label.substring(label.indexOf("|") + 1);
label = label.substring(0, label.indexOf("|"));
- if (features[j].description.indexOf(href) == -1)
+ if (sequenceFeature.description.indexOf(href) == -1)
{
- out.append("<a href=\"" + href + "\">" + label + "</a>");
+ out.append(" <a href=\"" + href + "\">" + label
+ + "</a>");
}
}
- if (features[j].getDescription().indexOf("</html>") == -1)
+ if (sequenceFeature.getDescription().indexOf("</html>") == -1)
{
out.append("</html>");
}
}
out.append(sequences[i].getName());
out.append("\t-1\t");
- out.append(features[j].begin);
+ out.append(sequenceFeature.begin);
out.append(TAB);
- out.append(features[j].end);
+ out.append(sequenceFeature.end);
out.append(TAB);
- out.append(features[j].type);
- if (!Float.isNaN(features[j].score))
+ out.append(sequenceFeature.type);
+ if (!Float.isNaN(sequenceFeature.score))
{
out.append(TAB);
- out.append(features[j].score);
+ out.append(sequenceFeature.score);
}
out.append(newline);
}
* @return
*/
public String printGffFormat(SequenceI[] sequences,
- Map<String, Object> visible)
+ Map<String, FeatureColourI> visible)
{
return printGffFormat(sequences, visible, true, true);
}
* @return
*/
public String printGffFormat(SequenceI[] sequences,
- Map<String, Object> visible, boolean outputVisibleOnly,
+ Map<String, FeatureColourI> visible, boolean outputVisibleOnly,
boolean includeNonPositionalFeatures)
{
StringBuilder out = new StringBuilder(256);
- out.append(String.format("%s %d\n", GFF_VERSION, gffVersion));
+ int version = gffVersion == 0 ? 2 : gffVersion;
+ out.append(String.format("%s %d\n", GFF_VERSION, version));
String source;
boolean isnonpos;
for (SequenceI seq : sequences)
AlignmentPanel ap;
+ private IProgressIndicator pIndicator;
+
+ private long pSessionId;
+
+ private boolean headless;
+
+
public HtmlSvgOutput(File file, AlignmentPanel ap)
{
this.av = ap.av;
public void generateHtmlSvgOutput(File file)
{
- IProgressIndicator pIndicator = ap.alignFrame;
- long pSessionId = System.currentTimeMillis();
+ pIndicator = ap.alignFrame;
+ pSessionId = System.currentTimeMillis();
try
{
- boolean headless = (System.getProperty("java.awt.headless") != null && System
+ headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
if (file == null)
{
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.waiting_for_user_to_select_output_file", "HTML"),
- pSessionId);
- }
+ setProgressMessage(MessageManager.formatMessage(
+ "status.waiting_for_user_to_select_output_file", "HTML"));
JalviewFileChooser chooser = getHTMLChooser();
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(ap.alignFrame.getTitle());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
file = chooser.getSelectedFile();
+ ap.alignFrame.repaint();
}
else
{
-
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", "HTML"),
- pSessionId);
- }
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "HTML"));
return;
}
}
-
- AlignmentDimension aDimension = ap.getAlignmentDimension();
- SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
- aDimension.getHeight());
- SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
- aDimension.getHeight());
-
- String renderStyle = jalview.bin.Cache.getDefault("HTML_RENDERING",
- "Prompt each time");
-
- // If we need to prompt, and if the GUI is visible then
- // Prompt for rendering style
- if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
- {
- HTMLOptions svgOption = new HTMLOptions();
- renderStyle = svgOption.getValue();
-
- if (renderStyle == null || svgOption.cancelled)
- {
- return;
- }
- }
-
- if (renderStyle.equalsIgnoreCase("lineart"))
- {
- g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
- SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
- g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
- SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
- }
- printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, g1,
- g2);
-
- String titleSvgData = g1.getSVGDocument();
- String alignSvgData = g2.getSVGDocument();
- String jsonData = null;
- boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
- .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
- if (isEmbbedBioJSON)
+ } catch (Exception e)
+ {
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "info.error_creating_file", "HTML"), pSessionId);
+ e.printStackTrace();
+ return;
+ }
+ final File fileX = file;
+ new Thread()
+ {
+ @Override
+ public void run()
{
- AlignExportSettingI exportSettings = new AlignExportSettingI()
+ try
{
- @Override
- public boolean isExportHiddenSequences()
+ setProgressMessage(null);
+ setProgressMessage(MessageManager
+.formatMessage(
+ "status.exporting_alignment_as_x_file", "HTML"));
+ AlignmentDimension aDimension = ap.getAlignmentDimension();
+ SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
+ aDimension.getHeight());
+ SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
+ aDimension.getHeight());
+
+ String renderStyle = jalview.bin.Cache.getDefault(
+ "HTML_RENDERING", "Prompt each time");
+
+ // If we need to prompt, and if the GUI is visible then
+ // Prompt for rendering style
+ if (renderStyle.equalsIgnoreCase("Prompt each time")
+ && !(System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
{
- return true;
+ HTMLOptions svgOption = new HTMLOptions();
+ renderStyle = svgOption.getValue();
+
+ if (renderStyle == null || svgOption.cancelled)
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "HTML"));
+ return;
+ }
}
- @Override
- public boolean isExportHiddenColumns()
+ if (renderStyle.equalsIgnoreCase("Lineart"))
{
- return true;
+ g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+ SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+ g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+ SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
}
-
- @Override
- public boolean isExportAnnotations()
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ g1, g2);
+
+ String titleSvgData = g1.getSVGDocument();
+ String alignSvgData = g2.getSVGDocument();
+ String jsonData = null;
+ boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
+ .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+ if (isEmbbedBioJSON)
{
- return true;
+ AlignExportSettingI exportSettings = new AlignExportSettingI()
+ {
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportFeatures()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportGroups()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+
+ };
+ AlignmentExportData exportData = jalview.gui.AlignFrame
+ .getAlignmentForExport(JSONFile.FILE_DESC, av,
+ exportSettings);
+ jsonData = new FormatAdapter(ap, exportData.getSettings())
+ .formatSequences(JSONFile.FILE_DESC,
+ exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ av.getColumnSelection());
}
-
- @Override
- public boolean isExportFeatures()
- {
- return true;
- }
-
- @Override
- public boolean isExportGroups()
+ String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
+ FileOutputStream out = new FileOutputStream(fileX);
+ out.write(htmlData.getBytes());
+ out.flush();
+ out.close();
+ if (!(System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
{
- return true;
+ jalview.util.BrowserLauncher.openURL("file:///" + fileX);
}
+ } catch (OutOfMemoryError err)
+ {
+ System.out.println("########################\n"
+ + "OUT OF MEMORY " + fileX + "\n"
+ + "########################");
+ new OOMWarning("Creating Image for " + fileX, err);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "info.error_creating_file", "HTML"), pSessionId);
+ }
+ setProgressMessage(MessageManager.formatMessage(
+ "status.export_complete", "HTML"));
+ }
+ }.start();
- @Override
- public boolean isCancelled()
- {
- return false;
- }
+ }
- };
- AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(JSONFile.FILE_DESC, av,
- exportSettings);
- jsonData = new FormatAdapter(ap, exportData.getSettings())
- .formatSequences(JSONFile.FILE_DESC,
- exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- av.getColumnSelection());
- }
- String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
- FileOutputStream out = new FileOutputStream(file);
- out.write(htmlData.getBytes());
- out.flush();
- out.close();
- if (!(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
- {
- jalview.util.BrowserLauncher.openURL("file:///" + file);
- }
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.export_complete", "HTML"), pSessionId);
- }
- } catch (OutOfMemoryError err)
+ private void setProgressMessage(String message)
+ {
+ if (pIndicator != null && !headless)
{
- System.out.println("########################\n" + "OUT OF MEMORY "
- + file + "\n" + "########################");
- new OOMWarning("Creating Image for " + file, err);
- } catch (Exception e)
+ pIndicator.setProgressBar(message, pSessionId);
+ }
+ else
{
- e.printStackTrace();
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "info.error_creating_file", "HTML"), pSessionId);
+ System.out.println(message);
}
}
} catch (IOException ex)
{
}
- ;
if (dta != null && dta.indexOf("*") > -1)
{
starterm = true;
// read as a FASTA (probably)
break;
}
- if ((data.indexOf("<") > -1)) // possible Markup Language data i.e HTML,
+ int lessThan = data.indexOf("<");
+ if ((lessThan > -1)) // possible Markup Language data i.e HTML,
// RNAML, XML
{
- // FIXME this is nuts - it consumes the rest of the file if no match
- boolean identified = false;
- do
- {
- if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
- {
- reply = HtmlFile.FILE_DESC;
- identified = true;
- break;
- }
-
- if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
- {
- reply = "RNAML";
- identified = true;
- break;
- }
- } while ((data = source.nextLine()) != null);
-
- if (identified)
+ String upper = data.toUpperCase();
+ if (upper.substring(lessThan).startsWith("<HTML"))
{
+ reply = HtmlFile.FILE_DESC;
break;
}
- if (data == null)
+ if (upper.substring(lessThan).startsWith("<RNAML"))
{
+ reply = "RNAML";
break;
}
}
fr = avpanel.cloneFeatureRenderer();
// Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : annots)
+ if (annots != null)
{
- if (annot != null && !annot.autoCalculated)
+ for (AlignmentAnnotation annot : annots)
{
- annotations.add(annot);
+ if (annot != null && !annot.autoCalculated)
+ {
+ annotations.add(annot);
+ }
}
}
globalColourScheme = ColourSchemeProperty.getColourName(viewport
package jalview.io;
import jalview.api.FeatureColourI;
-import jalview.schemes.FeatureColourAdapter;
+import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureSettingsAdapter;
import java.awt.Color;
{
if (type.equalsIgnoreCase(FEATURE_INSERTION))
{
- return new FeatureColourAdapter()
+ return new FeatureColour()
{
@Override
private String id;
private String dbRefType;
+
/**
* set to true to add derived sequence annotations (temp factor read from
* file, or computed secondary structure) to the alignment
sourceDBRef.setSource(DBRefSource.PDB);
sourceDBRef.setStartRes(pdbSequence.getStart());
sourceDBRef.setEndRes(pdbSequence.getEnd());
-
- SequenceI chainseq = pdbSequence.deriveSequence();
- chainseq.setSourceDBRef(sourceDBRef);
- chainseq.addPDBId(entry);
- chainseq.addDBRef(sourceDBRef);
-
+ pdbSequence.setSourceDBRef(sourceDBRef);
+ pdbSequence.addPDBId(entry);
+ pdbSequence.addDBRef(sourceDBRef);
+ SequenceI chainseq = pdbSequence;
seqs.addElement(chainseq);
-
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
if (chainannot != null && visibleChainAnnotation)
@SuppressWarnings("unchecked")
protected void replaceAndUpdateChains(List<SequenceI> prot,
- AlignmentI al,
- String pep, boolean b)
+ AlignmentI al, String pep, boolean b)
{
List<List<? extends Object>> replaced = AlignSeq
.replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
}
@SuppressWarnings({ "unchecked", "rawtypes" })
- private void processWithJmolParser(List<SequenceI> prot)
- throws Exception
+ private void processWithJmolParser(List<SequenceI> prot) throws Exception
{
try
{
Class cl = Class.forName("jalview.ext.jmol.JmolParser");
if (cl != null)
{
- final Constructor constructor = cl
-.getConstructor(new Class[] {
+ 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) };
+ new FileParse(getDataName(), type) };
StructureViewSettings.setShowSeqFeatures(false);
StructureViewSettings.setVisibleChainAnnotation(false);
} catch (ClassNotFoundException q)
{
}
+ StructureViewSettings.setShowSeqFeatures(true);
}
public PDBChain findChain(String id) throws Exception
*/
package jalview.io.packed;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.NewickFile;
/**
* @return the featureColours
*/
- public Map<String, Object> getFeatureColours()
+ public Map<String, FeatureColourI> getFeatureColours()
{
return featureColours;
}
* @param featureColours
* the featureColours to set
*/
- public void setFeatureColours(Map<String, Object> featureColours)
+ public void setFeatureColours(Map<String, FeatureColourI> featureColours)
{
this.featureColours = featureColours;
}
/**
* current set of feature colours
*/
- Map<String, Object> featureColours;
+ Map<String, FeatureColourI> featureColours;
/**
* original identity of each sequence in results
seqDetails = new Hashtable();
al = new ArrayList<AlignmentSet>();
parentDataset = null;
- featureColours = new HashMap<String, Object>();
+ featureColours = new HashMap<String, FeatureColourI>();
}
/**
*
* @param parentAlignment
*/
- public JalviewDataset(AlignmentI aldataset, Map<String, Object> fc,
+ public JalviewDataset(AlignmentI aldataset,
+ Map<String, FeatureColourI> fc,
Hashtable seqDets)
{
// TODO not used - remove?
* (may be null) alignment to associate new annotation and trees
* with.
*/
- public JalviewDataset(AlignmentI aldataset, Map<String, Object> fc,
+ public JalviewDataset(AlignmentI aldataset,
+ Map<String, FeatureColourI> fc,
Hashtable seqDets, AlignmentI parentAlignment)
{
this();
*/
package jalview.io.packed;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
// if not, create one.
if (context.featureColours == null)
{
- context.featureColours = new HashMap<String, Object>();
+ context.featureColours = new HashMap<String, FeatureColourI>();
}
try
{
/*
* Output tab components
*/
- protected JComboBox<String> epsRendering = new JComboBox<String>();
+ protected JComboBox<Object> epsRendering = new JComboBox<Object>();
protected JLabel userIdWidthlabel = new JLabel();
.getString("label.open_overview"));
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
- openoverv.setText(MessageManager.getString(("label.open_overview")));
+ openoverv.setText(MessageManager.getString("label.open_overview"));
JPanel jPanel2 = new JPanel();
jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
jPanel2.setLayout(new GridLayout(14, 1));
import javax.swing.event.ChangeListener;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
+import javax.swing.table.TableColumn;
@SuppressWarnings("serial")
/**
protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
- protected JTable tbl_summary = new JTable()
+ protected JTable tbl_local_pdb = new JTable();
+
+ protected JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
+
+ private JTabbedPane pnl_filter = new JTabbedPane();
+
+ protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
+ PreferenceSource.STRUCTURE_CHOOSER,
+ PDBFTSRestClient.getInstance());
+
+ protected FTSDataColumnI[] previousWantedFields;
+
+ private JTable tbl_summary = new JTable()
{
+ private boolean inLayout;
+
+ @Override
+ public boolean getScrollableTracksViewportWidth()
+ {
+ return hasExcessWidth();
+
+ }
+
+ @Override
+ public void doLayout()
+ {
+ if (hasExcessWidth())
+ {
+ autoResizeMode = AUTO_RESIZE_SUBSEQUENT_COLUMNS;
+ }
+ inLayout = true;
+ super.doLayout();
+ inLayout = false;
+ autoResizeMode = AUTO_RESIZE_OFF;
+ }
+
+ protected boolean hasExcessWidth()
+ {
+ return getPreferredSize().width < getParent().getWidth();
+ }
+
+ @Override
+ public void columnMarginChanged(ChangeEvent e)
+ {
+ if (isEditing())
+ {
+ removeEditor();
+ }
+ TableColumn resizingColumn = getTableHeader().getResizingColumn();
+ // Need to do this here, before the parent's
+ // layout manager calls getPreferredSize().
+ if (resizingColumn != null && autoResizeMode == AUTO_RESIZE_OFF
+ && !inLayout)
+ {
+ resizingColumn.setPreferredWidth(resizingColumn.getWidth());
+ }
+ resizeAndRepaint();
+ }
+
@Override
public String getToolTipText(MouseEvent evt)
{
protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
- protected JTable tbl_local_pdb = new JTable();
-
- protected JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
-
- private JTabbedPane pnl_filter = new JTabbedPane();
-
- private FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
- PreferenceSource.STRUCTURE_CHOOSER, PDBFTSRestClient.getInstance());
-
- protected FTSDataColumnI[] previousWantedFields;
-
public GStructureChooser()
{
try
}
});
- scrl_foundStructures.setPreferredSize(new Dimension(500, 300));
- scrl_foundStructures
- .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ scrl_foundStructures.setPreferredSize(new Dimension(800, 400));
- scrl_localPDB.setPreferredSize(new Dimension(500, 300));
+ scrl_localPDB.setPreferredSize(new Dimension(800, 400));
scrl_localPDB
.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
chk_invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
chk_rememberSettings.setVisible(false);
-
- txt_search.setToolTipText(MessageManager
- .getString("label.enter_pdb_id"));
+ txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.enter_pdb_id")));
cmb_filterOption.setToolTipText(MessageManager
.getString("info.select_filter_option"));
txt_search.getDocument().addDocumentListener(new DocumentListener()
btn_cancel.setEnabled(false);
btn_view.setVisible(false);
btn_cancel.setVisible(false);
- previousWantedFields = PDBFTSRestClient.getInstance()
- .getAllDefaulDisplayedDataColumns()
- .toArray(new FTSDataColumnI[0]);
+ previousWantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields().toArray(
+ new FTSDataColumnI[0]);
}
if (sourceTabbedPane.getTitleAt(index)
.equals(foundStructureSummary))
}
};
pnl_filter.addChangeListener(changeListener);
- pnl_filter.setPreferredSize(new Dimension(500, 300));
+ pnl_filter.setPreferredSize(new Dimension(800, 400));
pnl_filter.add(foundStructureSummary, scrl_foundStructures);
pnl_filter.add(configureCols, pdbDocFieldPrefs);
mainFrame.setVisible(true);
mainFrame.setContentPane(this);
mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
- Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+ Desktop.addInternalFrame(mainFrame, frameTitle, 900, 500);
}
public boolean wantedFieldsUpdated()
{
return true;
}
-
- return Arrays.equals(
- PDBFTSRestClient.getInstance()
- .getAllDefaulDisplayedDataColumns()
- .toArray(new FTSDataColumnI[0]),
- previousWantedFields) ? false : true;
+
+ FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields()
+ .toArray(new FTSDataColumnI[0]);
+ return Arrays.equals(currentWantedFields, previousWantedFields) ? false
+ : true;
}
}
}
+ public JTable getResultTable()
+ {
+ return tbl_summary;
+ }
public JComboBox<FilterOption> getCmbFilterOption()
{
return cmb_filterOption;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.renderer;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Calculate and display alignment rulers
+ *
+ * @author jprocter
+ *
+ */
+public class ScaleRenderer
+{
+ /**
+ * calculate positions markers on the alignment ruler
+ *
+ * @param av
+ * @param startx
+ * left-most column in visible view
+ * @param endx
+ * - right-most column in visible view
+ * @return List { Object { .. } } Boolean: true/false for major/minor mark,
+ * Integer: marker position in alignment column coords, String: null
+ * or a String to be rendered at the position.
+ */
+ public static List<Object[]> calculateMarks(AlignViewportI av,
+ int startx, int endx)
+ {
+ new ArrayList<Object[]>();
+
+ int scalestartx = (startx / 10) * 10;
+
+ SequenceI refSeq = av.getAlignment().getSeqrep();
+ int refSp = 0, refStartI = 0, refEndI = -1;
+ if (refSeq != null)
+ {
+ // find bounds and set origin appopriately
+ // locate first visible position for this sequence
+ int[] refbounds = av.getColumnSelection()
+ .locateVisibleBoundsOfSequence(refSeq);
+
+ refSp = refbounds[0];
+ refStartI = refbounds[4];
+ refEndI = refbounds[5];
+ scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
+ }
+
+ if (refSeq == null && scalestartx % 10 == 0)
+ {
+ scalestartx += 5;
+ }
+ List<Object[]> marks = new ArrayList<Object[]>();
+ String string;
+ int refN, iadj;
+ // todo: add a 'reference origin column' to set column number relative to
+ for (int i = scalestartx; i < endx; i += 5)
+ {
+ Object[] amark = new Object[3];
+ if (((i - refSp) % 10) == 0)
+ {
+ if (refSeq == null)
+ {
+ iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
+ string = String.valueOf(iadj);
+ }
+ else
+ {
+ iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
+ refN = refSeq.findPosition(iadj);
+ // TODO show bounds if position is a gap
+ // - ie L--R -> "1L|2R" for
+ // marker
+ if (iadj < refStartI)
+ {
+ string = String.valueOf(iadj - refStartI);
+ }
+ else if (iadj > refEndI)
+ {
+ string = "+" + String.valueOf(iadj - refEndI);
+ }
+ else
+ {
+ string = String.valueOf(refN) + refSeq.getCharAt(iadj);
+ }
+ }
+ amark[0] = Boolean.TRUE;
+ amark[1] = Integer.valueOf(i - startx - 1);
+ amark[2] = string;
+
+ }
+ else
+ {
+ amark[0] = Boolean.FALSE;
+ amark[1] = Integer.valueOf(i - startx - 1);
+ amark[2] = null;
+ }
+ marks.add(amark);
+ }
+ return marks;
+ }
+
+}
boolean av_validCharWidth, av_isShowSeqFeatureHeight;
+ private Integer currentColour;
+
protected void updateAvConfig()
{
av_charHeight = av.getCharHeight();
}
/**
- * This is used by the Molecule Viewer and Overview to get the accurate
- * colourof the rendered sequence
+ * This is used by the Molecule Viewer and Overview to get the accurate colour
+ * of the rendered sequence
*/
public synchronized int findFeatureColour(int initialCol,
final SequenceI seq, int column)
}
else
{
- return ((Integer) currentColour).intValue();
+ return currentColour.intValue();
}
}
}
- if (transparency != 1.0f && g != null && transparencyAvailable)
+ if (transparency != 1.0f && g != null)
{
Graphics2D g2 = (Graphics2D) g;
g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
}
}
- boolean transparencyAvailable = true;
-
- protected void setTransparencyAvailable(boolean isTransparencyAvailable)
- {
- transparencyAvailable = isTransparencyAvailable;
- }
-
- @Override
- public boolean isTransparencyAvailable()
- {
- return transparencyAvailable;
- }
-
/**
* Called when alignment in associated view has new/modified features to
* discover and display.
-#Thu Sep 03 10:55:37 BST 2015
+#Mon Jun 20 15:44:52 BST 2016
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
private boolean _has_hidden;
/**
+ * Field _viewreference.
+ */
+ private boolean _viewreference;
+
+ /**
+ * keeps track of state for field: _viewreference
+ */
+ private boolean _has_viewreference;
+
+ /**
* Field _featuresList.
*/
private java.util.Vector _featuresList;
}
/**
+ */
+ public void deleteViewreference()
+ {
+ this._has_viewreference = false;
+ }
+
+ /**
* Method enumerateFeatures.
*
* @return an Enumeration over all jalview.schemabinding.version2.Features
}
/**
+ * Returns the value of field 'viewreference'.
+ *
+ * @return the value of field 'Viewreference'.
+ */
+ public boolean getViewreference()
+ {
+ return this._viewreference;
+ }
+
+ /**
* Method hasColour.
*
* @return true if at least one Colour has been added
}
/**
+ * Method hasViewreference.
+ *
+ * @return true if at least one Viewreference has been added
+ */
+ public boolean hasViewreference()
+ {
+ return this._has_viewreference;
+ }
+
+ /**
* Returns the value of field 'hidden'.
*
* @return the value of field 'Hidden'.
}
/**
+ * Returns the value of field 'viewreference'.
+ *
+ * @return the value of field 'Viewreference'.
+ */
+ public boolean isViewreference()
+ {
+ return this._viewreference;
+ }
+
+ /**
*
*
* @param out
}
/**
+ * Sets the value of field 'viewreference'.
+ *
+ * @param viewreference
+ * the value of field 'viewreference'.
+ */
+ public void setViewreference(final boolean viewreference)
+ {
+ this._viewreference = viewreference;
+ this._has_viewreference = true;
+ }
+
+ /**
* Method unmarshal.
*
* @param reader
//- Imported classes and packages -/
//---------------------------------/
+import jalview.schemabinding.version2.AnnotationColours;
+
/**
* Class AnnotationColoursDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
+import jalview.schemabinding.version2.Features;
+
/**
* Class FeaturesDescriptor.
*
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
+ // -- _viewreference
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_viewreference", "viewreference",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ if (!target.hasViewreference())
+ {
+ return null;
+ }
+ return (target.getViewreference() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JSeq target = (JSeq) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteViewreference();
+ return;
+ }
+ target.setViewreference(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _viewreference
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
// -- initialize element descriptors
// -- _featuresList
desc.setImmutable(true);
handler = new org.exolab.castor.xml.XMLFieldHandler()
{
+ @Override
public java.lang.Object getValue(java.lang.Object object)
throws IllegalStateException
{
return target.getSchemeName();
}
+ @Override
public void setValue(java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
}
}
+ @Override
public java.lang.Object newInstance(java.lang.Object parent)
{
return null;
desc.setImmutable(true);
handler = new org.exolab.castor.xml.XMLFieldHandler()
{
+ @Override
public java.lang.Object getValue(java.lang.Object object)
throws IllegalStateException
{
return target.getVersion();
}
+ @Override
public void setValue(java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
}
}
+ @Override
public java.lang.Object newInstance(java.lang.Object parent)
{
return null;
org.exolab.castor.xml.NodeType.Element);
handler = new org.exolab.castor.xml.XMLFieldHandler()
{
+ @Override
public java.lang.Object getValue(java.lang.Object object)
throws IllegalStateException
{
return target.getColour();
}
+ @Override
public void setValue(java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
}
}
+ @Override
public void resetValue(Object object) throws IllegalStateException,
IllegalArgumentException
{
}
}
+ @Override
public java.lang.Object newInstance(java.lang.Object parent)
{
return new Colour();
*
* @return the access mode specified for this class.
*/
+ @Override
public org.exolab.castor.mapping.AccessMode getAccessMode()
{
return null;
*
* @return the identity field, null if this class has no identity.
*/
+ @Override
public org.exolab.castor.mapping.FieldDescriptor getIdentity()
{
return super.getIdentity();
*
* @return the Java class represented by this descriptor.
*/
+ @Override
public java.lang.Class getJavaClass()
{
return jalview.schemabinding.version2.JalviewUserColours.class;
*
* @return the namespace prefix to use when marshaling as XML.
*/
+ @Override
public java.lang.String getNameSpacePrefix()
{
return _nsPrefix;
*
* @return the namespace URI used when marshaling and unmarshaling as XML.
*/
+ @Override
public java.lang.String getNameSpaceURI()
{
return _nsURI;
* @return a specific validator for the class described by this
* ClassDescriptor.
*/
+ @Override
public org.exolab.castor.xml.TypeValidator getValidator()
{
return this;
*
* @return the XML Name for the Class being described.
*/
+ @Override
public java.lang.String getXMLName()
{
return _xmlName;
* @return true if XML schema definition of this Class is that of a global
* element or element with anonymous type definition.
*/
+ @Override
public boolean isElementDefinition()
{
return _elementDefinition;
//- Imported classes and packages -/
//---------------------------------/
+import jalview.schemabinding.version2.UserColourScheme;
+
/**
* Class UserColourSchemeDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
+import jalview.schemabinding.version2.VamsasModel;
+
/**
* Class VamsasModelDescriptor.
*
--- /dev/null
+package jalview.schemes;
+
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SequenceFeature;
+import jalview.util.Format;
+
+import java.awt.Color;
+import java.util.StringTokenizer;
+
+/**
+ * A class that wraps either a simple colour or a graduated colour
+ */
+public class FeatureColour implements FeatureColourI
+{
+ private static final String BAR = "|";
+
+ final private Color colour;
+
+ final private Color minColour;
+
+ final private Color maxColour;
+
+ private boolean graduatedColour;
+
+ private boolean colourByLabel;
+
+ private float threshold;
+
+ private float base;
+
+ private float range;
+
+ private boolean belowThreshold;
+
+ private boolean aboveThreshold;
+
+ private boolean thresholdIsMinOrMax;
+
+ private boolean isHighToLow;
+
+ private boolean autoScaled;
+
+ final private float minRed;
+
+ final private float minGreen;
+
+ final private float minBlue;
+
+ final private float deltaRed;
+
+ final private float deltaGreen;
+
+ final private float deltaBlue;
+
+ /**
+ * Parses a Jalview features file format colour descriptor
+ * [label|][mincolour|maxcolour
+ * |[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue] Examples:
+ * <ul>
+ * <li>red</li>
+ * <li>a28bbb</li>
+ * <li>25,125,213</li>
+ * <li>label</li>
+ * <li>label|||0.0|0.0|above|12.5</li>
+ * <li>label|||0.0|0.0|below|12.5</li>
+ * <li>red|green|12.0|26.0|none</li>
+ * <li>a28bbb|3eb555|12.0|26.0|above|12.5</li>
+ * <li>a28bbb|3eb555|abso|12.0|26.0|below|12.5</li>
+ * </ul>
+ *
+ * @param descriptor
+ * @return
+ * @throws IllegalArgumentException
+ * if not parseable
+ */
+ public static FeatureColour parseJalviewFeatureColour(String descriptor)
+ {
+ StringTokenizer gcol = new StringTokenizer(descriptor, "|", true);
+ float min = Float.MIN_VALUE;
+ float max = Float.MAX_VALUE;
+ boolean labelColour = false;
+
+ String mincol = gcol.nextToken();
+ if (mincol == "|")
+ {
+ throw new IllegalArgumentException(
+ "Expected either 'label' or a colour specification in the line: "
+ + descriptor);
+ }
+ String maxcol = null;
+ if (mincol.toLowerCase().indexOf("label") == 0)
+ {
+ labelColour = true;
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ // skip '|'
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+
+ if (!labelColour && !gcol.hasMoreTokens())
+ {
+ /*
+ * only a simple colour specification - parse it
+ */
+ Color colour = UserColourScheme.getColourFromString(descriptor);
+ if (colour == null)
+ {
+ throw new IllegalArgumentException("Invalid colour descriptor: "
+ + descriptor);
+ }
+ return new FeatureColour(colour);
+ }
+
+ /*
+ * autoScaled == true: colours range over actual score range
+ * autoScaled == false ('abso'): colours range over min/max range
+ */
+ boolean autoScaled = true;
+ String tok = null, minval, maxval;
+ if (mincol != null)
+ {
+ // at least four more tokens
+ if (mincol.equals("|"))
+ {
+ mincol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ maxcol = gcol.nextToken();
+ if (maxcol.equals("|"))
+ {
+ maxcol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ tok = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ if (tok.toLowerCase().startsWith("abso"))
+ {
+ minval = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ autoScaled = false;
+ }
+ else
+ {
+ minval = tok;
+ }
+ maxval = gcol.nextToken();
+ if (gcol.hasMoreTokens())
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ try
+ {
+ if (minval.length() > 0)
+ {
+ min = new Float(minval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(
+ "Couldn't parse the minimum value for graduated colour ("
+ + descriptor + ")");
+ }
+ try
+ {
+ if (maxval.length() > 0)
+ {
+ max = new Float(maxval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(
+ "Couldn't parse the maximum value for graduated colour ("
+ + descriptor + ")");
+ }
+ }
+ else
+ {
+ // add in some dummy min/max colours for the label-only
+ // colourscheme.
+ mincol = "FFFFFF";
+ maxcol = "000000";
+ }
+
+ /*
+ * construct the FeatureColour
+ */
+ FeatureColour featureColour;
+ try
+ {
+ featureColour = new FeatureColour(
+ new UserColourScheme(mincol).findColour('A'),
+ new UserColourScheme(maxcol).findColour('A'), min, max);
+ featureColour.setColourByLabel(labelColour);
+ featureColour.setAutoScaled(autoScaled);
+ // add in any additional parameters
+ String ttype = null, tval = null;
+ if (gcol.hasMoreTokens())
+ {
+ // threshold type and possibly a threshold value
+ ttype = gcol.nextToken();
+ if (ttype.toLowerCase().startsWith("below"))
+ {
+ featureColour.setBelowThreshold(true);
+ }
+ else if (ttype.toLowerCase().startsWith("above"))
+ {
+ featureColour.setAboveThreshold(true);
+ }
+ else
+ {
+ if (!ttype.toLowerCase().startsWith("no"))
+ {
+ System.err.println("Ignoring unrecognised threshold type : "
+ + ttype);
+ }
+ }
+ }
+ if (featureColour.hasThreshold())
+ {
+ try
+ {
+ gcol.nextToken();
+ tval = gcol.nextToken();
+ featureColour.setThreshold(new Float(tval).floatValue());
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't parse threshold value as a float: ("
+ + tval + ")");
+ }
+ }
+ if (gcol.hasMoreTokens())
+ {
+ System.err
+ .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+ while (gcol.hasMoreTokens())
+ {
+ System.err.println("|" + gcol.nextToken());
+ }
+ System.err.println("\n");
+ }
+ return featureColour;
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(e.getMessage());
+ }
+ }
+
+ /**
+ * Default constructor
+ */
+ public FeatureColour()
+ {
+ this((Color) null);
+ }
+
+ /**
+ * Constructor given a simple colour
+ *
+ * @param c
+ */
+ public FeatureColour(Color c)
+ {
+ minColour = Color.WHITE;
+ maxColour = Color.BLACK;
+ minRed = 0f;
+ minGreen = 0f;
+ minBlue = 0f;
+ deltaRed = 0f;
+ deltaGreen = 0f;
+ deltaBlue = 0f;
+ colour = c;
+ }
+
+ /**
+ * Constructor given a colour range and a score range
+ *
+ * @param low
+ * @param high
+ * @param min
+ * @param max
+ */
+ public FeatureColour(Color low, Color high, float min, float max)
+ {
+ graduatedColour = true;
+ colour = null;
+ minColour = low;
+ maxColour = high;
+ threshold = Float.NaN;
+ isHighToLow = min >= max;
+ minRed = low.getRed() / 255f;
+ minGreen = low.getGreen() / 255f;
+ minBlue = low.getBlue() / 255f;
+ deltaRed = (high.getRed() / 255f) - minRed;
+ deltaGreen = (high.getGreen() / 255f) - minGreen;
+ deltaBlue = (high.getBlue() / 255f) - minBlue;
+ if (isHighToLow)
+ {
+ base = max;
+ range = min - max;
+ }
+ else
+ {
+ base = min;
+ range = max - min;
+ }
+ }
+
+ /**
+ * Copy constructor
+ *
+ * @param fc
+ */
+ public FeatureColour(FeatureColour fc)
+ {
+ graduatedColour = fc.graduatedColour;
+ colour = fc.colour;
+ minColour = fc.minColour;
+ maxColour = fc.maxColour;
+ minRed = fc.minRed;
+ minGreen = fc.minGreen;
+ minBlue = fc.minBlue;
+ deltaRed = fc.deltaRed;
+ deltaGreen = fc.deltaGreen;
+ deltaBlue = fc.deltaBlue;
+ base = fc.base;
+ range = fc.range;
+ isHighToLow = fc.isHighToLow;
+ setAboveThreshold(fc.isAboveThreshold());
+ setBelowThreshold(fc.isBelowThreshold());
+ setThreshold(fc.getThreshold());
+ setAutoScaled(fc.isAutoScaled());
+ setColourByLabel(fc.isColourByLabel());
+ }
+
+ /**
+ * Copy constructor with new min/max ranges
+ * @param fc
+ * @param min
+ * @param max
+ */
+ public FeatureColour(FeatureColour fc, float min, float max)
+ {
+ this(fc);
+ graduatedColour = true;
+ updateBounds(min, max);
+ }
+
+ @Override
+ public boolean isGraduatedColour()
+ {
+ return graduatedColour;
+ }
+
+ /**
+ * Sets the 'graduated colour' flag. If true, also sets 'colour by label' to
+ * false.
+ */
+ void setGraduatedColour(boolean b)
+ {
+ graduatedColour = b;
+ if (b)
+ {
+ setColourByLabel(false);
+ }
+ }
+
+ @Override
+ public Color getColour()
+ {
+ return colour;
+ }
+
+ @Override
+ public Color getMinColour()
+ {
+ return minColour;
+ }
+
+ @Override
+ public Color getMaxColour()
+ {
+ return maxColour;
+ }
+
+ @Override
+ public boolean isColourByLabel()
+ {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the 'colour by label' flag. If true, also sets 'graduated colour' to
+ * false.
+ */
+ @Override
+ public void setColourByLabel(boolean b)
+ {
+ colourByLabel = b;
+ if (b)
+ {
+ setGraduatedColour(false);
+ }
+ }
+ @Override
+ public boolean isBelowThreshold()
+ {
+ return belowThreshold;
+ }
+
+ @Override
+ public void setBelowThreshold(boolean b)
+ {
+ belowThreshold = b;
+ if (b)
+ {
+ setAboveThreshold(false);
+ }
+ }
+
+ @Override
+ public boolean isAboveThreshold()
+ {
+ return aboveThreshold;
+ }
+
+ @Override
+ public void setAboveThreshold(boolean b)
+ {
+ aboveThreshold = b;
+ if (b)
+ {
+ setBelowThreshold(false);
+ }
+ }
+
+ @Override
+ public boolean isThresholdMinMax()
+ {
+ return thresholdIsMinOrMax;
+ }
+
+ @Override
+ public void setThresholdMinMax(boolean b)
+ {
+ thresholdIsMinOrMax = b;
+ }
+
+ @Override
+ public float getThreshold()
+ {
+ return threshold;
+ }
+
+ @Override
+ public void setThreshold(float f)
+ {
+ threshold = f;
+ }
+
+ @Override
+ public boolean isAutoScaled()
+ {
+ return autoScaled;
+ }
+
+ @Override
+ public void setAutoScaled(boolean b)
+ {
+ this.autoScaled = b;
+ }
+
+ /**
+ * Updates the base and range appropriately for the given minmax range
+ *
+ * @param min
+ * @param max
+ */
+ @Override
+ public void updateBounds(float min, float max)
+ {
+ if (max < min)
+ {
+ base = max;
+ range = min - max;
+ isHighToLow = true;
+ }
+ else
+ {
+ base = min;
+ range = max - min;
+ isHighToLow = false;
+ }
+ }
+
+ /**
+ * Returns the colour for the given instance of the feature. This may be a
+ * simple colour, a colour generated from the feature description (if
+ * isColourByLabel()), or a colour derived from the feature score (if
+ * isGraduatedColour()).
+ *
+ * @param feature
+ * @return
+ */
+ @Override
+ public Color getColor(SequenceFeature feature)
+ {
+ if (isColourByLabel())
+ {
+ return UserColourScheme
+ .createColourFromName(feature.getDescription());
+ }
+
+ if (!isGraduatedColour())
+ {
+ return getColour();
+ }
+
+ // todo should we check for above/below threshold here?
+ if (range == 0.0)
+ {
+ return getMaxColour();
+ }
+ float scr = feature.getScore();
+ if (Float.isNaN(scr))
+ {
+ return getMinColour();
+ }
+ float scl = (scr - base) / range;
+ if (isHighToLow)
+ {
+ scl = -scl;
+ }
+ if (scl < 0f)
+ {
+ scl = 0f;
+ }
+ if (scl > 1f)
+ {
+ scl = 1f;
+ }
+ return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen, minBlue + scl * deltaBlue);
+ }
+
+ /**
+ * Returns the maximum score of the graduated colour range
+ *
+ * @return
+ */
+ @Override
+ public float getMax()
+ {
+ // regenerate the original values passed in to the constructor
+ return (isHighToLow) ? base : (base + range);
+ }
+
+ /**
+ * Returns the minimum score of the graduated colour range
+ *
+ * @return
+ */
+ @Override
+ public float getMin()
+ {
+ // regenerate the original value passed in to the constructor
+ return (isHighToLow) ? (base + range) : base;
+ }
+
+ /**
+ * Answers true if the feature has a simple colour, or is coloured by label,
+ * or has a graduated colour and the score of this feature instance is within
+ * the range to render (if any), i.e. does not lie below or above any
+ * threshold set.
