<classpath>
<classpathentry kind="src" path="src"/>
<classpathentry kind="src" path="utils"/>
+ <classpathentry kind="src" path="test"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="lib" path="lib/activation.jar"/>
<classpathentry kind="lib" path="lib/axis.jar" sourcepath="D:/axis-1_2RC2-src/axis-1_2RC2"/>
<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="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.java"/>
<classpathentry kind="lib" path="/Users/jimp/git/jalview_clean/lib/VARNAv3-9-dev.jar"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="output" path="classes"/>
</classpath>
</buildCommand>
</buildSpec>
<natures>
+ <nature>org.eclipse.jdt.groovy.core.groovyNature</nature>
<nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r<head>\r<!-- InstanceBeginEditable name="doctitle" -->
-<TITLE>Applet Parameters</TITLE>
-<!-- InstanceEndEditable -->
\r<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">
\r<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
\r<style type="text/css">
\r<!--
\rtd {
\r font-family: Geneva, Arial, Helvetica, sans-serif;
\r font-size: 12px;
\r}
\r.plain {
\r font-family: Verdana, Arial, Helvetica, sans-serif;
\r font-size: 14px;
\r text-decoration: none;
\r}
\r.plain:hover{
\r background-color:#000000; color: #F2F2FF;
\r}
\r \r-->
\r</style>
\r\r<script language="JavaScript">
\rfunction genHref()
\r{
\rvar s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
\rfor(i=0; i<8; i++)
\r{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
\rwindow.location=href;
\r}
\rfunction getEventTarget(e)
\r{
\rif(!e)
\re = window.event;
\rif(e.target)
\rreturn e.target;
\rreturn e.srcElement;
\r}
\r\r</script>
\r</head>
\r\r<body alink="#000000" vlink="#000000" link="#000000">
\r<script type="text/javascript">
\rvar gaJsHost = (("https:" == document.location.protocol) ?
\r"https://ssl." : "http://www.");
\rdocument.write(unescape("%3Cscript src='" + gaJsHost +
\r"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
\r</script>
\r<script type="text/javascript">
\rtry{
\rvar pageTracker = _gat._getTracker("UA-9060947-1");
\rpageTracker._trackPageview();
\r} catch(err) {}
\r</script>
\r<div align="left">
\r <table width="805" height="100" cellpadding="5">
\r <tr>
\r <td background="../jalview.gif"> <a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
\r </tr>
\r </table>
\r <table width="805" border="0" cellpadding="5" cellspacing="5">
\r <tr>
\r <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
\r \r <div align="center">
\r <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
\r <tr>
\r <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
\r Version</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
\r history</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
\r Code</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
\r Mailing List</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a
\r href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
\r class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
\r bug reports to the discussion list.</em></td>
\r </tr>
\r <tr></tr>
\r <tr>
\r <!--<td align="left" valign="middle"><br>
\r Please send problems<br>and
\r bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
\r </tr>
\r </table>
\r\r </div>
\r\r <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
\r <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
\r </div>
\r </td>
\r <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p>
\r <strong>Quick Links:<ul><li>Download the applet jar file from <a
\r href="jalviewApplet.jar">here</a>
\r </li>
\r <li>Parameters are described <a href="#parameters">below</a></li>
\r <li>The javascript API is described <a
\r href="jalviewLiteJs.html">here</a></li>
\r </ul></strong>
\r </p>
\r +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<!-- InstanceBeginEditable name="doctitle" -->\r
+<TITLE>Applet Parameters</TITLE>\r
+<!-- InstanceEndEditable -->
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+<style type="text/css">
+<!--
+td {
+ font-family: Geneva, Arial, Helvetica, sans-serif;
+ font-size: 12px;
+}
+.plain {
+ font-family: Verdana, Arial, Helvetica, sans-serif;
+ font-size: 14px;
+ text-decoration: none;
+}
+.plain:hover{
+ background-color:#000000; color: #F2F2FF;
+}
+
+-->
+</style>
+
+<script language="JavaScript">
+function genHref()
+{
+var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
+for(i=0; i<8; i++)
+{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
+window.location=href;
+}
+function getEventTarget(e)
+{
+if(!e)
+e = window.event;
+if(e.target)
+return e.target;
+return e.srcElement;
+}
+
+</script>
+</head>
+
+<body alink="#000000" vlink="#000000" link="#000000">
+<script type="text/javascript">
+var gaJsHost = (("https:" == document.location.protocol) ?
+"https://ssl." : "http://www.");
+document.write(unescape("%3Cscript src='" + gaJsHost +
+"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+try{
+var pageTracker = _gat._getTracker("UA-9060947-1");
+pageTracker._trackPageview();
+} catch(err) {}
+</script>
+<div align="left">
+ <table width="805" height="100" cellpadding="5">
+ <tr>
+ <td background="../jalview.gif"> <a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
+ </tr>
+ </table>
+ <table width="805" border="0" cellpadding="5" cellspacing="5">
+ <tr>
+ <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
+
+ <div align="center">
+ <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
+ <tr>
+ <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
+ Version</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
+ history</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
+ Code</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
+ Mailing List</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a
+ href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+ class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
+ bug reports to the discussion list.</em></td>
+ </tr>
+ <tr></tr>
+ <tr>
+ <!--<td align="left" valign="middle"><br>
+ Please send problems<br>and
+ bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
+ </tr>
+ </table>
+
+ </div>
+
+ <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
+ <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
+ </div>
+ </td>
+ <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" --> \r
+ <p>
+ <strong>Quick Links:<ul><li>Download the applet jar file from <a
+ href="jalviewApplet.jar">here</a>
+ </li>
+ <li>Parameters are described <a href="#parameters">below</a></li>
+ <li>The javascript API is described <a
+ href="jalviewLiteJs.html">here</a></li>
+ </ul></strong>
+ </p>
+
<h3 align="left">Useful to know!!</h3>
<ul>
<li>Package all your data files into a single (or multiple) zip / jar
</font></li>
<li> Use Jalview for input to a HTML form. For an example of how to
code this using Javascript, click <a href="formComplete.html">here</a>.
