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+<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<!-- InstanceBeginEditable name="doctitle" -->
+<TITLE>JalviewLite Applet API and Form Complete Example</TITLE>
+<!-- InstanceEndEditable -->
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+</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;
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+function getEventTarget(e)
+{
+if(!e)
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+if(e.target)
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+<body alink="#000000" vlink="#000000" link="#000000">
+<script type="text/javascript">
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+pageTracker._trackPageview();
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+</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>
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+ </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" -->
+ <p> </p>
+ Click the Javascript buttons below to interact with the Applet
+ instance on the page.<br>
+ View the source in your browser to see how it has been done.<br>
+ The applet's public API methods are <a href="#api">listed below</a>
+ the following example.<br>
+ <applet code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar" name="Jalview">
+ <param name="file" value="plantfdx.fa">
+ <param name="features" value="plantfdx.features">
+ <param name="wrap" value="true">
+ <param name="showAnnotation" value="false">
+ <param name="windowHeight" value="500">
+ <param name="windowWidth" value="650">
+ <param name="showFullId" value="false">
+ <param name="RGB" value="F2F2FF">
+ <param name="linkLabel_1" value="SRS">
+ <param name="linkUrl_1"
+ value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+ <param name="linkLabel_2" value="Uniprot">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="hidefeaturegroups" value="uniprot" />
+ <param name="showbutton" value="false" />
+ </applet>
+ <form name="exampleForm"><br>
+ <br>
+ <center><strong>Using the Jalview Applet for Input
+ to an HTML Form</strong></center>
+ <div align="center"><input type="button"
+ onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
+ value="Fill Form from Jalview" /> <br>
+ <br>
+ <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
+ </form>
+ <center><strong>Make a new View and Get and Set
+ Group Display List</strong></center>
+ <form name="groupForm">
+ <div align="center"><input type="button"
+ onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
+ value="Get groups" /> <input type="button"
+ onClick="document.applets.Jalview.newView()" value="new View" /> <br>
+ <textarea name="groups" cols="55" rows="9"></textarea> <br>
+ <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
+ value="Display groups" /> <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
+ value="Hide groups" /></div>
+ </form>
+ <p><a name="api" /> Since Jalview 2.5, the public methods listed
+ below are available to be called via Javascript.</p>
+ <p>Unfortunately Javascript - Java communication is not possible
+ using Internet Explorer or Opera on Macs. Please use Safari or
+ Firefox.</p>
+ <p>If more than one Jalview window is open, Jalview returns the
+ alignment in the active window, unless you provide an AlignFrame
+ object reference.</p>
+ <p>The alignment output format can be either Fasta, PFAM, Clustal,
+ MSF, PIR, or BLC.</p>
+ <p>When referring to the Jalview applet in javascript, you must
+ either give Jalview a name in the applet tag or use the applets index.</p>
+
+ <pre>//get list of IDs of selected sequences
+public String getSelectedSequences()
+
+// list of IDs of selected sequences terminated by sep or, if sep is null, '¬' (&#172;)
+public String getSelectedSequences(sep)
+
+// get selected sequences as alignment as format with or without start-end suffix
+public String getSelectedSequencesAsAlignment(String format, boolean suffix)
+
+// get selected sequences as alignment from given view as format with or without start-end suffix
+public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, boolean suffix)
+
+// get alignment as format
+public String getAlignment(String format)
+
+// get alignment as format with jalview
+// start-end sequence suffix appended
+public String getAlignment(String format, String suffix)
+
+// get alignment displayed in alf as format
+public String getAlignmentFrom(AlignFrame alf, String format)
+
+// get alignment displayed in alf as format
+// with jalview start-end sequence suffix appended
+public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
+
+// add the given features or annotation to the current alignment
+public void loadAnnotation(String annotation)
+
+// add the given features or annotation to the given alignment view
+public void loadAnnotationFrom(AlignFrame alf, String annotation)
+
+// get the sequence features in the given format (Jalview or GFF)
+public String getFeatures(String format)
+
+// get the sequence features in alf in the given format (Jalview or GFF)
+public String getFeaturesFrom(AlignFrame alf, String format)
+
+// get current alignment's annotation as an annotation file
+public String getAnnotation()
+
+// get alignment view alf's annotation as an annotation file
+public String getAnnotationFrom(AlignFrame alf)
+
+// create a new view and return the alignFrame instance
+public AlignFrame newView()
+
+// create a new view named name and return the alignFrame instance
+public AlignFrame newView(String name)
+
+// create a new view on alf and return the alignFrame instance
+public AlignFrame newViewFrom(AlignFrame alf)
+
+// create a new view named name on alf
+// and return the alignFrame instance
+public AlignFrame newViewFrom(AlignFrame alf, String name)
+
+// load a new alignment
+public AlignFrame loadAlignment(String text, String title)
+
+// return separator separated list of feature groups
+// on the current alignment
+public String getFeatureGroups()
+
+// return separator separated list of feature groups on alf
+public String getFeatureGroupsOn(AlignFrame alf)
+
+// return separator separated list of feature groups
+// either visible or hidden
+public String getFeatureGroupsOfState(boolean state)
+
+// return separator separated list of feature groups
+// either visible or hidden on alf
+public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean state)
+
+// set the separator separated list of feature groups as
+// visible or hidden on the current alignment
+public void setFeatureGroupState(String groupList, boolean state)
+
+// set the separator separated list of feature groups
+// as visible or hidden on alf
+public void setFeatureGroupStateOn(AlignFrame alf, String groupList, boolean state)
+
+// helper functions
+
+// convert list to a separator separated array
+public String arrayToSeparatorList(String[] list)
+
+// get a string array from a list
+public String[] separatorListToArray(String list)
+
+// get the current separator
+public String getSeparator()
+
+// set the current separator
+public void setSeparator(String)
+
+//// JalviewLite global state methods and fields
+
+// return the build date as a string
+public static String getBuildDate()
+
+// return the JalviewLite version as a string
+public static String getVersion()
+
+// debug flag - controls output to standard out
+public static boolean debug
+
+</pre> <!-- InstanceEndEditable --></td>
+ </tr>
+ </table>
+</div>
+</body>
+<!-- InstanceEnd --></html>
git://source.jalview.org / jalview.git / blobdiff