+ *
+ * @param feature
+ * @return
+ */
+ @Override
+ public boolean isColored(SequenceFeature feature)
+ {
+ if (isColourByLabel() || !isGraduatedColour())
+ {
+ return true;
+ }
+
+ float val = feature.getScore();
+ if (Float.isNaN(val))
+ {
+ return true;
+ }
+ if (Float.isNaN(this.threshold))
+ {
+ return true;
+ }
+
+ if (isAboveThreshold() && val <= threshold)
+ {
+ return false;
+ }
+ if (isBelowThreshold() && val >= threshold)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ public boolean isSimpleColour()
+ {
+ return (!isColourByLabel() && !isGraduatedColour());
+ }
+
+ @Override
+ public boolean hasThreshold()
+ {
+ return isAboveThreshold() || isBelowThreshold();
+ }
+
+ @Override
+ public String toJalviewFormat(String featureType)
+ {
+ String colourString = null;
+ if (isSimpleColour())
+ {
+ colourString = Format.getHexString(getColour());
+ }
+ else
+ {
+ StringBuilder sb = new StringBuilder(32);
+ if (isColourByLabel())
+ {
+ sb.append("label");
+ if (hasThreshold())
+ {
+ sb.append(BAR).append(BAR).append(BAR);
+ }
+ }
+ if (isGraduatedColour())
+ {
+ sb.append(Format.getHexString(getMinColour())).append(BAR);
+ sb.append(Format.getHexString(getMaxColour())).append(BAR);
+ if (!isAutoScaled())
+ {
+ sb.append("abso").append(BAR);
+ }
+ }
+ if (hasThreshold() || isGraduatedColour())
+ {
+ sb.append(getMin()).append(BAR);
+ sb.append(getMax()).append(BAR);
+ if (isBelowThreshold())
+ {
+ sb.append("below").append(BAR).append(getThreshold());
+ }
+ else if (isAboveThreshold())
+ {
+ sb.append("above").append(BAR).append(getThreshold());
+ }
+ else
+ {
+ sb.append("none");
+ }
+ }
+ colourString = sb.toString();
+ }
+ return String.format("%s\t%s", featureType, colourString);
+ }
+
+}
+++ /dev/null
-package jalview.schemes;
-
-import jalview.api.FeatureColourI;
-
-import java.awt.Color;
-
-/**
- * A convenience class with implementations of FeatureColourI methods. Override
- * methods as required in subclasses.
- */
-public class FeatureColourAdapter implements FeatureColourI
-{
- @Override
- public boolean isGraduatedColour()
- {
- return isColourByLabel() || isAboveThreshold() || isBelowThreshold();
- }
-
- @Override
- public Color getColour()
- {
- return Color.BLACK;
- }
-
- @Override
- public Color getMinColour()
- {
- return Color.WHITE;
- }
-
- @Override
- public Color getMaxColour()
- {
- return Color.BLACK;
- }
-
- @Override
- public boolean isColourByLabel()
- {
- return false;
- }
-
- @Override
- public boolean isBelowThreshold()
- {
- return false;
- }
-
- @Override
- public boolean isAboveThreshold()
- {
- return false;
- }
-
- @Override
- public boolean isThresholdMinMax()
- {
- return false;
- }
-
- @Override
- public float getThreshold()
- {
- return 0f;
- }
-
- @Override
- public boolean isLowToHigh()
- {
- return true;
- }
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.schemes;
-
-import jalview.api.FeatureColourI;
-import jalview.datamodel.SequenceFeature;
-
-import java.awt.Color;
-
-/**
- * Value and/or thresholded colour scale used for colouring by annotation and
- * feature score
- *
- * @author JimP
- *
- */
-public class GraduatedColor
-{
- int thresholdState = AnnotationColourGradient.NO_THRESHOLD; // or
- // ABOVE_THRESHOLD
- // or
- // BELOW_THRESHOLD
-
- float lr, lg, lb, dr, dg, db;
-
- /**
- * linear scaling parameters, base, minimum colour threshold, range of linear
- * scale from lower to upper
- */
- float base, range, thrsh;
-
- /**
- * when true, colour from u to u-d rather than u to u+d
- */
- boolean tolow = false;
-
- /**
- * when false, min/max range has been manually set so should not be
- * dynamically adjusted.
- */
- boolean autoScale = true;
-
- /**
- * construct a graduatedColor object from simple parameters
- *
- * @param low
- * @param high
- * @param min
- * @param max
- * color low->high from min->max
- */
- public GraduatedColor(Color low, Color high, float min, float max)
- {
- thrsh = Float.NaN;
- tolow = min >= max;
- lr = low.getRed() / 255f;
- lg = low.getGreen() / 255f;
- lb = low.getBlue() / 255f;
- dr = (high.getRed() / 255f) - lr;
- dg = (high.getGreen() / 255f) - lg;
- db = (high.getBlue() / 255f) - lb;
- if (tolow)
- {
- base = max;
- range = min - max;
- }
- else
- {
- base = min;
- range = max - min;
- }
- }
-
- public GraduatedColor(GraduatedColor oldcs)
- {
- lr = oldcs.lr;
- lg = oldcs.lg;
- lb = oldcs.lb;
- dr = oldcs.dr;
- dg = oldcs.dg;
- db = oldcs.db;
- base = oldcs.base;
- range = oldcs.range;
- tolow = oldcs.tolow;
- thresholdState = oldcs.thresholdState;
- thrsh = oldcs.thrsh;
- autoScale = oldcs.autoScale;
- colourByLabel = oldcs.colourByLabel;
- }
-
- /**
- * make a new gradient from an old one with a different scale range
- *
- * @param oldcs
- * @param min
- * @param max
- */
- public GraduatedColor(GraduatedColor oldcs, float min, float max)
- {
- this(oldcs);
- updateBounds(min, max);
- }
-
- public GraduatedColor(FeatureColourI col)
- {
- setColourByLabel(col.isColourByLabel());
- }
-
- public Color getMinColor()
- {
- return new Color(lr, lg, lb);
- }
-
- public Color getMaxColor()
- {
- return new Color(lr + dr, lg + dg, lb + db);
- }
-
- /**
- *
- * @return true if original min/max scale was from high to low
- */
- public boolean getTolow()
- {
- return tolow;
- }
-
- public void setTolow(boolean tolower)
- {
- tolow = tolower;
- }
-
- public boolean isColored(SequenceFeature feature)
- {
- float val = feature.getScore();
- if (Float.isNaN(val))
- {
- return true;
- }
- if (this.thresholdState == AnnotationColourGradient.NO_THRESHOLD)
- {
- return true;
- }
- if (Float.isNaN(this.thrsh))
- {
- return true;
- }
- boolean rtn = thresholdState == AnnotationColourGradient.ABOVE_THRESHOLD;
- if (val <= thrsh)
- {
- return !rtn; // ? !tolow : tolow;
- }
- else
- {
- return rtn; // ? tolow : !tolow;
- }
- }
-
- /**
- * default implementor of a getColourFromString method. TODO: abstract an
- * interface enabling pluggable colour from string
- */
- private UserColourScheme ucs = null;
-
- private boolean colourByLabel = false;
-
- /**
- *
- * @return true if colourByLabel style is set
- */
- public boolean isColourByLabel()
- {
- return colourByLabel;
- }
-
- /**
- * @param colourByLabel
- * the colourByLabel to set
- */
- public void setColourByLabel(boolean colourByLabel)
- {
- this.colourByLabel = colourByLabel;
- }
-
- public Color findColor(SequenceFeature feature)
- {
- if (colourByLabel)
- {
- // TODO: allow user defined feature label colourschemes. Colour space is
- // {type,regex,%anytype%}x{description string, regex, keyword}
- if (ucs == null)
- {
- ucs = new UserColourScheme();
- }
- return ucs.createColourFromName(feature.getDescription());
- }
- if (range == 0.0)
- {
- return getMaxColor();
- }
- float scr = feature.getScore();
- if (Float.isNaN(scr))
- {
- return getMinColor();
- }
- float scl = (scr - base) / range;
- if (tolow)
- {
- scl = -scl;
- }
- if (scl < 0f)
- {
- scl = 0f;
- }
- if (scl > 1f)
- {
- scl = 1f;
- }
- return new Color(lr + scl * dr, lg + scl * dg, lb + scl * db);
- }
-
- public void setThresh(float value)
- {
- thrsh = value;
- }
-
- public float getThresh()
- {
- return thrsh;
- }
-
- public void setThreshType(int aboveThreshold)
- {
- thresholdState = aboveThreshold;
- }
-
- public int getThreshType()
- {
- return thresholdState;
- }
-
- public float getMax()
- {
- // regenerate the original values passed in to the constructor
- return (tolow) ? base : (base + range);
- }
-
- public float getMin()
- {
- // regenerate the original value passed in to the constructor
- return (tolow) ? (base + range) : base;
- }
-
- public boolean isAutoScale()
- {
- return autoScale;
- }
-
- public void setAutoScaled(boolean autoscale)
- {
- autoScale = autoscale;
- }
-
- /**
- * update the base and range appropriatly for the given minmax range
- *
- * @param a
- * float[] {min,max} array containing minmax range for the associated
- * score values
- */
- public void updateBounds(float min, float max)
- {
- if (max < min)
- {
- base = max;
- range = min - max;
- tolow = true;
- }
- else
- {
- base = min;
- range = max - min;
- tolow = false;
- }
- }
-}
// This loop will find the first rna structure annotation by which to colour
// the sequences.
AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+ if (annotations == null)
+ {
+ return;
+ }
for (int i = 0; i < annotations.length; i++)
{
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
import java.awt.event.ActionEvent;
adjusting = true;
Vector list = new Vector();
int index = 1;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns != null)
{
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
+ for (int i = 0; i < anns.length; i++)
{
- list.addElement(label);
- }
- else
- {
- list.addElement(label + "_" + (index++));
+ String label = anns[i].label;
+ if (!list.contains(label))
+ {
+ list.addElement(label);
+ }
+ else
+ {
+ list.addElement(label + "_" + (index++));
+ }
}
}
public static Color getColourFromString(String colour)
{
+ if (colour == null)
+ {
+ return null;
+ }
colour = colour.trim();
Color col = null;
}
- public Color createColourFromName(String name)
+ public static Color createColourFromName(String name)
{
int r, g, b;
}
return ala_copy;
}
+
+ public String getMappingDetailsOutput()
+ {
+ return mappingDetails;
+ }
+
+ public HashMap<Integer, int[]> getMapping()
+ {
+ return mapping;
+ }
}
if (isMapUsingSIFTs)
{
setProgressBar(null);
- setProgressBar("Obtaining mapping with SIFTS");
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"));
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
{
- StructureMapping mapping = getStructureMapping(seq, pdbFile,
- targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(mapping);
+ StructureMapping siftsMapping;
+ try
+ {
+ siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+ pdb, maxChain, sqmpping, maxAlignseq);
+ seqToStrucMapping.add(siftsMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ } catch (SiftsException e)
+ {
+ // fall back to NW alignment
+ System.err.println(e.getMessage());
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ targetChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ }
}
else
{
+ ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
for (PDBChain chain : pdb.getChains())
{
- StructureMapping mapping = getStructureMapping(seq, pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(mapping);
+ try
+ {
+ StructureMapping siftsMapping = getStructureMapping(seq,
+ pdbFile,
+ chain.id, pdb, chain, sqmpping, maxAlignseq);
+ foundSiftsMappings.add(siftsMapping);
+ } catch (SiftsException e)
+ {
+ System.err.println(e.getMessage());
+ }
+ }
+ if (!foundSiftsMappings.isEmpty())
+ {
+ seqToStrucMapping.addAll(foundSiftsMappings);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
+ sqmpping);
+ }
+ else
+ {
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
}
}
}
else
{
setProgressBar(null);
- setProgressBar("Obtaining mapping with NW alignment");
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_nw_alignment"));
seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
maxChain, pdb, maxAlignseq));
}
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq)
+ AlignSeq maxAlignseq) throws SiftsException
{
- String maxChainId = targetChainId;
- try
- {
StructureMapping curChainMapping = siftsClient
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
try
e.printStackTrace();
}
return curChainMapping;
- } catch (SiftsException e)
- {
- System.err.println(e.getMessage());
- System.err.println(">>> Now switching mapping with NW alignment...");
- setProgressBar(null);
- setProgressBar(">>> Now switching mapping with NW alignment...");
- return getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb,
- maxAlignseq);
- }
}
private StructureMapping getNWMappings(SequenceI seq,
for (String file : files)
{
notLoaded = file;
+ if (file == null)
+ {
+ continue;
+ }
try
{
StructureMapping[] sm = getSsm().getMapping(file);
--- /dev/null
+package jalview.util;
+
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+public class DnaUtils
+{
+
+ /**
+ * Parses an ENA/GenBank format location specifier and returns a list of
+ * [start, end] ranges. Throws an exception if not able to parse.
+ * <p>
+ * Currently we do not parse "order()" specifiers, or indeterminate ranges of
+ * the format "<start..end" or "start..>end" or "start.end" or
+ * "start^end"
+ *
+ * @param location
+ * @return
+ * @throws ParseException
+ * if unable to parse the location (the exception message is the
+ * location specifier being parsed); we use ParseException in
+ * preference to the unchecked IllegalArgumentException
+ * @see http://www.insdc.org/files/feature_table.html#3.4
+ */
+ public static List<int[]> parseLocation(String location)
+ throws ParseException
+ {
+ if (location.startsWith("join("))
+ {
+ return parseJoin(location);
+ }
+ else if (location.startsWith("complement("))
+ {
+ return parseComplement(location);
+ }
+ if (location.startsWith("order("))
+ {
+ throw new ParseException(location, 0);
+ }
+
+ /*
+ * try to parse m..n (or simply m)
+ */
+ String[] range = location.split("\\.\\.");
+ if (range.length == 1 || range.length == 2)
+ {
+ try
+ {
+ int start = Integer.valueOf(range[0]);
+ int end = range.length == 1 ? start : Integer.valueOf(range[1]);
+ return Collections.singletonList(new int[] { start, end });
+ } catch (NumberFormatException e)
+ {
+ /*
+ * could be a location like <1..888 or 1..>888
+ */
+ throw new ParseException(location, 0);
+ }
+ }
+ else
+ {
+ /*
+ * could be a location like 102.110 or 123^124
+ */
+ throw new ParseException(location, 0);
+ }
+ }
+
+ /**
+ * Parses a complement(locationSpec) into a list of start-end ranges
+ *
+ * @param location
+ * @return
+ * @throws ParseException
+ */
+ static List<int[]> parseComplement(String location) throws ParseException
+ {
+ /*
+ * take what is inside complement()
+ */
+ if (!location.endsWith(")"))
+ {
+ throw new ParseException(location, 0);
+ }
+ String toComplement = location.substring("complement(".length(),
+ location.length() - 1);
+ List<int[]> ranges = parseLocation(toComplement);
+
+ /*
+ * reverse the order and direction of ranges
+ */
+ Collections.reverse(ranges);
+ for (int[] range : ranges)
+ {
+ int temp = range[0];
+ range[0] = range[1];
+ range[1] = temp;
+ }
+ return ranges;
+ }
+
+ /**
+ * Parses a join(loc1,loc2,...,locn) into a list of start-end ranges
+ *
+ * @param location
+ * @return
+ * @throws ParseException
+ */
+ static List<int[]> parseJoin(String location) throws ParseException
+ {
+ List<int[]> ranges = new ArrayList<int[]>();
+
+ /*
+ * take what is inside join()
+ */
+ if (!location.endsWith(")"))
+ {
+ throw new ParseException(location, 0);
+ }
+ String joinedLocs = location.substring("join(".length(),
+ location.length() - 1);
+ String[] locations = joinedLocs.split(",");
+ for (String loc : locations)
+ {
+ List<int[]> range = parseLocation(loc);
+ ranges.addAll(range);
+ }
+ return ranges;
+ }
+
+}
TYPE type;
+ private IProgressIndicator pIndicator;
+
+ private long pSessionId;
+
+ private boolean headless;
+
public enum TYPE
{
EPS("EPS", MessageManager.getString("label.eps_file"), getEPSChooser()), PNG(
int height, File file, String fileTitle,
IProgressIndicator pIndicator, long pSessionId, boolean headless)
{
+ this.pIndicator = pIndicator;
this.type = type;
-
+ this.pSessionId = pSessionId;
+ this.headless = headless;
if (file == null)
{
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(
- MessageManager.formatMessage(
- "status.waiting_for_user_to_select_output_file",
- type.name), pSessionId);
- }
+ setProgressMessage(MessageManager.formatMessage(
+ "status.waiting_for_user_to_select_output_file", type.name));
JalviewFileChooser chooser;
chooser = type.getChooser();
chooser.setFileView(new jalview.io.JalviewFileView());
}
else
{
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", type.name),
- pSessionId);
- }
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", type.name));
}
}
try
{
out = new FileOutputStream(file);
+ setProgressMessage(null);
+ setProgressMessage(MessageManager.formatMessage(
+ "status.exporting_alignment_as_x_file", type.getName()));
if (type == TYPE.SVG)
{
setupSVG(width, height, fileTitle);
{
setupPNG(width, height);
}
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(
-MessageManager.formatMessage(
- "status.export_complete", type.getName()),
- pSessionId);
- }
+
} catch (Exception ex)
{
System.out.println("Error creating " + type.getName() + " file.");
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "info.error_creating_file", type.getName()), pSessionId);
+ setProgressMessage(MessageManager.formatMessage(
+ "info.error_creating_file", type.getName()));
}
}
}
if (renderStyle == null || eps.cancelled)
{
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "EPS"));
return;
}
}
pg.setAccurateTextMode(accurateText);
graphics = pg;
+ setProgressMessage(MessageManager.formatMessage(
+ "status.export_complete", type.getName()));
} catch (Exception ex)
{
}
Graphics2D ig2 = (Graphics2D) graphics;
ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
+ setProgressMessage(MessageManager.formatMessage(
+ "status.export_complete", type.getName()));
}
if (renderStyle == null || svgOption.cancelled)
{
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "SVG"));
return;
}
}
- if (renderStyle.equalsIgnoreCase("lineart"))
+ if (renderStyle.equalsIgnoreCase("Lineart"))
{
ig2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
}
+ setProgressMessage(MessageManager.formatMessage(
+ "status.export_complete", type.getName()));
graphics = g2;
}
"Encapsulated Postscript");
}
+ private void setProgressMessage(String message)
+ {
+ if (pIndicator != null && !headless)
+ {
+ pIndicator.setProgressBar(message, pSessionId);
+ }
+ }
+
static JalviewFileChooser getSVGChooser()
{
if (Jalview.isHeadlessMode())
*/
package jalview.util;
+import java.awt.Toolkit;
+import java.awt.event.MouseEvent;
+
/**
* System platform information used by Applet and Application
*
f.append(file.substring(lastp));
return f.toString();
}
+
+ public static boolean isControlDown(MouseEvent e)
+ {
+ return (jalview.util.Platform.isAMac() ? (Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask() & e.getModifiers()) != 0 : e
+ .isControlDown());
+ }
}
}
return result;
}
+
+ /**
+ * Compares two versions formatted as e.g. "3.4.5" and returns -1, 0 or 1 as
+ * the first version precedes, is equal to, or follows the second
+ *
+ * @param v1
+ * @param v2
+ * @return
+ */
+ public static int compareVersions(String v1, String v2)
+ {
+ return compareVersions(v1, v2, null);
+ }
+
+ /**
+ * Compares two versions formatted as e.g. "3.4.5b1" and returns -1, 0 or 1 as
+ * the first version precedes, is equal to, or follows the second
+ *
+ * @param v1
+ * @param v2
+ * @param pointSeparator
+ * a string used to delimit point increments in sub-tokens of the
+ * version
+ * @return
+ */
+ public static int compareVersions(String v1, String v2,
+ String pointSeparator)
+ {
+ if (v1 == null || v2 == null)
+ {
+ return 0;
+ }
+ String[] toks1 = v1.split("\\.");
+ String[] toks2 = v2.split("\\.");
+ int i = 0;
+ for (; i < toks1.length; i++)
+ {
+ if (i >= toks2.length)
+ {
+ /*
+ * extra tokens in v1
+ */
+ return 1;
+ }
+ String tok1 = toks1[i];
+ String tok2 = toks2[i];
+ if (pointSeparator != null)
+ {
+ /*
+ * convert e.g. 5b2 into decimal 5.2 for comparison purposes
+ */
+ tok1 = tok1.replace(pointSeparator, ".");
+ tok2 = tok2.replace(pointSeparator, ".");
+ }
+ try
+ {
+ float f1 = Float.valueOf(tok1);
+ float f2 = Float.valueOf(tok2);
+ int comp = Float.compare(f1, f2);
+ if (comp != 0)
+ {
+ return comp;
+ }
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Invalid version format found: "
+ + e.getMessage());
+ return 0;
+ }
+ }
+
+ if (i < toks2.length)
+ {
+ /*
+ * extra tokens in v2
+ */
+ return -1;
+ }
+
+ /*
+ * same length, all tokens match
+ */
+ return 0;
+ }
+
+ /**
+ * Converts the string to all lower-case except the first character which is
+ * upper-cased
+ *
+ * @param s
+ * @return
+ */
+ public static String toSentenceCase(String s)
+ {
+ if (s == null)
+ {
+ return s;
+ }
+ if (s.length() <= 1)
+ {
+ return s.toUpperCase();
+ }
+ return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
+ }
}
{
updateHiddenColumns();
}
+ isColSelChanged(true);
}
/**
*/
public boolean isColSelChanged(boolean b)
{
- int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel
- .hashCode();
+ int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
if (hc != -1 && hc != colselhash)
{
if (b)
colSel.hideSelectedColumns();
setSelectionGroup(null);
-
+ isColSelChanged(true);
}
public void hideColumns(int start, int end)
{
colSel.hideColumns(start, end);
}
+ isColSelChanged(true);
}
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
-
+ isColSelChanged(true);
}
public void showAllHiddenColumns()
{
colSel.revealAllHiddenColumns();
+ isColSelChanged(true);
}
// common hide/show seq stuff
}
/**
+ * Hides the specified sequence, or the sequences it represents
+ *
+ * @param sequence
+ * the sequence to hide, or keep as representative
+ * @param representGroup
+ * if true, hide the current selection group except for the
+ * representative sequence
+ */
+ public void hideSequences(SequenceI sequence, boolean representGroup)
+ {
+ if (selectionGroup == null || selectionGroup.getSize() < 1)
+ {
+ hideSequence(new SequenceI[] { sequence });
+ return;
+ }
+
+ if (representGroup)
+ {
+ hideRepSequences(sequence, selectionGroup);
+ setSelectionGroup(null);
+ return;
+ }
+
+ int gsize = selectionGroup.getSize();
+ SequenceI[] hseqs = selectionGroup.getSequences().toArray(
+ new SequenceI[gsize]);
+
+ hideSequence(hseqs);
+ setSelectionGroup(null);
+ sendSelection();
+ }
+
+ /**
* Set visibility for any annotations for the given sequence.
*
* @param sequenceI
protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
boolean visible)
{
- for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ if (anns != null)
{
- if (ann.sequenceRef == sequenceI)
+ for (AlignmentAnnotation ann : anns)
{
- ann.visible = visible;
+ if (ann.sequenceRef == sequenceI)
+ {
+ ann.visible = visible;
+ }
}
}
}
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
+ return getViewAsString(selectedRegionOnly, true);
+ }
+
+ @Override
+ public String[] getViewAsString(boolean selectedRegionOnly,
+ boolean exportHiddenSeqs)
+ {
String[] selection = null;
SequenceI[] seqs = null;
int i, iSize;
}
else
{
- if (hasHiddenRows())
+ if (hasHiddenRows() && exportHiddenSeqs)
{
- iSize = alignment.getHiddenSequences().getFullAlignment()
- .getHeight();
- seqs = alignment.getHiddenSequences().getFullAlignment()
- .getSequencesArray();
- end = alignment.getHiddenSequences().getFullAlignment().getWidth();
+ AlignmentI fullAlignment = alignment.getHiddenSequences()
+ .getFullAlignment();
+ iSize = fullAlignment.getHeight();
+ seqs = fullAlignment.getSequencesArray();
+ end = fullAlignment.getWidth();
}
else
{
}
}
}
+
+
}
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureRenderer;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.UserColourScheme;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
*/
protected float transparency = 1.0f;
- protected Map<String, Object> featureColours = new ConcurrentHashMap<String, Object>();
+ protected Map<String, FeatureColourI> featureColours = new ConcurrentHashMap<String, FeatureColourI>();
protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<String, Boolean>();
- protected Object currentColour;
-
- /*
- * feature types in ordering of rendering, where last means on top
- */
protected String[] renderOrder;
+ Map<String, Float> featureOrder = null;
+
protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
protected AlignmentViewport av;
- /*
- * map holds per feature type, {{min, max}, {min, max}} feature score
- * values for positional and non-positional features respectively
- */
- private Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
-
@Override
public AlignViewportI getViewport()
{
renderOrder = neworder;
}
+ protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+
public Map<String, float[][]> getMinMax()
{
return minmax;
List<String> allfeatures = new ArrayList<String>(allFeatures);
String[] oldRender = renderOrder;
renderOrder = new String[allfeatures.size()];
- Object mmrange, fc = null;
boolean initOrders = (featureOrder == null);
int opos = 0;
if (oldRender != null && oldRender.length > 0)
allfeatures.remove(oldRender[j]);
if (minmax != null)
{
- mmrange = minmax.get(oldRender[j]);
+ float[][] mmrange = minmax.get(oldRender[j]);
if (mmrange != null)
{
- fc = featureColours.get(oldRender[j]);
- if (fc != null && fc instanceof GraduatedColor
- && ((GraduatedColor) fc).isAutoScale())
+ FeatureColourI fc = featureColours.get(oldRender[j]);
+ if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
{
- ((GraduatedColor) fc).updateBounds(
- ((float[][]) mmrange)[0][0],
- ((float[][]) mmrange)[0][1]);
+ fc.updateBounds(mmrange[0][0], mmrange[0][1]);
}
}
}
if (minmax != null)
{
// update from new features minmax if necessary
- mmrange = minmax.get(newf[i]);
+ float[][] mmrange = minmax.get(newf[i]);
if (mmrange != null)
{
- fc = featureColours.get(newf[i]);
- if (fc != null && fc instanceof GraduatedColor
- && ((GraduatedColor) fc).isAutoScale())
+ FeatureColourI fc = featureColours.get(newf[i]);
+ if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
{
- ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
- ((float[][]) mmrange)[0][1]);
+ fc.updateBounds(mmrange[0][0], mmrange[0][1]);
}
}
}
setOrder(newf[i], i / (float) denom);
}
// set order from newly found feature from persisted ordering.
- sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
+ sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue();
if (i < iSize)
{
// only sort if we need to
/**
* get a feature style object for the given type string. Creates a
- * java.awt.Color for a featureType with no existing colourscheme. TODO:
- * replace return type with object implementing standard abstract colour/style
- * interface
+ * java.awt.Color for a featureType with no existing colourscheme.
*
* @param featureType
- * @return java.awt.Color or GraduatedColor
+ * @return
*/
@Override
- public Object getFeatureStyle(String featureType)
+ public FeatureColourI getFeatureStyle(String featureType)
{
- Object fc = featureColours.get(featureType);
+ FeatureColourI fc = featureColours.get(featureType);
if (fc == null)
{
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
- Color col = ucs.createColourFromName(featureType);
- featureColours.put(featureType, fc = col);
+ Color col = UserColourScheme.createColourFromName(featureType);
+ fc = new FeatureColour(col);
+ featureColours.put(featureType, fc);
}
return fc;
}
/**
- * return a nominal colour for this feature
- *
- * @param featureType
- * @return standard color, or maximum colour for graduated colourscheme
- */
- public Color getColour(String featureType)
- {
- Object fc = getFeatureStyle(featureType);
-
- if (fc instanceof Color)
- {
- return (Color) fc;
- }
- else
- {
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).getMaxColor();
- }
- }
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + featureType);
- }
-
- /**
* calculate the render colour for a specific feature using current feature
* settings.
*
*/
public Color getColour(SequenceFeature feature)
{
- Object fc = getFeatureStyle(feature.getType());
- if (fc instanceof Color)
- {
- return (Color) fc;
- }
- else
- {
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).findColor(feature);
- }
- }
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + feature.getType());
+ FeatureColourI fc = getFeatureStyle(feature.getType());
+ return fc.getColor(feature);
}
protected boolean showFeature(SequenceFeature sequenceFeature)
{
- Object fc = getFeatureStyle(sequenceFeature.type);
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).isColored(sequenceFeature);
- }
- else
- {
- return true;
- }
+ FeatureColourI fc = getFeatureStyle(sequenceFeature.type);
+ return fc.isColored(sequenceFeature);
}
protected boolean showFeatureOfType(String type)
}
@Override
- public void setColour(String featureType, Object col)
+ public void setColour(String featureType, FeatureColourI col)
{
- // overwrite
- // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
- // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
- // Object c = featureColours.get(featureType);
- // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
- // !((GraduatedColor)c).getMaxColor().equals(_col)))
- if (col instanceof FeatureColourI)
- {
- if (((FeatureColourI) col).isGraduatedColour())
- {
- col = new GraduatedColor((FeatureColourI) col);
- }
- else
- {
- col = ((FeatureColourI) col).getColour();
- }
- }
- featureColours.put(featureType, col);
+ featureColours.put(featureType, col);
}
public void setTransparency(float value)
return transparency;
}
- Map featureOrder = null;
-
/**
* analogous to colour - store a normalized ordering for all feature types in
* this rendering context.
{
if (featureOrder == null)
{
- featureOrder = new Hashtable();
+ featureOrder = new Hashtable<String, Float>();
}
featureOrder.put(type, new Float(position));
return position;
{
if (featureOrder.containsKey(type))
{
- return ((Float) featureOrder.get(type)).floatValue();
+ return featureOrder.get(type).floatValue();
}
}
return -1;
}
@Override
- public Map<String, Object> getFeatureColours()
+ public Map<String, FeatureColourI> getFeatureColours()
{
return featureColours;
}
* note visible feature ordering and colours before update
*/
List<String> visibleFeatures = getDisplayedFeatureTypes();
- Map<String, Object> visibleColours = new HashMap<String, Object>(
+ Map<String, FeatureColourI> visibleColours = new HashMap<String, FeatureColourI>(
getFeatureColours());
FeaturesDisplayedI av_featuresdisplayed = null;
for (int i = 0; i < data.length; i++)
{
String type = data[i][0].toString();
- setColour(type, data[i][1]); // todo : typesafety - feature color
- // interface object
+ setColour(type, (FeatureColourI) data[i][1]);
if (((Boolean) data[i][2]).booleanValue())
{
av_featuresdisplayed.setVisible(type);
return renderOrder != null;
}
+ /**
+ * Returns feature types in ordering of rendering, where last means on top
+ */
public List<String> getRenderOrder()
{
if (renderOrder == null)
{
if (featureGroups != null)
{
- ArrayList gp = new ArrayList();
+ List<String> gp = new ArrayList<String>();
- for (Object grp : featureGroups.keySet())
+ for (String grp : featureGroups.keySet())
{
Boolean state = featureGroups.get(grp);
if (state.booleanValue() == visible)
}
@Override
- public Hashtable getDisplayedFeatureCols()
+ public Map<String, FeatureColourI> getDisplayedFeatureCols()
{
- Hashtable fcols = new Hashtable();
+ Map<String, FeatureColourI> fcols = new Hashtable<String, FeatureColourI>();
if (getViewport().getFeaturesDisplayed() == null)
{
return fcols;
}
- Iterator<String> en = getViewport().getFeaturesDisplayed()
+ Iterator<String> features = getViewport().getFeaturesDisplayed()
.getVisibleFeatures();
- while (en.hasNext())
+ while (features.hasNext())
{
- String col = en.next();
- fcols.put(col, getColour(col));
+ String feature = features.next();
+ fcols.put(feature, getFeatureStyle(feature));
}
return fcols;
}
*/
package jalview.viewmodel.seqfeatures;
-import jalview.schemes.GraduatedColor;
+import jalview.api.FeatureColourI;
+import jalview.schemes.FeatureColour;
import java.util.Arrays;
-import java.util.Hashtable;
import java.util.Iterator;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
{
String[] renderOrder;
- Map featureGroups;
+ /*
+ * map of {groupName, isDisplayed}
+ */
+ Map<String, Boolean> featureGroups;
- Map featureColours;
+ /*
+ * map of {featureType, colourScheme}
+ */
+ Map<String, FeatureColourI> featureColours;
float transparency;
- Map featureOrder;
+ Map<String, Float> featureOrder;
public FeatureRendererSettings(String[] renderOrder,
- Hashtable featureGroups, Hashtable featureColours,
- float transparency, Hashtable featureOrder)
+ Map<String, Boolean> featureGroups,
+ Map<String, FeatureColourI> featureColours, float transparency,
+ Map<String, Float> featureOrder)
{
super();
this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
- this.featureGroups = new ConcurrentHashMap(featureGroups);
- this.featureColours = new ConcurrentHashMap(featureColours);
+ this.featureGroups = new ConcurrentHashMap<String, Boolean>(
+ featureGroups);
+ this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
+ featureColours);
this.transparency = transparency;
- this.featureOrder = new ConcurrentHashMap(featureOrder);
+ this.featureOrder = new ConcurrentHashMap<String, Float>(featureOrder);
}
/**
jalview.viewmodel.seqfeatures.FeatureRendererModel fr)
{
renderOrder = null;
- featureGroups = new ConcurrentHashMap();
- featureColours = new ConcurrentHashMap();
- featureOrder = new ConcurrentHashMap();
+ featureGroups = new ConcurrentHashMap<String, Boolean>();
+ featureColours = new ConcurrentHashMap<String, FeatureColourI>();
+ featureOrder = new ConcurrentHashMap<String, Float>();
if (fr.renderOrder != null)
{
this.renderOrder = new String[fr.renderOrder.length];
}
if (fr.featureGroups != null)
{
- this.featureGroups = new ConcurrentHashMap(fr.featureGroups);
+ this.featureGroups = new ConcurrentHashMap<String, Boolean>(
+ fr.featureGroups);
}
if (fr.featureColours != null)
{
- this.featureColours = new ConcurrentHashMap(fr.featureColours);
+ this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
+ fr.featureColours);
}
- Iterator en = fr.featureColours.keySet().iterator();
+ Iterator<String> en = fr.featureColours.keySet().iterator();
while (en.hasNext())
{
- Object next = en.next();
- Object val = featureColours.get(next);
- if (val instanceof GraduatedColor)
+ String next = en.next();
+ FeatureColourI val = featureColours.get(next);
+ // if (val instanceof GraduatedColor)
+ if (val.isGraduatedColour() || val.isColourByLabel()) // why this test?
{
- featureColours.put(next, new GraduatedColor((GraduatedColor) val));
+ featureColours.put(next, new FeatureColour((FeatureColour) val));
}
}
this.transparency = fr.transparency;
if (fr.featureOrder != null)
{
- this.featureOrder = new ConcurrentHashMap(fr.featureOrder);
+ this.featureOrder = new ConcurrentHashMap<String, Float>(
+ fr.featureOrder);
}
}
}
package jalview.workers;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
import java.awt.Color;
*/
public static void newCalculator(FeatureCounterI counter)
{
- if (Desktop.getCurrentAlignFrame() != null)
+ if (Jalview.getCurrentAlignFrame() != null)
{
- newCalculator(Desktop.getCurrentAlignFrame(), counter);
+ newCalculator(Jalview.getCurrentAlignFrame(), counter);
}
else
{
*/
public static void newCalculator(AnnotationProviderI calculator)
{
- if (Desktop.getCurrentAlignFrame() != null)
+ if (Jalview.getCurrentAlignFrame() != null)
{
- newCalculator(Desktop.getCurrentAlignFrame(), calculator);
+ newCalculator(Jalview.getCurrentAlignFrame(), calculator);
}
else
{
.getAlignmentAnnotation();
AlignmentAnnotation rnaStruc = null;
// select rna struct to use for calculation
- for (int i = 0; i < aa.length; i++)
+ if (aa != null)
{
- if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+ for (int i = 0; i < aa.length; i++)
{
- rnaStruc = aa[i];
- break;
+ if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+ {
+ rnaStruc = aa[i];
+ break;
+ }
}
}
// check to see if its valid
String[] defdb = null, otherdb = sfetcher
.getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
- Vector dasselsrc = (featureSettings != null) ? featureSettings
+ Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
.getSelectedSources() : new jalview.gui.DasSourceBrowser()
.getSelectedSources();
Enumeration<jalviewSourceI> en = dasselsrc.elements();
}
/**
+ * Constructor with only sequences provided
+ *
+ * @param sequences
+ */
+ public DBRefFetcher(SequenceI[] sequences)
+ {
+ this(sequences, null, null, null, false);
+ }
+
+ /**
* Add a listener to be notified when sequence fetching is complete
*
* @param l
import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.FeatureSettings;
+import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
{
for (int j = 0; j < dbref.length; j++)
{
- if (dbref[j].getSource().equals(
- jalview.datamodel.DBRefSource.UNIPROT))
+ if (dbref[j].getSource().equals(DBRefSource.UNIPROT))
{
refCount++;
break;
public void run()
{
running = true;
- boolean isNuclueotide = af.getViewport().getAlignment()
+ boolean isNucleotide = af.getViewport().getAlignment()
.isNucleotide();
- new jalview.ws.DBRefFetcher(sequences, af, null, af.featureSettings,
- isNuclueotide).fetchDBRefs(true);
+ new DBRefFetcher(sequences, af, null, af.featureSettings,
+ isNucleotide).fetchDBRefs(true);
startFetching();
setGuiFetchComplete();
{
jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
new jalviewSourceI[0]);
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
+ String active = Cache.getDefault("DAS_ACTIVE_SOURCE",
"uniprot");
StringTokenizer st = new StringTokenizer(active, "\t");
selectedSources = new Vector();
{
return null;
}
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
+ DBRefEntry[] uprefs = DBRefUtils.selectRefs(
seq.getDBRefs(), new String[] {
// jalview.datamodel.DBRefSource.PDB,
- jalview.datamodel.DBRefSource.UNIPROT,
+ DBRefSource.UNIPROT,
// jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
// sys sources
});
for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())
{
- if (jalview.util.DBRefUtils.isDasCoordinateSystem(
+ if (DBRefUtils.isDasCoordinateSystem(
csys.getAuthority(), uprefs[j]))
{
debug("Launched fetcher for coordinate system "
try
{
reply = dbFetch.fetchDataAsFile(
- emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null,
+ emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
".xml");
} catch (Exception e)
{
+
/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
public static final String FEATURE_RES_NUM = "RESNUM";
- private static String currentDefaultFomart = DBRefSource.PDB;
+ private static String currentDefaultFormat = DBRefSource.PDB;
/*
* (non-Javadoc)
stopQuery();
return null;
}
- String ext = getCurrentDefaultFomart().equalsIgnoreCase("mmcif") ? ".cif"
+ String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
: ".xml";
EBIFetchClient ebi = new EBIFetchClient();
file = ebi.fetchDataAsFile("pdb:" + id,
- getCurrentDefaultFomart().toLowerCase(), "raw", ext)
+ getCurrentDefaultFormat().toLowerCase(), ext)
.getAbsolutePath();
stopQuery();
if (file == null)
pdbAlignment = new FormatAdapter().readFile(file,
jalview.io.AppletFormatAdapter.FILE,
- getCurrentDefaultFomart());
+ getCurrentDefaultFormat());
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
}
/**
- * obtain human glyoxalase chain A sequence
+ * human glyoxalase
*/
@Override
public String getTestQuery()
{
- return "1QIPA";
+ return "1QIP";
}
@Override
return 0;
}
- public static String getCurrentDefaultFomart()
+ public static String getCurrentDefaultFormat()
{
- return currentDefaultFomart;
+ return currentDefaultFormat;
}
- public static void setCurrentDefaultFomart(String currentDefaultFomart)
+ public static void setCurrentDefaultFormat(String currentDefaultFomart)
{
- Pdb.currentDefaultFomart = currentDefaultFomart;
+ Pdb.currentDefaultFormat = currentDefaultFomart;
}
/**
// uniprotxml parameter required since december 2007
// uniprotkb dbname changed introduced december 2008
File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
- null, ".xml");
+ ".xml");
Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
if (entries != null)
*/
public class EBIFetchClient
{
- String format = "default";
-
- String style = "raw";
/**
* Creates a new EBIFetchClient object.
* the query formatted as db:query1;query2;query3
* @param format
* the format wanted
- * @param s
- * - unused parameter
+ * @param extension
+ * for the temporary file to hold response
* @return the file holding the response
* @throws OutOfMemoryError
*/
- public File fetchDataAsFile(String ids, String format, String s,
- String ext)
+ public File fetchDataAsFile(String ids, String format, String ext)
throws OutOfMemoryError
{
File outFile = null;
{
outFile = File.createTempFile("jalview", ext);
outFile.deleteOnExit();
- fetchData(ids, format, s, outFile);
+ fetchData(ids, format, outFile);
if (outFile.length() == 0)
{
outFile.delete();
}
/**
- * Single DB multiple record retrieval
+ * Fetches queries and either saves the response to a file or returns as
+ * string data
*
* @param ids
- * db:query1;query2;query3
* @param format
- * raw/xml
- * @param s
- * not used - remove?