- <br>
- </li>
+ <br>\r
+ </li>\r
<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>
- </ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.8</font></strong></p>
\r <ul>
\r <li><font size="2">Normalised sequence logo display
\r </font></li>
\r <li><font size="2">RNA secondary structure annotation row
\r </font></li>
\r </ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7.1</font></strong></p>
\r <ul>
\r<li><font size="2">Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></font></li>
\r<li>To use Jmol as the structure viewer for Jalview, you must include
\r the jar file in the applet archive argument thus:<br>
\r <pre>archive="jalviewApplet.jar,Jmol-12.2.4.jar"</pre></font>
\r </li>
\r <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have
\r Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the
\r original Jalview structure viewer will still be available. <br>
\r </li>
\r \r </ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>
\r <ul>
\r <li><font size="2">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>
\r <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></font>
\r </li>
\r <li><font size="2">New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
\r </font></li></ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
\r <ul>
\r <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series</font></li>
\r <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
\r the Jmol binary distribution available at the Jmol Sourceforge site,
\r or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
\r <li><font size="2">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).</font></li>
\r </ul>
- <br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>
\r <ul>
\r <li><font size="2">New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</font></li>
\r </ul>
\r <br><strong><font size="2">**NEW FEATURES** in Jalview 2.4</font></strong></p>
+ </ul>
+ <p><strong><font size="2">**NEW FEATURES** in Jalview 2.8</font></strong></p>
+ <ul>
+ <li><font size="2">Normalised sequence logo display
+ </font></li>
+ <li><font size="2">RNA secondary structure annotation row
+ </font></li>
+ </ul>
+ <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7.1</font></strong></p>
+ <ul>
+<li><font size="2">Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></font></li>
+<li>To use Jmol as the structure viewer for Jalview, you must include
+ the jar file in the applet archive argument thus:<br>
+ <pre>archive="jalviewApplet.jar,Jmol-12.2.4.jar"</pre></font>
+ </li>
+ <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have
+ Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the
+ original Jalview structure viewer will still be available. <br>
+ </li>
+
+ </ul>
+ <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>
+ <ul>
+ <li><font size="2">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></font>
+ </li>
+ <li><font size="2">New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
+ </font></li></ul>
+ <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
+ <ul>
+ <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series</font></li>
+ <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
+ 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><font size="2">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).</font></li>
+ </ul>
+ <br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>
+ <ul>
+ <li><font size="2">New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</font></li>
+ </ul>
+ <br><strong><font size="2">**NEW FEATURES** in Jalview 2.4</font></strong></p>
<ul>
<li><font size="2">New applet API methods for feature display control, views, and obtaining current selection via javascript.</font></li>
<li><font size="2">Group show and hide parameters:
<font size="2"><param name="PDBFile3" value="Third.pdb
D=SeqX B=SeqY C=SeqZ"> </font> <br>
</li>
- <li>Note parameter "PDBSeq" is no longer required.<br>
+ <li>Note parameter "PDBSeq" is no longer required.<br>\r
</li>
<li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="../versions.html">versions archive if you want to download the old Jmol applet</a>.</li>
<p> </p>
<font face="Courier New, Courier, mono"><param name="userDefinedColour"
value="D,E=red; K,R,H=0022FF; C=yellow"></font><br>
</li>
- <li>Param <font face="Courier New, Courier, mono">showFeatureSettings</font>
+ <li>Param <font face="Courier New, Courier, mono">showFeatureSettings</font>
- this will display the feature settings window when the applet starts.<br>
</li>
<li>Param <font face="Courier New, Courier, mono">Application_URL value="http://www.jalview.org/services/launchApp"<br>
<tr><td>showbutton</td>
<td>true</td>
<td>Show the jalview button on the page. When false, JalviewLite will open immediately.</td>
- </tr>\r </tr>\r <tr><td>sortByTree</td>\r <td>true or false (default is false)</td>\r <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>\r </tr>\r <tr>\r <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>\r </tr>\r <tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>\r <tr><td>showUnlinkedTreeNodes</td><td>true or false (default is false)</td><td>indicate if unassociated nodes should be highlighted in the tree view</td>\r </tr>\r <tr><td>heightScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. (<em>since 2.5.1</em>)</td>\r </tr>
- <tr><td>widthScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (<em>since 2.5.1</em>)</td>\r </tr>\r <tr><td>centrecolumnlabels</td>\r <td>true of false (default is false)</td>\r <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (<em>since 2.4</em>)</td>\r <tr><td>showUnconserved</td>\r <td>true of false (default is false)</td>\r <td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (<em>since 2.5</em>)</td>\r </tr>\r <tr><td>upperCase</td>\r <td><em>bold</em> or other value</td>\r <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>\r </tr>\r <tr><td>automaticScrolling</td>\r <td>true of false (default is true)</td>\r <td>When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (<em>since 2.6</em>)</td>\r </tr>\r \r <tr><td>showGroupConsensus</td>\r <td>true of false (default is false)</td>\r <td>When true, shows consensus annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>\r </tr>\r \r <tr><td>showGroupConservation</td>\r <td>true of false (default is false)</td>\r <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>showConsensusHistogram</td>\r <td>true of false (default is true)</td>\r <td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>showSequenceLogo</td>\r <td>true of false (default is false)</td>\r <td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>normaliseLogo</td>\r <td>true of false (default is false)</td>\r <td>When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (<em>since 2.7.1</em>)</td>\r </tr>\r <tr><td>oninit</td>\r <td><em>after_init()</em></td>\r <td>name of javascript function that will be called after the jalviewLite instance has completed its initialisation. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>relaxedidmatch</td>\r <td><em>true or false (default is false)</em></td>\r <td>When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID). (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>alignpdbfiles</td>\r <td><em>true or false (default is false)</em></td>\r <td>When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental] (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>externalstructureviewer</td>\r <td><em>true or false (default is false)</em></td>\r <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] (<em>since 2.7</em>)</td>\r \r </tr>\r <tr><td>annotationcolour_max</td>\r <td>colour name or RGB hex triplet (default is red)</td>\r <td>Default colour used for maximum value when shading by annotation. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>annotationcolour_min</td>\r <td>colour name or RGB hex triplet (default is orange)</td>\r <td>Default colour used for minimum value when shading by annotation. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>jalviewhelpurl</td>\r <td>absolute or relative url or javascript function prefixed by <em>javascript:</em> (default is http://www.jalview.org/help.html)</td>\r <td>Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>resolvetocodebase</td>\r <td>True or False (False)</td>\r <td>Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (<em>since 2.7</em>)</td>\r </tr>\r \r </table>
+ </tr>
+ </tr>
+ <tr><td>sortByTree</td>
+ <td>true or false (default is false)</td>
+ <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>
+ </tr>
+ <tr>
+ <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>
+ </tr>
+ <tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>
+ <tr><td>showUnlinkedTreeNodes</td><td>true or false (default is false)</td><td>indicate if unassociated nodes should be highlighted in the tree view</td>
+ </tr>
+ <tr><td>heightScale</td>
+ <td>1.0 or greater</td>
+ <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. (<em>since 2.5.1</em>)</td>
+ </tr>
+ <tr><td>widthScale</td>
+ <td>1.0 or greater</td>