- *
- * @return Raw string array result of query set
+ * @param outFile
+ * @return
+ * @throws OutOfMemoryError
*/
- public String[] fetchData(String ids, String format, String s)
+ String[] fetchData(String ids, String format, File outFile)
throws OutOfMemoryError
{
- return fetchData(ids, format, s, null);
+ StringBuilder querystring = new StringBuilder(ids.length());
+ String database = parseIds(ids, querystring);
+ if (database == null)
+ {
+ System.err.println("Invalid Query string : '" + ids + "'");
+ System.err.println("Should be of form 'dbname:q1;q2;q3;q4'");
+ return null;
+ }
+
+ // note: outFile is currently always specified, so return value is null
+ String[] rslt = fetchBatch(querystring.toString(), database, format, outFile);
+
+ return (rslt != null && rslt.length > 0 ? rslt : null);
}
- String[] fetchData(String ids, String f, String s, File outFile)
- throws OutOfMemoryError
+ /**
+ * Parses ids formatted as dbname:q1;q2;q3, returns the dbname and adds
+ * queries as comma-separated items to the querystring. dbname must be
+ * specified for at least one queryId. Returns null if a mixture of different
+ * dbnames is found (ignoring case).
+ *
+ * @param ids
+ * @param queryString
+ * @return
+ */
+ static String parseIds(String ids, StringBuilder queryString)
{
- // Need to split
- // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
- String[] rslts = new String[0];
+ String database = null;
StringTokenizer queries = new StringTokenizer(ids, ";");
- String db = null;
- StringBuffer querystring = null;
- int nq = 0;
+ boolean appending = queryString.length() > 0;
while (queries.hasMoreTokens())
{
String query = queries.nextToken();
- int p;
- if ((p = query.indexOf(':')) > -1)
+ int p = query.indexOf(':');
+ if (p > -1)
{
- db = query.substring(0, p);
+ String db = query.substring(0, p);
+ if (database != null && !db.equalsIgnoreCase(database))
+ {
+ /*
+ * different databases mixed in together - invalid
+ */
+ return null;
+ }
+ database = db;
query = query.substring(p + 1);
}
- if (querystring == null)
- {
- querystring = new StringBuffer(query);
- nq++;
- }
- else
- {
- querystring.append("," + query);
- nq++;
- }
- }
- if (db == null)
- {
- System.err.println("Invalid Query string : '" + ids
- + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
- return null;
- }
- String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile);
- if (rslt != null)
- {
- String[] nrslts = new String[rslt.length + rslts.length];
- System.arraycopy(rslts, 0, nrslts, 0, rslts.length);
- System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);
- rslts = nrslts;
+ queryString.append(appending ? "," : "");
+ queryString.append(query);
+ appending = true;
}
-
- return (rslts.length == 0 ? null : rslts);
+ return database;
}
- public String[] fetchBatch(String ids, String dbPath, String format, String s,
+ /**
+ * Fetches queries and either saves the response to a file or (if no file
+ * specified) returns as string data
+ *
+ * @param ids
+ * @param database
+ * @param format
+ * @param outFile
+ * @return
+ * @throws OutOfMemoryError
+ */
+ String[] fetchBatch(String ids, String database, String format,
File outFile) throws OutOfMemoryError
{
// long time = System.currentTimeMillis();
- /*
- * JAL-1855 dbfetch from ena_sequence, ena_coding
- */
- if (dbPath.equalsIgnoreCase(DBRefSource.EMBL))
- {
- dbPath = "ena_sequence";
- }
- else if (dbPath.equalsIgnoreCase(DBRefSource.EMBLCDS))
- {
- dbPath = "ena_coding";
- }
+ String url = buildUrl(ids, database, format);
try
{
- URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
- + dbPath.toLowerCase() + "/" + ids.toLowerCase()
- + (format != null ? "/" + format : ""));
+ URL rcall = new URL(url);
InputStream is = new BufferedInputStream(rcall.openStream());
if (outFile != null)
}
} catch (OutOfMemoryError er)
{
-
- System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + dbPath
+ System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
+ ":\n" + ids);
throw er;
} catch (Exception ex)
return null;
}
System.err.println("Unexpected exception when retrieving from "
- + dbPath
+ + database
+ "\nQuery was : '" + ids + "'");
ex.printStackTrace(System.err);
return null;
}
return null;
}
+
+ /**
+ * Constructs the URL to fetch from
+ *
+ * @param ids
+ * @param database
+ * @param format
+ * @return
+ */
+ static String buildUrl(String ids, String database, String format)
+ {
+ String url;
+ if (database.equalsIgnoreCase(DBRefSource.EMBL)
+ || database.equalsIgnoreCase(DBRefSource.EMBLCDS))
+ {
+ url = "http://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
+ + (format != null ? "&" + format : "");
+ }
+ else
+ {
+ url = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+ + database.toLowerCase() + "/" + ids.toLowerCase()
+ + (format != null ? "/" + format : "");
+ }
+ return url;
+ }
}
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
+import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
public Object[] getAlignment(Alignment dataset,
- Map<String, Object> featureColours)
+ Map<String, FeatureColourI> featureColours)
{
if (result != null && result.isFinished())
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
- Map<String, Object> featureColours = new HashMap<String, Object>();
+ Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())
*/
package jalview.ws.jws2;
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
annot.description += "<br/>" + threshNote;
}
annot.description += "</html>";
- Color col = new UserColourScheme(typeName)
- .createColourFromName(typeName + scr.getMethod());
+ Color col = UserColourScheme.createColourFromName(typeName
+ + scr.getMethod());
for (int p = 0, ps = annot.annotations.length; p < ps; p++)
{
if (annot.annotations[p] != null)
.cloneFeatureRenderer();
for (String ft : fc.keySet())
{
- Object gc = fr.getFeatureStyle(ft);
- if (gc instanceof Color)
+ FeatureColourI gc = fr.getFeatureStyle(ft);
+ if (gc.isSimpleColour())
{
// set graduated color as fading to white for minimum, and
// autoscaling to values on alignment
- GraduatedColor ggc = new GraduatedColor(Color.white,
- (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
+ FeatureColourI ggc = new FeatureColour(Color.white,
+ gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE);
ggc.setAutoScaled(true);
fr.setColour(ft, ggc);
}
});
wsmenu.add(aaConEnabled);
final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
- modifyParams
- .setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(false,
- aaui.getAAeditSettingsTooltip() + "</p>")
- + "</html>");
+ modifyParams.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ aaui.getAAeditSettingsTooltip()));
modifyParams.addActionListener(new ActionListener()
{
return (WebServiceName.indexOf("lustal") > -1); // cheat!
}
+ @Override
public void attachWSMenuEntry(JMenu rmsawsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
method.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
method.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
}
});
- methodR.setToolTipText(JvSwingUtils.wrapTooltip(
+ String tooltip = JvSwingUtils.wrapTooltip(
true,
- "<p><strong>"
+ "<strong>"
+ (preset.isModifiable() ? MessageManager
.getString("label.user_preset")
: MessageManager
.getString("label.service_preset"))
- + "</strong><br/>" + preset.getDescription()
- + "</p>"));
+ + "</strong><br/>"
+ + preset.getDescription());
+ methodR.setToolTipText(tooltip);
methodR.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame
private String type;
- private int wrapHeight;
-
private static final int MAX_ID_LENGTH = 30;
public String getSeqName()
this.type = type;
}
- public int getWrapHeight()
- {
- return wrapHeight;
- }
-
- public void setWrapHeight(int wrapHeight)
- {
- this.wrapHeight = wrapHeight;
- }
}
import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
-import jalview.xml.binding.sifts.Entry.ListDB.Db;
import java.io.File;
import java.io.FileInputStream;
-import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import java.util.TreeMap;
import java.util.zip.GZIPInputStream;
import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
-import javax.xml.stream.FactoryConfigurationError;
import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamReader;
import MCview.Atom;
import MCview.PDBChain;
-import MCview.PDBfile;
public class SiftsClient implements SiftsClientI
{
private String structId;
- private String segStartEnd;
-
private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
private static final int BUFFER_SIZE = 4096;
private static final int PDB_ATOM_POS = 1;
- private static final String NOT_FOUND = "Not_Found";
-
private static final String NOT_OBSERVED = "Not_Observed";
- private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
private final static String NEWLINE = System.lineSeparator();
private HashSet<String> curDBRefAccessionIdsString;
- public enum CoordinateSys
+ private enum CoordinateSys
{
UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
private String name;
}
};
- public enum ResidueDetailType
+ private enum ResidueDetailType
{
NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE(
"codeSecondaryStructure"), ANNOTATION("Annotation");
siftsEntry = parseSIFTs(siftsFile);
}
- /**
- * Construct an instance of SiftsClient using the supplied SIFTs file. Note:
- * The SIFTs file should correspond to the PDB Id in PDBfile instance
- *
- * @param pdbId
- * @param siftsFile
- * @throws SiftsException
- * @throws Exception
- */
- public SiftsClient(PDBfile pdb, File siftsFile) throws SiftsException
- {
- this.pdb = pdb;
- this.pdbId = pdb.getId();
- siftsEntry = parseSIFTs(siftsFile);
- }
/**
* Parse the given SIFTs File and return a JAXB POJO of parsed data
.createXMLStreamReader(gzis);
Unmarshaller um = jc.createUnmarshaller();
return (Entry) um.unmarshal(streamReader);
- } catch (JAXBException e)
- {
- e.printStackTrace();
- throw new SiftsException(e.getMessage());
- } catch (FileNotFoundException e)
- {
- e.printStackTrace();
- throw new SiftsException(e.getMessage());
- } catch (XMLStreamException e)
- {
- e.printStackTrace();
- throw new SiftsException(e.getMessage());
- } catch (FactoryConfigurationError e)
- {
- e.printStackTrace();
- throw new SiftsException(e.getMessage());
- } catch (IOException e)
+ } catch (Exception e)
{
e.printStackTrace();
throw new SiftsException(e.getMessage());
*/
public static File getSiftsFile(String pdbId) throws SiftsException
{
- File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase() + ".xml.gz");
+ String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
+ + pdbId.toLowerCase() + ".xml.gz";
+ File siftsFile = new File(siftsFileName);
if (siftsFile.exists())
{
// The line below is required for unit testing... don't comment it out!!!
if (isFileOlderThanThreshold(siftsFile,
SiftsSettings.getCacheThresholdInDays()))
{
- // System.out.println("Downloaded file is out of date, hence re-downloading...");
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ File oldSiftsFile = new File(siftsFileName + "_old");
+ siftsFile.renameTo(oldSiftsFile);
+ try
+ {
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ oldSiftsFile.delete();
+ return siftsFile;
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ oldSiftsFile.renameTo(siftsFile);
+ return new File(siftsFileName);
+ }
}
- return siftsFile;
}
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ try
+ {
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ } catch (IOException e)
+ {
+ throw new SiftsException(e.getMessage());
+ }
return siftsFile;
}
* @param pdbId
* @return downloaded SIFTs XML file
* @throws SiftsException
+ * @throws IOException
*/
- public static File downloadSiftsFile(String pdbId) throws SiftsException
+ public static File downloadSiftsFile(String pdbId) throws SiftsException,
+ IOException
{
if (pdbId.contains(".cif"))
{
{
siftsDownloadDir.mkdirs();
}
- try
- {
// System.out.println(">> Download ftp url : " + siftsFileFTPURL);
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
outputStream.close();
inputStream.close();
// System.out.println(">>> File downloaded : " + downloadedSiftsFile);
- } catch (IOException ex)
- {
- throw new SiftsException(ex.getMessage());
- }
return new File(downloadedSiftsFile);
}
DBRefEntry[] dbRefs = seq.getDBRefs();
if (dbRefs == null || dbRefs.length < 1)
{
- throw new SiftsException("Could not get source DB Ref");
+ throw new SiftsException(
+ "Source DBRef could not be determined. DBRefs might not have been retrieved.");
}
for (DBRefEntryI dbRef : dbRefs)
&& (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef
.getSource().equalsIgnoreCase(DBRefSource.PDB)))
{
+ seq.setSourceDBRef(dbRef);
return dbRef;
}
}
* - DBRefEntry to validate
* @return true validation is successful otherwise false is returned.
*/
- private boolean isValidDBRefEntry(DBRefEntryI entry)
+ boolean isValidDBRefEntry(DBRefEntryI entry)
{
return entry != null && entry.getAccessionId() != null
&& isFoundInSiftsEntry(entry.getAccessionId());
.getMapRegion();
for (MapRegion mapRegion : mapRegions)
{
- accessions.add(mapRegion.getDb().getDbAccessionId());
+ accessions
+ .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
}
}
}
public HashMap<Integer, int[]> getGreedyMapping(String entityId,
SequenceI seq, java.io.PrintStream os) throws SiftsException
{
- ArrayList<Integer> omitNonObserved = new ArrayList<Integer>();
+ List<Integer> omitNonObserved = new ArrayList<Integer>();
int nonObservedShiftIndex = 0;
// System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
jalview.util.Comparison.GapChars, seq.getSequenceAsString());
HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
DBRefEntryI sourceDBRef = seq.getSourceDBRef();
- if (sourceDBRef == null)
- {
- sourceDBRef = getValidSourceDBRef(seq);
- // TODO ensure sequence start/end is in the same coordinate system and
- // consistent with the choosen sourceDBRef
- }
+ sourceDBRef = getValidSourceDBRef(seq);
+ // TODO ensure sequence start/end is in the same coordinate system and
+ // consistent with the choosen sourceDBRef
// set sequence coordinate system - default value is UniProt
if (sourceDBRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
List<Segment> segments = entity.getSegment();
+ SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
+ omitNonObserved, nonObservedShiftIndex);
+ processSegments(segments, shp);
+ try
+ {
+ populateAtomPositions(entityId, mapping);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ if (seqCoordSys == CoordinateSys.UNIPROT)
+ {
+ padWithGaps(resNumMap, omitNonObserved);
+ }
+ int seqStart = UNASSIGNED;
+ int seqEnd = UNASSIGNED;
+ int pdbStart = UNASSIGNED;
+ int pdbEnd = UNASSIGNED;
+
+ Integer[] keys = mapping.keySet().toArray(new Integer[0]);
+ Arrays.sort(keys);
+ if (keys.length < 1)
+ {
+ throw new SiftsException(">>> Empty SIFTS mapping generated!!");
+ }
+ seqStart = keys[0];
+ seqEnd = keys[keys.length - 1];
+
+ String matchedSeq = originalSeq;
+ if (seqStart != UNASSIGNED)
+ {
+ pdbStart = mapping.get(seqStart)[PDB_RES_POS];
+ pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
+ int orignalSeqStart = seq.getStart();
+ if (orignalSeqStart >= 1)
+ {
+ int subSeqStart = (seqStart >= orignalSeqStart) ? seqStart
+ - orignalSeqStart : 0;
+ int subSeqEnd = seqEnd - (orignalSeqStart - 1);
+ subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length()
+ : subSeqEnd;
+ matchedSeq = originalSeq.substring(subSeqStart, subSeqEnd);
+ }
+ else
+ {
+ matchedSeq = originalSeq.substring(1, originalSeq.length());
+ }
+ }
+
+ StringBuilder targetStrucSeqs = new StringBuilder();
+ for (String res : resNumMap.values())
+ {
+ targetStrucSeqs.append(res);
+ }
+
+ if (os != null)
+ {
+ MappingOutputPojo mop = new MappingOutputPojo();
+ mop.setSeqStart(pdbStart);
+ mop.setSeqEnd(pdbEnd);
+ mop.setSeqName(seq.getName());
+ mop.setSeqResidue(matchedSeq);
+
+ mop.setStrStart(seqStart);
+ mop.setStrEnd(seqEnd);
+ mop.setStrName(structId);
+ mop.setStrResidue(targetStrucSeqs.toString());
+
+ mop.setType("pep");
+ os.print(getMappingOutput(mop).toString());
+ os.println();
+ }
+ return mapping;
+ }
+
+ void processSegments(List<Segment> segments, SegmentHelperPojo shp)
+ {
+ SequenceI seq = shp.getSeq();
+ HashMap<Integer, int[]> mapping = shp.getMapping();
+ TreeMap<Integer, String> resNumMap = shp.getResNumMap();
+ List<Integer> omitNonObserved = shp.getOmitNonObserved();
+ int nonObservedShiftIndex = shp.getNonObservedShiftIndex();
for (Segment segment : segments)
{
- segStartEnd = segment.getStart() + " - " + segment.getEnd();
- // System.out.println("Mapping segments : " + segment.getSegId() + "\\"
+ // System.out.println("Mapping segments : " + segment.getSegId() + "\\"s
// + segStartEnd);
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
}
}
}
- try
- {
- populateAtomPositions(entityId, mapping);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- if (seqCoordSys == CoordinateSys.UNIPROT)
- {
- padWithGaps(resNumMap, omitNonObserved);
- }
- int seqStart = UNASSIGNED;
- int seqEnd = UNASSIGNED;
- int pdbStart = UNASSIGNED;
- int pdbEnd = UNASSIGNED;
-
- Integer[] keys = mapping.keySet().toArray(new Integer[0]);
- Arrays.sort(keys);
- if (keys.length < 1)
- {
- throw new SiftsException(">>> Empty SIFTS mapping generated!!");
- }
- seqStart = keys[0];
- seqEnd = keys[keys.length - 1];
-
- String matchedSeq = originalSeq;
- if (seqStart != UNASSIGNED)
- {
- pdbStart = mapping.get(seqStart)[PDB_RES_POS];
- pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
- int orignalSeqStart = seq.getStart();
- if (orignalSeqStart >= 1)
- {
- int subSeqStart = (seqStart >= orignalSeqStart) ? seqStart
- - orignalSeqStart : 0;
- int subSeqEnd = seqEnd - (orignalSeqStart - 1);
- subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length()
- : subSeqEnd;
- matchedSeq = originalSeq.substring(subSeqStart, subSeqEnd);
- }
- else
- {
- matchedSeq = originalSeq.substring(1, originalSeq.length());
- }
- }
-
- StringBuilder targetStrucSeqs = new StringBuilder();
- for (String res : resNumMap.values())
- {
- targetStrucSeqs.append(res);
- }
-
- if (os != null)
- {
- MappingOutputPojo mop = new MappingOutputPojo();
- mop.setSeqStart(pdbStart);
- mop.setSeqEnd(pdbEnd);
- mop.setSeqName(seq.getName());
- mop.setSeqResidue(matchedSeq);
-
- mop.setStrStart(seqStart);
- mop.setStrEnd(seqEnd);
- mop.setStrName(structId);
- mop.setStrResidue(targetStrucSeqs.toString());
-
- mop.setType("pep");
- os.print(getMappingOutput(mop).toString());
- }
- return mapping;
}
-
/**
*
* @param chainId
* Two dimension array of residue index versus atom position
* @throws IllegalArgumentException
* Thrown if chainId or mapping is null
+ * @throws SiftsException
*/
- void populateAtomPositions(String chainId,
- HashMap<Integer, int[]> mapping) throws IllegalArgumentException
+ void populateAtomPositions(String chainId, Map<Integer, int[]> mapping)
+ throws IllegalArgumentException, SiftsException
{
try
{
map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
}
}
+ } catch (NullPointerException e)
+ {
+ throw new SiftsException(e.getMessage());
} catch (Exception e)
{
- e.printStackTrace();
+ throw new SiftsException(e.getMessage());
}
}
*/
private boolean isResidueObserved(Residue residue)
{
- HashSet<String> annotations = getResidueAnnotaitons(residue,
+ Set<String> annotations = getResidueAnnotaitons(residue,
ResidueDetailType.ANNOTATION);
if (annotations == null || annotations.isEmpty())
{
* @param type
* @return
*/
- private HashSet<String> getResidueAnnotaitons(Residue residue,
+ private Set<String> getResidueAnnotaitons(Residue residue,
ResidueDetailType type)
{
HashSet<String> foundAnnotations = new HashSet<String>();
private boolean isFoundInSiftsEntry(String accessionId)
{
+ Set<String> siftsDBRefs = getAllMappingAccession();
return accessionId != null
- && getAllMappingAccession().contains(accessionId);
+ && siftsDBRefs.contains(accessionId.toLowerCase());
}
/**
*
* @param resNumMap
*/
- void padWithGaps(TreeMap<Integer, String> resNumMap,
- ArrayList<Integer> omitNonObserved)
+ void padWithGaps(Map<Integer, String> resNumMap,
+ List<Integer> omitNonObserved)
{
if (resNumMap == null || resNumMap.isEmpty())
{
return;
}
Integer[] keys = resNumMap.keySet().toArray(new Integer[0]);
- Arrays.sort(keys);
+ // Arrays.sort(keys);
int firstIndex = keys[0];
int lastIndex = keys[keys.length - 1];
// System.out.println("Min value " + firstIndex);
@Override
public Entity getEntityById(String id) throws SiftsException
{
- // Sometimes SIFTS mappings are wrongly swapped between different chains of
- // a PDB entry. This results to wrong mappings being generated. The boolean
- // flag 'isGetEntityIdDirectly, determines whether an entity to process is
- // determined by a greedy heuristic search or by just matching the Chain Id
- // directly against the entity Id tag. Setting the default value to 'false'
- // utilise the heuristic search which always produces correct mappings but
- // less optimised processing, where as changing the value to 'true'
- // optimises performance but might result to incorrect mapping in some cases
- // where SIFTS mappings are wrongly swapped between different chains.
- boolean isGetEntityIdDirectly = false;
- if (isGetEntityIdDirectly)
- {
- List<Entity> entities = siftsEntry.getEntity();
- for (Entity entity : entities)
- {
- if (!entity.getEntityId().equalsIgnoreCase(id))
- {
- continue;
- }
- return entity;
- }
- }
+ // Determines an entity to process by performing a heuristic matching of all
+ // Entities with the given chainId and choosing the best matching Entity
Entity entity = getEntityByMostOptimalMatchedId(id);
if (entity != null)
{
return null;
}
- public class SiftsEntitySortPojo implements
+ private class SiftsEntitySortPojo implements
Comparable<SiftsEntitySortPojo>
{
public String entityId;
}
}
- @Override
- public String[] getEntryDBs()
+ private class SegmentHelperPojo
{
- System.out.println("\nListing DB entries...");
- List<String> availDbs = new ArrayList<String>();
- List<Db> dbs = siftsEntry.getListDB().getDb();
- for (Db db : dbs)
+ private SequenceI seq;
+
+ private HashMap<Integer, int[]> mapping;
+
+ private TreeMap<Integer, String> resNumMap;
+
+ private List<Integer> omitNonObserved;
+
+ private int nonObservedShiftIndex;
+
+ public SegmentHelperPojo(SequenceI seq,
+ HashMap<Integer, int[]> mapping,
+ TreeMap<Integer, String> resNumMap,
+ List<Integer> omitNonObserved, int nonObservedShiftIndex)
+ {
+ setSeq(seq);
+ setMapping(mapping);
+ setResNumMap(resNumMap);
+ setOmitNonObserved(omitNonObserved);
+ setNonObservedShiftIndex(nonObservedShiftIndex);
+ }
+
+ public SequenceI getSeq()
+ {
+ return seq;
+ }
+
+ public void setSeq(SequenceI seq)
+ {
+ this.seq = seq;
+ }
+
+ public HashMap<Integer, int[]> getMapping()
+ {
+ return mapping;
+ }
+
+ public void setMapping(HashMap<Integer, int[]> mapping)
+ {
+ this.mapping = mapping;
+ }
+
+ public TreeMap<Integer, String> getResNumMap()
+ {
+ return resNumMap;
+ }
+
+ public void setResNumMap(TreeMap<Integer, String> resNumMap)
+ {
+ this.resNumMap = resNumMap;
+ }
+
+ public List<Integer> getOmitNonObserved()
+ {
+ return omitNonObserved;
+ }
+
+ public void setOmitNonObserved(List<Integer> omitNonObserved)
{
- availDbs.add(db.getDbSource());
- System.out.println(db.getDbSource() + " | " + db.getDbCoordSys());
+ this.omitNonObserved = omitNonObserved;
+ }
+
+ public int getNonObservedShiftIndex()
+ {
+ return nonObservedShiftIndex;
+ }
+
+ public void setNonObservedShiftIndex(int nonObservedShiftIndex)
+ {
+ this.nonObservedShiftIndex = nonObservedShiftIndex;
}
- return availDbs.toArray(new String[0]);
}
@Override
output.append("Length of alignment = " + seqRes.length()).append(
NEWLINE);
output.append(new Format("Percentage ID = %2.2f").form(pid));
- output.append(NEWLINE);
return output;
}
}
@Override
- public String getDbEvidence()
- {
- return siftsEntry.getDbEvidence();
- }
-
- @Override
public String getDbSource()
{
return siftsEntry.getDbSource();
SequenceFeature sf = sfs[0];
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
- assertEquals("K->E", sf.getDescription());
+ assertEquals("p.Lys1Glu", sf.getDescription());
assertEquals("var1.125A>G", sf.getValue("ID"));
assertNull(sf.getValue("clinical_significance"));
assertEquals("ID=var1.125A>G", sf.getAttributes());
assertEquals(1, sf.links.size());
// link to variation is urlencoded
assertEquals(
- "K->E var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
+ "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
sf.links.get(0));
+ assertEquals("Jalview", sf.getFeatureGroup());
sf = sfs[1];
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
- assertEquals("K->Q", sf.getDescription());
+ assertEquals("p.Lys1Gln", sf.getDescription());
assertEquals("var2", sf.getValue("ID"));
assertEquals("Dodgy", sf.getValue("clinical_significance"));
assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
- "K->Q var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
+ "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
sf.links.get(0));
+ assertEquals("Jalview", sf.getFeatureGroup());
sf = sfs[2];
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
- assertEquals("K->N", sf.getDescription());
+ assertEquals("p.Lys1Asn", sf.getDescription());
assertEquals("var4", sf.getValue("ID"));
assertEquals("Benign", sf.getValue("clinical_significance"));
assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
- "K->N var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+ "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
sf.links.get(0));
+ assertEquals("Jalview", sf.getFeatureGroup());
sf = sfs[3];
assertEquals(3, sf.getBegin());
assertEquals(3, sf.getEnd());
- assertEquals("P->H", sf.getDescription());
+ assertEquals("p.Pro3His", sf.getDescription());
assertEquals("var6", sf.getValue("ID"));
assertEquals("Good", sf.getValue("clinical_significance"));
assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
- "P->H var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
sf.links.get(0));
// var5 generates two distinct protein variant features
+ assertEquals("Jalview", sf.getFeatureGroup());
sf = sfs[4];
assertEquals(3, sf.getBegin());
assertEquals(3, sf.getEnd());
- assertEquals("P->R", sf.getDescription());
+ assertEquals("p.Pro3Arg", sf.getDescription());
assertEquals("var6", sf.getValue("ID"));
assertEquals("Good", sf.getValue("clinical_significance"));
assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
- "P->R var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
sf.links.get(0));
+ assertEquals("Jalview", sf.getFeatureGroup());
}
/**
assertTrue(testee.equals("A12345,"));
assertTrue(testee.equals("A12345?"));
assertTrue(testee.equals("A12345_"));
+ /*
+ * case insensitive matching
+ */
+ assertTrue(testee.equals("a12345"));
/*
* matcher name = target name + word separator...
assertTrue(testee.equals("A12345"));
/*
+ * case insensitive matching
+ */
+ assertTrue(testee.equals("a12345"));
+
+ /*
* miscellaneous failing cases
*/
testee = sequenceIdMatcher.new SeqIdName("A12345");
assertFalse(testee.equals((Object) null));
assertFalse(testee.equals(""));
- assertFalse(testee.equals("a12345"));
assertFalse(testee.equals("A12346|A12345"));
+ /*
+ * case insensitive matching
+ */
+ assertTrue(testee.equals("a12345"));
testee = sequenceIdMatcher.new SeqIdName("A12345?B23456");
assertFalse(testee.equals("B23456"));
testee = sequenceIdMatcher.new SeqIdName("A12345<");
assertFalse(testee.equals("A12345?"));
assertTrue(testee.equals("A12345<")); // bug? inconsistent
+ /*
+ * case insensitive matching
+ */
+ assertTrue(testee.equals("a12345"));
}
}
--- /dev/null
+package jalview.bin;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import org.testng.annotations.Test;
+
+public class ArgsParserTest
+{
+ @Test(groups = "Functional")
+ public void testGetValue()
+ {
+ ArgsParser ap = new ArgsParser(new String[] { "-name", "Henry", "-job",
+ "Tester" });
+ assertEquals(4, ap.getSize());
+ assertNull(ap.getValue("rubbish"));
+ assertEquals("Tester", ap.getValue("job"));
+ // call to getValue removes the argument and its value
+ assertEquals(2, ap.getSize());
+ assertNull(ap.getValue("job"));
+ assertFalse(ap.contains("job"));
+ assertFalse(ap.contains("Tester"));
+
+ assertEquals("Henry", ap.getValue("name"));
+ assertEquals(0, ap.getSize());
+ assertNull(ap.getValue("name"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetValue_decoded()
+ {
+ ArgsParser ap = new ArgsParser(new String[] { "-name%241", "Henry",
+ "-job", "Test%203%2a" });
+ // parameter value is decoded
+ assertEquals("Test 3*", ap.getValue("job", true));
+ // parameter name is not decoded
+ assertNull(ap.getValue("name$1", true));
+ assertEquals("Henry", ap.getValue("name%241", true));
+ }
+
+ @Test(groups = "Functional")
+ public void testNextValue()
+ {
+ ArgsParser ap = new ArgsParser(new String[] { "-name", "Henry", "-job",
+ "Tester" });
+ assertEquals("name", ap.nextValue());
+ assertEquals("Henry", ap.nextValue());
+ assertEquals("job", ap.nextValue());
+ assertEquals("Tester", ap.nextValue());
+ }
+
+ @Test(groups = "Functional")
+ public void testContains()
+ {
+ ArgsParser ap = new ArgsParser(new String[] { "-name", "Henry", "-job",
+ "Tester" });
+ assertFalse(ap.contains("Susan"));
+ assertFalse(ap.contains("-name"));
+ assertTrue(ap.contains("name"));
+ // testing for contains removes the argument
+ assertFalse(ap.contains("name"));
+ }
+}
}
+ @Test(groups={"Functional"})
+ public void testLocateVisibleBoundsPathologicals()
+ {
+ // test some pathological cases we missed
+ AlignmentI al = new Alignment(new SequenceI[] { new Sequence("refseqGaptest","KTDVTI----------NFI-----G----L")});
+ ColumnSelection cs = new ColumnSelection();
+ cs.hideInsertionsFor(al.getSequenceAt(0));
+ assertEquals(
+ "G",
+ ""
+ + al.getSequenceAt(0).getCharAt(
+ cs.adjustForHiddenColumns(9)));
+
+
+ }
@Test(groups = { "Functional" })
public void testHideColumns()
{
cs.addElement(0);
assertEquals(0, cs.getMin());
}
+
+ @Test(groups = { "Functional" })
+ public void testEquals()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(0);
+ cs.addElement(513);
+ cs.addElement(1);
+ cs.hideColumns(3);
+ cs.hideColumns(7);
+ cs.hideColumns(5,9);
+
+ // same selections added in a different order
+ ColumnSelection cs2 = new ColumnSelection();
+ cs2.addElement(1);
+ cs2.addElement(513);
+ cs2.addElement(0);
+
+ // with no hidden columns
+ assertFalse(cs.equals(cs2));
+ assertFalse(cs2.equals(cs));
+
+ // with hidden columns added in a different order
+ cs2.hideColumns(6, 9);
+ cs2.hideColumns(5, 8);
+ cs2.hideColumns(3);
+
+ assertTrue(cs.equals(cs2));
+ assertTrue(cs.equals(cs));
+ assertTrue(cs2.equals(cs));
+ assertTrue(cs2.equals(cs2));
+
+ cs2.addElement(12);
+ assertFalse(cs.equals(cs2));
+ assertFalse(cs2.equals(cs));
+
+ cs2.removeElement(12);
+ assertTrue(cs.equals(cs2));
+
+ cs2.hideColumns(88);
+ assertFalse(cs.equals(cs2));
+ /*
+ * unhiding a column adds it to selection!
+ */
+ cs2.revealHiddenColumns(88);
+ assertFalse(cs.equals(cs2));
+ cs.addElement(88);
+ assertTrue(cs.equals(cs2));
+ }
}
*/
package jalview.datamodel;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.util.MapList;
assertTrue(ref1.equalRef(ref2));
assertTrue(ref2.equalRef(ref1));
}
+
+ /**
+ * Tests for the method that may update a DBRefEntry from another with a
+ * mapping or 'real' version
+ */
+ @Test(groups = { "Functional" })
+ public void testUpdateFrom()
+ {
+ DBRefEntry ref1 = new DBRefEntry("UNIPROT", "1", "V71633");
+
+ assertFalse(ref1.updateFrom(null));
+
+ /*
+ * equivalent other dbref
+ */
+ DBRefEntry ref2 = new DBRefEntry("uniprot", "1", "v71633");
+ assertTrue(ref1.updateFrom(ref2));
+ assertEquals("UNIPROT", ref1.getSource()); // unchanged
+ assertEquals("V71633", ref1.getAccessionId()); // unchanged
+
+ /*
+ * ref1 has no mapping, acquires mapping from ref2
+ */
+ Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
+ 1, 1 }, 3, 1));
+ ref2.setMap(map);
+ assertTrue(ref1.updateFrom(ref2));
+ assertSame(map, ref1.getMap()); // null mapping updated
+
+ /*
+ * ref1 has a mapping, does not acquire mapping from ref2
+ */
+ ref2.setMap(new Mapping(map));
+ assertTrue(ref1.updateFrom(ref2));
+ assertSame(map, ref1.getMap()); // non-null mapping not updated
+
+ /*
+ * ref2 has a different source, accession or version
+ */
+ ref2.setSource("pdb");
+ assertFalse(ref1.updateFrom(ref2));
+ ref2.setSource(ref1.getSource());
+ ref2.setAccessionId("P12345");
+ assertFalse(ref1.updateFrom(ref2));
+ ref2.setAccessionId(ref1.getAccessionId());
+ ref1.setVersion("2");
+ assertFalse(ref1.updateFrom(ref2));
+
+ /*
+ * a non-null version supersedes "0" or "source:0"
+ */
+ ref2.setVersion(null);
+ assertFalse(ref1.updateFrom(ref2));
+ assertEquals("2", ref1.getVersion());
+ ref2.setVersion("3");
+ ref1.setVersion("0");
+ assertTrue(ref1.updateFrom(ref2));
+ assertEquals("3", ref1.getVersion());
+ ref1.setVersion("UNIPROT:0");
+ assertTrue(ref1.updateFrom(ref2));
+ assertEquals("3", ref1.getVersion());
+
+ /*
+ * version "source:n" with n>0 is not superseded
+ */
+ ref1.setVersion("UNIPROT:1");
+ assertFalse(ref1.updateFrom(ref2));
+ assertEquals("UNIPROT:1", ref1.getVersion());
+
+ /*
+ * version "10" is not superseded
+ */
+ ref1.setVersion("10");
+ assertFalse(ref1.updateFrom(ref2));
+ assertEquals("10", ref1.getVersion());
+ }
}
--- /dev/null
+package jalview.datamodel;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+
+import jalview.gui.AlignViewport;
+
+import java.util.List;
+
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+@Test(singleThreaded = true)
+public class HiddenSequencesTest
+{
+ static int SEQ_COUNT = 10;
+
+ SequenceI[] seqs;
+
+ /**
+ * Set up an alignment of 10 sequences
+ */
+ @BeforeTest(alwaysRun = true)
+ public void setUp()
+ {
+ seqs = new SequenceI[SEQ_COUNT];
+ for (int i = 0; i < SEQ_COUNT; i++)
+ {
+ // sequence lengths are 1, 2, ... 10
+ seqs[i] = new Sequence("Seq" + i, "abcdefghijk".substring(0, i + 1));
+ }
+ }
+
+ /**
+ * Test the method that converts sequence alignment index to what it would be
+ * if all sequences were unhidden
+ */
+ @Test(groups = "Functional")
+ public void testAdjustForHiddenSeqs()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ for (int i = 0; i < SEQ_COUNT; i++)
+ {
+ assertEquals(i, hs.adjustForHiddenSeqs(i));
+ }
+
+ // hide seq1 and seq5 and seq6
+ hs.hideSequence(seqs[1]);
+ hs.hideSequence(seqs[5]);
+ hs.hideSequence(seqs[6]);
+
+ /*
+ * alignment is now seq0/2/3/4/7/8/9
+ */
+ assertEquals(7, al.getHeight());
+ assertEquals(0, hs.adjustForHiddenSeqs(0));
+ assertEquals(2, hs.adjustForHiddenSeqs(1));
+ assertEquals(3, hs.adjustForHiddenSeqs(2));
+ assertEquals(4, hs.adjustForHiddenSeqs(3));
+ assertEquals(7, hs.adjustForHiddenSeqs(4));
+ assertEquals(8, hs.adjustForHiddenSeqs(5));
+ assertEquals(9, hs.adjustForHiddenSeqs(6));
+ }
+
+ /**
+ * Test the method that increments the internal array size if a sequence is
+ * added to the alignment (ugh this should not be exposed to the light of day)
+ */
+ @Test(groups = "Functional")
+ public void testAdjustHeightSequenceAdded()
+ {
+ AlignmentI al = new Alignment(seqs);
+ assertEquals(SEQ_COUNT, al.getHeight());
+
+ HiddenSequences hs = al.getHiddenSequences();
+ // initially does nothing
+ hs.adjustHeightSequenceAdded();
+ assertNull(hs.hiddenSequences);
+
+ // hide one sequence
+ hs.hideSequence(seqs[3]);
+ assertEquals(1, hs.getSize());
+ assertEquals(SEQ_COUNT - 1, al.getHeight());
+ assertEquals(SEQ_COUNT, hs.hiddenSequences.length);
+
+ /*
+ * add a sequence to the alignment
+ * - the safe way to call hs.adjustHeightSequenceAdded!
+ * (implementation depends on alignment height having
+ * been already updated for the added sequence)
+ */
+ al.addSequence(new Sequence("a", "b"));
+ assertEquals(1, hs.getSize());
+ assertEquals(SEQ_COUNT, al.getHeight());
+ assertEquals(SEQ_COUNT + 1, hs.hiddenSequences.length);
+ }
+
+ /**
+ * Test the method that decrements the internal array size if a sequence is
+ * deleted from the alignment (ugh this should not be exposed to the light of
+ * day)
+ */
+ @Test(groups = "Functional")
+ public void testAdjustHeightSequenceDeleted()
+ {
+ AlignmentI al = new Alignment(seqs);
+ assertEquals(SEQ_COUNT, al.getHeight());
+
+ HiddenSequences hs = al.getHiddenSequences();
+ // initially does nothing
+ hs.adjustHeightSequenceAdded();
+ assertNull(hs.hiddenSequences);
+
+ // hide two sequences
+ hs.hideSequence(seqs[3]);
+ hs.hideSequence(seqs[5]);
+ assertEquals(2, hs.getSize());
+ assertTrue(hs.isHidden(seqs[3]));
+ assertTrue(hs.isHidden(seqs[5]));
+ assertEquals(SEQ_COUNT - 2, al.getHeight());
+ assertEquals(SEQ_COUNT, hs.hiddenSequences.length);
+
+ /*
+ * delete a visible sequence from the alignment
+ * - the safe way to call hs.adjustHeightSequenceDeleted!