+ <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (<em>since 2.5.1</em>)</td>
+ </tr>
+ <tr><td>centrecolumnlabels</td>
+ <td>true of false (default is false)</td>
+ <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (<em>since 2.4</em>)</td>
+ <tr><td>showUnconserved</td>
+ <td>true of false (default is false)</td>
+ <td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (<em>since 2.5</em>)</td>
+ </tr>
+ <tr><td>upperCase</td>
+ <td><em>bold</em> or other value</td>
+ <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>
+ </tr>
+ <tr><td>automaticScrolling</td>
+ <td>true of false (default is true)</td>
+ <td>When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (<em>since 2.6</em>)</td>
+ </tr>
+
+ <tr><td>showGroupConsensus</td>
+ <td>true of false (default is false)</td>
+ <td>When true, shows consensus annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
+ </tr>
+
+ <tr><td>showGroupConservation</td>
+ <td>true of false (default is false)</td>
+ <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>showConsensusHistogram</td>
+ <td>true of false (default is true)</td>
+ <td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>showSequenceLogo</td>
+ <td>true of false (default is false)</td>
+ <td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>normaliseLogo</td>
+ <td>true of false (default is false)</td>
+ <td>When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (<em>since 2.7.1</em>)</td>
+ </tr>
+ <tr><td>oninit</td>
+ <td><em>after_init()</em></td>
+ <td>name of javascript function that will be called after the jalviewLite instance has completed its initialisation. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>relaxedidmatch</td>
+ <td><em>true or false (default is false)</em></td>
+ <td>When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID). (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>alignpdbfiles</td>
+ <td><em>true or false (default is false)</em></td>
+ <td>When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental] (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>externalstructureviewer</td>
+ <td><em>true or false (default is false)</em></td>
+ <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] (<em>since 2.7</em>)</td>
+
+ </tr>
+ <tr><td>annotationcolour_max</td>
+ <td>colour name or RGB hex triplet (default is red)</td>
+ <td>Default colour used for maximum value when shading by annotation. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>annotationcolour_min</td>
+ <td>colour name or RGB hex triplet (default is orange)</td>
+ <td>Default colour used for minimum value when shading by annotation. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>jalviewhelpurl</td>
+ <td>absolute or relative url or javascript function prefixed by <em>javascript:</em> (default is http://www.jalview.org/help.html)</td>
+ <td>Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>resolvetocodebase</td>
+ <td>True or False (False)</td>
+ <td>Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>scoreFile</td>
+ <td>file</td>
+ <td>Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format</td>
+ </tr>
+ </table>
<p align="center"> </p>
- <!-- InstanceEndEditable --></td>\r </tr>\r </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
\ No newline at end of file
+ <!-- InstanceEndEditable --></td>
+ </tr>
+ </table>
+</div>
+</body>
+<!-- InstanceEnd --></html>
*/\r
package jalview.appletgui;\r
\r
-import java.net.*;\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
+import jalview.analysis.AAFrequency;\r
+import jalview.analysis.AlignmentSorter;\r
+import jalview.analysis.Conservation;\r
import jalview.api.SequenceStructureBinding;\r
import jalview.bin.JalviewLite;\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
+import jalview.commands.CommandI;\r
+import jalview.commands.EditCommand;\r
+import jalview.commands.OrderCommand;\r
+import jalview.commands.RemoveGapColCommand;\r
+import jalview.commands.RemoveGapsCommand;\r
+import jalview.commands.SlideSequencesCommand;\r
+import jalview.commands.TrimRegionCommand;\r
+import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.AlignmentOrder;\r
+import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.io.AnnotationFile;\r
+import jalview.io.AppletFormatAdapter;\r
+import jalview.io.FeaturesFile;\r
+import jalview.io.TCoffeeScoreFile;\r
+import jalview.schemes.Blosum62ColourScheme;\r
+import jalview.schemes.BuriedColourScheme;\r
+import jalview.schemes.ClustalxColourScheme;\r
+import jalview.schemes.ColourSchemeI;\r
+import jalview.schemes.HelixColourScheme;\r
+import jalview.schemes.HydrophobicColourScheme;\r
+import jalview.schemes.NucleotideColourScheme;\r
+import jalview.schemes.PIDColourScheme;\r
+import jalview.schemes.PurinePyrimidineColourScheme;\r
+import jalview.schemes.RNAHelicesColourChooser;\r
+import jalview.schemes.ResidueProperties;\r
+import jalview.schemes.StrandColourScheme;\r
+import jalview.schemes.TCoffeeColourScheme;\r
+import jalview.schemes.TaylorColourScheme;\r
+import jalview.schemes.TurnColourScheme;\r
+import jalview.schemes.ZappoColourScheme;\r
import jalview.structure.StructureSelectionManager;\r
\r
-public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
- ItemListener, KeyListener\r
+import java.awt.BorderLayout;\r
+import java.awt.Canvas;\r
+import java.awt.CheckboxMenuItem;\r
+import java.awt.Color;\r
+import java.awt.Font;\r
+import java.awt.FontMetrics;\r
+import java.awt.Frame;\r
+import java.awt.Graphics;\r
+import java.awt.Label;\r
+import java.awt.Menu;\r
+import java.awt.MenuBar;\r
+import java.awt.MenuItem;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.FocusEvent;\r
+import java.awt.event.FocusListener;\r
+import java.awt.event.ItemEvent;\r
+import java.awt.event.ItemListener;\r
+import java.awt.event.KeyEvent;\r
+import java.awt.event.KeyListener;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.io.IOException;\r
+import java.io.InputStreamReader;\r
+import java.net.URL;\r
+import java.net.URLEncoder;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.StringTokenizer;\r
+import java.util.Vector;\r
+\r
+public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener\r
{\r
public AlignmentPanel alignPanel;\r
\r
int DEFAULT_HEIGHT = 500;\r
\r
String jalviewServletURL;\r
+ \r
\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,\r
- String title, boolean embedded)\r
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)\r
{\r
-\r
if (applet != null)\r
{\r
jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
{\r
loadAnnotations();\r
}\r
+ else if( source == loadScores ) {\r
+ loadScores();\r
+ }\r
else if (source == outputAnnotations)\r
{\r
outputAnnotations(true);\r
{\r
changeColour(new Blosum62ColourScheme());\r
}\r
+ else if (source == tcoffeeColour) {\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ }\r
else if (source == annotationColour)\r
{\r
new AnnotationColourChooser(viewport, alignPanel);\r
jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
\r
}\r
+ \r
+ public void loadScores() {\r
+ //TODO\r
+ \r
+ }\r
\r
public String outputAnnotations(boolean displayTextbox)\r
{\r
\r
cs.setConsensus(viewport.getSequenceConsensusHash());\r
\r
- }\r
+ } \r
viewport.setGlobalColourScheme(cs);\r
\r
if (viewport.getColourAppliesToAllGroups())\r
{\r
try\r
{\r
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+ sg.cs = cs.getClass().newInstance();\r
} catch (Exception ex)\r
{\r
ex.printStackTrace();\r
MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
\r
MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+ \r
+ MenuItem loadScores = new MenuItem("Load Associated T-Coffee scores ...");\r
\r
MenuItem outputFeatures = new MenuItem("Export Features ...");\r
\r
MenuItem PIDColour = new MenuItem();\r
\r
MenuItem BLOSUM62Colour = new MenuItem();\r
+ \r
+ MenuItem tcoffeeColour = new MenuItem();\r
\r
MenuItem njTreeBlosumMenuItem = new MenuItem();\r
\r
\r
loadTree.addActionListener(this);\r
loadAnnotations.addActionListener(this);\r
+ loadScores.addActionListener(this);\r
outputFeatures.addActionListener(this);\r
outputAnnotations.addActionListener(this);\r
selectAllSequenceMenuItem.addActionListener(this);\r
PIDColour.addActionListener(this);\r
BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
BLOSUM62Colour.addActionListener(this);\r
- avDistanceTreeBlosumMenuItem\r
- .setLabel("Average Distance Using BLOSUM62");\r
+ tcoffeeColour.setLabel("T-Coffee Scores");\r
+ tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided\r
+ tcoffeeColour.addActionListener(this);\r
+ avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");\r
avDistanceTreeBlosumMenuItem.addActionListener(this);\r
njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
njTreeBlosumMenuItem.addActionListener(this);\r
fileMenu.add(inputText);\r
fileMenu.add(loadTree);\r
fileMenu.add(loadAnnotations);\r
-\r
+ fileMenu.add(loadScores);\r
+ \r
fileMenu.addSeparator();\r
fileMenu.add(outputTextboxMenu);\r
fileMenu.add(outputFeatures);\r
colourMenu.add(buriedColour);\r
colourMenu.add(nucleotideColour);\r
colourMenu.add(purinePyrimidineColour);\r