+ * (implementation depends on alignment height having
+ * been already updated for the removed sequence)
+ */
+ al.deleteSequence(seqs[2]);
+ assertEquals(2, hs.getSize());
+ // the visible alignment is unchanged:
+ assertEquals(SEQ_COUNT - 3, al.getHeight());
+ // sequences array size has decremented:
+ assertEquals(SEQ_COUNT - 1, hs.hiddenSequences.length);
+ }
+
+ /**
+ * Test the method that converts a 'full alignment' sequence index into the
+ * equivalent in the alignment with sequences hidden
+ */
+ @Test(groups = "Functional")
+ public void testFindIndexWithoutHiddenSeqs()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ for (int i = 0; i < SEQ_COUNT; i++)
+ {
+ assertEquals(i, hs.findIndexWithoutHiddenSeqs(i));
+ }
+
+ // hide seq1 and seq5 and seq6
+ hs.hideSequence(seqs[1]);
+ hs.hideSequence(seqs[5]);
+ hs.hideSequence(seqs[6]);
+
+ /*
+ * alignment is now seq0/2/3/4/7/8/9
+ */
+ assertEquals(7, al.getHeight());
+ assertEquals(0, hs.findIndexWithoutHiddenSeqs(0));
+ assertEquals(0, hs.findIndexWithoutHiddenSeqs(1));
+ assertEquals(1, hs.findIndexWithoutHiddenSeqs(2));
+ assertEquals(2, hs.findIndexWithoutHiddenSeqs(3));
+ assertEquals(3, hs.findIndexWithoutHiddenSeqs(4));
+ assertEquals(3, hs.findIndexWithoutHiddenSeqs(5));
+ assertEquals(3, hs.findIndexWithoutHiddenSeqs(6));
+ assertEquals(4, hs.findIndexWithoutHiddenSeqs(7));
+ assertEquals(5, hs.findIndexWithoutHiddenSeqs(8));
+ assertEquals(6, hs.findIndexWithoutHiddenSeqs(9));
+ }
+
+ /**
+ * Test the method that reconstructs (sort of) the full alignment including
+ * hidden sequences
+ */
+ @Test(groups = "Functional")
+ public void testGetFullAlignment()
+ {
+ AlignmentI al = new Alignment(seqs);
+ assertArrayEquals(seqs, al.getSequencesArray());
+ al.setProperty("a", "b");
+ al.addAnnotation(new AlignmentAnnotation("ann", "label", 12f));
+ al.setSeqrep(seqs[4]);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(seqs[8], false);
+ al.addGroup(sg);
+ ((Alignment) al).hasRNAStructure = true;
+
+ HiddenSequences hs = al.getHiddenSequences();
+ AlignmentI al2 = hs.getFullAlignment();
+ // new alignment but with original sequences
+ assertNotSame(al, al2);
+ assertArrayEquals(al.getSequencesArray(), al2.getSequencesArray());
+
+ hs.hideSequence(seqs[4]);
+ hs.hideSequence(seqs[9]);
+ al2 = hs.getFullAlignment();
+ assertNotSame(al, al2);
+ assertArrayEquals(seqs, al2.getSequencesArray());
+ assertNotNull(al2.getProperties());
+ assertSame(al.getProperties(), al2.getProperties());
+ assertNotNull(al2.getAlignmentAnnotation());
+ assertSame(al.getAlignmentAnnotation(), al2.getAlignmentAnnotation());
+ assertSame(seqs[4], al2.getSeqrep());
+ assertNotNull(al2.getGroups());
+ assertSame(al.getGroups(), al2.getGroups());
+ assertTrue(al2.hasRNAStructure());
+ }
+
+ /**
+ * Test the method that returns the hidden sequence at a given index in the
+ * full alignment
+ *
+ * @return either the sequence (if hidden) or null (if not hidden)
+ */
+ @Test(groups = "Functional")
+ public void testGetHiddenSequence()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ assertNull(hs.getHiddenSequence(0));
+ hs.hideSequence(seqs[3]);
+ assertSame(seqs[3], hs.getHiddenSequence(3));
+ assertNull(hs.getHiddenSequence(2));
+ assertNull(hs.getHiddenSequence(4));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSize()
+ {
+ }
+
+ @Test(groups = "Functional")
+ public void testGetWidth()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ assertEquals(0, hs.getWidth());
+ hs.hideSequence(seqs[6]);
+ hs.hideSequence(seqs[8]);
+ assertEquals(9, hs.getWidth());
+ }
+
+ /**
+ * Test the method that adds a sequence to the hidden sequences and deletes it
+ * from the alignment, and its converse
+ */
+ @Test(groups = "Functional")
+ public void testHideShowSequence()
+ {
+ AlignmentI al = new Alignment(seqs);
+ assertTrue(al.getSequences().contains(seqs[1]));
+ HiddenSequences hs = al.getHiddenSequences();
+ assertEquals(0, hs.getSize());
+ assertEquals(10, al.getHeight());
+
+ /*
+ * hide the second sequence in the alignment
+ */
+ hs.hideSequence(seqs[1]);
+ assertFalse(hs.isHidden(seqs[0]));
+ assertTrue(hs.isHidden(seqs[1]));
+ assertFalse(al.getSequences().contains(seqs[1]));
+ assertEquals(1, hs.getSize());
+ assertEquals(9, al.getHeight());
+ assertSame(seqs[2], al.getSequenceAt(1));
+
+ /*
+ * hide what is now the second sequence in the alignment
+ */
+ hs.hideSequence(seqs[2]);
+ assertFalse(hs.isHidden(seqs[0]));
+ assertTrue(hs.isHidden(seqs[1]));
+ assertTrue(hs.isHidden(seqs[2]));
+ assertFalse(al.getSequences().contains(seqs[1]));
+ assertFalse(al.getSequences().contains(seqs[2]));
+ assertEquals(2, hs.getSize());
+ assertEquals(8, al.getHeight());
+
+ /*
+ * perform 'reveal' on what is now the second sequence in the alignment
+ * this should unhide the two sequences that precede it
+ */
+ List<SequenceI> revealed = hs.showSequence(1, null);
+ assertEquals(2, revealed.size());
+ assertTrue(revealed.contains(seqs[1]));
+ assertTrue(revealed.contains(seqs[2]));
+ assertEquals(0, hs.getSize());
+ assertEquals(10, al.getHeight());
+ }
+
+ @Test(groups = "Functional")
+ public void testIsHidden()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ hs.hideSequence(seqs[7]);
+ hs.hideSequence(seqs[4]);
+ assertTrue(hs.isHidden(seqs[4]));
+ assertFalse(hs.isHidden(seqs[5]));
+ assertFalse(hs.isHidden(seqs[6]));
+ assertTrue(hs.isHidden(seqs[7]));
+ assertFalse(hs.isHidden(null));
+ assertFalse(hs.isHidden(new Sequence("", "")));
+ }
+
+ /**
+ * Test hiding and unhiding a group with a representative sequence. The
+ * representative should be left visible when the group is hidden, and
+ * included in the selected group when it is unhidden.
+ */
+ @Test(groups = "Functional")
+ public void testHideShowSequence_withHiddenRepSequence()
+ {
+ AlignmentI al = new Alignment(seqs);
+
+ /*
+ * represent seqs 2-4 with seq3
+ * this hides seq2 and seq4 but not seq3
+ */
+ AlignViewport av = new AlignViewport(al);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(seqs[1], false);
+ sg.addSequence(seqs[2], false);
+ sg.addSequence(seqs[3], false);
+ av.setSelectionGroup(sg);
+
+ /*
+ * hiding group with reference sequence is done via AlignViewport
+ */
+ av.hideSequences(seqs[2], true);
+ HiddenSequences hs = al.getHiddenSequences();
+ assertEquals(2, hs.getSize());
+ assertTrue(hs.isHidden(seqs[1]));
+ assertFalse(hs.isHidden(seqs[2]));
+ assertTrue(hs.isHidden(seqs[3]));
+
+ /*
+ * should now be no sequences selected in the alignment
+ */
+ assertNull(av.getSelectionGroup());
+
+ /*
+ * visible alignment is now seq0/2/4/5/6/7/8/9
+ * 'reveal sequences' at the representative sequence (index = 1)
+ * this should unhide the one above i.e. seq1
+ * and return a selection list including seq2
+ *
+ * note have to call via AlignViewport to get the expected
+ * resulting sequence selection
+ */
+ av.showSequence(1);
+
+ /*
+ * only seq3 is now hidden
+ */
+ assertEquals(1, hs.getSize());
+ assertTrue(hs.isHidden(seqs[3]));
+ assertEquals(SEQ_COUNT - 1, al.getHeight());
+ sg = av.getSelectionGroup();
+
+ /*
+ * unhidden and representative sequence selected
+ * (this behaviour may change! JAL-2133)
+ */
+ assertEquals(2, sg.getSize());
+ assertTrue(sg.getSequences().contains(seqs[1]));
+ assertTrue(sg.getSequences().contains(seqs[2]));
+ assertFalse(sg.getSequences().contains(seqs[3]));
+ }
+}
{
}
- @AfterMethod
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
}
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import jalview.datamodel.PDBEntry.Type;
+import jalview.util.MapList;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Vector;
+import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
sq.setStart(3);
sq.setEnd(4);
+ sq.setDescription("Test sequence description..");
+ sq.setVamsasId("TestVamsasId");
+ sq.setSourceDBRef(new DBRefEntry("PDB", "version0", "1TST"));
+
+ sq.addDBRef(new DBRefEntry("PDB", "version1", "1Tst"));
+ sq.addDBRef(new DBRefEntry("PDB", "version2", "2Tst"));
+ sq.addDBRef(new DBRefEntry("PDB", "version3", "3Tst"));
+ sq.addDBRef(new DBRefEntry("PDB", "version4", "4Tst"));
+
+ sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
+ sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
+ sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
+ sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version1", "1Tst"));
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version2", "2Tst"));
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version3", "3Tst"));
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version4", "4Tst"));
+
+ sq.getDatasetSequence().addPDBId(
+ new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
+ sq.getDatasetSequence().addPDBId(
+ new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
+ sq.getDatasetSequence().addPDBId(
+ new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
+ sq.getDatasetSequence().addPDBId(
+ new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+
+ ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
+ System.out.println(">>>>>> " + sq.getSequenceAsString().length());
+ annotsList.add(new Annotation("A", "A", 'X', 0.1f));
+ annotsList.add(new Annotation("A", "A", 'X', 0.1f));
+ Annotation[] annots = annotsList.toArray(new Annotation[0]);
+ sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
+ "Test annot description", annots));
+ sq.getDatasetSequence().addAlignmentAnnotation(
+ new AlignmentAnnotation("Test annot", "Test annot description",
+ annots));
+ Assert.assertEquals(sq.getDescription(), "Test sequence description..");
+ Assert.assertEquals(sq.getDBRefs().length, 4);
+ 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().getAllPDBEntries().size(),
+ 4);
+ Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
+
Sequence derived = (Sequence) sq.deriveSequence();
+
+ Assert.assertEquals(derived.getDescription(),
+ "Test sequence description..");
+ Assert.assertEquals(derived.getDBRefs().length, 4);
+ 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().getAllPDBEntries()
+ .size(), 4);
+ Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
+
assertEquals("CD", derived.getSequenceAsString());
assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
assertEquals(' ', sq.getCharAt(5));
assertEquals(' ', sq.getCharAt(-1));
}
+
+ /**
+ * Tests for adding (or updating) dbrefs
+ *
+ * @see DBRefEntry#updateFrom(DBRefEntry)
+ */
+ @Test(groups = { "Functional" })
+ public void testAddDBRef()
+ {
+ SequenceI sq = new Sequence("", "abcde");
+ assertNull(sq.getDBRefs());
+ DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
+ sq.addDBRef(dbref);
+ assertEquals(1, sq.getDBRefs().length);
+ assertSame(dbref, sq.getDBRefs()[0]);
+
+ /*
+ * change of version - new entry
+ */
+ DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
+ sq.addDBRef(dbref2);
+ assertEquals(2, sq.getDBRefs().length);
+ assertSame(dbref, sq.getDBRefs()[0]);
+ assertSame(dbref2, sq.getDBRefs()[1]);
+
+ /*
+ * matches existing entry - not added
+ */
+ sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
+ assertEquals(2, sq.getDBRefs().length);
+
+ /*
+ * different source = new entry
+ */
+ DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
+ sq.addDBRef(dbref3);
+ assertEquals(3, sq.getDBRefs().length);
+ assertSame(dbref3, sq.getDBRefs()[2]);
+
+ /*
+ * different ref = new entry
+ */
+ DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
+ sq.addDBRef(dbref4);
+ assertEquals(4, sq.getDBRefs().length);
+ assertSame(dbref4, sq.getDBRefs()[3]);
+
+ /*
+ * matching ref with a mapping - map updated
+ */
+ DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
+ Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
+ 1, 1 }, 3, 1));
+ dbref5.setMap(map);
+ sq.addDBRef(dbref5);
+ assertEquals(4, sq.getDBRefs().length);
+ assertSame(dbref4, sq.getDBRefs()[3]);
+ assertSame(map, dbref4.getMap());
+
+ /*
+ * 'real' version replaces "0" version
+ */
+ dbref2.setVersion("0");
+ DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
+ dbref2.getAccessionId());
+ sq.addDBRef(dbref6);
+ assertEquals(4, sq.getDBRefs().length);
+ assertSame(dbref2, sq.getDBRefs()[1]);
+ assertEquals("3", dbref2.getVersion());
+
+ /*
+ * 'real' version replaces "source:0" version
+ */
+ dbref3.setVersion("Uniprot:0");
+ DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
+ dbref3.getAccessionId());
+ sq.addDBRef(dbref7);
+ assertEquals(4, sq.getDBRefs().length);
+ assertSame(dbref3, sq.getDBRefs()[2]);
+ assertEquals("3", dbref2.getVersion());
+ }
}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;
-import jalview.util.MappingUtils;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Vector;
+import java.util.List;
import org.testng.annotations.Test;
* Make a (CDS) Feature with 4 locations
*/
EmblFeature cds = new EmblFeature();
- Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
- cds.setLocations(locs);
-
- /*
- * single range [10-20]
- */
- EmblFeatureLocations loc = new EmblFeatureLocations();
- loc.setLocationType("single");
- loc.setLocationComplement(false);
- Vector<EmblFeatureLocElement> elements = new Vector<EmblFeatureLocElement>();
- EmblFeatureLocElement locElement = new EmblFeatureLocElement();
- BasePosition b1 = new BasePosition();
- b1.setPos("10");
- BasePosition b2 = new BasePosition();
- b2.setPos("20");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * complement range [30-40]
- */
- loc = new EmblFeatureLocations();
- loc.setLocationType("single");
- loc.setLocationComplement(true);
- elements = new Vector<EmblFeatureLocElement>();
- locElement = new EmblFeatureLocElement();
- b1 = new BasePosition();
- b1.setPos("30");
- b2 = new BasePosition();
- b2.setPos("40");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * join range [50-60], [70-80]
- */
- loc = new EmblFeatureLocations();
- loc.setLocationType("join");
- loc.setLocationComplement(false);
- elements = new Vector<EmblFeatureLocElement>();
- locElement = new EmblFeatureLocElement();
- b1 = new BasePosition();
- b1.setPos("50");
- b2 = new BasePosition();
- b2.setPos("60");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- locElement = new EmblFeatureLocElement();
- b1 = new BasePosition();
- b1.setPos("70");
- b2 = new BasePosition();
- b2.setPos("80");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * complement range [90-100], [110-120]
- * this should be the same as complement(join(90..100,110.120))
- * which is "join 90-100 and 110-120, then complement"
- */
- loc = new EmblFeatureLocations();
- loc.setLocationType("join");
- loc.setLocationComplement(true);
- elements = new Vector<EmblFeatureLocElement>();
- locElement = new EmblFeatureLocElement();
- b1 = new BasePosition();
- b1.setPos("90");
- b2 = new BasePosition();
- b2.setPos("100");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- locElement = new EmblFeatureLocElement();
- b1 = new BasePosition();
- b1.setPos("110");
- b2 = new BasePosition();
- b2.setPos("120");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
+ cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
int[] exons = testee.getCdsRanges(cds);
- assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110, 100, 90]",
+ assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
Arrays.toString(exons));
}
@Test(groups = "Functional")
- public void testGetCdsRanges_badData()
+ public void testParseCodingFeature()
{
- EmblEntry testee = new EmblEntry();
+ // not the whole sequence but enough for this test...
+ SequenceI dna = new Sequence("J03321", "GGATCCGTAAGTTAGACGAAATT");
+ List<SequenceI> peptides = new ArrayList<SequenceI>();
+ SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
+ EmblFile ef = EmblTestHelper.getEmblFile();
/*
- * Make a (CDS) Feature with 4 locations
- */
- EmblFeature cds = new EmblFeature();
- Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
- cds.setLocations(locs);
-
- /*
- * single range [10-20]
- */
- EmblFeatureLocations loc = new EmblFeatureLocations();
- loc.setLocationType("single");
- loc.setLocationComplement(false);
- Vector<EmblFeatureLocElement> elements = new Vector<EmblFeatureLocElement>();
- EmblFeatureLocElement locElement = new EmblFeatureLocElement();
- BasePosition b1 = new BasePosition();
- b1.setPos("10");
- BasePosition b2 = new BasePosition();
- b2.setPos("20");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * single range with missing end position - should be skipped
- */
- loc = new EmblFeatureLocations();
- loc.setLocationType("single");
- loc.setLocationComplement(false);
- elements = new Vector<EmblFeatureLocElement>();
- locElement = new EmblFeatureLocElement();
- b1 = new BasePosition();
- b1.setPos("30");
- locElement.setBasePositions(new BasePosition[] { b1 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * single range with extra base position - should be skipped
+ * parse two CDS features, one with two Uniprot cross-refs,
+ * the other with one
*/
- loc = new EmblFeatureLocations();
- loc.setLocationType("single");
- loc.setLocationComplement(false);
- elements = new Vector<EmblFeatureLocElement>();
- locElement = new EmblFeatureLocElement();
- b1 = new BasePosition();
- b1.setPos("30");
- locElement.setBasePositions(new BasePosition[] { b1, b1, b1 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * single valid range [50-60] to finish
- */
- loc = new EmblFeatureLocations();
- loc.setLocationType("single");
- loc.setLocationComplement(false);
- elements = new Vector<EmblFeatureLocElement>();
- locElement = new EmblFeatureLocElement();
- b1 = new BasePosition();
- b1.setPos("50");
- b2 = new BasePosition();
- b2.setPos("60");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- int[] exons = testee.getCdsRanges(cds);
- assertEquals("[10, 20, 50, 60]", Arrays.toString(exons));
- }
-
- /**
- * Test retrieval of exon locations matching an accession id
- */
- @Test(groups = "Functional")
- public void testGetCdsRanges_forAccession()
- {
EmblEntry testee = new EmblEntry();
- String accession = "A1234";
- testee.setAccession(accession);
- /*
- * Make a (CDS) Feature with 4 locations
- */
- EmblFeature cds = new EmblFeature();
- Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
- cds.setLocations(locs);
-
- /*
- * single range [10-20] for 'this' accession
- */
- EmblFeatureLocations loc = new EmblFeatureLocations();
- loc.setLocationType("single");
- loc.setLocationComplement(false);
- Vector<EmblFeatureLocElement> elements = new Vector<EmblFeatureLocElement>();
- EmblFeatureLocElement locElement = new EmblFeatureLocElement();
- locElement.setAccession(accession);
- BasePosition b1 = new BasePosition();
- b1.setPos("10");
- BasePosition b2 = new BasePosition();
- b2.setPos("20");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * complement range [30-40] - no accession
- */
- loc = new EmblFeatureLocations();
- loc.setLocationType("single");
- loc.setLocationComplement(true);
- elements = new Vector<EmblFeatureLocElement>();
- locElement = new EmblFeatureLocElement();
- b1 = new BasePosition();
- b1.setPos("30");
- b2 = new BasePosition();
- b2.setPos("40");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * join range [50-60] this accession, [70-80] another
- */
- loc = new EmblFeatureLocations();
- loc.setLocationType("join");
- loc.setLocationComplement(false);
- elements = new Vector<EmblFeatureLocElement>();
- locElement = new EmblFeatureLocElement();
- locElement.setAccession(accession);
- b1 = new BasePosition();
- b1.setPos("50");
- b2 = new BasePosition();
- b2.setPos("60");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- locElement = new EmblFeatureLocElement();
- locElement.setAccession("notme");
- b1 = new BasePosition();
- b1.setPos("70");
- b2 = new BasePosition();
- b2.setPos("80");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * complement range [90-100] wrong accession, [110-120] good
- * this should be the same as complement(join(90..100,110.120))
- * which is "join 90-100 and 110-120, then complement"
- */
- loc = new EmblFeatureLocations();
- loc.setLocationType("join");
- loc.setLocationComplement(true);
- elements = new Vector<EmblFeatureLocElement>();
- locElement = new EmblFeatureLocElement();
- locElement.setAccession("wrong");
- b1 = new BasePosition();
- b1.setPos("90");
- b2 = new BasePosition();
- b2.setPos("100");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- locElement = new EmblFeatureLocElement();
- locElement.setAccession(accession);
- b1 = new BasePosition();
- b1.setPos("110");
- b2 = new BasePosition();
- b2.setPos("120");
- locElement.setBasePositions(new BasePosition[] { b1, b2 });
- elements.add(locElement);
- loc.setLocElements(elements);
- locs.add(loc);
-
- /*
- * verify we pick out only ranges for A1234
- */
- int[] exons = testee.getCdsRanges(cds);
- assertEquals("[10, 20, 50, 60, 120, 110]",
- Arrays.toString(exons));
+ for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
+ {
+ if ("CDS".equals(feature.getName()))
+ {
+ testee.parseCodingFeature(feature, "EMBL", dna, peptides, matcher);
+ }
+ }
+
+ /*
+ * peptides should now have five entries:
+ * EMBL product and two Uniprot accessions for the first CDS / translation
+ * EMBL product and one Uniprot accession for the second CDS / translation
+ */
+ assertEquals(5, peptides.size());
+ assertEquals("CAA30420.1", peptides.get(0).getName());
+ assertEquals("MLCF", peptides.get(0).getSequenceAsString());
+ assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
+ assertEquals("MLCF", peptides.get(1).getSequenceAsString());
+ assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
+ assertEquals("MLCF", peptides.get(2).getSequenceAsString());
+ assertEquals("CAA30421.1", peptides.get(3).getName());
+ assertEquals("MSSS", peptides.get(3).getSequenceAsString());
+ assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
+ assertEquals("MSSS", peptides.get(4).getSequenceAsString());
+
+ /*
+ * verify dna sequence has dbrefs with mappings to the peptide 'products'
+ */
+ DBRefEntry[] dbrefs = dna.getDBRefs();
+ assertEquals(3, dbrefs.length);
+ DBRefEntry dbRefEntry = dbrefs[0];
+ assertEquals("UNIPROT", dbRefEntry.getSource());
+ assertEquals("B0BCM4", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
+ List<int[]> fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
+ assertEquals(1, fromRanges.size());
+ assertEquals(57, fromRanges.get(0)[0]);
+ assertEquals(46, fromRanges.get(0)[1]);
+ List<int[]> toRanges = dbRefEntry.getMap().getMap().getToRanges();
+ assertEquals(1, toRanges.size());
+ assertEquals(1, toRanges.get(0)[0]);
+ assertEquals(4, toRanges.get(0)[1]);
+
+ dbRefEntry = dbrefs[1];
+ assertEquals("UNIPROT", dbRefEntry.getSource());
+ assertEquals("P0CE20", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
+ fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
+ assertEquals(1, fromRanges.size());
+ assertEquals(57, fromRanges.get(0)[0]);
+ assertEquals(46, fromRanges.get(0)[1]);
+ toRanges = dbRefEntry.getMap().getMap().getToRanges();
+ assertEquals(1, toRanges.size());
+ assertEquals(1, toRanges.get(0)[0]);
+ assertEquals(4, toRanges.get(0)[1]);
+
+ dbRefEntry = dbrefs[2];
+ assertEquals("UNIPROT", dbRefEntry.getSource());
+ assertEquals("B0BCM3", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
+ fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
+ assertEquals(1, fromRanges.size());
+ assertEquals(4, fromRanges.get(0)[0]);
+ assertEquals(15, fromRanges.get(0)[1]);
+ toRanges = dbRefEntry.getMap().getMap().getToRanges();
+ assertEquals(1, toRanges.size());
+ assertEquals(1, toRanges.get(0)[0]);
+ assertEquals(4, toRanges.get(0)[1]);
}
}
package jalview.datamodel.xdb.embl;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.DBRefEntry;
-import java.io.StringReader;
import java.util.Vector;
import org.testng.annotations.Test;
public class EmblFileTest
{
- // adapted from http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
- private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
- + "<EMBL_Services>"
- + "<entry accession=\"X53828\" version=\"3\" lastUpdated=\"2005-04-18\" releaseCreated=\"25\" releaseLastUpdated=\"83\">"
- + "<description>Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)</description>"
- + "<keyword>L-lactate dehydrogenase</keyword><keyword>chutney</keyword>"
- + "<dbreference db=\"EuropePMC\" primary=\"PMC1460223\" secondary=\"9649548\" />"
- + "<dbreference db=\"MD5\" primary=\"d3b68\" />"
- + "<feature name=\"CDS\"><dbreference db=\"GOA\" primary=\"P00340\" secondary=\"2.1\" /><dbreference db=\"InterPro\" primary=\"IPR001236\" />"
- + "<qualifier name=\"note\"><value>L-lactate dehydrogenase A-chain</value><value>pickle</value></qualifier>"
- + "<qualifier name=\"translation\"><value>MSLKDHLIHN</value><evidence>Keith</evidence></qualifier>"
- + "<location type=\"single\" complement=\"true\">"
- + "<locationElement type=\"range\" accession=\"X53828\" version=\"1\" complement=\"false\">"
- + "<basePosition type=\"simple\">60</basePosition><basePosition type=\"join\">1058</basePosition>"
- + "</locationElement></location></feature>"
- + "<sequence type=\"mRNA\" version=\"2\">GTGACG</sequence></entry></EMBL_Services>";
@Test(groups = { "Functional" })
public void testGetEmblFile()
{
- Vector<EmblEntry> entries = EmblFile.getEmblFile(
- new StringReader(TESTDATA)).getEntries();
+ Vector<EmblEntry> entries = EmblTestHelper.getEmblFile().getEntries();
assertEquals(1, entries.size());
EmblEntry entry = entries.get(0);
- assertEquals("X53828", entry.getAccession());
- assertEquals(
- "Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)",
- entry.getDesc());
- assertEquals("2005-04-18", entry.getLastUpdated());
+ assertEquals("X07547", entry.getAccession());
+ assertEquals("C. trachomatis plasmid", entry.getDescription());
+ assertEquals("STD", entry.getDataClass());
+ assertEquals("PRO", entry.getTaxonomicDivision());
+ assertEquals("1999-02-10", entry.getLastUpdatedDate());
+ assertEquals("58", entry.getLastUpdatedRelease());
+ assertEquals("1988-11-10", entry.getFirstPublicDate());
+ assertEquals("18", entry.getFirstPublicRelease());
+ assertEquals("genomic DNA", entry.getMoleculeType());
+ assertEquals("1", entry.getSequenceVersion());
+ assertEquals("8", entry.getEntryVersion());
+ assertEquals("linear", entry.getTopology());
+ assertEquals("7499", entry.getSequenceLength());
/*
* FIXME these assertions fail - values are null - why?? Adding or removing
* attributes in the test XML modifies behaviour. eg. inserting an attribute
* _before_ lastUpdated results in a null value in this field.
*/
- // assertEquals("25", entry.getRCreated());
- // assertEquals("83", entry.getRLastUpdated());
+ assertEquals("1988-11-10", entry.getFirstPublicDate());
+ assertEquals("18", entry.getFirstPublicRelease());
assertEquals(2, entry.getKeywords().size());
- assertEquals("L-lactate dehydrogenase", entry.getKeywords().get(0));
- assertEquals("chutney", entry.getKeywords().get(1));
+ assertEquals("plasmid", entry.getKeywords().get(0));
+ assertEquals("unidentified reading frame", entry.getKeywords().get(1));
/*
* dbrefs
assertEquals(2, entry.getDbRefs().size());
DBRefEntry dbref = entry.getDbRefs().get(0);
assertEquals("EuropePMC", dbref.getSource());
- assertEquals("PMC1460223", dbref.getAccessionId());
- assertEquals("9649548", dbref.getVersion());
+ assertEquals("PMC107176", dbref.getAccessionId());
+ assertEquals("9573186", dbref.getVersion());
dbref = entry.getDbRefs().get(1);
assertEquals("MD5", dbref.getSource());
- assertEquals("d3b68", dbref.getAccessionId());
+ assertEquals("ac73317", dbref.getAccessionId());
// blank version has been converted to "0"
assertEquals("0", dbref.getVersion());
/*
- * sequence features
+ * two sequence features for CDS
+ */
+ assertEquals(2, entry.getFeatures().size());
+ /*
+ * first CDS
*/
- assertEquals(1, entry.getFeatures().size());
EmblFeature ef = entry.getFeatures().get(0);
assertEquals("CDS", ef.getName());
+ assertEquals("complement(46..57)", ef.getLocation());
assertEquals(2, ef.getDbRefs().size());
dbref = ef.getDbRefs().get(0);
- assertEquals("GOA", dbref.getSource());
- assertEquals("P00340", dbref.getAccessionId());
+ assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
+ assertEquals("B0BCM4", dbref.getAccessionId());
assertEquals("2.1", dbref.getVersion());
dbref = ef.getDbRefs().get(1);
- assertEquals("InterPro", dbref.getSource());
- assertEquals("IPR001236", dbref.getAccessionId());
- // blank version converted to "0":
+ assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
+ assertEquals("P0CE20", dbref.getAccessionId());
+ // blank version gets converted to "0":
assertEquals("0", dbref.getVersion());
- assertEquals(2, ef.getQualifiers().size());
-
- // feature qualifiers
+ // CDS feature qualifiers
+ assertEquals(3, ef.getQualifiers().size());
Qualifier q = ef.getQualifiers().get(0);
assertEquals("note", q.getName());
assertEquals(2, q.getValues().length);
- assertEquals("L-lactate dehydrogenase A-chain", q.getValues()[0]);
+ assertEquals("ORF 8 (AA 1-330)", q.getValues()[0]);
assertEquals("pickle", q.getValues()[1]);
assertNull(q.getEvidence());
q = ef.getQualifiers().get(1);
+ assertEquals("protein_id", q.getName());
+ assertEquals(1, q.getValues().length);
+ assertEquals("CAA30420.1", q.getValues()[0]);
+ q = ef.getQualifiers().get(2);
assertEquals("translation", q.getName());
assertEquals(1, q.getValues().length);
- assertEquals("MSLKDHLIHN", q.getValues()[0]);
+ assertEquals("MLCF", q.getValues()[0]);
assertEquals(1, q.getEvidence().length);
assertEquals("Keith", q.getEvidence()[0]);
- // feature locations
- assertEquals(1, ef.getLocations().size());
- EmblFeatureLocations fl = ef.getLocations().get(0);
- assertEquals("single", fl.getLocationType());
- assertTrue(fl.isLocationComplement());
- assertEquals(1, fl.getLocElements().size());
- EmblFeatureLocElement le = fl.getLocElements().get(0);
- assertEquals("range", le.getType());
- assertEquals("X53828", le.getAccession());
- assertEquals("1", le.getVersion());
- assertFalse(le.isComplement());
- assertEquals(2, le.getBasePositions().length);
- BasePosition bp = le.getBasePositions()[0];
- assertEquals("simple", bp.getType());
- assertEquals("60", bp.getPos());
- bp = le.getBasePositions()[1];
- assertEquals("join", bp.getType());
- assertEquals("1058", bp.getPos());
+ /*
+ * second CDS
+ */
+ ef = entry.getFeatures().get(1);
+ assertEquals("CDS", ef.getName());
+ assertEquals("4..15", ef.getLocation());
+ assertEquals(1, ef.getDbRefs().size());
+ dbref = ef.getDbRefs().get(0);
+ assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
+ assertEquals("B0BCM3", dbref.getAccessionId());
+ assertEquals("0", dbref.getVersion());
+ assertEquals(2, ef.getQualifiers().size());
+ q = ef.getQualifiers().get(0);
+ assertEquals("protein_id", q.getName());
+ assertEquals(1, q.getValues().length);
+ assertEquals("CAA30421.1", q.getValues()[0]);
+ q = ef.getQualifiers().get(1);
+ assertEquals("translation", q.getName());
+ assertEquals(1, q.getValues().length);
+ assertEquals("MSSS", q.getValues()[0]);
/*
- * Sequence
+ * Sequence - verify newline not converted to space (JAL-2029)
*/
EmblSequence seq = entry.getSequence();
- assertEquals("mRNA", seq.getType());
- assertEquals("2", seq.getVersion());
- assertEquals("GTGACG", seq.getSequence());
+ assertEquals(
+ "GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
+ seq.getSequence());
/*
* getSequence() converts empty DBRefEntry.version to "0"
--- /dev/null
+package jalview.datamodel.xdb.embl;
+
+import java.io.StringReader;
+
+public class EmblTestHelper
+{
+ // 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>"
+ + "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
+ + " dataClass=\"STD\" taxonomicDivision=\"PRO\""
+ + " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
+ + " firstPublic=\"1988-11-10\" firstPublicRelease=\"18\""
+ + " lastUpdated=\"1999-02-10\" lastUpdatedRelease=\"58\">"
+ + "<secondaryAccession>X07574</secondaryAccession>"
+ + "<description>C. trachomatis plasmid</description>"
+ + "<keyword>plasmid</keyword><keyword>unidentified reading frame</keyword>"
+ + "<xref db=\"EuropePMC\" id=\"PMC107176\" secondaryId=\"9573186\" />"
+ + "<xref db=\"MD5\" id=\"ac73317\" />"
+ /*
+ * first CDS (range and translation changed to keep test data manageable)
+ */
+ + "<feature name=\"CDS\" location=\"complement(46..57)\">"
+ // test the case of >1 cross-ref to the same database (JAL-2029)
+ + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM4\" secondaryId=\"2.1\" />"
+ + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"P0CE20\" />"
+ + "<qualifier name=\"note\"><value>ORF 8 (AA 1-330)</value><value>pickle</value></qualifier>"
+ + "<qualifier name=\"protein_id\"><value>CAA30420.1</value></qualifier>"
+ + "<qualifier name=\"translation\"><value>MLCF</value><evidence>Keith</evidence></qualifier>"
+ + "</feature>"
+ /*
+ * second CDS (range and translation changed to keep test data manageable)
+ */
+ + "<feature name=\"CDS\" location=\"4..15\">"
+ + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM3\" />"
+ + "<qualifier name=\"protein_id\"><value>CAA30421.1</value></qualifier>"
+ + "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
+ + "</feature>"
+ /*
+ * sequence (modified for test purposes)
+ * emulates EMBL XML 1.2 which splits sequence data every 60 characters
+ * see EmblSequence.setSequence
+ */
+ + "<sequence>GGTATGTCCTCTAGTACAAAC\n"
+ + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
+ + "</sequence></entry></ROOT>";
+
+ static EmblFile getEmblFile()
+ {
+ return EmblFile.getEmblFile(new StringReader(TESTDATA));
+ }
+}
public class EnsemblCdnaTest
{
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceOntologyFactory.setInstance(null);
public class EnsemblCdsTest
{
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceOntologyFactory.setInstance(null);
public class EnsemblGeneTest
{
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceOntologyFactory.setInstance(null);
public class EnsemblGenomeTest
{
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceOntologyFactory.setInstance(null);
{
@Test(suiteName = "live")
- public void testLiveCheckEnsembl()
+ public void testIsEnsemblAvailable()
{
EnsemblRestClient sf = new EnsemblRestClient()
{
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.gff.SequenceOntologyLite;
import java.lang.reflect.Method;
-import java.net.MalformedURLException;
-import java.net.URL;
import java.util.Arrays;
-import java.util.List;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceOntologyFactory.setInstance(null);
}
}
- @Test(suiteName = "live")
- public void testLiveCheckEnsembl()
- {
- EnsemblRestClient sf = new EnsemblRestClient()
- {
-
- @Override
- public String getDbName()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public AlignmentI getSequenceRecords(String queries) throws Exception
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected URL getUrl(List<String> ids) throws MalformedURLException
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected boolean useGetRequest()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- protected String getRequestMimeType(boolean b)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected String getResponseMimeType()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- };
- boolean isAvailable = sf.isEnsemblAvailable();
- System.out.println("Ensembl is "
- + (isAvailable ? "UP!"
- : "DOWN or unreachable ******************* BAD!"));
- }
-
@Test(groups = "Functional")
public void getGenomicRangesFromFeatures()
{
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
public class TestAnnotate3D
{
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Network" }, enabled = true)
public void test1GIDbyId() throws Exception
{
// use same ID as standard tests given at
testRNAMLcontent(ids, null);
}
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Network" }, enabled = true)
public void testIdVsContent2GIS() throws Exception
{
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
*
* @throws Exception
*/
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Network" }, enabled = true)
public void testPDBfileVsRNAML() throws Exception
{
PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
testRNAMLcontent(readers, pdbf);
}
- @Test(groups = { "Functional" }, enabled = false)
private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
throws Exception
{
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.ext.so.SequenceOntology;
-import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
-import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
{
private SequenceOntologyI so;
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp() {
long now = System.currentTimeMillis();
- SequenceOntologyFactory.setInstance(new SequenceOntology());
+ try
+ {
+ so = new SequenceOntology();
+ } catch (Throwable t)
+ {
+ System.out.println("SOTest error ");
+ t.printStackTrace(System.err);
+ }
long elapsed = System.currentTimeMillis() - now;
System.out.println("Load and cache of Sequence Ontology took "
+ elapsed + "ms");
- so = SequenceOntologyFactory.getInstance();
- }
-
- @AfterClass
- public void tearDown()
- {
- SequenceOntologyFactory.setInstance(null);
}
@Test(groups = "Functional")
public void getPrimaryKeyColumIndexTest()
{
Collection<FTSDataColumnI> wantedFields = ftsRestClient
- .getAllDefaulDisplayedDataColumns();
+ .getAllDefaultDisplayedFTSDataColumns();
int foundIndex = -1;
try
{
@Test(groups = { "Functional" })
public void getAllDefaulDisplayedDataColumns()
{
- Assert.assertNotNull(ftsRestClient.getAllDefaulDisplayedDataColumns());
- Assert.assertTrue(!ftsRestClient.getAllDefaulDisplayedDataColumns()
+ Assert.assertNotNull(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
+ Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
.isEmpty());
- Assert.assertEquals(ftsRestClient.getAllDefaulDisplayedDataColumns()
+ Assert.assertEquals(ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
.size(), 7);
}
public void getDataColumnsFieldsAsCommaDelimitedString()
{
Collection<FTSDataColumnI> wantedFields = ftsRestClient
- .getAllDefaulDisplayedDataColumns();
+ .getAllDefaultDisplayedFTSDataColumns();
String actual = ftsRestClient
.getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
Assert.assertEquals(actual,
- "id,entry name,protein names,genes,organism,length,reviewed");
+ "id,entry name,protein names,genes,organism,reviewed,length");
}
Collection<FTSDataColumnI> searchalbeFields = ftsRestClient
.getSearchableDataColumns();
Assert.assertNotNull(searchalbeFields);
- Assert.assertEquals(searchalbeFields.size(), 30);
+ Assert.assertEquals(searchalbeFields.size(), 22);
}
@Test(groups = { "Functional" })
public void getDefaultResponsePageSize()
{
int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
- Assert.assertEquals(defaultResSize, 100);
+ Assert.assertEquals(defaultResSize, 500);
}
@Test(groups = { "Functional" })
FTSDataColumnI foundDataCol = ftsRestClient
.getDataColumnByNameOrCode("Protein names");
Assert.assertNotNull(foundDataCol);
- Assert.assertEquals(foundDataCol.getDataColumnClass(), String.class);
+ Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
+ String.class);
foundDataCol = ftsRestClient.getDataColumnByNameOrCode("length");
Assert.assertNotNull(foundDataCol);
- Assert.assertEquals(foundDataCol.getDataColumnClass(), Integer.class);
+ Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
+ Integer.class);
// foundDataCol = ftsRestClient.getDataColumnByNameOrCode("length");
// Assert.assertNotNull(foundDataCol);
// Assert.assertEquals(foundDataCol.getDataColumnClass(), Double.class);
.getSearchableDataColumns();
for (FTSDataColumnI foundCol : searchableCols)
{
+ System.out.println(foundCol.toString());
uniqueSet.add(foundCol);
uniqueSet.add(foundCol);
}
Assert.assertTrue(!uniqueSet.isEmpty());
- Assert.assertEquals(uniqueSet.size(), 30);
+ Assert.assertEquals(uniqueSet.size(), 22);
}
@Test(groups = { "Functional" })
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.fts.service.pdb.PDBFTSPanel;
-
import javax.swing.JInternalFrame;
import javax.swing.JTextField;
{
}
- @AfterMethod
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
}
{
}
- @AfterMethod
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
}
--- /dev/null
+package jalview.gui;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class AlignFrameTest
+{
+
+ @Test
+ public void testHideFeatureColumns()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
+ SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
+ seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5,
+ Float.NaN, null));
+ seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10,
+ Float.NaN, null));
+ seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
+ Float.NaN, null));
+ seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
+ Float.NaN, null));
+ AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+ AlignFrame af = new AlignFrame(al, al.getWidth(), al.getHeight());
+
+ /*
+ * hiding a feature not present does nothing
+ */
+ assertFalse(af.hideFeatureColumns("exon", true));
+ assertTrue(af.getViewport().getColumnSelection().isEmpty());
+ assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
+ .isEmpty());
+ assertFalse(af.hideFeatureColumns("exon", false));
+ assertTrue(af.getViewport().getColumnSelection().isEmpty());
+ assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
+ .isEmpty());
+
+ /*
+ * hiding a feature in all columns does nothing
+ */
+ assertFalse(af.hideFeatureColumns("Metal", true));
+ assertTrue(af.getViewport().getColumnSelection().isEmpty());
+ List<int[]> hidden = af.getViewport().getColumnSelection()
+ .getHiddenColumns();
+ assertTrue(hidden.isEmpty());
+
+ /*
+ * hide a feature present in some columns
+ * sequence positions [2-4], [7-9] are column positions
+ * [1-3], [6-8] base zero
+ */
+ assertTrue(af.hideFeatureColumns("Turn", true));
+ hidden = af.getViewport().getColumnSelection()
+ .getHiddenColumns();
+ assertEquals(2, hidden.size());
+ assertEquals(1, hidden.get(0)[0]);
+ assertEquals(3, hidden.get(0)[1]);
+ assertEquals(6, hidden.get(1)[0]);
+ assertEquals(8, hidden.get(1)[1]);
+ }
+}
{
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
PaintRefresher.components.clear();
}
- @AfterMethod
+ @AfterMethod(alwaysRun = true)
public void tearDown()
{
PaintRefresher.components.clear();
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
seq.setPDBId(pdbIds);
}
- @AfterMethod
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
seq.setDBRefs(null);
query = StructureChooser.buildQuery(seq);
assertEquals("text:4kqy", query);
+
+ DBRefEntry uniprotDBRef = new DBRefEntry();
+ uniprotDBRef.setAccessionId("P12345");
+ uniprotDBRef.setSource(DBRefSource.UNIPROT);
+ seq.addDBRef(uniprotDBRef);
+
+ DBRefEntry pdbDBRef = new DBRefEntry();
+ pdbDBRef.setAccessionId("1XYZ");
+ pdbDBRef.setSource(DBRefSource.PDB);
+ seq.addDBRef(pdbDBRef);
+
+ for (int x = 1; x < 5; x++)
+ {
+ DBRefEntry dbRef = new DBRefEntry();
+ dbRef.setAccessionId("XYZ_" + x);
+ seq.addDBRef(dbRef);
+ }
+ query = StructureChooser.buildQuery(seq);
+ assertEquals(
+ "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
+ query);
}
@Test(groups = { "Functional" })
assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
}
+
+ @Test(groups = { "Functional" })
+ public void sanitizeSeqNameTest()
+ {
+ String name = "ab_cdEF|fwxyz012349";
+ assertEquals(name, StructureChooser.sanitizeSeqName(name));
+
+ // remove a [nn] substring
+ name = "abcde12[345]fg";
+ assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
+
+ // remove characters other than a-zA-Z0-9 | or _
+ name = "ab[cd],.\t£$*!- \\\"@:e";
+ assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
+
+ name = "abcde12[345a]fg";
+ assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
+ }
}
--- /dev/null
+HEADER IRON-SULFUR PROTEIN 19-MAR-98 1A70
+TITLE SPINACH FERREDOXIN
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: FERREDOXIN;
+COMPND 3 CHAIN: A;
+COMPND 4 ENGINEERED: YES;
+COMPND 5 MUTATION: YES
+SOURCE MOL_ID: 1;
+SOURCE 2 ORGANISM_SCIENTIFIC: SPINACIA OLERACEA;
+SOURCE 3 ORGANISM_COMMON: SPINACH;
+SOURCE 4 ORGANISM_TAXID: 3562;
+SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
+SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
+KEYWDS IRON-SULFUR PROTEIN, PHOTOSYNTHESIS, ELECTRON TRANSPORT
+EXPDTA X-RAY DIFFRACTION
+AUTHOR C.BINDA,A.CODA,A.MATTEVI,A.ALIVERTI,G.ZANETTI
+REVDAT 3 24-FEB-09 1A70 1 VERSN
+REVDAT 2 13-JAN-99 1A70 3 ATOM SOURCE COMPND REMARK
+REVDAT 2 2 3 HETATM JRNL KEYWDS TER
+REVDAT 2 3 3 CONECT
+REVDAT 1 25-NOV-98 1A70 0
+JRNL AUTH C.BINDA,A.CODA,A.ALIVERTI,G.ZANETTI,A.MATTEVI
+JRNL TITL STRUCTURE OF THE MUTANT E92K OF [2FE-2S]
+JRNL TITL 2 FERREDOXIN I FROM SPINACIA OLERACEA AT 1.7 A
+JRNL TITL 3 RESOLUTION.
+JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 54 1353 1998
+JRNL REFN ISSN 0907-4449
+JRNL PMID 10089511
+JRNL DOI 10.1107/S0907444998005137
+REMARK 1
+REMARK 2
+REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
+REMARK 3
+REMARK 3 REFINEMENT.
+REMARK 3 PROGRAM : TNT V. 5-D
+REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS
+REMARK 3
+REMARK 3 DATA USED IN REFINEMENT.
+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00
+REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
+REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6
+REMARK 3 NUMBER OF REFLECTIONS : 11755
+REMARK 3
+REMARK 3 USING DATA ABOVE SIGMA CUTOFF.
+REMARK 3 CROSS-VALIDATION METHOD : A POSTERIORI
+REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY 10TH REFLECTION
+REMARK 3 R VALUE (WORKING + TEST SET) : 0.190
+REMARK 3 R VALUE (WORKING SET) : 0.182
+REMARK 3 FREE R VALUE : 0.200
+REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
+REMARK 3 FREE R VALUE TEST SET COUNT : 1090
+REMARK 3
+REMARK 3 USING ALL DATA, NO SIGMA CUTOFF.
+REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2010
+REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1960
+REMARK 3 FREE R VALUE (NO CUTOFF) : 0.259
+REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.00
+REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1176
+REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11755
+REMARK 3
+REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
+REMARK 3 PROTEIN ATOMS : 732
+REMARK 3 NUCLEIC ACID ATOMS : 0
+REMARK 3 HETEROGEN ATOMS : 4
+REMARK 3 SOLVENT ATOMS : 81
+REMARK 3
+REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 5.100
+REMARK 3
+REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT
+REMARK 3 BOND LENGTHS (A) : 0.019 ; 70.000; 620
+REMARK 3 BOND ANGLES (DEGREES) : 2.994 ; 90.000; 855
+REMARK 3 TORSION ANGLES (DEGREES) : 18.500; 0.000 ; 300
+REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL
+REMARK 3 TRIGONAL CARBON PLANES (A) : 0.021 ; 70.000; 13
+REMARK 3 GENERAL PLANES (A) : 0.021 ; 240.000; 94
+REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 4.300 ; 2.100 ; 620
+REMARK 3 NON-BONDED CONTACTS (A) : 0.039 ; 125.000; 9
+REMARK 3
+REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL
+REMARK 3
+REMARK 3 BULK SOLVENT MODELING.
+REMARK 3 METHOD USED : BABINET SCALING
+REMARK 3 KSOL : 0.80
+REMARK 3 BSOL : 150.00
+REMARK 3
+REMARK 3 RESTRAINT LIBRARIES.
+REMARK 3 STEREOCHEMISTRY : TNT PROTGEO
+REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL V1.0
+REMARK 3
+REMARK 3 OTHER REFINEMENT REMARKS: NULL
+REMARK 4
+REMARK 4 1A70 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
+REMARK 100
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
+REMARK 200
+REMARK 200 EXPERIMENTAL DETAILS
+REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
+REMARK 200 DATE OF DATA COLLECTION : JUN-96
+REMARK 200 TEMPERATURE (KELVIN) : 293
+REMARK 200 PH : 7.5
+REMARK 200 NUMBER OF CRYSTALS USED : 1
+REMARK 200
+REMARK 200 SYNCHROTRON (Y/N) : N
+REMARK 200 RADIATION SOURCE : ROTATING ANODE
+REMARK 200 BEAMLINE : NULL
+REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R
+REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
+REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
+REMARK 200 MONOCHROMATOR : GRAPHITE(002)
+REMARK 200 OPTICS : MIRRORS
+REMARK 200
+REMARK 200 DETECTOR TYPE : IMAGE PLATE
+REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
+REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
+REMARK 200 DATA SCALING SOFTWARE : AGROVATA
+REMARK 200
+REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11755
+REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700
+REMARK 200 RESOLUTION RANGE LOW (A) : NULL
+REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
+REMARK 200
+REMARK 200 OVERALL.
+REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6
+REMARK 200 DATA REDUNDANCY : 2.500
+REMARK 200 R MERGE (I) : 0.07800
+REMARK 200 R SYM (I) : 0.11200
+REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000
+REMARK 200
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80
+REMARK 200 COMPLETENESS FOR SHELL (%) : 68.0
+REMARK 200 DATA REDUNDANCY IN SHELL : 2.50
+REMARK 200 R MERGE FOR SHELL (I) : 0.20200
+REMARK 200 R SYM FOR SHELL (I) : 0.30500
+REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
+REMARK 200
+REMARK 200 DIFFRACTION PROTOCOL: NULL
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
+REMARK 200 SOFTWARE USED: AMORE
+REMARK 200 STARTING MODEL: PDB ENTRY 1FRR
+REMARK 200
+REMARK 200 REMARK: NULL
+REMARK 280
+REMARK 280 CRYSTAL
+REMARK 280 SOLVENT CONTENT, VS (%): 50.00
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.50
+REMARK 280
+REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 2.6M
+REMARK 280 AMMONIUM SULPHATE IN 50MM PHOSPHATE BUFFER, PH 7.5
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
+REMARK 290
+REMARK 290 SYMOP SYMMETRY
+REMARK 290 NNNMMM OPERATOR
+REMARK 290 1555 X,Y,Z
+REMARK 290 2555 -X+1/2,-Y,Z+1/2
+REMARK 290 3555 -X,Y+1/2,-Z+1/2
+REMARK 290 4555 X+1/2,-Y+1/2,-Z
+REMARK 290
+REMARK 290 WHERE NNN -> OPERATOR NUMBER
+REMARK 290 MMM -> TRANSLATION VECTOR
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+REMARK 290 RELATED MOLECULES.
+REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 15.50000
+REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.76000
+REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.59000
+REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.76000
+REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.50000
+REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.59000
+REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
+REMARK 290
+REMARK 290 REMARK: NULL
+REMARK 300
+REMARK 300 BIOMOLECULE: 1
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
+REMARK 300 BURIED SURFACE AREA.
+REMARK 350
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
+REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
+REMARK 350
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
+REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
+REMARK 500 ASP A 20 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES
+REMARK 500 ASP A 34 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES
+REMARK 500 ASP A 34 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES
+REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES
+REMARK 500 ASP A 59 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES
+REMARK 500 ASP A 65 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES
+REMARK 500 ASP A 84 CB - CG - OD1 ANGL. DEV. = 12.2 DEGREES
+REMARK 500 ASP A 84 CB - CG - OD2 ANGL. DEV. = -14.6 DEGREES
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: TORSION ANGLES
+REMARK 500
+REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
+REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
+REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
+REMARK 500
+REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
+REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
+REMARK 500
+REMARK 500 M RES CSSEQI PSI PHI
+REMARK 500 SER A 38 -77.42 -141.70
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CHIRAL CENTERS
+REMARK 500
+REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
+REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
+REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
+REMARK 500
+REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
+REMARK 500 ALA A 1 115.2 ALPHA-CARBON
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 525
+REMARK 525 SOLVENT
+REMARK 525
+REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
+REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
+REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
+REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
+REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
+REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
+REMARK 525 NUMBER; I=INSERTION CODE):
+REMARK 525
+REMARK 525 M RES CSSEQI
+REMARK 525 HOH A1653 DISTANCE = 5.18 ANGSTROMS
+REMARK 525 HOH A1666 DISTANCE = 5.57 ANGSTROMS
+REMARK 525 HOH A1680 DISTANCE = 8.72 ANGSTROMS
+REMARK 800
+REMARK 800 SITE
+REMARK 800 SITE_IDENTIFIER: AC1
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 1602
+DBREF 1A70 A 1 97 UNP P00221 FER1_SPIOL 51 147
+SEQADV 1A70 LYS A 92 UNP P00221 GLU 142 ENGINEERED
+SEQRES 1 A 97 ALA ALA TYR LYS VAL THR LEU VAL THR PRO THR GLY ASN
+SEQRES 2 A 97 VAL GLU PHE GLN CYS PRO ASP ASP VAL TYR ILE LEU ASP
+SEQRES 3 A 97 ALA ALA GLU GLU GLU GLY ILE ASP LEU PRO TYR SER CYS
+SEQRES 4 A 97 ARG ALA GLY SER CYS SER SER CYS ALA GLY LYS LEU LYS
+SEQRES 5 A 97 THR GLY SER LEU ASN GLN ASP ASP GLN SER PHE LEU ASP
+SEQRES 6 A 97 ASP ASP GLN ILE ASP GLU GLY TRP VAL LEU THR CYS ALA
+SEQRES 7 A 97 ALA TYR PRO VAL SER ASP VAL THR ILE GLU THR HIS LYS
+SEQRES 8 A 97 LYS GLU GLU LEU THR ALA
+HET FES A1602 4
+HETNAM FES FE2/S2 (INORGANIC) CLUSTER
+FORMUL 2 FES FE2 S2
+FORMUL 3 HOH *81(H2 O)
+HELIX 1 1 ILE A 24 GLU A 30 1 7
+HELIX 2 2 ASP A 66 GLU A 71 1 6
+HELIX 3 3 THR A 76 ALA A 78 5 3
+HELIX 4 4 LYS A 92 GLU A 94 5 3
+SHEET 1 A 5 GLY A 12 PRO A 19 0
+SHEET 2 A 5 ALA A 2 THR A 9 -1 N THR A 9 O GLY A 12
+SHEET 3 A 5 VAL A 85 GLU A 88 1 N VAL A 85 O THR A 6
+SHEET 4 A 5 ALA A 48 THR A 53 -1 N THR A 53 O THR A 86
+SHEET 5 A 5 TRP A 73 LEU A 75 -1 N VAL A 74 O GLY A 49
+LINK FE1 FES A1602 SG CYS A 39 1555 1555 2.32
+LINK FE1 FES A1602 SG CYS A 44 1555 1555 2.28
+LINK FE2 FES A1602 SG CYS A 47 1555 1555 2.36
+LINK FE2 FES A1602 SG CYS A 77 1555 1555 2.27
+SITE 1 AC1 8 SER A 38 CYS A 39 ARG A 40 GLY A 42
+SITE 2 AC1 8 SER A 43 CYS A 44 CYS A 47 CYS A 77
+CRYST1 31.000 39.180 83.520 90.00 90.00 90.00 P 21 21 21 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.032258 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.025523 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.011973 0.00000
+ATOM 1 N ALA A 1 1.578 -4.284 5.235 1.00 64.26 N
+ATOM 2 CA ALA A 1 2.384 -5.448 5.549 1.00 56.75 C
+ATOM 3 C ALA A 1 3.756 -4.955 5.925 1.00 52.65 C
+ATOM 4 O ALA A 1 3.885 -4.610 7.073 1.00 48.15 O
+ATOM 5 CB ALA A 1 1.801 -6.118 6.780 1.00 57.60 C
+ATOM 6 N ALA A 2 4.702 -4.829 4.989 1.00 44.72 N
+ATOM 7 CA ALA A 2 6.033 -4.319 5.297 1.00 39.74 C
+ATOM 8 C ALA A 2 6.471 -3.432 4.151 1.00 38.97 C
+ATOM 9 O ALA A 2 6.000 -3.558 3.005 1.00 35.65 O
+ATOM 10 CB ALA A 2 6.977 -5.471 5.509 1.00 39.07 C
+ATOM 11 N TYR A 3 7.381 -2.517 4.408 1.00 35.77 N
+ATOM 12 CA TYR A 3 7.706 -1.626 3.320 1.00 34.41 C
+ATOM 13 C TYR A 3 9.186 -1.384 3.280 1.00 33.59 C
+ATOM 14 O TYR A 3 9.923 -1.779 4.188 1.00 31.95 O
+ATOM 15 CB TYR A 3 6.953 -0.249 3.319 1.00 39.83 C
+ATOM 16 CG TYR A 3 5.433 -0.309 3.472 1.00 45.38 C
+ATOM 17 CD1 TYR A 3 4.627 -0.464 2.343 1.00 44.25 C
+ATOM 18 CD2 TYR A 3 4.849 -0.181 4.741 1.00 42.82 C
+ATOM 19 CE1 TYR A 3 3.235 -0.498 2.478 1.00 44.87 C
+ATOM 20 CE2 TYR A 3 3.455 -0.215 4.877 1.00 31.11 C
+ATOM 21 CZ TYR A 3 2.650 -0.374 3.744 1.00 36.82 C
+ATOM 22 OH TYR A 3 1.297 -0.407 3.867 1.00 45.94 O
+ATOM 23 N LYS A 4 9.588 -0.749 2.216 1.00 25.97 N
+ATOM 24 CA LYS A 4 10.996 -0.492 1.999 1.00 26.02 C
+ATOM 25 C LYS A 4 11.389 0.887 2.512 1.00 27.15 C
+ATOM 26 O LYS A 4 10.856 1.920 2.077 1.00 29.78 O
+ATOM 27 CB LYS A 4 11.330 -0.599 0.521 1.00 28.74 C
+ATOM 28 CG LYS A 4 12.767 -0.182 0.231 1.00 41.18 C
+ATOM 29 CD LYS A 4 13.579 -1.258 -0.483 1.00 65.99 C
+ATOM 30 CE LYS A 4 13.898 -2.462 0.403 1.00 71.21 C
+ATOM 31 NZ LYS A 4 15.116 -3.169 -0.011 1.00100.00 N
+ATOM 32 N VAL A 5 12.331 0.863 3.439 1.00 25.81 N
+ATOM 33 CA VAL A 5 12.856 2.091 4.022 1.00 21.97 C
+ATOM 34 C VAL A 5 14.205 2.397 3.480 1.00 24.32 C
+ATOM 35 O VAL A 5 15.049 1.515 3.638 1.00 28.20 O
+ATOM 36 CB VAL A 5 12.952 2.019 5.546 1.00 26.13 C
+ATOM 37 CG1 VAL A 5 13.589 3.279 6.154 1.00 24.03 C
+ATOM 38 CG2 VAL A 5 11.587 1.886 6.220 1.00 28.00 C
+ATOM 39 N THR A 6 14.446 3.585 2.881 1.00 23.42 N
+ATOM 40 CA THR A 6 15.819 3.958 2.510 1.00 22.77 C
+ATOM 41 C THR A 6 16.295 5.055 3.506 1.00 27.61 C
+ATOM 42 O THR A 6 15.661 6.102 3.654 1.00 28.00 O
+ATOM 43 CB THR A 6 15.821 4.529 1.094 1.00 26.23 C
+ATOM 44 OG1 THR A 6 15.370 3.515 0.217 1.00 27.15 O
+ATOM 45 CG2 THR A 6 17.230 4.964 0.813 1.00 27.17 C
+ATOM 46 N LEU A 7 17.379 4.897 4.238 1.00 20.82 N
+ATOM 47 CA LEU A 7 17.815 5.979 5.096 1.00 18.17 C
+ATOM 48 C LEU A 7 19.102 6.537 4.478 1.00 26.80 C
+ATOM 49 O LEU A 7 20.054 5.815 4.166 1.00 31.28 O
+ATOM 50 CB LEU A 7 18.204 5.474 6.533 1.00 24.27 C
+ATOM 51 CG LEU A 7 17.064 4.808 7.373 1.00 25.99 C
+ATOM 52 CD1 LEU A 7 17.597 4.132 8.670 1.00 28.24 C
+ATOM 53 CD2 LEU A 7 15.847 5.760 7.582 1.00 23.18 C
+ATOM 54 N VAL A 8 19.178 7.825 4.390 1.00 24.64 N
+ATOM 55 CA VAL A 8 20.351 8.582 3.937 1.00 24.53 C
+ATOM 56 C VAL A 8 21.067 9.037 5.189 1.00 25.60 C
+ATOM 57 O VAL A 8 20.609 10.034 5.788 1.00 24.85 O
+ATOM 58 CB VAL A 8 19.949 9.817 3.074 1.00 26.13 C
+ATOM 59 CG1 VAL A 8 21.154 10.667 2.669 1.00 26.51 C
+ATOM 60 CG2 VAL A 8 19.153 9.301 1.862 1.00 23.87 C
+ATOM 61 N THR A 9 22.132 8.282 5.580 1.00 23.15 N
+ATOM 62 CA THR A 9 22.863 8.664 6.790 1.00 23.40 C
+ATOM 63 C THR A 9 24.173 9.314 6.438 1.00 33.13 C
+ATOM 64 O THR A 9 24.654 9.241 5.303 1.00 31.04 O
+ATOM 65 CB THR A 9 23.218 7.469 7.641 1.00 29.07 C
+ATOM 66 OG1 THR A 9 24.437 6.916 7.123 1.00 34.25 O
+ATOM 67 CG2 THR A 9 22.097 6.424 7.576 1.00 23.85 C
+ATOM 68 N PRO A 10 24.773 9.907 7.443 1.00 32.74 N
+ATOM 69 CA PRO A 10 26.012 10.626 7.192 1.00 40.21 C
+ATOM 70 C PRO A 10 27.145 9.843 6.552 1.00 39.02 C
+ATOM 71 O PRO A 10 27.994 10.367 5.811 1.00 40.41 O
+ATOM 72 CB PRO A 10 26.365 11.354 8.512 1.00 40.85 C
+ATOM 73 CG PRO A 10 25.100 11.360 9.383 1.00 38.81 C
+ATOM 74 CD PRO A 10 24.169 10.310 8.772 1.00 29.25 C
+ATOM 75 N THR A 11 27.149 8.583 6.860 1.00 29.69 N
+ATOM 76 CA THR A 11 28.191 7.741 6.370 1.00 31.68 C
+ATOM 77 C THR A 11 27.680 6.836 5.253 1.00 40.26 C
+ATOM 78 O THR A 11 28.315 5.815 4.937 1.00 32.78 O
+ATOM 79 CB THR A 11 28.745 6.892 7.546 1.00 35.16 C
+ATOM 80 OG1 THR A 11 27.737 6.011 8.077 1.00 41.86 O
+ATOM 81 CG2 THR A 11 29.280 7.785 8.637 1.00 34.63 C
+ATOM 82 N GLY A 12 26.479 7.095 4.715 1.00 29.29 N
+ATOM 83 CA GLY A 12 26.019 6.151 3.680 1.00 27.67 C
+ATOM 84 C GLY A 12 24.548 5.765 3.657 1.00 31.61 C
+ATOM 85 O GLY A 12 23.861 5.746 4.657 1.00 27.16 O
+ATOM 86 N ASN A 13 24.028 5.411 2.492 1.00 27.49 N
+ATOM 87 CA ASN A 13 22.641 4.967 2.352 1.00 28.15 C
+ATOM 88 C ASN A 13 22.472 3.508 2.820 1.00 34.35 C
+ATOM 89 O ASN A 13 23.261 2.592 2.523 1.00 34.29 O
+ATOM 90 CB ASN A 13 22.229 5.041 0.859 1.00 22.27 C
+ATOM 91 CG ASN A 13 22.215 6.448 0.279 1.00 28.56 C
+ATOM 92 OD1 ASN A 13 22.151 7.484 0.966 1.00 29.38 O
+ATOM 93 ND2 ASN A 13 22.260 6.532 -1.054 1.00 29.02 N
+ATOM 94 N VAL A 14 21.376 3.154 3.448 1.00 24.93 N
+ATOM 95 CA VAL A 14 21.199 1.768 3.845 1.00 24.17 C
+ATOM 96 C VAL A 14 19.689 1.494 3.624 1.00 35.26 C
+ATOM 97 O VAL A 14 18.847 2.366 3.880 1.00 34.14 O
+ATOM 98 CB VAL A 14 21.457 1.553 5.350 1.00 35.72 C
+ATOM 99 CG1 VAL A 14 22.781 2.158 5.819 1.00 45.19 C
+ATOM 100 CG2 VAL A 14 20.379 2.191 6.228 1.00 37.45 C
+ATOM 101 N GLU A 15 19.318 0.319 3.133 1.00 25.56 N
+ATOM 102 CA GLU A 15 17.873 -0.022 2.949 1.00 24.81 C
+ATOM 103 C GLU A 15 17.513 -1.257 3.780 1.00 28.51 C
+ATOM 104 O GLU A 15 18.367 -2.054 4.152 1.00 39.92 O
+ATOM 105 CB GLU A 15 17.528 -0.396 1.499 1.00 26.55 C
+ATOM 106 CG GLU A 15 18.058 0.554 0.428 1.00 76.87 C
+ATOM 107 CD GLU A 15 17.768 0.033 -0.987 1.00100.00 C
+ATOM 108 OE1 GLU A 15 17.197 -1.116 -1.149 1.00 68.35 O
+ATOM 109 OE2 GLU A 15 18.097 0.737 -2.014 1.00100.00 O
+ATOM 110 N PHE A 16 16.247 -1.431 4.065 1.00 26.52 N
+ATOM 111 CA PHE A 16 15.777 -2.608 4.823 1.00 28.30 C
+ATOM 112 C PHE A 16 14.244 -2.584 4.803 1.00 33.00 C
+ATOM 113 O PHE A 16 13.635 -1.520 4.649 1.00 30.39 O
+ATOM 114 CB PHE A 16 16.306 -2.569 6.266 1.00 32.53 C
+ATOM 115 CG PHE A 16 15.886 -1.332 7.078 1.00 25.02 C
+ATOM 116 CD1 PHE A 16 14.640 -1.297 7.723 1.00 32.70 C
+ATOM 117 CD2 PHE A 16 16.753 -0.235 7.192 1.00 28.27 C
+ATOM 118 CE1 PHE A 16 14.269 -0.176 8.481 1.00 33.73 C
+ATOM 119 CE2 PHE A 16 16.383 0.883 7.952 1.00 30.83 C
+ATOM 120 CZ PHE A 16 15.142 0.913 8.597 1.00 28.38 C
+ATOM 121 N GLN A 17 13.645 -3.759 4.941 1.00 35.55 N
+ATOM 122 CA GLN A 17 12.164 -3.892 4.941 1.00 33.09 C
+ATOM 123 C GLN A 17 11.622 -3.664 6.368 1.00 36.52 C
+ATOM 124 O GLN A 17 12.161 -4.187 7.348 1.00 34.16 O
+ATOM 125 CB GLN A 17 11.745 -5.297 4.473 1.00 40.84 C
+ATOM 126 CG GLN A 17 12.118 -5.610 3.015 1.00 75.19 C
+ATOM 127 CD GLN A 17 11.176 -5.056 1.937 1.00100.00 C
+ATOM 128 OE1 GLN A 17 10.033 -5.500 1.819 1.00 91.53 O
+ATOM 129 NE2 GLN A 17 11.600 -4.099 1.131 1.00 56.40 N
+ATOM 130 N CYS A 18 10.541 -2.882 6.483 1.00 32.45 N
+ATOM 131 CA CYS A 18 9.949 -2.554 7.813 1.00 34.72 C
+ATOM 132 C CYS A 18 8.464 -2.778 7.839 1.00 34.29 C
+ATOM 133 O CYS A 18 7.700 -2.208 7.075 1.00 31.05 O
+ATOM 134 CB CYS A 18 10.249 -1.090 8.161 1.00 29.02 C
+ATOM 135 SG CYS A 18 9.658 -0.587 9.853 1.00 28.94 S
+ATOM 136 N PRO A 19 8.085 -3.629 8.787 1.00 33.32 N
+ATOM 137 CA PRO A 19 6.690 -3.963 9.026 1.00 32.10 C
+ATOM 138 C PRO A 19 6.006 -2.702 9.499 1.00 40.78 C
+ATOM 139 O PRO A 19 6.592 -1.893 10.222 1.00 36.47 O
+ATOM 140 CB PRO A 19 6.661 -5.023 10.134 1.00 34.58 C
+ATOM 141 CG PRO A 19 8.108 -5.439 10.360 1.00 38.47 C
+ATOM 142 CD PRO A 19 9.005 -4.461 9.587 1.00 36.38 C
+ATOM 143 N ASP A 20 4.761 -2.545 9.044 1.00 34.47 N
+ATOM 144 CA ASP A 20 3.939 -1.390 9.316 1.00 33.10 C
+ATOM 145 C ASP A 20 3.594 -1.249 10.782 1.00 37.33 C
+ATOM 146 O ASP A 20 3.007 -0.234 11.167 1.00 33.51 O
+ATOM 147 CB ASP A 20 2.776 -1.182 8.329 1.00 44.18 C
+ATOM 148 CG ASP A 20 1.663 -2.172 8.473 1.00 58.88 C
+ATOM 149 OD1 ASP A 20 1.737 -3.155 9.206 1.00 56.81 O
+ATOM 150 OD2 ASP A 20 0.598 -1.806 7.784 1.00 79.64 O
+ATOM 151 N ASP A 21 3.977 -2.293 11.543 1.00 35.64 N
+ATOM 152 CA ASP A 21 3.728 -2.237 12.962 1.00 40.82 C
+ATOM 153 C ASP A 21 4.983 -2.105 13.764 1.00 45.13 C
+ATOM 154 O ASP A 21 4.965 -2.495 14.923 1.00 45.86 O
+ATOM 155 CB ASP A 21 2.706 -3.233 13.568 1.00 39.20 C
+ATOM 156 CG ASP A 21 3.075 -4.710 13.573 1.00 64.17 C
+ATOM 157 OD1 ASP A 21 4.036 -5.157 12.965 1.00 61.46 O
+ATOM 158 OD2 ASP A 21 2.230 -5.476 14.256 1.00 79.00 O
+ATOM 159 N VAL A 22 6.067 -1.601 13.191 1.00 30.02 N
+ATOM 160 CA VAL A 22 7.303 -1.467 13.989 1.00 23.17 C
+ATOM 161 C VAL A 22 7.875 -0.083 13.703 1.00 37.42 C
+ATOM 162 O VAL A 22 7.841 0.425 12.545 1.00 29.14 O
+ATOM 163 CB VAL A 22 8.279 -2.554 13.524 1.00 35.95 C
+ATOM 164 CG1 VAL A 22 9.671 -2.333 14.072 1.00 33.42 C
+ATOM 165 CG2 VAL A 22 7.790 -3.977 13.845 1.00 40.60 C
+ATOM 166 N TYR A 23 8.319 0.603 14.747 1.00 31.07 N
+ATOM 167 CA TYR A 23 8.868 1.922 14.526 1.00 23.20 C
+ATOM 168 C TYR A 23 10.146 1.813 13.697 1.00 20.53 C
+ATOM 169 O TYR A 23 10.967 0.886 13.815 1.00 22.64 O
+ATOM 170 CB TYR A 23 9.207 2.601 15.864 1.00 24.89 C
+ATOM 171 CG TYR A 23 8.048 2.917 16.813 1.00 29.11 C
+ATOM 172 CD1 TYR A 23 6.967 3.710 16.422 1.00 25.37 C
+ATOM 173 CD2 TYR A 23 8.087 2.419 18.126 1.00 29.47 C
+ATOM 174 CE1 TYR A 23 5.959 3.981 17.342 1.00 33.05 C
+ATOM 175 CE2 TYR A 23 7.167 2.794 19.097 1.00 27.42 C
+ATOM 176 CZ TYR A 23 6.100 3.579 18.677 1.00 29.98 C
+ATOM 177 OH TYR A 23 5.135 3.895 19.566 1.00 32.49 O
+ATOM 178 N ILE A 24 10.358 2.857 12.891 1.00 26.63 N
+ATOM 179 CA ILE A 24 11.544 3.002 12.045 1.00 23.62 C
+ATOM 180 C ILE A 24 12.848 2.723 12.839 1.00 27.47 C
+ATOM 181 O ILE A 24 13.721 1.942 12.446 1.00 25.11 O
+ATOM 182 CB ILE A 24 11.530 4.355 11.265 1.00 27.34 C
+ATOM 183 CG1 ILE A 24 10.308 4.326 10.338 1.00 27.39 C
+ATOM 184 CG2 ILE A 24 12.839 4.618 10.484 1.00 25.71 C
+ATOM 185 CD1 ILE A 24 10.409 5.326 9.248 1.00 35.33 C
+ATOM 186 N LEU A 25 13.016 3.398 13.982 1.00 21.68 N
+ATOM 187 CA LEU A 25 14.226 3.232 14.751 1.00 23.19 C
+ATOM 188 C LEU A 25 14.494 1.805 15.152 1.00 19.67 C
+ATOM 189 O LEU A 25 15.622 1.287 15.036 1.00 21.97 O
+ATOM 190 CB LEU A 25 14.214 4.251 15.971 1.00 25.03 C
+ATOM 191 CG LEU A 25 15.399 4.134 16.985 1.00 33.85 C
+ATOM 192 CD1 LEU A 25 16.767 4.626 16.432 1.00 28.22 C
+ATOM 193 CD2 LEU A 25 15.003 4.794 18.321 1.00 23.35 C
+ATOM 194 N ASP A 26 13.445 1.170 15.740 1.00 21.80 N
+ATOM 195 CA ASP A 26 13.567 -0.238 16.197 1.00 24.22 C
+ATOM 196 C ASP A 26 13.968 -1.184 15.076 1.00 28.12 C
+ATOM 197 O ASP A 26 14.887 -2.035 15.191 1.00 26.29 O
+ATOM 198 CB ASP A 26 12.229 -0.815 16.715 1.00 26.64 C
+ATOM 199 CG ASP A 26 11.713 -0.170 18.009 1.00 37.98 C
+ATOM 200 OD1 ASP A 26 12.168 0.845 18.458 1.00 46.55 O
+ATOM 201 OD2 ASP A 26 10.581 -0.638 18.464 1.00 44.33 O
+ATOM 202 N ALA A 27 13.266 -0.995 13.938 1.00 28.45 N
+ATOM 203 CA ALA A 27 13.559 -1.804 12.709 1.00 30.31 C
+ATOM 204 C ALA A 27 15.013 -1.637 12.266 1.00 24.55 C
+ATOM 205 O ALA A 27 15.704 -2.620 11.990 1.00 26.78 O
+ATOM 206 CB ALA A 27 12.584 -1.510 11.550 1.00 27.80 C
+ATOM 207 N ALA A 28 15.467 -0.370 12.227 1.00 21.71 N
+ATOM 208 CA ALA A 28 16.844 -0.113 11.872 1.00 22.96 C
+ATOM 209 C ALA A 28 17.837 -0.801 12.830 1.00 31.14 C
+ATOM 210 O ALA A 28 18.866 -1.394 12.440 1.00 29.37 O
+ATOM 211 CB ALA A 28 17.190 1.365 11.769 1.00 30.64 C
+ATOM 212 N GLU A 29 17.519 -0.733 14.138 1.00 32.57 N
+ATOM 213 CA GLU A 29 18.383 -1.339 15.157 1.00 33.34 C
+ATOM 214 C GLU A 29 18.598 -2.824 14.926 1.00 23.91 C
+ATOM 215 O GLU A 29 19.748 -3.285 14.959 1.00 29.83 O
+ATOM 216 CB GLU A 29 17.921 -0.963 16.602 1.00 25.60 C
+ATOM 217 CG GLU A 29 18.305 0.502 16.913 1.00 24.44 C
+ATOM 218 CD GLU A 29 17.457 1.018 18.046 1.00 25.19 C
+ATOM 219 OE1 GLU A 29 16.460 0.426 18.438 1.00 24.78 O
+ATOM 220 OE2 GLU A 29 17.923 2.098 18.586 1.00 23.81 O
+ATOM 221 N GLU A 30 17.448 -3.455 14.709 1.00 27.47 N
+ATOM 222 CA GLU A 30 17.286 -4.882 14.380 1.00 37.83 C
+ATOM 223 C GLU A 30 18.140 -5.359 13.188 1.00 40.11 C
+ATOM 224 O GLU A 30 18.573 -6.495 13.120 1.00 39.63 O
+ATOM 225 CB GLU A 30 15.794 -5.252 14.170 1.00 40.07 C
+ATOM 226 CG GLU A 30 14.957 -5.155 15.458 1.00 42.44 C
+ATOM 227 CD GLU A 30 13.539 -5.612 15.275 1.00 56.36 C
+ATOM 228 OE1 GLU A 30 13.164 -6.260 14.314 1.00 50.54 O
+ATOM 229 OE2 GLU A 30 12.725 -5.114 16.174 1.00 36.99 O
+ATOM 230 N GLU A 31 18.344 -4.473 12.222 1.00 38.32 N
+ATOM 231 CA GLU A 31 19.177 -4.703 11.071 1.00 35.60 C
+ATOM 232 C GLU A 31 20.646 -4.398 11.378 1.00 52.16 C
+ATOM 233 O GLU A 31 21.518 -4.562 10.510 1.00 49.05 O
+ATOM 234 CB GLU A 31 18.620 -3.894 9.866 1.00 32.36 C
+ATOM 235 CG GLU A 31 17.343 -4.552 9.270 1.00 42.97 C
+ATOM 236 CD GLU A 31 17.511 -6.010 8.860 1.00 67.41 C
+ATOM 237 OE1 GLU A 31 18.482 -6.441 8.262 1.00 80.04 O
+ATOM 238 OE2 GLU A 31 16.571 -6.805 9.318 1.00 80.93 O
+ATOM 239 N GLY A 32 20.934 -3.911 12.608 1.00 36.45 N
+ATOM 240 CA GLY A 32 22.297 -3.587 13.006 1.00 31.78 C
+ATOM 241 C GLY A 32 22.778 -2.203 12.703 1.00 31.69 C
+ATOM 242 O GLY A 32 23.972 -1.976 12.642 1.00 34.57 O
+ATOM 243 N ILE A 33 21.850 -1.251 12.501 1.00 35.35 N
+ATOM 244 CA ILE A 33 22.177 0.144 12.177 1.00 28.42 C
+ATOM 245 C ILE A 33 22.256 1.009 13.444 1.00 33.98 C
+ATOM 246 O ILE A 33 21.378 0.942 14.287 1.00 32.45 O
+ATOM 247 CB ILE A 33 21.135 0.765 11.251 1.00 31.00 C
+ATOM 248 CG1 ILE A 33 20.902 -0.025 9.950 1.00 47.25 C
+ATOM 249 CG2 ILE A 33 21.426 2.216 10.846 1.00 27.16 C
+ATOM 250 CD1 ILE A 33 19.920 0.766 9.061 1.00 51.98 C
+ATOM 251 N ASP A 34 23.258 1.860 13.579 1.00 31.29 N
+ATOM 252 CA ASP A 34 23.303 2.712 14.757 1.00 34.35 C
+ATOM 253 C ASP A 34 22.744 4.100 14.464 1.00 43.06 C
+ATOM 254 O ASP A 34 23.349 4.874 13.724 1.00 33.14 O
+ATOM 255 CB ASP A 34 24.761 2.854 15.196 1.00 38.16 C
+ATOM 256 CG ASP A 34 24.920 3.628 16.465 1.00 60.77 C
+ATOM 257 OD1 ASP A 34 24.013 4.180 17.048 1.00 67.71 O
+ATOM 258 OD2 ASP A 34 26.160 3.670 16.870 1.00100.00 O
+ATOM 259 N LEU A 35 21.606 4.432 15.063 1.00 25.84 N
+ATOM 260 CA LEU A 35 20.982 5.725 14.886 1.00 25.49 C
+ATOM 261 C LEU A 35 20.972 6.503 16.230 1.00 30.02 C
+ATOM 262 O LEU A 35 20.894 5.970 17.324 1.00 30.20 O
+ATOM 263 CB LEU A 35 19.524 5.626 14.330 1.00 29.86 C
+ATOM 264 CG LEU A 35 19.326 4.995 12.913 1.00 34.99 C
+ATOM 265 CD1 LEU A 35 17.826 5.101 12.508 1.00 25.92 C
+ATOM 266 CD2 LEU A 35 20.204 5.766 11.885 1.00 28.46 C
+ATOM 267 N PRO A 36 20.991 7.774 16.189 1.00 24.98 N
+ATOM 268 CA PRO A 36 20.915 8.450 17.496 1.00 27.92 C
+ATOM 269 C PRO A 36 19.519 8.369 18.150 1.00 34.05 C
+ATOM 270 O PRO A 36 18.406 8.438 17.518 1.00 24.43 O
+ATOM 271 CB PRO A 36 21.187 9.939 17.172 1.00 25.14 C
+ATOM 272 CG PRO A 36 21.223 10.101 15.644 1.00 33.38 C
+ATOM 273 CD PRO A 36 21.123 8.723 15.027 1.00 27.27 C
+ATOM 274 N TYR A 37 19.578 8.381 19.481 1.00 24.54 N
+ATOM 275 CA TYR A 37 18.347 8.494 20.237 1.00 24.90 C
+ATOM 276 C TYR A 37 18.650 8.899 21.687 1.00 44.09 C
+ATOM 277 O TYR A 37 19.790 8.838 22.140 1.00 28.24 O
+ATOM 278 CB TYR A 37 17.491 7.256 20.362 1.00 18.81 C
+ATOM 279 CG TYR A 37 18.233 6.159 21.122 1.00 24.63 C
+ATOM 280 CD1 TYR A 37 19.137 5.311 20.464 1.00 26.04 C
+ATOM 281 CD2 TYR A 37 18.018 5.944 22.486 1.00 29.97 C
+ATOM 282 CE1 TYR A 37 19.817 4.294 21.132 1.00 30.23 C
+ATOM 283 CE2 TYR A 37 18.673 4.912 23.167 1.00 24.88 C
+ATOM 284 CZ TYR A 37 19.581 4.091 22.501 1.00 30.95 C
+ATOM 285 OH TYR A 37 20.213 3.062 23.175 1.00 38.22 O
+ATOM 286 N SER A 38 17.595 9.277 22.418 1.00 29.18 N
+ATOM 287 CA SER A 38 17.725 9.558 23.845 1.00 32.26 C
+ATOM 288 C SER A 38 16.490 9.055 24.659 1.00 25.30 C
+ATOM 289 O SER A 38 16.606 7.975 25.282 1.00 25.32 O
+ATOM 290 CB SER A 38 18.302 10.927 24.200 1.00 22.00 C
+ATOM 291 OG SER A 38 17.293 11.869 24.016 1.00 33.52 O
+ATOM 292 N CYS A 39 15.380 9.816 24.591 1.00 23.71 N
+ATOM 293 CA CYS A 39 14.183 9.490 25.362 1.00 26.55 C
+ATOM 294 C CYS A 39 13.438 8.285 24.842 1.00 34.48 C
+ATOM 295 O CYS A 39 12.786 7.587 25.618 1.00 26.18 O
+ATOM 296 CB CYS A 39 13.199 10.697 25.491 1.00 29.83 C
+ATOM 297 SG CYS A 39 12.242 11.025 23.939 1.00 29.79 S
+ATOM 298 N ARG A 40 13.487 8.054 23.495 1.00 24.58 N
+ATOM 299 CA ARG A 40 12.723 6.913 22.913 1.00 28.18 C
+ATOM 300 C ARG A 40 11.205 7.064 23.170 1.00 30.09 C
+ATOM 301 O ARG A 40 10.487 6.085 23.025 1.00 31.35 O
+ATOM 302 CB ARG A 40 13.215 5.463 23.156 1.00 26.06 C
+ATOM 303 CG ARG A 40 14.725 5.291 22.954 1.00 26.48 C
+ATOM 304 CD ARG A 40 15.197 3.855 23.177 1.00 29.25 C
+ATOM 305 NE ARG A 40 14.665 2.882 22.173 1.00 29.50 N
+ATOM 306 CZ ARG A 40 15.384 2.358 21.164 1.00 24.32 C
+ATOM 307 NH1 ARG A 40 16.675 2.663 20.962 1.00 22.08 N
+ATOM 308 NH2 ARG A 40 14.730 1.522 20.369 1.00 24.44 N
+ATOM 309 N ALA A 41 10.703 8.251 23.551 1.00 30.98 N
+ATOM 310 CA ALA A 41 9.258 8.340 23.833 1.00 35.10 C
+ATOM 311 C ALA A 41 8.586 9.429 23.005 1.00 32.60 C
+ATOM 312 O ALA A 41 7.617 9.978 23.480 1.00 33.61 O
+ATOM 313 CB ALA A 41 9.061 8.685 25.305 1.00 32.00 C
+ATOM 314 N GLY A 42 9.184 9.924 21.887 1.00 37.71 N
+ATOM 315 CA GLY A 42 8.569 11.038 21.100 1.00 32.94 C
+ATOM 316 C GLY A 42 8.463 12.452 21.726 1.00 33.79 C
+ATOM 317 O GLY A 42 7.614 13.321 21.347 1.00 27.19 O
+ATOM 318 N SER A 43 9.383 12.734 22.670 1.00 29.21 N
+ATOM 319 CA SER A 43 9.217 14.009 23.222 1.00 27.72 C
+ATOM 320 C SER A 43 10.468 14.838 23.104 1.00 36.35 C
+ATOM 321 O SER A 43 10.575 15.886 23.772 1.00 37.69 O
+ATOM 322 CB SER A 43 8.702 13.848 24.657 1.00 41.18 C
+ATOM 323 OG SER A 43 9.762 13.391 25.438 1.00 37.35 O
+ATOM 324 N CYS A 44 11.424 14.383 22.281 1.00 24.01 N
+ATOM 325 CA CYS A 44 12.645 15.163 22.186 1.00 26.72 C
+ATOM 326 C CYS A 44 13.177 15.352 20.744 1.00 34.67 C
+ATOM 327 O CYS A 44 12.489 14.868 19.850 1.00 30.25 O
+ATOM 328 CB CYS A 44 13.745 14.604 23.122 1.00 22.69 C
+ATOM 329 SG CYS A 44 14.770 13.299 22.485 1.00 24.81 S
+ATOM 330 N SER A 45 14.308 16.078 20.499 1.00 24.73 N
+ATOM 331 CA SER A 45 14.777 16.268 19.112 1.00 26.39 C
+ATOM 332 C SER A 45 15.868 15.266 18.722 1.00 30.37 C
+ATOM 333 O SER A 45 16.412 15.218 17.615 1.00 28.25 O
+ATOM 334 CB SER A 45 15.275 17.674 18.949 1.00 27.38 C
+ATOM 335 OG SER A 45 16.431 17.813 19.806 1.00 29.38 O
+ATOM 336 N SER A 46 16.301 14.457 19.674 1.00 21.91 N
+ATOM 337 CA SER A 46 17.426 13.616 19.381 1.00 21.12 C
+ATOM 338 C SER A 46 17.353 12.724 18.144 1.00 25.42 C
+ATOM 339 O SER A 46 18.410 12.471 17.586 1.00 26.31 O
+ATOM 340 CB SER A 46 17.834 12.702 20.561 1.00 28.46 C
+ATOM 341 OG SER A 46 18.253 13.537 21.616 1.00 36.10 O
+ATOM 342 N CYS A 47 16.247 12.026 17.904 1.00 21.93 N
+ATOM 343 CA CYS A 47 16.202 11.056 16.827 1.00 21.80 C
+ATOM 344 C CYS A 47 15.649 11.698 15.536 1.00 21.02 C
+ATOM 345 O CYS A 47 15.149 10.997 14.648 1.00 23.37 O
+ATOM 346 CB CYS A 47 15.227 9.940 17.245 1.00 20.46 C
+ATOM 347 SG CYS A 47 13.560 10.572 17.479 1.00 24.27 S
+ATOM 348 N ALA A 48 15.664 12.998 15.481 1.00 23.57 N
+ATOM 349 CA ALA A 48 15.062 13.721 14.300 1.00 27.12 C
+ATOM 350 C ALA A 48 15.728 13.356 12.956 1.00 23.33 C
+ATOM 351 O ALA A 48 16.985 13.288 12.810 1.00 22.29 O
+ATOM 352 CB ALA A 48 15.001 15.246 14.459 1.00 23.21 C
+ATOM 353 N GLY A 49 14.841 13.313 11.994 1.00 26.74 N
+ATOM 354 CA GLY A 49 15.186 13.132 10.580 1.00 29.02 C
+ATOM 355 C GLY A 49 14.265 14.081 9.719 1.00 28.23 C
+ATOM 356 O GLY A 49 13.303 14.752 10.210 1.00 20.19 O
+ATOM 357 N LYS A 50 14.518 14.061 8.367 1.00 22.94 N
+ATOM 358 CA LYS A 50 13.710 14.863 7.373 1.00 21.93 C
+ATOM 359 C LYS A 50 13.181 13.817 6.316 1.00 27.46 C
+ATOM 360 O LYS A 50 13.986 13.010 5.743 1.00 22.40 O
+ATOM 361 CB LYS A 50 14.564 15.966 6.685 1.00 22.08 C
+ATOM 362 CG LYS A 50 14.605 17.254 7.500 1.00 70.03 C
+ATOM 363 CD LYS A 50 13.535 18.294 7.153 1.00 70.65 C
+ATOM 364 CE LYS A 50 14.198 19.537 6.556 1.00 95.81 C
+ATOM 365 NZ LYS A 50 13.315 20.498 5.873 1.00100.00 N