+ colourMenu.add(tcoffeeColour);\r
colourMenu.add(userDefinedColour);\r
colourMenu.addSeparator();\r
colourMenu.add(conservationMenuItem);\r
public String getSequenceSetId() {\r
return viewport.getSequenceSetId();\r
}\r
+ \r
+ \r
+ /**\r
+ * Load the (T-Coffee) score file from the specified url \r
+ * \r
+ * @param url The absolute path from where download and read the score file\r
+ * @throws IOException \r
+ */\r
+ public void loadScoreFile( URL url ) throws IOException {\r
+ // TODO: refactor to string/standard jalview data importer\r
+ TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) );\r
+ if( file == null ) {\r
+ // TODO: raise a dialog box here rather than bomb out.\r
+ \r
+ throw new RuntimeException("The file provided does not match the T-Coffee scores file format");\r
+ }\r
+ \r
+ /*\r
+ * check that the score matrix matches the alignment dimensions\r
+ */\r
+ AlignmentI aln; \r
+ if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {\r
+ // TODO: raise a dialog box here rather than bomb out.\r
+ throw new RuntimeException("The scores matrix does not match the alignment dimensions");\r
+ \r
+ }\r
+ \r
+ // TODO add parameter to indicate if matching should be done\r
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
+ {\r
+ tcoffeeColour.setEnabled(true);\r
+ // switch to this color\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ }\r
+ }\r
+ \r
+ \r
}\r
*/
package jalview.appletgui;
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
{
if (cs != null)
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i);
+ resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+
+import java.awt.Button;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dialog;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.MouseEvent;
+import java.util.Vector;
public class UserDefinedColours extends Panel implements ActionListener,
AdjustmentListener
{
try
{
- col = oldColourScheme.findColour(aa.charAt(0), -1);
+ col = oldColourScheme.findColour(aa.charAt(0), -1, null);
} catch (Exception ex)
{
}
\r
if (protocol == jalview.io.AppletFormatAdapter.PASTE)\r
{\r
- newAlignFrame.setTitle("Sequences from "\r
- + applet.getDocumentBase());\r
+ newAlignFrame.setTitle("Sequences from " + applet.getDocumentBase());\r
}\r
\r
newAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
}\r
}\r
\r
+\r
+ /*\r
+ * Try to load T-Coffee score file\r
+ */\r
+ String sScoreFile = applet.getParameter("scoreFile");\r
+ if( sScoreFile != null && !"".equals(sScoreFile) ) {\r
+ try {\r
+ URL urlScore = new URL(sScoreFile);\r
+ newAlignFrame.loadScoreFile(urlScore);\r
+ \r
+ }\r
+ catch( Exception e ) {\r
+ // TODO error message log (shows a warning dialogbox?)\r
+ System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());\r
+ }\r
+ }\r
+ \r
+\r
// ///////////////////////////\r
// modify display of features\r
// we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed\r
annotations = temp;
}
+ @Override
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * returns all annotation on the alignment
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
{
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
-public interface AlignmentI
+public interface AlignmentI extends AnnotatedCollectionI
{
/**
* Calculates the number of sequences in an alignment
--- /dev/null
+package jalview.datamodel;
+
+import java.util.List;
+
+public interface AnnotatedCollectionI
+{
+
+ /**
+ * TODO: decide if null is a valid response if there is no annotation on the object
+ * @return null
+ */
+ AlignmentAnnotation[] getAlignmentAnnotation();
+
+}
*/
package jalview.datamodel;
-import java.util.*;
+import jalview.analysis.AlignSeq;
-import jalview.analysis.*;
+import java.util.Enumeration;
+import java.util.Vector;
/**
*
* to the residues of this sequence
*/
Vector annotation;
+
+ /**
+ * The index of the sequence in a MSA
+ */
+ int index = -1;
/** array of seuqence features - may not be null for a valid sequence object */
public SequenceFeature[] sequenceFeatures;
}
}
+ /**
+ * @return The index (zero-based) on this sequence in the MSA.
+ * It returns {@code -1} if this information is not available.
+ */
+ public int getIndex() { return index; }
+
+ /**
+ * Defines the position of this sequence in the MSA.
+ * Use the value {@code -1} if this information is undefined.
+ *
+ * @param The position for this sequence. This value is zero-based (zero for this first sequence)
+ */
+ public void setIndex(int value) { index = value; }
}
* @author $author$
* @version $Revision$
*/
-public class SequenceGroup
+public class SequenceGroup implements AnnotatedCollectionI
{
String groupName;
{
return;
}
-
+ if (cs!=null)
+ {
+ cs.alignmentChanged(this);
+ }
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
{
return normaliseSequenceLogo;
}
+ @Override
+ /**
+ * returns a new array with all annotation involving this group
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ // TODO add in other methods like 'getAlignmentAnnotation(String label), etc'
+ ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
+ for (SequenceI seq:(Vector<SequenceI>)sequences)
+ {
+ for (AlignmentAnnotation al: seq.getAnnotation())
+ {
+ if (al.groupRef==this)
+ {
+ annot.add(al);
+ }
+ }
+ }
+ if (consensus!=null)
+ {
+ annot.add(consensus);
+ }
+ if (conservation!=null)
+ {
+ annot.add(conservation);
+ }
+ return annot.toArray(new AlignmentAnnotation[0]);
+ }
}
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.Vector;
/**
* DOCUMENT ME!
* null or mapping from entry's numbering to local start/end
*/
public void transferAnnotation(SequenceI entry, Mapping mp);
+
+ /**
+ * @param index The sequence index in the MSA
+ */
+ public void setIndex(int index);
+
+ /**
+ * @return The index of the sequence in the alignment
+ */
+ public int getIndex();
}
import jalview.io.JalviewFileView;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
AlignViewport viewport;
Vector alignPanels = new Vector();
-
+
/**
* Last format used to load or save alignments in this window
*/
*/
public void changeColour(ColourSchemeI cs)
{
+ // TODO: compare with applet and pull up to model method
int threshold = 0;
if (cs != null)
{
try
{
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ sg.cs = cs.getClass().newInstance();
} catch (Exception ex)
{
}
}
}
}
-
+
+ @Override
+ public void loadScores_actionPerformed(ActionEvent e)
+ {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Select a T-Coffee scores ascii file");
+ chooser.setToolTipText("Load a score file");
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String sFilePath = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", sFilePath);
+
+
+ try
+ {
+ TCoffeeScoreFile result = TCoffeeScoreFile.load(new File(sFilePath));
+ if( result == null ) {
+ // TODO: raise a dialog box here rather than bomb out.
+
+ throw new RuntimeException("The file provided does not match the T-Coffee scores file format");
+ }
+
+ /*
+ * check that the score matrix matches the alignment dimensions
+ */
+ AlignmentI aln;
+ if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
+ // TODO: raise a dialog box here rather than bomb out.
+ throw new RuntimeException("The scores matrix does not match the alignment dimensions");
+ }
+ if (result.annotateAlignment(alignPanel.getAlignment(), true))
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ // switch to this color
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ } else {
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.setSelected(false);
+ }
+ }
+ catch (Exception ex) {
+ JOptionPane.showMessageDialog(
+ Desktop.desktop,
+ ex.getMessage(),
+ "Problem reading tree file",
+ JOptionPane.WARNING_MESSAGE);
+
+ ex.printStackTrace();
+ }
+ }
+
+ }
+
+
+ @Override
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) {
+ changeColour( new TCoffeeColourScheme(alignPanel.getAlignment()) );
+ }
+
+// /**
+// * Load the (T-Coffee) score file from the specified url
+// *
+// * @param url The absolute path from where download and read the score file
+// * @throws IOException
+// */
+// public void loadScoreFile(URL url ) throws IOException {
+//
+// TCoffeeScoreFile result = new TCoffeeScoreFile();
+// result.parse( new InputStreamReader( url.openStream() ) );
+// tcoffeeScoreFile = result;
+// }
+
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
return ShowNewickTree(nf, title, 600, 500, 4, 5);
*/
package jalview.gui;
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
/**
* DOCUMENT ME!
{
if (cs != null)
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i);
+ resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
*/
package jalview.gui;
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.JalviewFileChooser;
+import jalview.jbgui.GUserDefinedColours;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
/**
* DOCUMENT ME!
{
try
{
- col = oldColourScheme.findColour(aa.charAt(0), -1);
+ col = oldColourScheme.findColour(aa.charAt(0), -1, null);
} catch (Exception ex)
{
}
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* DOCUMENT ME!
/**
* Sequences to be added to form a new alignment.
*/
- protected Vector seqs;
+ protected Vector<SequenceI> seqs;
/**
* annotation to be added to generated alignment object
public AlignFile(String inFile, String type) throws IOException
{
super(inFile, type);
-
initData();
-
parse();
+ // sets the index of each sequence in the alignment
+ for( int i=0,c=seqs.size(); i<c; i++ ) {
+ seqs.get(i).setIndex(i);
+ }
}
/**
super(source);
initData();
parse();
+ // sets the index of each sequence in the alignment
+ for( int i=0,c=seqs.size(); i<c; i++ ) {
+ seqs.get(i).setIndex(i);
+ }
}
/**
* Return the seqs Vector
*/
- public Vector getSeqs()
+ public Vector<SequenceI> getSeqs()
{
return seqs;
}
--- /dev/null
+package jalview.io;
+
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * A file parse for T-Coffee score ascii format. This file contains the alignment consensus
+ * for each resude in any sequence.
+ * <p>
+ * This file is procuded by <code>t_coffee</code> providing the option
+ * <code>-output=score_ascii </code> to the program command line
+ *
+ * An example file is the following
+ *
+ * <pre>
+ * T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
+ * Cedric Notredame
+ * CPU TIME:0 sec.
+ * SCORE=90
+ * *
+ * BAD AVG GOOD
+ * *
+ * 1PHT : 89
+ * 1BB9 : 90
+ * 1UHC : 94
+ * 1YCS : 94
+ * 1OOT : 93
+ * 1ABO : 94
+ * 1FYN : 94
+ * 1QCF : 94
+ * cons : 90
+ *
+ * 1PHT 999999999999999999999999998762112222543211112134
+ * 1BB9 99999999999999999999999999987-------4322----2234
+ * 1UHC 99999999999999999999999999987-------5321----2246
+ * 1YCS 99999999999999999999999999986-------4321----1-35
+ * 1OOT 999999999999999999999999999861-------3------1135
+ * 1ABO 99999999999999999999999999986-------422-------34
+ * 1FYN 99999999999999999999999999985-------32--------35
+ * 1QCF 99999999999999999999999999974-------2---------24
+ * cons 999999999999999999999999999851000110321100001134
+ *
+ *
+ * 1PHT ----------5666642367889999999999889
+ * 1BB9 1111111111676653-355679999999999889
+ * 1UHC ----------788774--66789999999999889
+ * 1YCS ----------78777--356789999999999889
+ * 1OOT ----------78877--356789999999997-67
+ * 1ABO ----------687774--56779999999999889
+ * 1FYN ----------6888842356789999999999889
+ * 1QCF ----------6878742356789999999999889
+ * cons 00100000006877641356789999999999889
+ * </pre>
+ *
+ *
+ * @author Paolo Di Tommaso
+ *
+ */
+public class TCoffeeScoreFile {
+
+ /** The {@link Header} structure holder */
+ Header header;
+
+ /**
+ * Holds the consensues values for each sequences. It uses a LinkedHashMap to maintaint the
+ * insertion order.
+ */
+ LinkedHashMap<String,StringBuilder> scores = new LinkedHashMap<String,StringBuilder>();
+
+ Integer fWidth;
+
+ /**
+ * Parse the specified file.
+ *
+ * @param file The file to be parsed
+ */
+ public static TCoffeeScoreFile load(File file) {
+ try {
+ return load(new FileReader(file));
+ }
+ catch (FileNotFoundException e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+ /**
+ * Parse the provided reader for the T-Coffee scores file format
+ *
+ * @param reader
+ */
+ public static TCoffeeScoreFile load(Reader reader) {
+
+ try {
+ BufferedReader in = (BufferedReader) (reader instanceof BufferedReader ? reader : new BufferedReader(reader));
+ TCoffeeScoreFile result = new TCoffeeScoreFile();
+ result.doParsing(in);
+ return result.header != null && result.scores != null ? result : null;
+ }
+ catch( Exception e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+ /**
+ * @return The 'height' of the score matrix i.e. the numbers of score rows that should matches
+ * the number of sequences in the alignment
+ */
+ public int getHeight() {
+ // the last entry will always be the 'global' alingment consensus scores, so it is removed
+ // from the 'height' count to make this value compatible with the number of sequences in the MSA
+ return scores != null && scores.size() > 0 ? scores.size()-1 : 0;
+ }
+
+ /**
+ * @return The 'width' of the score matrix i.e. the number of columns.
+ * Since teh score value are supposd to be calculated for an 'aligned' MSA, all the entries
+ * have to have the same width.
+ */
+ public int getWidth() {
+ return fWidth != null ? fWidth : 0;
+ }
+
+ /**
+ * The default constructor is marked as {@code protected} since this class is meant to created
+ * through the {@link #load(File)} or {@link #load(Reader)} factory methods
+ */
+ protected TCoffeeScoreFile() { }
+
+ /**
+ * Get the string of score values for the specified seqeunce ID.
+ * @param id The sequence ID
+ * @return The scores as a string of values e.g. {@code 99999987-------432}.
+ * It return an empty string when the specified ID is missing.
+ */
+ public String getScoresFor( String id ) {
+ return scores.containsKey(id) ? scores.get(id).toString() : "";
+ }
+
+ /**
+ * @return The list of score string as a {@link List} object, in the same ordeer of the insertion i.e. in the MSA
+ */
+ public List<String> getScoresList() {
+ List<String> result = new ArrayList<String>( scores.size() );
+ for( Map.Entry<String,StringBuilder> it : scores.entrySet() ) {
+ result.add(it.getValue().toString());
+ }
+
+ return result;
+ }
+
+ /**
+ * @return The parsed score values a matrix of bytes
+ */
+ public byte[][] getScoresArray() {
+ byte[][] result = new byte[ scores.size() ][];
+
+ int rowCount = 0;
+ for( Map.Entry<String,StringBuilder> it : scores.entrySet() ) {
+ String line = it.getValue().toString();
+ byte[] seqValues = new byte[ line.length() ];
+ for( int j=0, c=line.length(); j<c; j++ ) {
+
+ byte val = (byte)(line.charAt(j) - '0');
+
+ seqValues[j] = ( val >= 0 && val <= 9 ) ? val : -1;
+ }
+
+ result[rowCount++] = seqValues;
+ }
+
+ return result;
+ }
+
+
+ private void doParsing(BufferedReader in) throws IOException {
+
+ /*
+ * read the header
+ */
+ header = readHeader(in);
+
+ if( header == null ) { return; }
+
+
+ /*
+ * initilize the structure
+ */
+ for( Map.Entry<String,Integer> entry : header.scores.entrySet() ) {
+ scores.put( entry.getKey(), new StringBuilder());
+ }
+
+ /*
+ * go with the reading
+ */
+ Block block;
+ while( (block = readBlock(in, header.scores.size())) != null ) {
+
+ /*
+ * append sequences read in the block
+ */
+ for( Map.Entry<String,String> entry : block.items.entrySet() ) {
+ StringBuilder scoreStringBuilder = scores.get(entry.getKey());
+ if( scoreStringBuilder == null ) {
+ throw new RuntimeException(String.format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section", entry.getKey()));
+ }
+
+ scoreStringBuilder.append( entry.getValue() );
+ }
+ }
+
+ /*
+ * verify that all rows have the same width
+ */
+ for( StringBuilder str : scores.values() ) {
+ if( fWidth == null ) {
+ fWidth = str.length();
+ }
+ else if( fWidth != str.length() ) {
+ throw new RuntimeException("Invalid T-Coffee score file: All the score sequences must have the same length");
+ }
+ }
+
+
+
+ }
+
+
+ static int parseInt( String str ) {
+ try {
+ return Integer.parseInt(str);
+ }
+ catch( NumberFormatException e ) {
+ // TODO report a warning ?