+ATOM 366 N LEU A 51 11.843 13.756 6.190 1.00 23.93 N
+ATOM 367 CA LEU A 51 11.182 12.820 5.242 1.00 22.04 C
+ATOM 368 C LEU A 51 11.343 13.464 3.811 1.00 26.89 C
+ATOM 369 O LEU A 51 11.019 14.617 3.489 1.00 26.02 O
+ATOM 370 CB LEU A 51 9.711 12.786 5.619 1.00 23.42 C
+ATOM 371 CG LEU A 51 8.853 12.151 4.557 1.00 26.07 C
+ATOM 372 CD1 LEU A 51 9.040 10.663 4.609 1.00 32.32 C
+ATOM 373 CD2 LEU A 51 7.389 12.360 4.843 1.00 35.33 C
+ATOM 374 N LYS A 52 11.980 12.719 2.963 1.00 24.44 N
+ATOM 375 CA LYS A 52 12.215 13.149 1.602 1.00 23.16 C
+ATOM 376 C LYS A 52 11.098 12.677 0.642 1.00 30.50 C
+ATOM 377 O LYS A 52 10.510 13.473 -0.152 1.00 32.15 O
+ATOM 378 CB LYS A 52 13.547 12.573 1.200 1.00 24.68 C
+ATOM 379 CG LYS A 52 14.590 13.069 2.203 1.00 61.41 C
+ATOM 380 CD LYS A 52 14.704 14.575 2.120 1.00 88.91 C
+ATOM 381 CE LYS A 52 15.163 15.276 3.378 1.00 99.36 C
+ATOM 382 NZ LYS A 52 15.668 16.630 3.069 1.00100.00 N
+ATOM 383 N THR A 53 10.723 11.429 0.796 1.00 22.25 N
+ATOM 384 CA THR A 53 9.693 10.822 -0.062 1.00 24.34 C
+ATOM 385 C THR A 53 8.818 9.802 0.661 1.00 27.89 C
+ATOM 386 O THR A 53 9.369 8.972 1.390 1.00 28.95 O
+ATOM 387 CB THR A 53 10.434 9.920 -1.104 1.00 31.58 C
+ATOM 388 OG1 THR A 53 11.485 10.615 -1.745 1.00 36.65 O
+ATOM 389 CG2 THR A 53 9.392 9.465 -2.097 1.00 28.92 C
+ATOM 390 N GLY A 54 7.520 9.785 0.437 1.00 23.82 N
+ATOM 391 CA GLY A 54 6.697 8.779 1.103 1.00 22.96 C
+ATOM 392 C GLY A 54 5.747 9.381 2.211 1.00 21.97 C
+ATOM 393 O GLY A 54 5.664 10.588 2.423 1.00 25.52 O
+ATOM 394 N SER A 55 5.072 8.494 2.960 1.00 25.22 N
+ATOM 395 CA SER A 55 4.154 8.875 4.011 1.00 28.49 C
+ATOM 396 C SER A 55 4.486 8.103 5.302 1.00 24.34 C
+ATOM 397 O SER A 55 4.973 6.965 5.258 1.00 27.68 O
+ATOM 398 CB SER A 55 2.761 8.352 3.609 1.00 29.79 C
+ATOM 399 OG SER A 55 2.398 8.865 2.336 1.00 41.45 O
+ATOM 400 N LEU A 56 4.183 8.723 6.426 1.00 26.66 N
+ATOM 401 CA LEU A 56 4.424 8.134 7.760 1.00 25.62 C
+ATOM 402 C LEU A 56 3.240 8.370 8.687 1.00 30.33 C
+ATOM 403 O LEU A 56 2.434 9.273 8.469 1.00 29.36 O
+ATOM 404 CB LEU A 56 5.559 8.867 8.490 1.00 26.75 C
+ATOM 405 CG LEU A 56 6.906 8.861 7.782 1.00 34.83 C
+ATOM 406 CD1 LEU A 56 7.858 9.937 8.326 1.00 29.42 C
+ATOM 407 CD2 LEU A 56 7.639 7.531 7.941 1.00 28.43 C
+ATOM 408 N ASN A 57 3.150 7.556 9.719 1.00 28.09 N
+ATOM 409 CA ASN A 57 2.162 7.782 10.791 1.00 24.87 C
+ATOM 410 C ASN A 57 2.970 8.183 12.032 1.00 23.91 C
+ATOM 411 O ASN A 57 3.748 7.365 12.556 1.00 25.64 O
+ATOM 412 CB ASN A 57 1.327 6.524 11.056 1.00 26.11 C
+ATOM 413 CG ASN A 57 0.408 6.647 12.288 1.00 35.12 C
+ATOM 414 OD1 ASN A 57 0.559 7.569 13.092 1.00 40.95 O
+ATOM 415 ND2 ASN A 57 -0.544 5.753 12.492 1.00 41.01 N
+ATOM 416 N GLN A 58 2.776 9.444 12.447 1.00 27.37 N
+ATOM 417 CA GLN A 58 3.511 10.052 13.595 1.00 31.76 C
+ATOM 418 C GLN A 58 2.582 10.362 14.800 1.00 34.04 C
+ATOM 419 O GLN A 58 2.879 11.183 15.671 1.00 29.19 O
+ATOM 420 CB GLN A 58 4.233 11.333 13.150 1.00 25.80 C
+ATOM 421 CG GLN A 58 5.444 11.050 12.242 1.00 28.40 C
+ATOM 422 CD GLN A 58 6.459 12.201 12.190 1.00 47.72 C
+ATOM 423 OE1 GLN A 58 6.420 13.019 11.268 1.00 34.30 O
+ATOM 424 NE2 GLN A 58 7.377 12.316 13.133 1.00 26.13 N
+ATOM 425 N ASP A 59 1.433 9.693 14.869 1.00 36.72 N
+ATOM 426 CA ASP A 59 0.490 9.937 15.971 1.00 38.66 C
+ATOM 427 C ASP A 59 1.091 9.815 17.356 1.00 35.94 C
+ATOM 428 O ASP A 59 0.654 10.514 18.266 1.00 39.04 O
+ATOM 429 CB ASP A 59 -0.584 8.841 15.935 1.00 42.70 C
+ATOM 430 CG ASP A 59 -1.530 8.991 14.788 1.00 46.32 C
+ATOM 431 OD1 ASP A 59 -1.658 10.028 14.186 1.00 38.83 O
+ATOM 432 OD2 ASP A 59 -2.364 7.994 14.691 1.00 59.49 O
+ATOM 433 N ASP A 60 1.995 8.847 17.545 1.00 24.98 N
+ATOM 434 CA ASP A 60 2.571 8.658 18.857 1.00 24.28 C
+ATOM 435 C ASP A 60 3.580 9.740 19.204 1.00 40.65 C
+ATOM 436 O ASP A 60 4.138 9.656 20.278 1.00 43.03 O
+ATOM 437 CB ASP A 60 3.322 7.326 18.890 1.00 27.18 C
+ATOM 438 CG ASP A 60 2.315 6.216 18.808 1.00 57.16 C
+ATOM 439 OD1 ASP A 60 1.117 6.432 18.881 1.00 51.58 O
+ATOM 440 OD2 ASP A 60 2.833 5.017 18.626 1.00 41.88 O
+ATOM 441 N GLN A 61 3.968 10.668 18.334 1.00 27.55 N
+ATOM 442 CA GLN A 61 4.973 11.625 18.768 1.00 30.08 C
+ATOM 443 C GLN A 61 4.316 12.872 19.438 1.00 40.72 C
+ATOM 444 O GLN A 61 3.179 13.216 19.124 1.00 34.19 O
+ATOM 445 CB GLN A 61 5.776 12.028 17.544 1.00 33.63 C
+ATOM 446 CG GLN A 61 5.117 13.131 16.681 1.00 25.93 C
+ATOM 447 CD GLN A 61 5.331 14.519 17.217 1.00 28.73 C
+ATOM 448 OE1 GLN A 61 6.402 14.827 17.721 1.00 30.35 O
+ATOM 449 NE2 GLN A 61 4.427 15.450 16.881 1.00 35.06 N
+ATOM 450 N SER A 62 4.967 13.636 20.333 1.00 27.75 N
+ATOM 451 CA SER A 62 4.283 14.824 20.910 1.00 30.90 C
+ATOM 452 C SER A 62 5.077 16.100 20.909 1.00 36.75 C
+ATOM 453 O SER A 62 4.690 17.110 21.441 1.00 52.66 O
+ATOM 454 CB SER A 62 3.864 14.633 22.379 1.00 35.95 C
+ATOM 455 OG SER A 62 4.952 14.105 23.125 1.00 46.21 O
+ATOM 456 N PHE A 63 6.252 16.067 20.384 1.00 29.60 N
+ATOM 457 CA PHE A 63 7.102 17.228 20.417 1.00 27.99 C
+ATOM 458 C PHE A 63 6.946 18.183 19.229 1.00 31.11 C
+ATOM 459 O PHE A 63 7.002 19.359 19.419 1.00 27.26 O
+ATOM 460 CB PHE A 63 8.530 16.630 20.559 1.00 25.49 C
+ATOM 461 CG PHE A 63 9.618 17.648 20.427 1.00 30.88 C
+ATOM 462 CD1 PHE A 63 9.947 18.463 21.509 1.00 26.86 C
+ATOM 463 CD2 PHE A 63 10.321 17.816 19.230 1.00 29.02 C
+ATOM 464 CE1 PHE A 63 11.013 19.366 21.435 1.00 29.07 C
+ATOM 465 CE2 PHE A 63 11.373 18.727 19.142 1.00 29.76 C
+ATOM 466 CZ PHE A 63 11.726 19.519 20.243 1.00 33.72 C
+ATOM 467 N LEU A 64 6.865 17.724 17.971 1.00 25.68 N
+ATOM 468 CA LEU A 64 6.831 18.662 16.842 1.00 24.82 C
+ATOM 469 C LEU A 64 5.450 19.287 16.739 1.00 26.70 C
+ATOM 470 O LEU A 64 4.460 18.591 16.986 1.00 31.40 O
+ATOM 471 CB LEU A 64 7.034 17.871 15.491 1.00 22.47 C
+ATOM 472 CG LEU A 64 8.369 17.086 15.396 1.00 29.46 C
+ATOM 473 CD1 LEU A 64 8.417 16.185 14.142 1.00 30.53 C
+ATOM 474 CD2 LEU A 64 9.647 17.977 15.456 1.00 24.48 C
+ATOM 475 N ASP A 65 5.405 20.538 16.305 1.00 28.62 N
+ATOM 476 CA ASP A 65 4.152 21.243 16.006 1.00 34.60 C
+ATOM 477 C ASP A 65 3.666 20.894 14.548 1.00 41.36 C
+ATOM 478 O ASP A 65 4.444 20.342 13.747 1.00 26.86 O
+ATOM 479 CB ASP A 65 4.279 22.755 16.344 1.00 31.77 C
+ATOM 480 CG ASP A 65 5.013 23.596 15.359 1.00 47.04 C
+ATOM 481 OD1 ASP A 65 5.134 23.317 14.193 1.00 48.63 O
+ATOM 482 OD2 ASP A 65 5.539 24.667 15.877 1.00 71.08 O
+ATOM 483 N ASP A 66 2.394 21.176 14.206 1.00 31.65 N
+ATOM 484 CA ASP A 66 1.862 20.859 12.888 1.00 33.85 C
+ATOM 485 C ASP A 66 2.718 21.427 11.772 1.00 38.51 C
+ATOM 486 O ASP A 66 2.894 20.807 10.719 1.00 38.50 O
+ATOM 487 CB ASP A 66 0.336 21.139 12.705 1.00 35.51 C
+ATOM 488 CG ASP A 66 -0.498 20.102 13.425 1.00 95.83 C
+ATOM 489 OD1 ASP A 66 -0.319 18.893 13.287 1.00100.00 O
+ATOM 490 OD2 ASP A 66 -1.318 20.615 14.323 1.00 84.76 O
+ATOM 491 N ASP A 67 3.271 22.611 12.040 1.00 33.26 N
+ATOM 492 CA ASP A 67 4.128 23.303 11.083 1.00 33.10 C
+ATOM 493 C ASP A 67 5.410 22.560 10.803 1.00 45.29 C
+ATOM 494 O ASP A 67 5.837 22.433 9.647 1.00 34.92 O
+ATOM 495 CB ASP A 67 4.521 24.678 11.546 1.00 31.04 C
+ATOM 496 CG ASP A 67 3.513 25.724 11.117 1.00 90.55 C
+ATOM 497 OD1 ASP A 67 2.330 25.355 10.766 1.00 92.64 O
+ATOM 498 OD2 ASP A 67 3.854 26.959 11.106 1.00100.00 O
+ATOM 499 N GLN A 68 6.015 22.094 11.853 1.00 38.59 N
+ATOM 500 CA GLN A 68 7.260 21.369 11.718 1.00 32.76 C
+ATOM 501 C GLN A 68 7.016 20.090 10.901 1.00 26.08 C
+ATOM 502 O GLN A 68 7.814 19.732 10.023 1.00 30.32 O
+ATOM 503 CB GLN A 68 7.820 21.057 13.091 1.00 22.57 C
+ATOM 504 CG GLN A 68 8.535 22.262 13.705 1.00 26.78 C
+ATOM 505 CD GLN A 68 8.904 22.067 15.173 1.00 35.57 C
+ATOM 506 OE1 GLN A 68 8.118 21.511 15.936 1.00 29.91 O
+ATOM 507 NE2 GLN A 68 10.069 22.499 15.619 1.00 29.90 N
+ATOM 508 N ILE A 69 5.903 19.435 11.205 1.00 25.11 N
+ATOM 509 CA ILE A 69 5.499 18.196 10.509 1.00 27.87 C
+ATOM 510 C ILE A 69 5.327 18.483 9.019 1.00 34.66 C
+ATOM 511 O ILE A 69 5.811 17.729 8.162 1.00 29.47 O
+ATOM 512 CB ILE A 69 4.171 17.674 11.063 1.00 32.70 C
+ATOM 513 CG1 ILE A 69 4.302 17.089 12.470 1.00 40.33 C
+ATOM 514 CG2 ILE A 69 3.565 16.559 10.207 1.00 29.13 C
+ATOM 515 CD1 ILE A 69 5.045 15.752 12.495 1.00 32.83 C
+ATOM 516 N ASP A 70 4.637 19.573 8.776 1.00 31.86 N
+ATOM 517 CA ASP A 70 4.370 20.072 7.426 1.00 38.31 C
+ATOM 518 C ASP A 70 5.714 20.306 6.684 1.00 40.55 C
+ATOM 519 O ASP A 70 5.839 20.039 5.474 1.00 48.39 O
+ATOM 520 CB ASP A 70 3.604 21.400 7.532 1.00 52.17 C
+ATOM 521 CG ASP A 70 2.078 21.257 7.683 1.00 55.19 C
+ATOM 522 OD1 ASP A 70 1.545 20.107 7.915 1.00 80.92 O
+ATOM 523 OD2 ASP A 70 1.323 22.303 7.572 1.00 63.35 O
+ATOM 524 N GLU A 71 6.703 20.810 7.446 1.00 34.13 N
+ATOM 525 CA GLU A 71 8.074 21.120 6.933 1.00 34.15 C
+ATOM 526 C GLU A 71 8.794 19.823 6.526 1.00 30.41 C
+ATOM 527 O GLU A 71 9.763 19.846 5.748 1.00 35.23 O
+ATOM 528 CB GLU A 71 8.924 21.851 8.000 1.00 41.29 C
+ATOM 529 CG GLU A 71 8.882 23.387 7.868 1.00 64.85 C
+ATOM 530 CD GLU A 71 10.268 24.068 7.864 1.00100.00 C
+ATOM 531 OE1 GLU A 71 11.290 23.479 8.387 1.00 55.31 O
+ATOM 532 OE2 GLU A 71 10.413 25.243 7.337 1.00100.00 O
+ATOM 533 N GLY A 72 8.295 18.726 7.081 1.00 27.79 N
+ATOM 534 CA GLY A 72 8.784 17.369 6.766 1.00 32.80 C
+ATOM 535 C GLY A 72 9.646 16.761 7.895 1.00 32.09 C
+ATOM 536 O GLY A 72 10.348 15.757 7.699 1.00 25.25 O
+ATOM 537 N TRP A 73 9.595 17.356 9.076 1.00 22.23 N
+ATOM 538 CA TRP A 73 10.383 16.849 10.220 1.00 21.49 C
+ATOM 539 C TRP A 73 9.765 15.543 10.734 1.00 26.19 C
+ATOM 540 O TRP A 73 8.548 15.414 10.743 1.00 26.06 O
+ATOM 541 CB TRP A 73 10.454 17.886 11.341 1.00 23.52 C
+ATOM 542 CG TRP A 73 11.396 19.048 11.007 1.00 26.22 C
+ATOM 543 CD1 TRP A 73 11.039 20.269 10.605 1.00 28.20 C
+ATOM 544 CD2 TRP A 73 12.823 19.008 11.067 1.00 24.95 C
+ATOM 545 NE1 TRP A 73 12.238 21.017 10.401 1.00 28.21 N
+ATOM 546 CE2 TRP A 73 13.272 20.262 10.674 1.00 34.89 C
+ATOM 547 CE3 TRP A 73 13.768 18.030 11.414 1.00 24.84 C
+ATOM 548 CZ2 TRP A 73 14.626 20.610 10.598 1.00 32.01 C
+ATOM 549 CZ3 TRP A 73 15.133 18.390 11.338 1.00 28.18 C
+ATOM 550 CH2 TRP A 73 15.540 19.620 10.948 1.00 32.61 C
+ATOM 551 N VAL A 74 10.593 14.559 11.200 1.00 23.35 N
+ATOM 552 CA VAL A 74 10.113 13.267 11.705 1.00 26.91 C
+ATOM 553 C VAL A 74 10.908 12.880 12.956 1.00 21.84 C
+ATOM 554 O VAL A 74 12.136 13.080 12.973 1.00 22.56 O
+ATOM 555 CB VAL A 74 10.512 12.092 10.734 1.00 34.43 C
+ATOM 556 CG1 VAL A 74 9.845 10.767 11.131 1.00 31.94 C
+ATOM 557 CG2 VAL A 74 10.272 12.404 9.276 1.00 34.41 C
+ATOM 558 N LEU A 75 10.212 12.238 13.882 1.00 23.50 N
+ATOM 559 CA LEU A 75 10.892 11.635 15.066 1.00 25.89 C
+ATOM 560 C LEU A 75 10.923 10.134 14.847 1.00 21.88 C
+ATOM 561 O LEU A 75 9.878 9.418 14.894 1.00 24.28 O
+ATOM 562 CB LEU A 75 10.252 12.047 16.425 1.00 24.52 C
+ATOM 563 CG LEU A 75 10.262 13.564 16.716 1.00 29.19 C
+ATOM 564 CD1 LEU A 75 9.589 13.895 18.095 1.00 27.15 C
+ATOM 565 CD2 LEU A 75 11.679 14.128 16.642 1.00 24.99 C
+ATOM 566 N THR A 76 12.124 9.633 14.510 1.00 20.95 N
+ATOM 567 CA THR A 76 12.251 8.258 14.122 1.00 22.14 C
+ATOM 568 C THR A 76 11.899 7.212 15.221 1.00 25.69 C
+ATOM 569 O THR A 76 11.533 6.102 14.878 1.00 20.55 O
+ATOM 570 CB THR A 76 13.595 7.943 13.417 1.00 29.14 C
+ATOM 571 OG1 THR A 76 14.619 8.070 14.358 1.00 22.12 O
+ATOM 572 CG2 THR A 76 13.851 8.815 12.151 1.00 21.65 C
+ATOM 573 N CYS A 77 11.936 7.604 16.523 1.00 19.42 N
+ATOM 574 CA CYS A 77 11.573 6.588 17.500 1.00 23.31 C
+ATOM 575 C CYS A 77 10.080 6.382 17.585 1.00 23.91 C
+ATOM 576 O CYS A 77 9.604 5.521 18.330 1.00 27.19 O
+ATOM 577 CB CYS A 77 12.096 7.056 18.896 1.00 26.08 C
+ATOM 578 SG CYS A 77 11.280 8.530 19.603 1.00 24.96 S
+ATOM 579 N ALA A 78 9.316 7.248 16.935 1.00 20.23 N
+ATOM 580 CA ALA A 78 7.844 7.176 17.084 1.00 26.31 C
+ATOM 581 C ALA A 78 7.033 7.191 15.789 1.00 36.64 C
+ATOM 582 O ALA A 78 5.853 7.565 15.774 1.00 30.28 O
+ATOM 583 CB ALA A 78 7.355 8.353 17.931 1.00 24.52 C
+ATOM 584 N ALA A 79 7.710 6.814 14.700 1.00 29.72 N
+ATOM 585 CA ALA A 79 7.111 6.869 13.368 1.00 32.19 C
+ATOM 586 C ALA A 79 6.958 5.506 12.733 1.00 25.32 C
+ATOM 587 O ALA A 79 7.919 4.711 12.753 1.00 24.70 O
+ATOM 588 CB ALA A 79 7.896 7.902 12.468 1.00 25.97 C
+ATOM 589 N TYR A 80 5.749 5.231 12.211 1.00 25.90 N
+ATOM 590 CA TYR A 80 5.484 4.014 11.425 1.00 24.76 C
+ATOM 591 C TYR A 80 5.417 4.400 9.929 1.00 24.61 C
+ATOM 592 O TYR A 80 4.854 5.446 9.553 1.00 25.82 O
+ATOM 593 CB TYR A 80 4.219 3.175 11.706 1.00 26.45 C
+ATOM 594 CG TYR A 80 4.106 2.676 13.134 1.00 31.84 C
+ATOM 595 CD1 TYR A 80 4.830 1.580 13.624 1.00 34.25 C
+ATOM 596 CD2 TYR A 80 3.242 3.365 13.990 1.00 34.72 C
+ATOM 597 CE1 TYR A 80 4.714 1.193 14.964 1.00 30.56 C
+ATOM 598 CE2 TYR A 80 3.065 2.963 15.314 1.00 30.24 C
+ATOM 599 CZ TYR A 80 3.790 1.866 15.770 1.00 35.29 C
+ATOM 600 OH TYR A 80 3.624 1.546 17.078 1.00 51.62 O
+ATOM 601 N PRO A 81 6.018 3.558 9.080 1.00 27.26 N
+ATOM 602 CA PRO A 81 5.949 3.836 7.625 1.00 29.66 C
+ATOM 603 C PRO A 81 4.575 3.430 7.093 1.00 31.14 C
+ATOM 604 O PRO A 81 4.053 2.403 7.575 1.00 29.26 O
+ATOM 605 CB PRO A 81 6.936 2.848 6.980 1.00 28.79 C
+ATOM 606 CG PRO A 81 7.194 1.736 8.003 1.00 31.75 C
+ATOM 607 CD PRO A 81 6.736 2.280 9.352 1.00 26.94 C
+ATOM 608 N VAL A 82 3.960 4.235 6.214 1.00 27.18 N
+ATOM 609 CA VAL A 82 2.685 3.782 5.638 1.00 35.74 C
+ATOM 610 C VAL A 82 2.831 3.398 4.139 1.00 42.39 C
+ATOM 611 O VAL A 82 1.907 3.001 3.426 1.00 34.16 O
+ATOM 612 CB VAL A 82 1.424 4.610 5.984 1.00 36.83 C
+ATOM 613 CG1 VAL A 82 1.091 4.669 7.474 1.00 37.46 C
+ATOM 614 CG2 VAL A 82 1.473 6.001 5.423 1.00 34.29 C
+ATOM 615 N SER A 83 4.039 3.560 3.645 1.00 36.29 N
+ATOM 616 CA SER A 83 4.438 3.307 2.273 1.00 34.79 C
+ATOM 617 C SER A 83 5.941 3.232 2.282 1.00 35.38 C
+ATOM 618 O SER A 83 6.586 3.383 3.330 1.00 27.25 O
+ATOM 619 CB SER A 83 4.139 4.497 1.347 1.00 30.61 C
+ATOM 620 OG SER A 83 5.019 5.647 1.485 1.00 28.06 O
+ATOM 621 N ASP A 84 6.494 3.021 1.094 1.00 26.06 N
+ATOM 622 CA ASP A 84 7.922 3.058 1.040 1.00 30.29 C
+ATOM 623 C ASP A 84 8.379 4.468 1.376 1.00 30.65 C
+ATOM 624 O ASP A 84 7.718 5.431 0.999 1.00 31.40 O
+ATOM 625 CB ASP A 84 8.418 2.707 -0.338 1.00 29.55 C
+ATOM 626 CG ASP A 84 8.195 1.254 -0.617 1.00 40.79 C
+ATOM 627 OD1 ASP A 84 7.890 0.313 0.155 1.00 34.20 O
+ATOM 628 OD2 ASP A 84 8.405 1.151 -1.879 1.00 47.36 O
+ATOM 629 N VAL A 85 9.526 4.644 2.031 1.00 22.99 N
+ATOM 630 CA VAL A 85 9.939 6.010 2.333 1.00 20.82 C
+ATOM 631 C VAL A 85 11.478 6.190 2.308 1.00 24.03 C
+ATOM 632 O VAL A 85 12.262 5.206 2.513 1.00 27.17 O
+ATOM 633 CB VAL A 85 9.478 6.435 3.755 1.00 28.89 C
+ATOM 634 CG1 VAL A 85 7.965 6.527 3.938 1.00 26.65 C
+ATOM 635 CG2 VAL A 85 10.152 5.504 4.814 1.00 29.90 C
+ATOM 636 N THR A 86 11.848 7.460 1.993 1.00 20.22 N
+ATOM 637 CA THR A 86 13.198 7.883 2.071 1.00 21.23 C
+ATOM 638 C THR A 86 13.330 8.952 3.174 1.00 25.70 C
+ATOM 639 O THR A 86 12.605 9.949 3.191 1.00 22.59 O
+ATOM 640 CB THR A 86 13.718 8.431 0.769 1.00 23.30 C
+ATOM 641 OG1 THR A 86 13.519 7.475 -0.260 1.00 26.36 O
+ATOM 642 CG2 THR A 86 15.210 8.768 0.824 1.00 22.87 C
+ATOM 643 N ILE A 87 14.262 8.733 4.102 1.00 22.97 N
+ATOM 644 CA ILE A 87 14.463 9.665 5.240 1.00 23.87 C
+ATOM 645 C ILE A 87 15.949 10.014 5.452 1.00 19.36 C
+ATOM 646 O ILE A 87 16.814 9.140 5.475 1.00 24.47 O
+ATOM 647 CB ILE A 87 13.972 9.014 6.543 1.00 21.55 C
+ATOM 648 CG1 ILE A 87 12.454 8.826 6.572 1.00 27.50 C
+ATOM 649 CG2 ILE A 87 14.331 9.833 7.785 1.00 20.65 C
+ATOM 650 CD1 ILE A 87 11.969 7.924 7.710 1.00 31.38 C
+ATOM 651 N GLU A 88 16.242 11.311 5.598 1.00 21.01 N
+ATOM 652 CA GLU A 88 17.622 11.757 5.934 1.00 22.22 C
+ATOM 653 C GLU A 88 17.735 11.750 7.465 1.00 27.78 C
+ATOM 654 O GLU A 88 16.941 12.400 8.152 1.00 24.12 O
+ATOM 655 CB GLU A 88 17.905 13.188 5.441 1.00 28.56 C
+ATOM 656 CG GLU A 88 17.653 13.397 3.950 1.00 41.70 C
+ATOM 657 CD GLU A 88 18.260 14.697 3.405 1.00 48.78 C
+ATOM 658 OE1 GLU A 88 18.764 15.569 4.210 1.00 55.59 O
+ATOM 659 OE2 GLU A 88 18.265 14.913 2.133 1.00 95.14 O
+ATOM 660 N THR A 89 18.708 11.014 7.991 1.00 21.38 N
+ATOM 661 CA THR A 89 18.881 10.871 9.468 1.00 25.41 C
+ATOM 662 C THR A 89 19.936 11.870 10.028 1.00 30.23 C
+ATOM 663 O THR A 89 20.541 12.649 9.288 1.00 22.22 O
+ATOM 664 CB THR A 89 19.313 9.435 9.803 1.00 24.95 C
+ATOM 665 OG1 THR A 89 20.566 9.146 9.196 1.00 26.36 O
+ATOM 666 CG2 THR A 89 18.316 8.369 9.323 1.00 23.11 C
+ATOM 667 N HIS A 90 20.129 11.829 11.361 1.00 29.25 N
+ATOM 668 CA HIS A 90 21.114 12.699 12.096 1.00 30.89 C
+ATOM 669 C HIS A 90 20.896 14.194 11.746 1.00 19.65 C
+ATOM 670 O HIS A 90 21.807 14.876 11.254 1.00 24.29 O
+ATOM 671 CB HIS A 90 22.552 12.359 11.680 1.00 23.67 C
+ATOM 672 CG HIS A 90 22.966 10.925 12.015 1.00 28.74 C
+ATOM 673 ND1 HIS A 90 22.367 9.824 11.412 1.00 25.05 N
+ATOM 674 CD2 HIS A 90 23.901 10.429 12.868 1.00 25.95 C
+ATOM 675 CE1 HIS A 90 22.932 8.732 11.896 1.00 26.62 C
+ATOM 676 NE2 HIS A 90 23.848 9.075 12.766 1.00 27.96 N
+ATOM 677 N LYS A 91 19.692 14.702 12.017 1.00 21.85 N
+ATOM 678 CA LYS A 91 19.328 16.104 11.671 1.00 24.48 C
+ATOM 679 C LYS A 91 18.969 16.961 12.899 1.00 22.53 C
+ATOM 680 O LYS A 91 18.507 18.105 12.767 1.00 24.20 O
+ATOM 681 CB LYS A 91 18.092 16.125 10.769 1.00 24.74 C
+ATOM 682 CG LYS A 91 18.394 15.720 9.329 1.00 33.72 C
+ATOM 683 CD LYS A 91 19.267 16.737 8.594 1.00 33.40 C
+ATOM 684 CE LYS A 91 19.650 16.284 7.184 1.00 56.58 C
+ATOM 685 NZ LYS A 91 20.051 17.398 6.313 1.00 70.22 N
+ATOM 686 N LYS A 92 19.193 16.402 14.066 1.00 29.41 N
+ATOM 687 CA LYS A 92 18.862 17.064 15.343 1.00 29.57 C
+ATOM 688 C LYS A 92 19.404 18.499 15.416 1.00 31.36 C
+ATOM 689 O LYS A 92 18.727 19.418 15.897 1.00 30.72 O
+ATOM 690 CB LYS A 92 19.478 16.299 16.516 1.00 28.26 C
+ATOM 691 CG LYS A 92 19.717 17.184 17.743 1.00 42.15 C
+ATOM 692 CD LYS A 92 19.736 16.395 19.054 1.00 58.10 C
+ATOM 693 CE LYS A 92 21.130 16.311 19.680 1.00 74.57 C
+ATOM 694 NZ LYS A 92 21.096 16.204 21.146 1.00 73.77 N
+ATOM 695 N GLU A 93 20.609 18.655 14.934 1.00 25.37 N
+ATOM 696 CA GLU A 93 21.334 19.926 15.008 1.00 33.41 C
+ATOM 697 C GLU A 93 20.816 20.964 13.971 1.00 34.04 C
+ATOM 698 O GLU A 93 21.217 22.136 13.972 1.00 37.10 O
+ATOM 699 CB GLU A 93 22.827 19.630 14.806 1.00 36.08 C
+ATOM 700 CG GLU A 93 23.635 19.664 16.121 1.00100.00 C
+ATOM 701 CD GLU A 93 23.858 18.339 16.907 1.00100.00 C
+ATOM 702 OE1 GLU A 93 22.862 17.695 17.423 1.00100.00 O
+ATOM 703 OE2 GLU A 93 25.060 17.880 17.081 1.00100.00 O
+ATOM 704 N GLU A 94 19.911 20.554 13.095 1.00 33.03 N
+ATOM 705 CA GLU A 94 19.390 21.462 12.044 1.00 33.87 C
+ATOM 706 C GLU A 94 17.957 21.905 12.326 1.00 30.08 C
+ATOM 707 O GLU A 94 17.403 22.771 11.634 1.00 29.33 O
+ATOM 708 CB GLU A 94 19.373 20.759 10.693 1.00 36.71 C
+ATOM 709 CG GLU A 94 20.771 20.470 10.160 1.00 52.81 C
+ATOM 710 CD GLU A 94 20.788 20.210 8.656 1.00100.00 C
+ATOM 711 OE1 GLU A 94 19.722 20.405 7.957 1.00 57.89 O
+ATOM 712 OE2 GLU A 94 21.868 19.796 8.088 1.00 85.85 O
+ATOM 713 N LEU A 95 17.393 21.306 13.332 1.00 26.01 N
+ATOM 714 CA LEU A 95 16.011 21.563 13.709 1.00 26.71 C
+ATOM 715 C LEU A 95 15.801 23.027 14.206 1.00 33.16 C
+ATOM 716 O LEU A 95 16.584 23.603 15.002 1.00 28.74 O
+ATOM 717 CB LEU A 95 15.601 20.616 14.840 1.00 24.05 C
+ATOM 718 CG LEU A 95 14.137 20.768 15.253 1.00 37.37 C
+ATOM 719 CD1 LEU A 95 13.161 20.208 14.216 1.00 39.22 C
+ATOM 720 CD2 LEU A 95 13.808 20.048 16.563 1.00 48.43 C
+ATOM 721 N THR A 96 14.690 23.657 13.803 1.00 24.29 N
+ATOM 722 CA THR A 96 14.357 24.971 14.259 1.00 20.50 C
+ATOM 723 C THR A 96 12.842 25.027 14.364 1.00 29.60 C
+ATOM 724 O THR A 96 12.150 24.097 13.856 1.00 27.87 O
+ATOM 725 CB THR A 96 14.675 26.113 13.293 1.00 29.55 C
+ATOM 726 OG1 THR A 96 13.917 25.851 12.128 1.00 30.05 O
+ATOM 727 CG2 THR A 96 16.120 26.211 13.007 1.00 23.85 C
+ATOM 728 N ALA A 97 12.313 26.090 15.052 1.00 27.16 N
+ATOM 729 CA ALA A 97 10.851 26.183 15.191 1.00 37.74 C
+ATOM 730 C ALA A 97 10.166 26.814 14.004 1.00 64.29 C
+ATOM 731 O ALA A 97 9.815 27.983 14.121 1.00100.00 O
+ATOM 732 CB ALA A 97 10.299 26.681 16.508 1.00 35.84 C
+TER 733 ALA A 97
+HETATM 734 FE1 FES A1602 13.398 11.548 21.999 1.00 26.97 FE
+HETATM 735 FE2 FES A1602 12.925 10.090 19.701 1.00 26.54 FE
+HETATM 736 S1 FES A1602 14.657 9.885 21.071 1.00 26.27 S
+HETATM 737 S2 FES A1602 11.681 11.837 20.546 1.00 27.47 S
+HETATM 738 O HOH A1603 20.314 3.189 17.662 1.00 28.40 O
+HETATM 739 O HOH A1604 19.136 13.499 14.797 1.00 27.63 O
+HETATM 740 O HOH A1605 15.839 17.655 22.569 1.00 31.32 O
+HETATM 741 O HOH A1606 13.340 -3.911 18.366 1.00 31.87 O
+HETATM 742 O HOH A1607 17.589 8.577 14.886 1.00 25.57 O
+HETATM 743 O HOH A1608 3.158 6.964 15.663 1.00 32.70 O
+HETATM 744 O HOH A1609 12.607 3.196 0.028 1.00 35.81 O
+HETATM 745 O HOH A1610 17.941 10.294 12.971 1.00 28.21 O
+HETATM 746 O HOH A1611 1.926 1.370 9.724 1.00 37.77 O
+HETATM 747 O HOH A1612 11.412 3.410 19.732 1.00 37.42 O
+HETATM 748 O HOH A1613 8.807 17.793 25.373 1.00 41.85 O
+HETATM 749 O HOH A1614 3.590 11.528 5.863 1.00 39.49 O
+HETATM 750 O HOH A1615 25.052 1.593 11.348 1.00 43.97 O
+HETATM 751 O HOH A1616 -6.196 7.375 14.972 1.00 75.86 O
+HETATM 752 O HOH A1617 8.534 -0.956 17.306 1.00 37.45 O
+HETATM 753 O HOH A1618 6.639 15.107 8.525 1.00 36.12 O
+HETATM 754 O HOH A1619 22.246 2.005 21.737 1.00 36.05 O
+HETATM 755 O HOH A1620 14.535 -4.507 10.197 1.00 55.68 O
+HETATM 756 O HOH A1621 4.876 2.526 -1.355 1.00 41.58 O
+HETATM 757 O HOH A1622 11.330 5.913 -0.990 1.00 42.42 O
+HETATM 758 O HOH A1623 8.224 5.865 20.826 1.00 41.41 O
+HETATM 759 O HOH A1624 22.831 5.923 19.420 1.00 45.06 O
+HETATM 760 O HOH A1625 14.917 23.836 10.267 1.00 40.43 O
+HETATM 761 O HOH A1626 11.139 24.357 10.914 1.00 63.90 O
+HETATM 762 O HOH A1627 11.625 17.756 3.797 1.00 64.36 O
+HETATM 763 O HOH A1628 0.872 11.720 21.228 1.00 66.38 O
+HETATM 764 O HOH A1629 -0.211 4.813 15.867 1.00 63.96 O
+HETATM 765 O HOH A1630 20.658 -7.095 8.049 1.00 67.10 O
+HETATM 766 O HOH A1631 24.043 4.181 -2.687 1.00 53.06 O
+HETATM 767 O HOH A1632 21.936 6.378 21.945 1.00 55.43 O
+HETATM 768 O HOH A1633 19.025 24.652 14.863 1.00 51.35 O
+HETATM 769 O HOH A1634 11.308 8.680 28.143 1.00 44.39 O
+HETATM 770 O HOH A1635 -0.428 0.927 5.386 1.00 85.08 O
+HETATM 771 O HOH A1636 21.798 10.879 23.320 1.00 52.42 O
+HETATM 772 O HOH A1637 3.239 6.955 -0.065 1.00 55.66 O
+HETATM 773 O HOH A1638 22.779 2.365 18.908 1.00 43.93 O
+HETATM 774 O HOH A1639 24.188 5.146 11.189 1.00 45.31 O
+HETATM 775 O HOH A1640 -1.683 -0.913 1.878 1.00 69.36 O
+HETATM 776 O HOH A1641 8.696 6.563 -1.677 1.00 58.88 O
+HETATM 777 O HOH A1642 7.367 26.197 14.480 1.00 49.47 O
+HETATM 778 O HOH A1643 6.591 -1.657 -1.410 1.00 85.37 O
+HETATM 779 O HOH A1644 7.606 18.977 3.435 1.00 63.19 O
+HETATM 780 O HOH A1645 -3.822 10.414 11.859 1.00 57.70 O
+HETATM 781 O HOH A1646 21.749 12.594 6.625 1.00 51.80 O
+HETATM 782 O HOH A1647 23.131 4.812 23.785 1.00 50.20 O
+HETATM 783 O HOH A1648 16.610 3.001 -2.612 1.00 56.90 O
+HETATM 784 O HOH A1649 22.528 16.502 13.897 1.00 55.79 O
+HETATM 785 O HOH A1650 26.500 7.848 10.348 1.00 68.43 O
+HETATM 786 O HOH A1651 3.851 12.983 3.178 1.00 49.71 O
+HETATM 787 O HOH A1652 19.786 18.726 20.646 1.00 45.90 O
+HETATM 788 O HOH A1653 18.145 27.680 9.755 1.00 64.26 O
+HETATM 789 O HOH A1654 17.574 -8.112 7.017 1.00 76.51 O
+HETATM 790 O HOH A1655 22.282 13.839 15.539 1.00 60.51 O
+HETATM 791 O HOH A1656 21.110 -7.809 14.066 1.00 66.51 O
+HETATM 792 O HOH A1657 25.732 22.369 16.313 1.00 59.47 O
+HETATM 793 O HOH A1658 13.415 9.318 -2.947 1.00 59.85 O
+HETATM 794 O HOH A1659 13.899 22.771 7.168 1.00 63.98 O
+HETATM 795 O HOH A1660 27.481 5.665 17.885 1.00 79.40 O
+HETATM 796 O HOH A1661 8.580 -4.372 17.408 1.00 60.41 O
+HETATM 797 O HOH A1662 24.876 4.074 8.926 1.00 71.07 O
+HETATM 798 O HOH A1663 10.525 -6.340 15.708 1.00 53.48 O
+HETATM 799 O HOH A1664 -1.284 5.529 19.201 1.00 68.40 O
+HETATM 800 O HOH A1665 15.014 11.978 -2.461 1.00 64.00 O
+HETATM 801 O HOH A1666 14.106 -9.236 2.519 1.00 67.28 O
+HETATM 802 O HOH A1667 14.062 29.978 13.852 1.00 84.39 O
+HETATM 803 O HOH A1668 6.500 2.082 -3.927 1.00 73.15 O
+HETATM 804 O HOH A1669 -3.999 12.915 12.023 1.00 70.07 O
+HETATM 805 O HOH A1670 22.522 10.655 20.491 1.00 62.92 O
+HETATM 806 O HOH A1671 5.802 -4.428 16.828 1.00 64.57 O
+HETATM 807 O HOH A1672 -0.285 -5.312 2.050 1.00 83.51 O
+HETATM 808 O HOH A1673 -0.266 3.144 11.216 1.00 68.25 O
+HETATM 809 O HOH A1674 25.407 13.378 14.852 1.00 80.99 O
+HETATM 810 O HOH A1675 15.568 7.564 -2.586 1.00 71.16 O
+HETATM 811 O HOH A1676 4.787 10.976 22.962 1.00 65.51 O
+HETATM 812 O HOH A1677 25.854 23.790 19.080 1.00 69.96 O
+HETATM 813 O HOH A1678 6.047 15.849 24.673 1.00 76.93 O
+HETATM 814 O HOH A1679 3.270 10.385 25.458 1.00 68.03 O
+HETATM 815 O HOH A1680 17.147 -11.645 -0.378 1.00 76.39 O
+HETATM 816 O HOH A1681 3.889 11.272 28.440 1.00 57.34 O
+HETATM 817 O HOH A1682 0.829 10.575 6.206 1.00 61.71 O
+HETATM 818 O HOH A1683 -2.192 14.658 14.063 1.00 83.95 O
+CONECT 297 734
+CONECT 329 734
+CONECT 347 735
+CONECT 578 735
+CONECT 734 297 329 736 737
+CONECT 735 347 578 736 737
+CONECT 736 734 735
+CONECT 737 734 735
+MASTER 253 0 1 4 5 0 2 6 817 1 8 8
+END
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
import java.awt.Color;
import java.io.File;
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
FeaturesFile featuresFile = new FeaturesFile(
"examples/exampleFeatures.txt", FormatAdapter.FILE);
*/
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("26 feature group colours not found", 26, colours.size());
- assertEquals(colours.get("Cath"), new Color(0x93b1d1));
- assertEquals(colours.get("ASX-MOTIF"), new Color(0x6addbb));
+ assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
+ assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
/*
* verify (some) features on sequences
*/
SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures(); // FER_CAPAA
- assertEquals(7, sfs.length);
+ assertEquals(8, sfs.length);
SequenceFeature sf = sfs[0];
+ assertEquals("Pfam family%LINK%", sf.description);
+ assertEquals(0, sf.begin);
+ assertEquals(0, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("Pfam", sf.type);
+ assertEquals(1, sf.links.size());
+ assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
+ sf.links.get(0));
+
+ sf = sfs[1];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(39, sf.begin);
assertEquals(39, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[1];
+ sf = sfs[2];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(44, sf.begin);
assertEquals(44, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[2];
+ sf = sfs[3];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(47, sf.begin);
assertEquals(47, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[3];
+ sf = sfs[4];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(77, sf.begin);
assertEquals(77, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[4];
+ sf = sfs[5];
assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
sf.description);
- assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111",
- sf.links.get(0).toString());
+ assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
+ sf.links.get(0));
assertEquals(8, sf.begin);
assertEquals(83, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Pfam", sf.type);
- sf = sfs[5];
+ sf = sfs[6];
assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
assertEquals(3, sf.begin);
assertEquals(93, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Cath", sf.type);
- sf = sfs[6];
+ sf = sfs[7];
assertEquals(
"High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
sf.description);
assertEquals(
"PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
- sf.links.get(0).toString());
+ sf.links.get(0));
assertEquals(89, sf.begin);
assertEquals(89, sf.end);
assertEquals("netphos", sf.featureGroup);
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
// GFF2 uses space as name/value separator in column 9
String gffData = "METAL\tcc9900\n" + "GFF\n"
// verify colours read or synthesized
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("1 feature group colours not found", 1, colours.size());
- assertEquals(colours.get("METAL"), new Color(0xcc9900));
+ assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
// verify feature on FER_CAPAA
SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
}
/**
- * Test various ways of describing a feature colour scheme
- *
- * @throws Exception
- */
- @Test(groups = { "Functional" })
- public void testParseGraduatedColourScheme() throws Exception
- {
- FeaturesFile ff = new FeaturesFile();
-
- // colour by label:
- GraduatedColor gc = ff.parseGraduatedColourScheme(
- "BETA-TURN-IR\t9a6a94", "label");
- assertTrue(gc.isColourByLabel());
- assertEquals(Color.white, gc.getMinColor());
- assertEquals(Color.black, gc.getMaxColor());
- assertTrue(gc.isAutoScale());
-
- // using colour name, rgb, etc:
- String spec = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
- gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
- assertFalse(gc.isColourByLabel());
- assertEquals(Color.blue, gc.getMinColor());
- assertEquals(new Color(255, 0, 255), gc.getMaxColor());
- assertFalse(gc.isAutoScale());
- assertFalse(gc.getTolow());
- assertEquals(20.0f, gc.getMin(), 0.001f);
- assertEquals(95.0f, gc.getMax(), 0.001f);
- assertEquals(AnnotationColourGradient.BELOW_THRESHOLD,
- gc.getThreshType());
- assertEquals(66.0f, gc.getThresh(), 0.001f);
-
- // inverse gradient high to low:
- spec = "blue|255,0,255|95.0|20.0|below|66.0";
- gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
- assertTrue(gc.isAutoScale());
- assertTrue(gc.getTolow());
- }
-
- /**
* Test parsing a features file with GFF formatted content only