+ return 0;
+ }
+ }
+
+ /**
+ * Reaad the header section in the T-Coffee score file format
+ *
+ * @param reader The scores reader
+ * @return The parser {@link Header} instance
+ * @throws RuntimeException when the header is not in the expected format
+ */
+ static Header readHeader(BufferedReader reader) {
+
+ Header result = null;
+ try {
+ result = new Header();
+ result.head = reader.readLine();
+
+ String line;
+
+ while( (line = reader.readLine()) != null ) {
+ if( line.startsWith("SCORE=")) {
+ result.score = parseInt( line.substring(6).trim() );
+ break;
+ }
+ }
+
+ if( (line=reader.readLine())==null || !"*".equals(line.trim())) return null;
+ if( (line=reader.readLine())==null || !"BAD AVG GOOD".equals(line.trim())) return null;
+ if( (line=reader.readLine())==null || !"*".equals(line.trim())) return null;
+
+ /*
+ * now are expected a list if sequences ID up to the first blank line
+ */
+ while( (line=reader.readLine()) != null ) {
+ if( "".equals(line) ) {
+ break;
+ }
+
+ int p = line.indexOf(":");
+ if( p == -1 ) {
+ // TODO report a warning
+ continue;
+ }
+
+ String id = line.substring(0,p).trim();
+ int val = parseInt(line.substring(p+1).trim());
+ if( "".equals(id) ) {
+ // TODO report warning
+ continue;
+ }
+
+ result.scores.put(id,val);
+ }
+
+ }
+ catch( IOException e ) {
+ throw new RuntimeException("Cannot parse T-Coffee score ascii file", e);
+ }
+
+ return result;
+ }
+
+ /**
+ * Read a scores block ihe provided stream.
+ *
+ * @param reader The stream to parse
+ * @param size The expected number of the sequence to be read
+ * @return The {@link Block} instance read or {link null} null if the end of file has reached.
+ * @throws IOException Something went wrong on the 'wire'
+ */
+ static Block readBlock( BufferedReader reader, int size ) throws IOException {
+ Block result = new Block(size);
+ String line;
+
+ /*
+ * read blank lines (eventually)
+ */
+ while( (line=reader.readLine()) != null && "".equals(line.trim())) {
+ // consume blank lines
+ }
+
+ if( line == null ) return null;
+
+ /*
+ * read the scores block
+ */
+ do {
+ if( "".equals(line.trim()) ) {
+ // terminated
+ break;
+ }
+
+ // split the line on the first blank
+ // the first part have to contain the sequence id
+ // theramining part are the scores values
+ int p = line.indexOf(" ");
+ if( p == -1 ) {
+ //TODO This is an unexpected condition, log a warning or throw an exception ?
+ continue;
+ }
+
+ String id = line.substring(0,p).trim();
+ String val = line.substring(p+1).trim();
+
+ result.items.put(id, val);
+
+ } while( (line = reader.readLine()) != null );
+
+
+ return result;
+ }
+
+ /*
+ * The score file header
+ */
+ static class Header {
+ String head;
+ int score;
+
+ LinkedHashMap<String,Integer> scores = new LinkedHashMap<String,Integer>();
+
+ public int getScoreAvg() { return score; }
+
+ public int getScoreFor( String ID ) {
+
+ return scores.containsKey(ID) ? scores.get(ID) : -1;
+
+ }
+ }
+
+ /*
+ * Hold a single block values block in the score file
+ */
+ static class Block {
+ int size;
+ Map<String,String> items;
+
+ public Block( int size ) {
+ this.size = size;
+ this.items = new HashMap<String,String>(size);
+ }
+
+ String getScoresFor( String id ) {
+ return items.get(id);
+ }
+
+ String getConsensus() {
+ return items.get("cons");
+ }
+ }
+ /**
+ * TCOFFEE score colourscheme
+ */
+ static final Color[] colors = {
+ new Color( 102, 102, 255 ), // #6666FF
+ new Color( 0, 255, 0), // #00FF00
+ new Color( 102, 255, 0), // #66FF00
+ new Color( 204, 255, 0), // #CCFF00
+ new Color( 255, 255, 0), // #FFFF00
+ new Color( 255, 204, 0), // #FFCC00
+ new Color( 255, 153, 0), // #FF9900
+ new Color( 255, 102, 0), // #FF6600
+ new Color( 255, 51, 0), // #FF3300
+ new Color( 255, 34, 0) // #FF2000
+ };
+ public final static String TCOFFEE_SCORE="TCoffeeScore";
+ /**
+ * generate annotation for this TCoffee score set on the given alignment
+ * @param al alignment to annotate
+ * @param matchids if true, annotate sequences based on matching sequence names
+ * @return true if alignment annotation was modified, false otherwise.
+ */
+ public boolean annotateAlignment(AlignmentI al, boolean matchids)
+ {
+ boolean added=false;
+ int i=0;
+ SequenceIdMatcher sidmatcher = new SequenceIdMatcher(al.getSequencesArray());
+ byte[][] scoreMatrix=getScoresArray();
+ // for 2.8 - we locate any existing TCoffee annotation and remove it first before adding this.
+ for (Map.Entry<String,StringBuilder> id:scores.entrySet())
+ {
+ byte[] srow=scoreMatrix[i];
+ SequenceI s;
+ if (matchids)
+ {
+ s=sidmatcher.findIdMatch(id.getKey());
+ } else {
+ s=al.getSequenceAt(i);
+ }
+ i++;
+ if (s==null && i!=scores.size() && !id.getKey().equals("cons"))
+ {
+ System.err.println("No "+(matchids ? "match ":" sequences left ")+" for TCoffee score set : "+id.getKey());
+ continue;
+ }
+ int jSize=al.getWidth()< srow.length ? al.getWidth() : srow.length;
+ Annotation[] annotations=new Annotation[al.getWidth()];
+ for (int j=0;j<jSize;j++) {
+ byte val = srow[j];
+ annotations[j]=new Annotation(s==null ? ""+val:null,s==null ? ""+val:null,(char) val,val*1f,val >= 0 && val < colors.length ? colors[val] : Color.white);
+ }
+ AlignmentAnnotation aa=null;
+ if (s!=null)
+ {
+ // TODO - set per sequence score
+ aa=new AlignmentAnnotation(TCOFFEE_SCORE, "Score for "+id.getKey(), annotations);
+
+ aa.setSequenceRef(s);
+ aa.visible=false;
+ aa.belowAlignment=false;
+ } else {
+ aa=new AlignmentAnnotation("T-COFFEE", "TCoffee column reliability score", annotations);
+ aa.belowAlignment=true;
+ aa.visible=true;
+
+ }
+ al.addAnnotation(aa);
+ added=true;
+ }
+ return added;
+ }
+
+
+}
*/
package jalview.jbgui;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.schemes.*;
+import jalview.schemes.ColourSchemeProperty;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.GridLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTabbedPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
public class GAlignFrame extends JInternalFrame
{
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+
+
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
JMenuItem epsFile = new JMenuItem();
JMenuItem LoadtreeMenuItem = new JMenuItem();
+
+ JMenuItem loadScoresMenuItem = new JMenuItem();
public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
colours.add(nucleotideColour);
colours.add(purinePyrimidineColour);
// colours.add(covariationColour);
+ colours.add(tcoffeeColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
nucleotideColour.setSelected(true);
break;
+
+ case ColourSchemeProperty.TCOFFEE:
+ tcoffeeColour.setSelected(true);
+ break;
case ColourSchemeProperty.PURINEPYRIMIDINE:
purinePyrimidineColour.setSelected(true);
nucleotideColour_actionPerformed(e);
}
});
+
+ tcoffeeColour.setText("T-Coffee scores");
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener( new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ tcoffeeColorScheme_actionPerformed(e);
+ }
+ } );
+
+
deleteGroups.setText("Undefine groups");
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
}
});
LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load Associated Tree");
+ LoadtreeMenuItem.setText("Load Associated Tree");
LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
LoadtreeMenuItem_actionPerformed(e);
}
});
+
+ loadScoresMenuItem.setActionCommand("Load T-Coffee scores");
+ loadScoresMenuItem.setText("Load T-Coffee scores");
+ loadScoresMenuItem.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ loadScores_actionPerformed(e);
+ }
+ });
+
scaleAbove.setVisible(false);
scaleAbove.setText("Scale Above");
scaleAbove.addActionListener(new java.awt.event.ActionListener()
fileMenu.add(exportAnnotations);
fileMenu.add(LoadtreeMenuItem);
fileMenu.add(associatedData);
+ fileMenu.add(loadScoresMenuItem);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
editMenu.add(undoMenuItem);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
// colourMenu.add(covariationColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
+
+ }
+
+ /**
+ * Template method to handle the 'load T-Coffee scores' menu event.
+ * <p>
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event The raised event
+ */
+ protected void loadScores_actionPerformed(ActionEvent event) {
+
+ }
+
+
+ /**
+ * Template method to handle the 'Color T-Coffee scores' menu event.
+ * <p>
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event The raised event
+ */
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
+
}
+
protected void jpred_actionPerformed(ActionEvent e)
{
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.Color;
public class AnnotationColourGradient extends ResidueColourScheme
{
*
* @return DOCUMENT ME!
*/
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour = Color.white;
if (colourScheme != null)
{
- currentColour = colourScheme.findColour(c, j);
+ currentColour = colourScheme.findColour(c, j, seq);
}
else if (range != 0)
{
*/
package jalview.schemes;
-import java.awt.*;
-
-import jalview.analysis.*;
+import jalview.analysis.AAFrequency;
+import java.awt.Color;
+import jalview.datamodel.SequenceI;
public class Blosum62ColourScheme extends ResidueColourScheme
{
public Blosum62ColourScheme()
super();
}
- public Color findColour(char res, int j)
+ @Override
+ public Color findColour(char res, int j, SequenceI seq)
{
if ('a' <= res && res <= 'z')
{
*/
package jalview.schemes;
-import java.util.*;
+import jalview.datamodel.SequenceI;
-import java.awt.*;
-
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Vector;
public class ClustalxColourScheme extends ResidueColourScheme // implements
// IParameterizable
ResidueColour[19] = colours[0]; // V
}
+ @Override
public Color findColour(char c)
{
return Color.pink;
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
*/
package jalview.schemes;
-import java.awt.*;
+import java.awt.Color;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceI;
public interface ColourSchemeI
{
public Color findColour(char c);
- public Color findColour(char c, int j);
+ public Color findColour(char c, int j, SequenceI seq);
public void setConsensus(java.util.Hashtable[] h);
public void setThreshold(int ct, boolean ignoreGaps);
+ public void alignmentChanged(AnnotatedCollectionI alignment);
+
}
*/
package jalview.schemes;
-import java.awt.*;
+import java.awt.Color;
/**
* ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
public static final int PURINEPYRIMIDINE = 13;
public static final int COVARIATION = 14;
+
+ public static final int TCOFFEE = 15;
+
/**
* index of first colourscheme (includes 'None')
{
ret = NUCLEOTIDE;
}
+ else if (name.equalsIgnoreCase("T-Coffee scores"))
+ {
+ ret = TCOFFEE;
+ }
+
else if (name.equalsIgnoreCase("User Defined"))
{
ret = USER_DEFINED;
}
/**
- * DOCUMENT ME!
+ * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
*
* @param seqs
- * DOCUMENT ME!
+ * sequences to be coloured by colourscheme
* @param width
- * DOCUMENT ME!
+ * geometry of alignment
* @param index
- * DOCUMENT ME!
+ * colourscheme number
*
- * @return DOCUMENT ME!
+ * @return null or an instance of the colourscheme configured to colour given sequence set
*/
public static ColourSchemeI getColour(java.util.Vector seqs, int width,
int index)
{
+ // TODO 3.0 2.8 refactor signature to take an alignmentI like container so colourschemes based on annotation can be initialised
ColourSchemeI cs = null;
switch (index)
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public Color findColour(char c)
{
// System.out.println("called"); log.debug
*
* @return DOCUMENT ME!
*/
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
if ((threshold == 0) || aboveThreshold(c, j))
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.analysis.AAFrequency;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import java.awt.Color;
public class PIDColourScheme extends ResidueColourScheme
{
this.thresholds = ResidueProperties.pidThresholds;
}
- public Color findColour(char c, int j)
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
if ('a' <= c && c <= 'z')
{
*/
package jalview.schemes;
-import java.util.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceI;
-import java.awt.*;
-
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Hashtable;
/**
* DOCUMENT ME!
: colors[ResidueProperties.aaIndex[c]];
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
return currentColour;
}
+ @Override public void alignmentChanged(AnnotatedCollectionI alignment) {};
/**
* Get the percentage threshold for this colour scheme
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
if (threshold > 0)
{
--- /dev/null
+package jalview.schemes;
+
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.TCoffeeScoreFile;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.IdentityHashMap;
+import java.util.TreeMap;
+
+/**
+ * Defines the color score for T-Coffee MSA
+ * <p>
+ * See http://tcoffee.org
+ *
+ *
+ * @author Paolo Di Tommaso
+ *
+ */
+public class TCoffeeColourScheme extends ResidueColourScheme {
+
+ static final Color[] colors = {
+ new Color( 102, 102, 255 ), // #6666FF
+ new Color( 0, 255, 0), // #00FF00
+ new Color( 102, 255, 0), // #66FF00
+ new Color( 204, 255, 0), // #CCFF00
+ new Color( 255, 255, 0), // #FFFF00
+ new Color( 255, 204, 0), // #FFCC00
+ new Color( 255, 153, 0), // #FF9900
+ new Color( 255, 102, 0), // #FF6600
+ new Color( 255, 51, 0), // #FF3300
+ new Color( 255, 34, 0) // #FF2000
+ };
+
+
+ IdentityHashMap<SequenceI, Color[]> seqMap;
+ /**
+ * the color scheme needs to look at the alignment to get and cache T-COFFEE scores
+ *
+ * @param alignment - annotated sequences to be searched
+ */
+ public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
+ alignmentChanged(alignment);
+ }
+ @Override public void alignmentChanged(AnnotatedCollectionI alignment)
+ {
+ // assume only one set of TCOFFEE scores - but could have more than one potentially.
+ ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+ // Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
+ seqMap = new IdentityHashMap<SequenceI, Color[]>();
+ for (AlignmentAnnotation al:alignment.getAlignmentAnnotation())
+ {
+ if (al.sequenceRef!=null && !al.belowAlignment && al.label!=null && (al.label==TCoffeeScoreFile.TCOFFEE_SCORE || al.label.equals(TCoffeeScoreFile.TCOFFEE_SCORE)))
+ {
+ annots.add(al);
+ Color[] scores=new Color[al.annotations.length];
+ int i=0;
+ for (Annotation an:al.annotations)
+ {
+ scores[i++]=(an!=null) ? an.colour : Color.white;
+ }
+ seqMap.put(al.sequenceRef, scores);
+ }
+ }
+ }
+ @Override
+ public Color findColour(char c, int j, SequenceI seq) {
+ Color[] cols;
+
+ if( seqMap==null || (cols=seqMap.get(seq))==null) {
+ return Color.white;
+ }
+
+ if( j < 0 || j>= cols.length ) {
+ return Color.white;
+ }
+ return cols[j];
+ }
+}
*/
package jalview.schemes;
-import java.util.*;
-
-import java.awt.*;
+import java.awt.Color;
+import java.util.StringTokenizer;
+import jalview.datamodel.SequenceI;
public class UserColourScheme extends ResidueColourScheme
{
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
int index = ResidueProperties.aaIndex[c];
--- /dev/null
+package jalview.io;
+
+import static org.junit.Assert.*;
+import jalview.io.TCoffeeScoreFile.Block;
+import jalview.io.TCoffeeScoreFile.Header;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.List;
+
+import org.junit.Test;
+
+public class TCoffeeScoreFileTest {
+
+ final static File SCORE_FILE = new File("./test/jalview/io/tcoffee.score_ascii");
+
+ @Test
+ public void testReadHeader() throws FileNotFoundException {
+
+ Header header = TCoffeeScoreFile.readHeader( new BufferedReader(new FileReader(SCORE_FILE)) );
+ assertNotNull(header);
+ assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
+ assertEquals( 90, header.score );
+ assertEquals( 89, header.getScoreFor("1PHT") );
+ assertEquals( 90, header.getScoreFor("1BB9") );
+ assertEquals( 94, header.getScoreFor("1UHC") );
+ assertEquals( 94, header.getScoreFor("1YCS") );
+ assertEquals( 93, header.getScoreFor("1OOT") );
+ assertEquals( 94, header.getScoreFor("1ABO") );
+ assertEquals( 94, header.getScoreFor("1FYN") );
+ assertEquals( 94, header.getScoreFor("1QCF") );
+ assertEquals( 90, header.getScoreFor("cons") );
+ }
+
+
+ @Test
+ public void testWrongFile() {
+ TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.fasta_aln"));
+ assertNull(result);
+ }
+
+ @Test
+ public void testHeightAndWidth() {
+ TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.score_ascii"));
+ assertNotNull(result);
+ assertEquals( 8, result.getHeight() );
+ assertEquals( 83, result.getWidth() );
+ }
+
+ @Test
+ public void testReadBlock( ) throws IOException {
+
+ String BLOCK = "\n" +
+ "\n" +
+ "\n" +
+ "1PHT 999999999999999999999999998762112222543211112134\n" +
+ "1BB9 99999999999999999999999999987-------4322----2234 \n" +
+ "1UHC 99999999999999999999999999987-------5321----2246\n" +
+ "1YCS 99999999999999999999999999986-------4321----1-35\n" +
+ "1OOT 999999999999999999999999999861-------3------1135 \n" +
+ "1ABO 99999999999999999999999999986-------422-------34\n" +
+ "1FYN 99999999999999999999999999985-------32--------35\n" +
+ "1QCF 99999999999999999999999999974-------2---------24\n" +
+ "cons 999999999999999999999999999851000110321100001134\n" +
+ "\n" +
+ "\n";
+
+ Block block = TCoffeeScoreFile.readBlock(new BufferedReader(new StringReader(BLOCK)), 0);
+ assertNotNull(block);
+ assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
+ assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
+ assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
+ assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
+ assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
+ assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
+ assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
+ assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
+ assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
+ }
+
+ @Test
+ public void testParse() throws FileNotFoundException {
+
+ TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+ assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
+ assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
+ assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
+ assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
+ assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
+ assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
+ assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
+ assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
+ assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
+ }
+
+
+ @Test
+ public void testGetAsList() throws FileNotFoundException {
+
+ TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+ List<String> scores = parser.getScoresList();
+ assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
+ assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
+ assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
+ assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
+ assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
+ assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
+ assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
+ assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
+ assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
+
+ }
+
+
+ @Test
+ public void testGetAsArray() throws FileNotFoundException {
+
+ TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+ byte[][] scores = parser.getScoresArray();
+
+ assertEquals( 9, scores[0][0] );
+ assertEquals( 9, scores[1][0] );
+ assertEquals( 9, scores[2][0] );
+ assertEquals( 9, scores[3][0] );
+ assertEquals( 9, scores[4][0] );
+ assertEquals( 9, scores[5][0] );
+ assertEquals( 9, scores[6][0] );
+ assertEquals( 9, scores[7][0] );
+ assertEquals( 9, scores[8][0] );
+
+ assertEquals( 5, scores[0][36] );
+ assertEquals( 4, scores[1][36] );
+ assertEquals( 5, scores[2][36] );
+ assertEquals( 4, scores[3][36] );
+ assertEquals( -1, scores[4][36] );
+ assertEquals( 4, scores[5][36] );
+ assertEquals( 3, scores[6][36] );
+ assertEquals( 2, scores[7][36] );
+ assertEquals( 3, scores[8][36] );
+
+ }
+
+
+
+}
--- /dev/null
+>1PHT
+YQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEI--
+--------GWLNGYNETTGERGDFPGTYVEYIG
+>1BB9
+FKVQAQHDYTATDTDELQLKAGDVVLVIP-------FQNP----EEQDEG
+WLMGVKESDWNQHK-ELEKCRGVFPENFTERVQ
+>1UHC
+QVYFAVYTFKARNPNELSVSANQKLKILE-------FKDV----TGNT--
+--------EWWLAE--VNGKKGYVPSNYIRKTE
+>1YCS
+GVIYALWDYEPQNDDELPMKEGDCMTIIH-------REDE----D-EI--
+--------EWWWA--RLNDKEGYVPRNLLGLYP
+>1OOT
+PKAVALYSFAGEESGDLPFRKGDVITILKK-------S------DSQN--
+--------DWWTG--RVNGREGIFPANYVE-LV
+>1ABO
+NLFVALYDFVASGDNTLSITKGEKLRVLG-------YNH-------NG--
+--------EWCEAQ--TKNGQGWVPSNYITPVN
+>1FYN
+TLFVALYDYEARTEDDLSFHKGEKFQILN-------SS--------EG--
+--------DWWEARSLTTGETGYIPSNYVAPVD
+>1QCF
+IIVVALYDYEAIHHEDLSFQKGDQMVVLE-------E---------SG--
+--------EWWKARSLATRKEGYIPSNYVARVD
\ No newline at end of file
--- /dev/null
+T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
+Cedric Notredame
+CPU TIME:0 sec.
+SCORE=90
+*
+ BAD AVG GOOD
+*
+1PHT : 89
+1BB9 : 90
+1UHC : 94
+1YCS : 94
+1OOT : 93
+1ABO : 94
+1FYN : 94
+1QCF : 94
+cons : 90
+
+1PHT 999999999999999999999999998762112222543211112134
+1BB9 99999999999999999999999999987-------4322----2234
+1UHC 99999999999999999999999999987-------5321----2246
+1YCS 99999999999999999999999999986-------4321----1-35
+1OOT 999999999999999999999999999861-------3------1135
+1ABO 99999999999999999999999999986-------422-------34
+1FYN 99999999999999999999999999985-------32--------35
+1QCF 99999999999999999999999999974-------2---------24
+cons 999999999999999999999999999851000110321100001134
+
+
+1PHT ----------5666642367889999999999889
+1BB9 1111111111676653-355679999999999889
+1UHC ----------788774--66789999999999889
+1YCS ----------78777--356789999999999889
+1OOT ----------78877--356789999999997-67
+1ABO ----------687774--56779999999999889
+1FYN ----------6888842356789999999999889
+1QCF ----------6878742356789999999999889
+cons 00100000006877641356789999999999889
git://source.jalview.org / jalview.git / commitdiff