*
* @throws Exception
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
// GFF3 uses '=' separator for name/value pairs in colum 9
String gffData = "##gff-version 3\n"
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
/*
parseResult);
checkDatasetfromSimpleGff3(dataset);
}
+
+ @Test(groups = { "Functional" })
+ public void testPrintJalviewFormat() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
+ .getFeatureColours();
+ String features = "METAL\tcc9900\n"
+ + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
+ + "Pfam\tred\n"
+ + "STARTGROUP\tuniprot\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
+ + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+ + "ENDGROUP\tuniprot\n";
+ FeaturesFile featuresFile = new FeaturesFile(features,
+ FormatAdapter.PASTE);
+ featuresFile.parse(al.getDataset(), colours, false);
+
+ /*
+ * first with no features displayed
+ */
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ Map<String, FeatureColourI> visible = fr
+ .getDisplayedFeatureCols();
+ String exported = featuresFile.printJalviewFormat(
+ al.getSequencesArray(), visible);
+ String expected = "No Features Visible";
+ assertEquals(expected, exported);
+
+ /*
+ * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
+ */
+ fr.setVisible("METAL");
+ fr.setVisible("GAMMA-TURN");
+ visible = fr.getDisplayedFeatureCols();
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
+ visible);
+ expected = "METAL\tcc9900\n"
+ + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "ENDGROUP\tuniprot\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now set Pfam visible
+ */
+ fr.setVisible("Pfam");
+ visible = fr.getDisplayedFeatureCols();
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
+ visible);
+ /*
+ * note the order of feature types is uncontrolled - derives from
+ * FeaturesDisplayed.featuresDisplayed which is a HashSet
+ */
+ expected = "METAL\tcc9900\n"
+ + "Pfam\tff0000\n"
+ + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ + "ENDGROUP\tuniprot\n";
+ assertEquals(expected, exported);
+ }
}
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
*/
package jalview.io;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
}
/**
- * Additional tests for (a) Jalview features file with no colour
- * specifications (old style 'groups' file) and (b) Jalview features file with
- * embedded GFF
+ * Additional tests for Jalview features file
*/
@Test(groups = "Functional")
public void testIdentify_featureFile()
{
IdentifyFile ider = new IdentifyFile();
- // Jalview format with features only, no feature colours
+ /*
+ * Jalview format with features only, no feature colours
+ */
String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
- Assert.assertEquals(IdentifyFile.FeaturesFile, ider.identify(data, AppletFormatAdapter.PASTE));
+ assertEquals(IdentifyFile.FeaturesFile,
+ ider.identify(data, AppletFormatAdapter.PASTE));
- // Jalview feature colour followed by GFF format feature data
+ /*
+ * Jalview feature colour followed by GFF format feature data
+ */
data = "METAL\tcc9900\n" + "GFF\n"
+ "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
- Assert.assertEquals(IdentifyFile.FeaturesFile,
+ assertEquals(IdentifyFile.FeaturesFile,
+ ider.identify(data, AppletFormatAdapter.PASTE));
+
+ /*
+ * Feature with '<' in the name (JAL-2098)
+ */
+ data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
+ assertEquals(IdentifyFile.FeaturesFile,
ider.identify(data, AppletFormatAdapter.PASTE));
}
passedCount = 0;
}
- @AfterTest
+ @AfterTest(alwaysRun = true)
public void tearDown() throws Exception
{
testJsonFile = null;
*/
package jalview.io;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenSequences;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Jalview2XML;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.AlignmentViewport;
import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+@Test(singleThreaded = true)
public class Jalview2xmlTests
{
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-
}
- public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
+ int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
{
int numdsann = 0;
for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
*
* @throws Exception
*/
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Functional" }, enabled = true)
public void testStoreAndRecoverExpandedviews() throws Exception
{
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
}
+ /**
+ * Test save and reload of a project with a different representative sequence
+ * in each view.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverReferenceSeqSettings() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ String afid = af.getViewport().getSequenceSetId();
+
+ /*
+ * remember representative and hidden sequences marked
+ * on each panel
+ */
+ Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
+ Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
+
+ /*
+ * mark sequence 2, 3, 4.. in panels 1, 2, 3...
+ * as reference sequence for itself and the preceding sequence
+ */
+ int n = 1;
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ AlignViewportI av = ap.getAlignViewport();
+ AlignmentI alignment = ap.getAlignment();
+ int repIndex = n % alignment.getHeight();
+ SequenceI rep = alignment.getSequenceAt(repIndex);
+ refseqs.put(ap.getViewName(), rep);
+ List<String> hiddenNames = new ArrayList<String>();
+ hiddenSeqNames.put(ap.getViewName(), hiddenNames);
+
+ /*
+ * hide rep sequence and the one before it
+ */
+ SequenceI seqToHide = alignment.getSequenceAt(repIndex);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(seqToHide, false);
+ SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
+ sg.addSequence(precedingSeq, false);
+ av.setSelectionGroup(sg);
+ ((AlignmentViewport) av).hideSequences(seqToHide, true);
+
+ /*
+ * record names of hidden sequences
+ */
+ HiddenSequences hs = alignment.getHiddenSequences();
+ for (SequenceI seq : hs.hiddenSequences)
+ {
+ if (seq != null)
+ {
+ hiddenNames.add(seq.getName());
+ }
+ }
+ // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
+ // todo refactor this to an alignment view controller
+ av.setDisplayReferenceSeq(true);
+ av.setColourByReferenceSeq(true);
+ av.getAlignment().setSeqrep(rep);
+
+ n++;
+ }
+ File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
+ ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the expanded view state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), FormatAdapter.FILE);
+ afid = af.getViewport().getSequenceSetId();
+
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ // check representative
+ AlignmentI alignment = ap.getAlignment();
+ SequenceI rep = alignment.getSeqrep();
+ Assert.assertNotNull(rep,
+ "Couldn't restore sequence representative from project");
+ // can't use a strong equals here, because by definition, the sequence IDs
+ // will be different.
+ // could set vamsas session save/restore flag to preserve IDs across
+ // load/saves.
+ Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
+ rep.toString(),
+ "Representative wasn't the same when recovered.");
+ Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
+ "Display reference sequence view setting not set.");
+ Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
+ "Colour By Reference Seq view setting not set.");
+
+ /*
+ * verify hidden sequences in restored panel
+ */
+ List<String> hidden = hiddenSeqNames.get(ap.getViewName());
+ HiddenSequences hs = alignment.getHiddenSequences();
+ assertEquals(
+ "wrong number of restored hidden sequences in "
+ + ap.getViewName(),
+ hidden.size(), hs.getSize());
+ }
+ }
+
@Test(groups = { "Functional" })
public void testIsVersionStringLaterThan()
{
*/
assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
assertTrue(Jalview2XML.isVersionStringLaterThan(null,
"Development Build"));
assertTrue(Jalview2XML.isVersionStringLaterThan(null,
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
{
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
+
+import jalview.datamodel.SequenceFeature;
+import jalview.util.Format;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class FeatureColourTest
+{
+ @Test(groups = { "Functional" })
+ public void testCopyConstructor()
+ {
+ /*
+ * plain colour
+ */
+ FeatureColour fc = new FeatureColour(Color.RED);
+ FeatureColour fc1 = new FeatureColour(fc);
+ assertTrue(fc1.getColour().equals(Color.RED));
+ assertFalse(fc1.isGraduatedColour());
+ assertFalse(fc1.isColourByLabel());
+
+ /*
+ * min-max colour
+ */
+ fc = new FeatureColour(Color.gray, Color.black, 10f, 20f);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(12f);
+ fc1 = new FeatureColour(fc);
+ assertTrue(fc1.isGraduatedColour());
+ assertFalse(fc1.isColourByLabel());
+ assertTrue(fc1.isAboveThreshold());
+ assertEquals(12f, fc1.getThreshold());
+ assertEquals(Color.gray, fc1.getMinColour());
+ assertEquals(Color.black, fc1.getMaxColour());
+ assertEquals(10f, fc1.getMin());
+ assertEquals(20f, fc1.getMax());
+
+ /*
+ * colour by label
+ */
+ fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ fc1 = new FeatureColour(fc);
+ assertTrue(fc1.isColourByLabel());
+ assertFalse(fc1.isGraduatedColour());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsColored_simpleColour()
+ {
+ FeatureColour fc = new FeatureColour(Color.RED);
+ assertTrue(fc.isColored(new SequenceFeature()));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsColored_colourByLabel()
+ {
+ FeatureColour fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ assertTrue(fc.isColored(new SequenceFeature()));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsColored_aboveThreshold()
+ {
+ // graduated colour range from score 20 to 100
+ FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 20f,
+ 100f);
+
+ // score 0 is adjusted to bottom of range
+ SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 0f,
+ null);
+ assertTrue(fc.isColored(sf));
+ assertEquals(Color.WHITE, fc.getColor(sf));
+
+ // score 120 is adjusted to top of range
+ sf.setScore(120f);
+ assertEquals(Color.BLACK, fc.getColor(sf));
+
+ // value below threshold is still rendered
+ // setting threshold has no effect yet...
+ fc.setThreshold(60f);
+ sf.setScore(36f);
+ assertTrue(fc.isColored(sf));
+ assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+
+ // now apply threshold:
+ fc.setAboveThreshold(true);
+ assertFalse(fc.isColored(sf));
+ // colour is still returned though ?!?
+ assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+
+ sf.setScore(84); // above threshold now
+ assertTrue(fc.isColored(sf));
+ assertEquals(new Color(51, 51, 51), fc.getColor(sf));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetColor_simpleColour()
+ {
+ FeatureColour fc = new FeatureColour(Color.RED);
+ assertEquals(Color.RED, fc.getColor(new SequenceFeature()));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetColor_colourByLabel()
+ {
+ FeatureColour fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
+ null);
+ Color expected = UserColourScheme.createColourFromName("desc");
+ assertEquals(expected, fc.getColor(sf));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetColor_Graduated()
+ {
+ // graduated colour from score 0 to 100, gray(128, 128, 128) to red(255, 0, 0)
+ FeatureColour fc = new FeatureColour(Color.GRAY, Color.RED, 0f, 100f);
+ // feature score is 75 which is 3/4 of the way from GRAY to RED
+ SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
+ null);
+ // the colour gradient is computed in float values from 0-1 (where 1 == 255)
+ float red = 128 / 255f + 3 / 4f * (255 - 128) / 255f;
+ float green = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
+ float blue = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
+ Color expected = new Color(red, green, blue);
+ assertEquals(expected, fc.getColor(sf));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetColor_belowThreshold()
+ {
+ // gradient from [50, 150] from WHITE(255, 255, 255) to BLACK(0, 0, 0)
+ FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 50f,
+ 150f);
+ SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f,
+ null);
+ fc.setThreshold(100f); // ignore for now
+ assertTrue(fc.isColored(sf));
+ assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+
+ fc.setAboveThreshold(true); // feature lies below threshold
+ assertFalse(fc.isColored(sf));
+ assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+ }
+
+ /**
+ * Test output of feature colours to Jalview features file format
+ */
+ @Test(groups = { "Functional" })
+ public void testToJalviewFormat()
+ {
+ /*
+ * plain colour - to RGB hex code
+ */
+ FeatureColour fc = new FeatureColour(Color.RED);
+ String redHex = Format.getHexString(Color.RED);
+ String hexColour = redHex;
+ assertEquals("domain\t" + hexColour, fc.toJalviewFormat("domain"));
+
+ /*
+ * colour by label (no threshold)
+ */
+ fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
+
+ /*
+ * colour by label (autoscaled) (an odd state you can reach by selecting
+ * 'above threshold', then deselecting 'threshold is min/max' then 'colour
+ * by label')
+ */
+ fc.setAutoScaled(true);
+ assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
+
+ /*
+ * colour by label (above threshold) (min/max values are output though not
+ * used by this scheme)
+ */
+ fc.setAutoScaled(false);
+ fc.setThreshold(12.5f);
+ fc.setAboveThreshold(true);
+ assertEquals("domain\tlabel|||0.0|0.0|above|12.5",
+ fc.toJalviewFormat("domain"));
+
+ /*
+ * colour by label (below threshold)
+ */
+ fc.setBelowThreshold(true);
+ assertEquals("domain\tlabel|||0.0|0.0|below|12.5",
+ fc.toJalviewFormat("domain"));
+
+ /*
+ * graduated colour, no threshold
+ */
+ fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
+ String greenHex = Format.getHexString(Color.GREEN);
+ String expected = String.format("domain\t%s|%s|abso|12.0|25.0|none",
+ greenHex, redHex);
+ assertEquals(expected, fc.toJalviewFormat("domain"));
+
+ /*
+ * colour ranges over the actual score ranges (not min/max)
+ */
+ fc.setAutoScaled(true);
+ expected = String.format("domain\t%s|%s|12.0|25.0|none", greenHex,
+ redHex);
+ assertEquals(expected, fc.toJalviewFormat("domain"));
+
+ /*
+ * graduated colour below threshold
+ */
+ fc.setThreshold(12.5f);
+ fc.setBelowThreshold(true);
+ expected = String.format("domain\t%s|%s|12.0|25.0|below|12.5",
+ greenHex, redHex);
+ assertEquals(expected, fc.toJalviewFormat("domain"));
+
+ /*
+ * graduated colour above threshold
+ */
+ fc.setThreshold(12.5f);
+ fc.setAboveThreshold(true);
+ fc.setAutoScaled(false);
+ expected = String.format("domain\t%s|%s|abso|12.0|25.0|above|12.5",
+ greenHex, redHex);
+ assertEquals(expected, fc.toJalviewFormat("domain"));
+ }
+
+ /**
+ * Test parsing of feature colours from Jalview features file format
+ */
+ @Test(groups = { "Functional" })
+ public void testParseJalviewFeatureColour()
+ {
+ /*
+ * simple colour by name
+ */
+ FeatureColour fc = FeatureColour.parseJalviewFeatureColour("red");
+ assertTrue(fc.isSimpleColour());
+ assertEquals(Color.RED, fc.getColour());
+
+ /*
+ * simple colour by hex code
+ */
+ fc = FeatureColour.parseJalviewFeatureColour(Format
+ .getHexString(Color.RED));
+ assertTrue(fc.isSimpleColour());
+ assertEquals(Color.RED, fc.getColour());
+
+ /*
+ * simple colour by rgb triplet
+ */
+ fc = FeatureColour.parseJalviewFeatureColour("255,0,0");
+ assertTrue(fc.isSimpleColour());
+ assertEquals(Color.RED, fc.getColour());
+
+ /*
+ * malformed colour
+ */
+ try
+ {
+ fc = FeatureColour.parseJalviewFeatureColour("oops");
+ fail("expected exception");
+ } catch (IllegalArgumentException e)
+ {
+ assertEquals("Invalid colour descriptor: oops", e.getMessage());
+ }
+
+ /*
+ * colour by label (no threshold)
+ */
+ fc = FeatureColour.parseJalviewFeatureColour("label");
+ assertTrue(fc.isColourByLabel());
+ assertFalse(fc.hasThreshold());
+
+ /*
+ * colour by label (with threshold)
+ */
+ fc = FeatureColour
+ .parseJalviewFeatureColour("label|||0.0|0.0|above|12.0");
+ assertTrue(fc.isColourByLabel());
+ assertTrue(fc.isAboveThreshold());
+ assertEquals(12.0f, fc.getThreshold());
+
+ /*
+ * graduated colour (by name) (no threshold)
+ */
+ fc = FeatureColour.parseJalviewFeatureColour("red|green|10.0|20.0");
+ assertTrue(fc.isGraduatedColour());
+ assertFalse(fc.hasThreshold());
+ assertEquals(Color.RED, fc.getMinColour());
+ assertEquals(Color.GREEN, fc.getMaxColour());
+ assertEquals(10f, fc.getMin());
+ assertEquals(20f, fc.getMax());
+ assertTrue(fc.isAutoScaled());
+
+ /*
+ * graduated colour (by hex code) (above threshold)
+ */
+ String descriptor = String.format("%s|%s|10.0|20.0|above|15",
+ Format.getHexString(Color.RED),
+ Format.getHexString(Color.GREEN));
+ fc = FeatureColour.parseJalviewFeatureColour(descriptor);
+ assertTrue(fc.isGraduatedColour());
+ assertTrue(fc.hasThreshold());
+ assertTrue(fc.isAboveThreshold());
+ assertEquals(15f, fc.getThreshold());
+ assertEquals(Color.RED, fc.getMinColour());
+ assertEquals(Color.GREEN, fc.getMaxColour());
+ assertEquals(10f, fc.getMin());
+ assertEquals(20f, fc.getMax());
+ assertTrue(fc.isAutoScaled());
+
+ /*
+ * graduated colour (by RGB triplet) (below threshold), absolute scale
+ */
+ descriptor = String.format("255,0,0|0,255,0|abso|10.0|20.0|below|15");
+ fc = FeatureColour.parseJalviewFeatureColour(descriptor);
+ assertTrue(fc.isGraduatedColour());
+ assertFalse(fc.isAutoScaled());
+ assertTrue(fc.hasThreshold());
+ assertTrue(fc.isBelowThreshold());
+ assertEquals(15f, fc.getThreshold());
+ assertEquals(Color.RED, fc.getMinColour());
+ assertEquals(Color.GREEN, fc.getMaxColour());
+ assertEquals(10f, fc.getMin());
+ assertEquals(20f, fc.getMax());
+
+ descriptor = String
+ .format("blue|255,0,255|absolute|20.0|95.0|below|66.0");
+ fc = FeatureColour.parseJalviewFeatureColour(descriptor);
+ assertTrue(fc.isGraduatedColour());
+ }
+}
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+public class UserColourSchemeTest
+{
+
+ @Test(groups = "functional")
+ public void testGetColourFromString()
+ {
+ /*
+ * by colour name - if known to AWT, and included in
+ *
+ * @see ColourSchemeProperty.getAWTColorFromName()
+ */
+ assertSame(Color.RED, UserColourScheme.getColourFromString("red"));
+ assertSame(Color.RED, UserColourScheme.getColourFromString("Red"));
+ assertSame(Color.RED, UserColourScheme.getColourFromString(" RED "));
+
+ /*
+ * by RGB hex code
+ */
+ String hexColour = Integer.toHexString(Color.RED.getRGB() & 0xffffff);
+ assertEquals(Color.RED, UserColourScheme.getColourFromString(hexColour));
+ // 'hex' prefixes _not_ wanted here
+ assertNull(UserColourScheme.getColourFromString("0x" + hexColour));
+ assertNull(UserColourScheme.getColourFromString("#" + hexColour));
+
+ /*
+ * by RGB triplet
+ */
+ String rgb = String.format("%d,%d,%d", Color.red.getRed(),
+ Color.red.getGreen(), Color.red.getBlue());
+ assertEquals(Color.RED, UserColourScheme.getColourFromString(rgb));
+
+ /*
+ * odds and ends
+ */
+ assertNull(UserColourScheme.getColourFromString(null));
+ assertNull(UserColourScheme.getColourFromString("rubbish"));
+ assertEquals(Color.WHITE, UserColourScheme.getColourFromString("-1"));
+ assertNull(UserColourScheme.getColourFromString(String
+ .valueOf(Integer.MAX_VALUE)));
+ }
+}
--- /dev/null
+package jalview.util;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.fail;
+
+import java.text.ParseException;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class DnaUtilsTest
+{
+ /**
+ * Tests for parsing an ENA/GenBank location specifier
+ *
+ * @throws ParseException
+ *
+ * @see http://www.insdc.org/files/feature_table.html#3.4
+ */
+ @Test(groups = { "Functional" })
+ public void testParseLocation() throws ParseException
+ {
+ /*
+ * single locus
+ */
+ List<int[]> ranges = DnaUtils.parseLocation("467");
+ assertEquals(1, ranges.size());
+ assertEquals(467, ranges.get(0)[0]);
+ assertEquals(467, ranges.get(0)[1]);
+
+ /*
+ * simple range
+ */
+ ranges = DnaUtils.parseLocation("12..78");
+ assertEquals(1, ranges.size());
+ assertEquals(12, ranges.get(0)[0]);
+ assertEquals(78, ranges.get(0)[1]);
+
+ /*
+ * join of simple ranges
+ */
+ ranges = DnaUtils.parseLocation("join(12..78,134..202,322..345)");
+ assertEquals(3, ranges.size());
+ assertEquals(12, ranges.get(0)[0]);
+ assertEquals(78, ranges.get(0)[1]);
+ assertEquals(134, ranges.get(1)[0]);
+ assertEquals(202, ranges.get(1)[1]);
+ assertEquals(322, ranges.get(2)[0]);
+ assertEquals(345, ranges.get(2)[1]);
+
+ /*
+ * complement of a simple range
+ */
+ ranges = DnaUtils.parseLocation("complement(34..126)");
+ assertEquals(1, ranges.size());
+ assertEquals(126, ranges.get(0)[0]);
+ assertEquals(34, ranges.get(0)[1]);
+
+ /*
+ * complement of a join
+ */
+ ranges = DnaUtils
+ .parseLocation("complement(join(2691..4571,4918..5163))");
+ assertEquals(2, ranges.size());
+ assertEquals(5163, ranges.get(0)[0]);
+ assertEquals(4918, ranges.get(0)[1]);
+ assertEquals(4571, ranges.get(1)[0]);
+ assertEquals(2691, ranges.get(1)[1]);
+
+ /*
+ * join of two complements
+ */
+ ranges = DnaUtils
+ .parseLocation("join(complement(4918..5163),complement(2691..4571))");
+ assertEquals(2, ranges.size());
+ assertEquals(5163, ranges.get(0)[0]);
+ assertEquals(4918, ranges.get(0)[1]);
+ assertEquals(4571, ranges.get(1)[0]);
+ assertEquals(2691, ranges.get(1)[1]);
+
+ /*
+ * join complement to non-complement
+ * @see http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation/ Transpliced Genes
+ */
+ ranges = DnaUtils
+ .parseLocation("join(complement(36618..36700),86988..87064)");
+ assertEquals(2, ranges.size());
+ assertEquals(36700, ranges.get(0)[0]);
+ assertEquals(36618, ranges.get(0)[1]);
+ assertEquals(86988, ranges.get(1)[0]);
+ assertEquals(87064, ranges.get(1)[1]);
+
+ /*
+ * valid things we don't yet handle
+ */
+ checkForParseException("<34..126");
+ checkForParseException("35..>126");
+ checkForParseException("34.126");
+ checkForParseException("34^126");
+ checkForParseException("order(34..126,130..180)");
+
+ /*
+ * invalid things
+ */
+ checkForParseException("");
+ checkForParseException("JOIN(1..2)");
+ checkForParseException("join(1..2");
+ checkForParseException("join(1..2(");
+ checkForParseException("complement(1..2");
+ checkForParseException("complement(1..2(");
+ try
+ {
+ assertNull(DnaUtils.parseLocation(null));
+ fail("Expected exception");
+ } catch (NullPointerException e)
+ {
+ // expected
+ }
+
+ /*
+ * nested joins are not allowed; just as well since this fails to parse
+ * (splitting tokens by comma fragments the inner join expression)
+ */
+ checkForParseException("join(1..2,join(4..5,10..12),18..22)");
+ /*
+ * complement may not enclose multiple ranges
+ * parsing fails for the same reason
+ */
+ checkForParseException("join(complement(36618..36700,4000..4200),86988..87064)");
+ }
+
+ /**
+ * Verifies that a ParseException is thrown when the given location is parsed
+ *
+ * @param location
+ */
+ void checkForParseException(String location)
+ {
+ try
+ {
+ DnaUtils.parseLocation(location);
+ fail("Expected exception");
+ } catch (ParseException e)
+ {
+ // expected;
+ }
+ }
+
+}
assertEquals(0,
StringUtils.parseInt(String.valueOf(Integer.MAX_VALUE) + "1"));
}
+
+ @Test(groups = { "Functional" })
+ public void testCompareVersions()
+ {
+ assertEquals(0, StringUtils.compareVersions(null, null));
+ assertEquals(0, StringUtils.compareVersions("2.8.3", null));
+
+ /*
+ * same version returns 0
+ */
+ assertEquals(0, StringUtils.compareVersions("2.8", "2.8"));
+ assertEquals(0, StringUtils.compareVersions("2.8.3", "2.8.3"));
+ assertEquals(0, StringUtils.compareVersions("2.8.3b1", "2.8.3b1", "b"));
+ assertEquals(0, StringUtils.compareVersions("2.8.3B1", "2.8.3b1", "b"));
+ assertEquals(0, StringUtils.compareVersions("2.8.3b1", "2.8.3B1", "b"));
+
+ /*
+ * v1 < v2 returns -1
+ */
+ assertEquals(-1, StringUtils.compareVersions("2.8.3", "2.8.4"));
+ assertEquals(-1, StringUtils.compareVersions("2.8.3", "2.9"));
+ assertEquals(-1, StringUtils.compareVersions("2.8.3", "2.9.2"));
+ assertEquals(-1, StringUtils.compareVersions("2.8", "2.8.3"));
+ assertEquals(-1, StringUtils.compareVersions("2.8.3", "2.8.3b1", "b"));
+ assertEquals(-1, StringUtils.compareVersions("2.8.3b1", "2.8.3b2", "b"));
+ assertEquals(-1, StringUtils.compareVersions("2.8", "2.8.0", "b"));
+ assertEquals(-1, StringUtils.compareVersions("2", "12"));
+ assertEquals(-1, StringUtils.compareVersions("3.2.4", "3.12.11"));
+
+ /*
+ * v1 > v2 returns +1
+ */
+ assertEquals(1, StringUtils.compareVersions("2.8.3", "2.8"));
+ assertEquals(1, StringUtils.compareVersions("2.8.0", "2.8"));
+ assertEquals(1, StringUtils.compareVersions("2.8.4", "2.8.3"));
+ assertEquals(1, StringUtils.compareVersions("2.8.3b1", "2.8.3", "b"));
+ assertEquals(1, StringUtils.compareVersions("2.8.3", "2.8.2b1", "b"));
+ assertEquals(1, StringUtils.compareVersions("2.8.0b2", "2.8.0b1", "b"));
+ assertEquals(1, StringUtils.compareVersions("12", "2"));
+ assertEquals(1, StringUtils.compareVersions("3.12.11", "3.2.4"));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testToSentenceCase()
+ {
+ assertEquals("John", StringUtils.toSentenceCase("john"));
+ assertEquals("John", StringUtils.toSentenceCase("JOHN"));
+ assertEquals("John and james",
+ StringUtils.toSentenceCase("JOHN and JAMES"));
+ assertEquals("J", StringUtils.toSentenceCase("j"));
+ assertEquals("", StringUtils.toSentenceCase(""));
+ assertNull(StringUtils.toSentenceCase(null));
+ }
}
}
}
+ @Test(groups = { "Network" }, enabled = true)
+ public void testPdbSeqRetrieve() throws Exception
+ {
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ testRetrieveProteinSeqFromPDB();
+ }
+
+ @Test(groups = { "Network" }, enabled = true)
+ public void testmmCifSeqRetrieve() throws Exception
+ {
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.FALSE.toString());
+ testRetrieveProteinSeqFromPDB();
+ }
+
+ private void testRetrieveProteinSeqFromPDB() throws Exception
+ {
+ List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
+ AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
+ assertTrue(response != null);
+ assertTrue(response.getHeight() == 4);
+ for (SequenceI sq : response.getSequences())
+ {
+ assertTrue("No annotation transfered to sequence.",
+ sq.getAnnotation().length > 0);
+ assertTrue("No PDBEntry on sequence.",
+ sq.getAllPDBEntries().size() > 0);
+ org.testng.Assert
+ .assertEquals(sq.getEnd() - sq.getStart() + 1,
+ sq.getLength(),
+ "Sequence start/end doesn't match number of residues in sequence");
+ }
+ }
+
}
--- /dev/null
+package jalview.ws.ebi;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
+import org.testng.annotations.Test;
+
+public class EBIFetchClientTest
+{
+ /**
+ * Test method that constructs URL to fetch from
+ */
+ @Test(groups = "Functional")
+ public void testBuildUrl()
+ {
+ /*
+ * EMBL
+ */
+ assertEquals("http://www.ebi.ac.uk/ena/data/view/x53838&display=xml",
+ EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
+
+ /*
+ * EMBLCDS
+ */
+ assertEquals("http://www.ebi.ac.uk/ena/data/view/caa37824&display=xml",
+ EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
+
+ /*
+ * Uniprot
+ */
+ assertEquals(
+ "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprot/p00340/uniprotxml",
+ EBIFetchClient.buildUrl("P00340", "UNIPROT", "uniprotxml"));
+
+ /*
+ * PDB / pdb
+ */
+ assertEquals("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/pdb",
+ EBIFetchClient.buildUrl("3A6S", "PDB", "pdb"));
+
+ /*
+ * PDB / mmCIF
+ */
+ assertEquals(
+ "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/mmCIF",
+ EBIFetchClient.buildUrl("3A6S", "PDB", "mmCIF"));
+ }
+
+ /**
+ * Test method that parses db:id;id;id
+ */
+ @Test(groups = "Functional")
+ public void testParseIds()
+ {
+ /*
+ * pdb, two accessions
+ */
+ StringBuilder queries = new StringBuilder();
+ String db = EBIFetchClient.parseIds("pdb:3a6s;1A70", queries);
+ assertEquals("pdb", db);
+ assertEquals("3a6s,1A70", queries.toString());
+
+ /*
+ * pdb specified on second accession
+ */
+ queries.setLength(0);
+ queries = new StringBuilder();
+ db = EBIFetchClient.parseIds("3a6s;pdb:1A70", queries);
+ assertEquals("pdb", db);
+ assertEquals("3a6s,1A70", queries.toString());
+
+ /*
+ * uniprot, one accession
+ */
+ queries.setLength(0);
+ db = EBIFetchClient.parseIds("uniprot:P00340", queries);
+ assertEquals("uniprot", db);
+ assertEquals("P00340", queries.toString());
+
+ /*
+ * uniprot, one accession, appending to existing queries
+ */
+ queries.setLength(0);
+ queries.append("P30419");
+ db = EBIFetchClient.parseIds("uniprot:P00340", queries);
+ assertEquals("uniprot", db);
+ assertEquals("P30419,P00340", queries.toString());
+
+ /*
+ * pdb and uniprot mixed - rejected
+ */
+ queries.setLength(0);
+ db = EBIFetchClient.parseIds("pdb:3a6s;1a70;uniprot:P00340", queries);
+ assertNull(db);
+ assertEquals("3a6s,1a70", queries.toString());
+
+ /*
+ * pdb and PDB mixed - ok
+ */
+ queries.setLength(0);
+ db = EBIFetchClient.parseIds("pdb:3a6s;pdb:1a70;PDB:1QIP", queries);
+ assertEquals("PDB", db);
+ assertEquals("3a6s,1a70,1QIP", queries.toString());
+
+ /*
+ * no database (improper format)
+ */
+ queries.setLength(0);
+ db = EBIFetchClient.parseIds("P00340", queries);
+ assertNull(db);
+ assertEquals("P00340", queries.toString());
+ }
+}
{
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
if (af != null)
import jalview.ws.params.AutoCalcSetting;
import java.awt.Component;
+import java.io.File;
import java.util.ArrayList;
import java.util.List;
public class RNAStructExportImport
{
+ private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
+
public static String testseqs = "examples/RF00031_folded.stk";
public static Jws2Discoverer disc;
// public?
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
if (af != null)
{
af.setVisible(false);
af.dispose();
+ File f = new File(JAR_FILE_NAME);
+ if (f.exists())
+ {
+ f.delete();
+ }
}
}
// write out parameters
jalview.gui.AlignFrame nalf = null;
assertTrue("Couldn't write out the Jar file",
- new Jalview2XML(false).saveAlignment(af,
- "testRnalifold_param.jar", "trial parameter writeout"));
+ new Jalview2XML(false).saveAlignment(af, JAR_FILE_NAME,
+ "trial parameter writeout"));
assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
- false).loadJalviewAlign("testRnalifold_param.jar")) != null);
+ false).loadJalviewAlign(JAR_FILE_NAME)) != null);
if (nalf != null)
{
AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
*/
package jalview.ws.sifts;
+import jalview.api.DBRefEntryI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.structure.StructureMapping;
-import java.io.ByteArrayOutputStream;
import java.io.File;
-import java.io.PrintStream;
+import java.io.IOException;
+import java.util.ArrayList;
import java.util.HashMap;
import org.testng.Assert;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
+import MCview.Atom;
import MCview.PDBfile;
public class SiftsClientTest
{
- private final ByteArrayOutputStream outContent = new ByteArrayOutputStream();
public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
.getProperty("user.home")
@BeforeTest(alwaysRun = true)
public void populateExpectedMapping() throws SiftsException
{
- for (int x = 1; x <= 97; x++)
- {
- expectedMapping.put(50 + x, new int[] { x, u });
- }
+ expectedMapping.put(51, new int[] { 1, 2 });
+ expectedMapping.put(52, new int[] { 2, 7 });
+ expectedMapping.put(53, new int[] { 3, 12 });
+ expectedMapping.put(54, new int[] { 4, 24 });
+ expectedMapping.put(55, new int[] { 5, 33 });
+ expectedMapping.put(56, new int[] { 6, 40 });
+ expectedMapping.put(57, new int[] { 7, 47 });
+ expectedMapping.put(58, new int[] { 8, 55 });
+ expectedMapping.put(59, new int[] { 9, 62 });
+ expectedMapping.put(60, new int[] { 10, 69 });
+ expectedMapping.put(61, new int[] { 11, 76 });
+ expectedMapping.put(62, new int[] { 12, 83 });
+ expectedMapping.put(63, new int[] { 13, 87 });
+ expectedMapping.put(64, new int[] { 14, 95 });
+ expectedMapping.put(65, new int[] { 15, 102 });
+ expectedMapping.put(66, new int[] { 16, 111 });
+ expectedMapping.put(67, new int[] { 17, 122 });
+ expectedMapping.put(68, new int[] { 18, 131 });
+ expectedMapping.put(69, new int[] { 19, 137 });
+ expectedMapping.put(70, new int[] { 20, 144 });
+ expectedMapping.put(71, new int[] { 21, 152 });
+ expectedMapping.put(72, new int[] { 22, 160 });
+ expectedMapping.put(73, new int[] { 23, 167 });
+ expectedMapping.put(74, new int[] { 24, 179 });
+ expectedMapping.put(75, new int[] { 25, 187 });
+ expectedMapping.put(76, new int[] { 26, 195 });
+ expectedMapping.put(77, new int[] { 27, 203 });
+ expectedMapping.put(78, new int[] { 28, 208 });
+ expectedMapping.put(79, new int[] { 29, 213 });
+ expectedMapping.put(80, new int[] { 30, 222 });
+ expectedMapping.put(81, new int[] { 31, 231 });
+ expectedMapping.put(82, new int[] { 32, 240 });
+ expectedMapping.put(83, new int[] { 33, 244 });
+ expectedMapping.put(84, new int[] { 34, 252 });
+ expectedMapping.put(85, new int[] { 35, 260 });
+ expectedMapping.put(86, new int[] { 36, 268 });
+ expectedMapping.put(87, new int[] { 37, 275 });
+ expectedMapping.put(88, new int[] { 38, 287 });
+ expectedMapping.put(89, new int[] { 39, 293 });
+ expectedMapping.put(90, new int[] { 40, 299 });
+ expectedMapping.put(91, new int[] { 41, 310 });
+ expectedMapping.put(92, new int[] { 42, 315 });
+ expectedMapping.put(93, new int[] { 43, 319 });
+ expectedMapping.put(94, new int[] { 44, 325 });
+ expectedMapping.put(95, new int[] { 45, 331 });
+ expectedMapping.put(96, new int[] { 46, 337 });
+ expectedMapping.put(97, new int[] { 47, 343 });
+ expectedMapping.put(98, new int[] { 48, 349 });
+ expectedMapping.put(99, new int[] { 49, 354 });
+ expectedMapping.put(100, new int[] { 50, 358 });
+ expectedMapping.put(101, new int[] { 51, 367 });
+ expectedMapping.put(102, new int[] { 52, 375 });
+ expectedMapping.put(103, new int[] { 53, 384 });
+ expectedMapping.put(104, new int[] { 54, 391 });
+ expectedMapping.put(105, new int[] { 55, 395 });
+ expectedMapping.put(106, new int[] { 56, 401 });
+ expectedMapping.put(107, new int[] { 57, 409 });
+ expectedMapping.put(108, new int[] { 58, 417 });
+ expectedMapping.put(109, new int[] { 59, 426 });
+ expectedMapping.put(110, new int[] { 60, 434 });
+ expectedMapping.put(111, new int[] { 61, 442 });
+ expectedMapping.put(112, new int[] { 62, 451 });
+ expectedMapping.put(113, new int[] { 63, 457 });
+ expectedMapping.put(114, new int[] { 64, 468 });
+ expectedMapping.put(115, new int[] { 65, 476 });
+ expectedMapping.put(116, new int[] { 66, 484 });
+ expectedMapping.put(117, new int[] { 67, 492 });
+ expectedMapping.put(118, new int[] { 68, 500 });
+ expectedMapping.put(119, new int[] { 69, 509 });
+ expectedMapping.put(120, new int[] { 70, 517 });
+ expectedMapping.put(121, new int[] { 71, 525 });
+ expectedMapping.put(122, new int[] { 72, 534 });
+ expectedMapping.put(123, new int[] { 73, 538 });
+ expectedMapping.put(124, new int[] { 74, 552 });
+ expectedMapping.put(125, new int[] { 75, 559 });
+ expectedMapping.put(126, new int[] { 76, 567 });
+ expectedMapping.put(127, new int[] { 77, 574 });
+ expectedMapping.put(128, new int[] { 78, 580 });
+ expectedMapping.put(129, new int[] { 79, 585 });
+ expectedMapping.put(130, new int[] { 80, 590 });
+ expectedMapping.put(131, new int[] { 81, 602 });
+ expectedMapping.put(132, new int[] { 82, 609 });
+ expectedMapping.put(133, new int[] { 83, 616 });
+ expectedMapping.put(134, new int[] { 84, 622 });
+ expectedMapping.put(135, new int[] { 85, 630 });
+ expectedMapping.put(136, new int[] { 86, 637 });
+ expectedMapping.put(137, new int[] { 87, 644 });
+ expectedMapping.put(138, new int[] { 88, 652 });
+ expectedMapping.put(139, new int[] { 89, 661 });
+ expectedMapping.put(140, new int[] { 90, 668 });
+ expectedMapping.put(141, new int[] { 91, 678 });
+ expectedMapping.put(142, new int[] { 92, 687 });
+ expectedMapping.put(143, new int[] { 93, 696 });
+ expectedMapping.put(144, new int[] { 94, 705 });
+ expectedMapping.put(145, new int[] { 95, 714 });
+ expectedMapping.put(146, new int[] { 96, 722 });
+ expectedMapping.put(147, new int[] { 97, 729 });
}
@BeforeTest(alwaysRun = true)
{
// SIFTs entries are updated weekly - so use saved SIFTs file to enforce
// test reproducibility
+ new SiftsSettings();
SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
"sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
-
- File testSiftsFile = new File("test/jalview/io/" + testPDBId
- + ".xml.gz");
- PDBfile pdbFile = new PDBfile(false, false, false);
- pdbFile.setId(testPDBId);
- siftsClient = new SiftsClient(pdbFile, testSiftsFile);
+ SiftsSettings.setMapWithSifts(true);
+ SiftsSettings.setCacheThresholdInDays("2");
+ SiftsSettings.setFailSafePIDThreshold("70");
+ PDBfile pdbFile;
+ try
+ {
+ pdbFile = new PDBfile(false, false, false, "test/jalview/io/"
+ + testPDBId + ".pdb", AppletFormatAdapter.FILE);
+ siftsClient = new SiftsClient(pdbFile);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
}
@AfterTest(alwaysRun = true)
siftsClient = null;
}
- @BeforeTest(alwaysRun = true)
- public void setUpStreams()
- {
- System.setOut(new PrintStream(outContent));
- }
-
- @AfterTest(alwaysRun = true)
- public void cleanUpStreams()
- {
- System.setOut(null);
- }
-
@Test(groups = { "Functional" })
public void getSIFTsFileTest() throws SiftsException
{
- Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
- SiftsClient.getSiftsFile(testPDBId);
- Assert.assertFalse(outContent.toString().contains(
- ">>> SIFTS File already downloaded for " + testPDBId));
-
- // test for SIFTs file caching
- SiftsClient.getSiftsFile(testPDBId);
- Assert.assertTrue(outContent.toString().contains(
- ">>> SIFTS File already downloaded for " + testPDBId));
+ File siftsFile;
+ try
+ {
+ siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ // test for SIFTs file caching
+ SiftsSettings.setCacheThresholdInDays("0");
+ siftsFile = SiftsClient.getSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ SiftsSettings.setCacheThresholdInDays("2");
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
}
@Test(groups = { "Functional" })
// Assert that file isn't yet downloaded - if already downloaded, assert it
// is deleted
Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
- File siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
- FileAssert.assertFile(siftsFile);
- SiftsClient.downloadSiftsFile(testPDBId);
+ File siftsFile;
+ try
+ {
+ siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ SiftsClient.downloadSiftsFile(testPDBId);
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
}
+
@Test(groups = { "Functional" })
public void getAllMappingAccessionTest()
{
HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
"A", testSeq,
null);
- Assert.assertEquals(actualMapping, expectedMapping);
Assert.assertEquals(testSeq.getStart(), 1);
Assert.assertEquals(testSeq.getEnd(), 147);
+ Assert.assertEquals(actualMapping, expectedMapping);
} catch (Exception e)
{
e.printStackTrace();
@Test(groups = { "Functional" })
private void getAtomIndexTest()
{
- // siftsClient.getAtomIndex(1, null);
- // Assert.assertTrue(true);
+ ArrayList<Atom> atoms = new ArrayList<Atom>();
+ Atom atom = new Atom(u, u, u);
+ atom.resNumber = 43;
+ atom.atomIndex = 7;
+ atoms.add(atom);
+ int actualAtomIndex = siftsClient.getAtomIndex(1, atoms);
+ Assert.assertEquals(actualAtomIndex, -1);
+ actualAtomIndex = siftsClient.getAtomIndex(43, atoms);
+ Assert.assertEquals(actualAtomIndex, 7);
}
@Test(
}
- @Test(groups = { "Functional" })
- private void populateAtomPositionsTest()
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = SiftsException.class)
+ private void populateAtomPositionsNullTest1()
+ throws IllegalArgumentException, SiftsException
{
+ siftsClient.populateAtomPositions(null, null);
+ }
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = SiftsException.class)
+ private void populateAtomPositionsNullTest2()
+ throws IllegalArgumentException, SiftsException
+ {
+ siftsClient.populateAtomPositions("A", null);
}
@Test(groups = { "Functional" })
public void getValidSourceDBRefTest()
{
+ try
+ {
+ DBRefEntryI actualValidSrcDBRef = siftsClient
+ .getValidSourceDBRef(testSeq);
+ DBRefEntryI expectedDBRef = new DBRefEntry();
+ expectedDBRef.setSource(DBRefSource.UNIPROT);
+ expectedDBRef.setAccessionId("P00221");
+ expectedDBRef.setStartRes(1);
+ expectedDBRef.setEndRes(147);
+ expectedDBRef.setVersion("");
+ Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
+ } catch (Exception e)
+ {
+ }
+ }
+
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = SiftsException.class)
+ public void getValidSourceDBRefExceptionTest() throws SiftsException
+ {
+ SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
+ try
+ {
+ siftsClient.getValidSourceDBRef(invalidTestSeq);
+ } catch (SiftsException e)
+ {
+ throw new SiftsException(e.getMessage());
+ }
+ }
+
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = SiftsException.class)
+ public void getValidSourceDBRefExceptionXTest() throws SiftsException
+ {
+ SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
+ DBRefEntry invalidDBRef = new DBRefEntry();
+ invalidDBRef.setAccessionId("BLAR");
+ invalidTestSeq.addDBRef(invalidDBRef);
+ try
+ {
+ siftsClient.getValidSourceDBRef(invalidTestSeq);
+ } catch (SiftsException e)
+ {
+ throw new SiftsException(e.getMessage());
+ }
}
@Test(groups = { "Functional" })
public void isValidDBRefEntryTest()
{
+ DBRefEntryI validDBRef = new DBRefEntry();
+ validDBRef.setSource(DBRefSource.UNIPROT);
+ validDBRef.setAccessionId("P00221");
+ validDBRef.setStartRes(1);
+ validDBRef.setEndRes(147);
+ validDBRef.setVersion("");
+ Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
+ }
+ @Test(groups = { "Functional" })
+ public void getSiftsStructureMappingTest()
+ {
+ try
+ {
+ Assert.assertTrue(SiftsSettings.isMapWithSifts());
+ StructureMapping strucMapping = siftsClient.getSiftsStructureMapping(
+ testSeq, testPDBId, "A");
+ String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
+ + "Method: SIFTS\n\n"
+ + "P00221 : 1 - 97 Maps to \n"
+ + "1A70|A : 51 - 147\n\n"
+ + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
+ + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
+ + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"
+
+ + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n"
+ + " |||||||||||||||||||||||||| |||||\n"
+ + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" +
+
+ "Length of alignment = 97\n" + "Percentage ID = 98.97\n";
+
+ Assert.assertEquals(strucMapping.getMappingDetailsOutput(),
+ expectedMappingOutput);
+ Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
+ } catch (SiftsException e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getEntityCountTest()
+ {
+ int actualEntityCount = siftsClient.getEntityCount();
+ System.out.println("actual entity count : " + actualEntityCount);
+ Assert.assertEquals(actualEntityCount, 1);
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDbAccessionIdTest()
+ {
+ String actualDbAccId = siftsClient.getDbAccessionId();
+ System.out.println("Actual Db Accession Id: " + actualDbAccId);
+ Assert.assertEquals(actualDbAccId, "1a70");
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDbCoordSysTest()
+ {
+ String actualDbCoordSys = siftsClient.getDbCoordSys();
+ System.out.println("Actual DbCoordSys: " + actualDbCoordSys);
+ Assert.assertEquals(actualDbCoordSys, "PDBe");
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDbSourceTest()
+ {
+ String actualDbSource = siftsClient.getDbSource();
+ System.out.println("Actual DbSource: " + actualDbSource);
+ Assert.assertEquals(actualDbSource, "PDBe");
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDbVersionTest()
+ {
+ String actualDbVersion = siftsClient.getDbVersion();
+ System.out.println("Actual DbVersion: " + actualDbVersion);
+ Assert.assertEquals(actualDbVersion, "2.0");
}
}
--- /dev/null
+
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * A class to check help file cross-references, and external URLs if internet
+ * access is available
+ *
+ * @author gmcarstairs
+ *
+ */
+public class HelpLinksChecker
+{
+ private static final String HELP_HS = "help.hs";
+
+ private static final String HELP_TOC_XML = "helpTOC.xml";
+
+ private static final String HELP_JHM = "help.jhm";
+
+ private static boolean internetAvailable = true;
+
+ private int targetCount = 0;
+
+ private int mapCount = 0;
+
+ private int internalHrefCount = 0;
+
+ private int anchorRefCount = 0;
+
+ private int externalHrefCount = 0;
+
+ private int invalidMapUrlCount = 0;
+
+ private int invalidTargetCount = 0;
+
+ private int invalidImageCount = 0;
+
+ private int invalidInternalHrefCount = 0;
+
+ private int invalidExternalHrefCount = 0;
+
+ /**
+ * The only parameter should be a path to the root of the help directory in
+ * the workspace
+ *
+ * @param args
+ * [0] path to the /html folder in the workspace
+ * @param args
+ * [1] (optional) -nointernet to suppress external link checking for
+ * a fast check of internal links only
+ * @throws IOException
+ */
+ public static void main(String[] args) throws IOException
+ {
+ if (args.length == 0 || args.length > 2
+ || (args.length == 2 && !args[1].equals("-nointernet")))
+ {
+ System.out.println("Usage: <pathToHelpFolder> [-nointernet]");
+ return;
+ }
+
+ if (args.length == 2)
+ {
+ internetAvailable = false;
+ }
+
+ new HelpLinksChecker().checkLinks(args[0]);
+ }
+
+ /**
+ * Checks help links and reports results
+ *
+ * @param helpDirectoryPath
+ * @throws IOException
+ */
+ void checkLinks(String helpDirectoryPath) throws IOException
+ {
+ System.out.println("Checking help file links");
+ File helpFolder = new File(helpDirectoryPath);
+ if (!helpFolder.exists())
+ {
+ System.out.println("Can't find " + helpDirectoryPath);
+ return;
+ }
+
+ internetAvailable &= connectToUrl("http://www.example.com");
+
+ Map<String, String> tocTargets = checkHelpMappings(helpFolder);
+
+ Map<String, String> unusedTargets = new HashMap<String, String>(
+ tocTargets);
+
+ checkTableOfContents(helpFolder, tocTargets, unusedTargets);
+
+ checkHelpSet(helpFolder, tocTargets, unusedTargets);
+
+ checkHtmlFolder(new File(helpFolder, "html"));
+
+ reportResults(unusedTargets);
+ }
+
+ /**
+ * Checks all html files in the given directory or its sub-directories
+ *
+ * @param folder
+ * @throws IOException
+ */
+ private void checkHtmlFolder(File folder) throws IOException
+ {
+ File[] files = folder.listFiles();
+ for (File f : files)
+ {
+ if (f.isDirectory())
+ {
+ checkHtmlFolder(f);
+ }
+ else
+ {
+ if (f.getAbsolutePath().endsWith(".html"))
+ {
+ checkHtmlFile(f, folder);
+ }
+ }
+ }
+ }
+
+ /**
+ * Checks that any image attribute in help.hs is a valid target
+ *
+ * @param helpFolder
+ * @param tocTargets
+ * @param unusedTargets
+ * used targets are removed from here
+ */
+ private void checkHelpSet(File helpFolder,
+ Map<String, String> tocTargets, Map<String, String> unusedTargets)
+ throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(new File(
+ helpFolder, HELP_HS)));
+ String data = br.readLine();
+ int lineNo = 0;
+
+ while (data != null)
+ {
+ lineNo++;
+ String image = getAttribute(data, "image");
+ if (image != null)
+ {
+ unusedTargets.remove(image);
+ if (!tocTargets.containsKey(image))
+ {
+ System.out.println(String.format(
+ "Invalid image '%s' at line %d of %s", image, lineNo,
+ HELP_HS));
+ invalidImageCount++;
+ }
+ }
+ data = br.readLine();
+ }
+ br.close();
+ }
+
+ /**
+ * Print counts to sysout
+ *
+ * @param unusedTargets
+ */
+ private void reportResults(Map<String, String> unusedTargets)
+ {
+ System.out.println("\nResults:");
+ System.out.println(targetCount + " distinct help targets");
+ System.out.println(mapCount + " help mappings");
+ System.out.println(invalidTargetCount + " invalid targets");
+ System.out.println(unusedTargets.size() + " unused targets");
+ for (String target : unusedTargets.keySet())
+ {
+ System.out.println(String.format(" %s: %s", target,
+ unusedTargets.get(target)));
+ }
+ System.out.println(invalidMapUrlCount + " invalid map urls");
+ System.out.println(invalidImageCount + " invalid image attributes");
+ System.out.println(String.format(
+ "%d internal href links (%d with anchors - not checked)",
+ internalHrefCount, anchorRefCount));
+ System.out.println(invalidInternalHrefCount
+ + " invalid internal href links");
+ System.out.println(externalHrefCount + " external href links");
+ if (internetAvailable)
+ {
+ System.out.println(invalidExternalHrefCount
+ + " invalid external href links");
+ }
+ else
+ {
+ System.out
+ .println("External links not verified as internet not available");
+ }
+
+ }
+
+ /**
+ * Reads the given html file and checks any href attibute values are either
+ * <ul>
+ * <li>a valid relative file path, or</li>
+ * <li>a valid absolute URL (if external link checking is enabled)</li>
+ * </ul>
+ *
+ * @param htmlFile
+ * @param htmlFolder
+ * the parent folder (for validation of relative paths)
+ */
+ private void checkHtmlFile(File htmlFile, File htmlFolder)
+ throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(htmlFile));
+ String data = br.readLine();
+ int lineNo = 0;
+ while (data != null)
+ {
+ lineNo++;
+ String href = getAttribute(data, "href");
+ if (href != null)
+ {
+ String anchor = null;
+ int anchorPos = href.indexOf("#");
+ if (anchorPos != -1)
+ {
+ anchor = href.substring(anchorPos + 1);
+ href = href.substring(0, anchorPos);
+ }
+ boolean badLink = false;
+ if (href.startsWith("http"))
+ {
+ externalHrefCount++;
+ if (internetAvailable)
+ {
+ if (!connectToUrl(href))
+ {
+ badLink = true;
+ invalidExternalHrefCount++;
+ }
+ }
+ }
+ else
+ {
+ internalHrefCount++;
+ File hrefFile = href.equals("") ? htmlFile : new File(htmlFolder,
+ href);
+ if (!hrefFile.exists())
+ {
+ badLink = true;
+ invalidInternalHrefCount++;
+ }
+ if (anchor != null)
+ {
+ anchorRefCount++;
+ if (!badLink)
+ {
+ if (!checkAnchorExists(hrefFile, anchor))
+ {
+ System.out.println(String.format(
+ "Invalid anchor: %s at line %d of %s", anchor,
+ lineNo, getPath(htmlFile)));
+ }
+ }
+ }
+ }
+ if (badLink)
+ {
+ System.out.println(String.format(
+ "Invalid href %s at line %d of %s", href, lineNo,
+ getPath(htmlFile)));
+ }
+ }
+ data = br.readLine();
+ }
+ br.close();
+ }
+
+ /**
+ * Reads the file and checks for the presence of the given html anchor
+ *
+ * @param hrefFile
+ * @param anchor
+ * @return true if anchor is found else false
+ */
+ private boolean checkAnchorExists(File hrefFile, String anchor)
+ {
+ String nameAnchor = "<a name=\"" + anchor + "\"";
+ String idAnchor = "<a id=\"" + anchor + "\"";
+ boolean found = false;
+ try
+ {
+ BufferedReader br = new BufferedReader(new FileReader(hrefFile));
+ String data = br.readLine();
+ while (data != null)
+ {
+ if (data.contains(nameAnchor) || data.contains(idAnchor))
+ {
+ found = true;
+ break;
+ }
+ data = br.readLine();
+ }
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ return found;
+ }
+
+ /**
+ * Returns the part of the file path starting from /help/
+ *
+ * @param helpFile
+ * @return
+ */
+ private String getPath(File helpFile)
+ {
+ String path = helpFile.getPath();
+ int helpPos = path.indexOf("/help/");
+ return helpPos == -1 ? path : path.substring(helpPos);
+ }
+
+ /**
+ * Returns true if the URL returns an input stream, or false if the URL
+ * returns an error code or we cannot connect to it (e.g. no internet
+ * available)
+ *
+ * @param url
+ * @return
+ */
+ private boolean connectToUrl(String url)
+ {
+ try
+ {
+ URL u = new URL(url);
+ InputStream connection = u.openStream();
+ connection.close();
+ return true;
+ } catch (Throwable t)
+ {
+ return false;
+ }
+ }
+
+ /**
+ * Reads file help.jhm and checks that
+ * <ul>
+ * <li>each target attribute is in tocTargets</li>
+ * <li>each url attribute is a valid relative file link</li>
+ * </ul>
+ *
+ * @param helpFolder
+ */
+ private Map<String, String> checkHelpMappings(File helpFolder)
+ throws IOException
+ {
+ Map<String, String> targets = new HashMap<String, String>();
+ BufferedReader br = new BufferedReader(new FileReader(new File(
+ helpFolder, HELP_JHM)));
+ String data = br.readLine();
+ int lineNo = 0;
+ while (data != null)
+ {
+ lineNo++;
+
+ /*
+ * record target, check for duplicates
+ */
+ String target = getAttribute(data, "target");
+ if (target != null)
+ {
+ mapCount++;
+ if (targets.containsKey(target))
+ {
+ System.out.println(String.format(
+ "Duplicate target mapping to %s at line %d of %s",
+ target, lineNo, HELP_JHM));
+ }
+ else
+ {
+ targetCount++;
+ }
+ }
+
+ /*
+ * validate url
+ */
+ String url = getAttribute(data, "url");
+ if (url != null)
+ {
+ targets.put(target, url);
+ int anchorPos = url.indexOf("#");
+ if (anchorPos != -1)
+ {
+ url = url.substring(0, anchorPos);
+ }
+ if (!new File(helpFolder, url).exists())
+ {
+ System.out.println(String.format(
+ "Invalid url path '%s' at line %d of %s", url, lineNo,
+ HELP_JHM));
+ invalidMapUrlCount++;
+ }
+ }
+ data = br.readLine();
+ }
+ br.close();
+ return targets;
+ }
+
+ /**
+ * Reads file helpTOC.xml and reports any invalid targets
+ *
+ * @param helpFolder
+ * @param tocTargets
+ * @param unusedTargets
+ * used targets are removed from this map
+ *
+ * @return
+ * @throws IOException
+ */
+ private void checkTableOfContents(File helpFolder,
+ Map<String, String> tocTargets, Map<String, String> unusedTargets)
+ throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(new File(
+ helpFolder, HELP_TOC_XML)));
+ String data = br.readLine();
+ int lineNo = 0;
+ while (data != null)
+ {
+ lineNo++;
+ /*
+ * assuming no more than one "target" per line of file here
+ */
+ String target = getAttribute(data, "target");
+ if (target != null)
+ {
+ unusedTargets.remove(target);
+ if (!tocTargets.containsKey(target))
+ {
+ System.out.println(String.format(
+ "Invalid target '%s' at line %d of %s", target, lineNo,
+ HELP_TOC_XML));
+ invalidTargetCount++;
+ }
+ }
+ data = br.readLine();
+ }
+ br.close();
+ }
+
+ /**
+ * Returns the value of an attribute if found in the data, else null
+ *
+ * @param data
+ * @param attName
+ * @return
+ */
+ private static String getAttribute(String data, String attName)
+ {
+ /*
+ * make a partial attempt at ignoring within <!-- html comments -->
+ * (doesn't work if multi-line)
+ */
+ int commentStartPos = data.indexOf("<!--");
+ int commentEndPos = commentStartPos == -1 ? -1 : data.substring(
+ commentStartPos + 4).indexOf("-->");
+ String value = null;
+ String match = attName + "=\"";
+ int attPos = data.indexOf(match);
+ if (attPos > 0
+ && (commentStartPos == -1 || attPos < commentStartPos || attPos > commentEndPos))
+ {
+ data = data.substring(attPos + match.length());
+ value = data.substring(0, data.indexOf("\""));
+ }
+ return value;
+ }
+}
<string><![CDATA[664]]></string>
</property>
<property name="sourceName">
- <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+ <string><![CDATA[groovy-all-2.4.6-indy.jar]]></string>
</property>
<property name="overrideUnixPermissions">
<boolean>false</boolean>
<boolean>true</boolean>
</property>
<property name="destinationName">
- <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+ <string><![CDATA[groovy-all-2.4.6-indy.jar]]></string>
</property>
<property name="fileSize">
<long>6149494</long>
</property>
</object>
</method>
+ <method name="addElement">
+ <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1000ddddfab939">
+ <property name="belongsToUninstallPhase">
+ <boolean>false</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ <property name="unixPermissions">
+ <string><![CDATA[664]]></string>
+ </property>
+ <property name="sourceName">
+ <string><![CDATA[servlet-api-3.1.jar]]></string>
+ </property>
+ <property name="overrideUnixPermissions">
+ <boolean>false</boolean>
+ </property>
+ <property name="sourcePath">
+ <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ </property>
+ <property name="shouldUninstall">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="destinationName">
+ <string><![CDATA[servlet-api-3.1.jar]]></string>
+ </property>
+ <property name="fileSize">
+ <long>16046</long>
+ </property>
+ <property name="macBinary">
+ <boolean>false</boolean>
+ </property>
+ <property name="targetCheckKind">
+ <int>0</int>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ </object>
+ </method>
</object>
</property>
<property name="rulesFailedMessage">
<object refID="1f46efeefab93"/>
<object refID="1936efeefab93"/>
<object refID="1000ddddfab93"/>
+ <object refID="1000ddddfab939"/>
<object refID="10936efeefab93"/>
<object refID="11936efeefab93"/>
<object refID="12936efeefab93"/>
<object refID="1f46efeefab93"/>
<object refID="1936efeefab93"/>
<object refID="1000ddddfab93"/>
+ <object refID="1000ddddfab939"/>
<object refID="10936efeefab93"/>
<object refID="11936efeefab93"/>
<object refID="12936efeefab93"/>
--- /dev/null
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Properties;
+import java.util.TreeSet;
+
+/**
+ * This class scans Java source files for calls to MessageManager and reports
+ * <ul>
+ * <li>calls using keys not found in Messages.properties</li>
+ * <li>any unused keys in Messages.properties</li>
+ * </ul>
+ * It does not handle dynamically constructed keys, these are reported as
+ * possible errors for manual inspection. <br>
+ * For comparing translated bundles with Messages.properties, see i18nAnt.xml
+ *
+ * @author gmcarstairs
+ *
+ */
+public class MessageBundleChecker
+{
+ /*
+ * number of text lines to read at a time in order to parse
+ * code that is split over several lines
+ */
+ static int bufferSize = 3;
+
+ static final String METHOD1 = "MessageManager.getString(";
+
+ static final String METHOD2 = "MessageManager.getStringOrReturn(";
+
+ static final String METHOD3 = "MessageManager.formatMessage(";
+
+ static final String[] METHODS = { METHOD1, METHOD2, METHOD3 };
+
+ /*
+ * root of the Java source folders we want to scan
+ */
+ String sourcePath;
+
+ /*
+ * contents of Messages.properties
+ */
+ private Properties messages;
+
+ /*
+ * keys from Messages.properties
+ * we remove entries from here as they are found to be used
+ * any left over are unused entries
+ */
+ private TreeSet<String> messageKeys;
+
+ private int javaCount;
+
+ private HashSet<String> invalidKeys;
+
+ /**
+ * Runs the scan given the path to the root of Java source directories
+ *
+ * @param args
+ * [0] path to the source folder to scan
+ * @param args
+ * [1] (optional) read buffer size (default is 3); increasing this
+ * may detect more results but will give higher error counts due to
+ * double counting of the same code
+ * @throws IOException
+ */
+ public static void main(String[] args) throws IOException
+ {
+ if (args.length != 1 && args.length != 2)
+ {
+ System.out.println("Usage: <pathToSourceFolder> [readBufferSize]");
+ return;
+ }
+ if (args.length == 2)
+ {
+ bufferSize = Integer.valueOf(args[1]);
+ }
+ new MessageBundleChecker().doMain(args[0]);
+ }
+
+ /**
+ * Main method to perform the work
+ *
+ * @param srcPath
+ * @throws IOException
+ */
+ private void doMain(String srcPath) throws IOException
+ {
+ System.out.println("Scanning " + srcPath
+ + " for calls to MessageManager");
+ sourcePath = srcPath;
+ loadMessages();
+ File dir = new File(srcPath);
+ if (!dir.exists())
+ {
+ System.out.println(srcPath + " not found");
+ return;
+ }
+ invalidKeys = new HashSet<String>();
+ if (dir.isDirectory())
+ {
+ scanDirectory(dir);
+ }
+ else
+ {
+ scanFile(dir);
+ }
+ reportResults();
+ }
+
+ /**
+ * Prints out counts to sysout
+ */
+ private void reportResults()
+ {
+ System.out.println("\nScanned " + javaCount + " source files");
+ System.out.println("Message.properties has " + messages.size()
+ + " keys");
+ System.out.println("Found " + invalidKeys.size()
+ + " possibly invalid parameter calls");
+
+ System.out.println(messageKeys.size()
+ + " keys not found, possibly unused");
+ for (String key : messageKeys)
+ {
+ System.out.println(" " + key);
+ }
+ }
+
+ /**
+ * Scan all files within a directory
+ *
+ * @param dir
+ * @throws IOException
+ */
+ private void scanDirectory(File dir) throws IOException
+ {
+ File[] files = dir.listFiles();
+ if (files != null)
+ {
+ for (File f : files)
+ {
+ if (f.isDirectory())
+ {
+ scanDirectory(f);
+ }
+ else
+ {
+ scanFile(f);
+ }
+ }
+ }
+ }
+
+ /**
+ * Scan a Java file
+ *
+ * @param f
+ */
+ private void scanFile(File f) throws IOException
+ {
+ String path = f.getPath();
+ if (!path.endsWith(".java"))
+ {
+ return;
+ }
+ javaCount++;
+
+ String[] lines = new String[bufferSize];
+ BufferedReader br = new BufferedReader(new FileReader(f));
+ for (int i = 0; i < bufferSize; i++)
+ {
+ String readLine = br.readLine();
+ lines[i] = stripCommentsAndTrim(readLine);
+ }
+
+ int lineNo = 0;
+
+ while (lines[bufferSize - 1] != null)
+ {
+ lineNo++;
+ inspectSourceLines(path, lineNo, lines);
+
+ for (int i = 0; i < bufferSize - 1; i++)
+ {
+ lines[i] = lines[i + 1];
+ }
+ lines[bufferSize - 1] = stripCommentsAndTrim(br.readLine());
+ }
+ br.close();
+
+ }
+
+ /*
+ * removes anything after (and including) '//'
+ */
+ private String stripCommentsAndTrim(String line)
+ {
+ if (line != null)
+ {
+ int pos = line.indexOf("//");
+ if (pos != -1)
+ {
+ line = line.substring(0, pos);
+ }
+ line = line.replace("\t", " ").trim();
+ }
+ return line;
+ }
+
+ /**
+ * Look for calls to MessageManager methods, possibly split over two or more
+ * lines
+ *
+ * @param path
+ * @param lineNo
+ * @param lines
+ */
+ private void inspectSourceLines(String path, int lineNo, String[] lines)
+ {
+ String lineNos = String.format("%d-%d", lineNo, lineNo + lines.length
+ - 1);
+ String combined = combineLines(lines);
+ for (String method : METHODS)
+ {
+ int pos = combined.indexOf(method);
+ if (pos == -1)
+ {
+ continue;
+ }
+ String methodArgs = combined.substring(pos + method.length());
+ if ("".equals(methodArgs))
+ {
+ /*
+ * continues on next line - catch in the next read loop iteration
+ */
+ continue;
+ }
+ if (!methodArgs.startsWith("\""))
+ {
+ System.out.println(String.format(
+ "Possible dynamic key at %s line %s %s",
+ path.substring(sourcePath.length()), lineNos, combined));
+ continue;
+ }
+ methodArgs = methodArgs.substring(1);
+ int quotePos = methodArgs.indexOf("\"");
+ if (quotePos == -1)
+ {
+ System.out.println(String.format("Trouble parsing %s line %s %s",
+ path.substring(sourcePath.length()), lineNos, combined));
+ continue;
+ }
+ String messageKey = methodArgs.substring(0, quotePos);
+ if (!this.messages.containsKey(messageKey))
+ {
+ System.out.println(String.format(
+ "Unmatched key '%s' at line %s of %s", messageKey, lineNos,
+ path.substring(sourcePath.length())));
+ if (!invalidKeys.contains(messageKey))
+ {
+ invalidKeys.add(messageKey);
+ }
+ }
+ messageKeys.remove(messageKey);
+ }
+ }
+
+ private String combineLines(String[] lines)
+ {
+ String combined = "";
+ if (lines != null)
+ {
+ for (String line : lines)
+ {
+ if (line != null)
+ {
+ combined += line;
+ }
+ }
+ }
+ return combined;
+ }
+
+ /**
+ * Loads properties from Message.properties
+ *
+ * @throws IOException
+ */
+ void loadMessages() throws IOException
+ {
+ messages = new Properties();
+ FileReader reader = new FileReader(new File(sourcePath,
+ "../resources/lang/Messages.properties"));
+ messages.load(reader);
+ reader.close();
+
+ messageKeys = new TreeSet<String>();
+ for (Object key : messages.keySet())
+ {
+ messageKeys.add((String) key);
+ }
+
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff
