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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- <p> </p>
- <strong>JalviewLite Javascript API<br></strong>
- <p>The jalviewLite applet's application programming interface (API) includes two components. A <a href="javascript/jalview.js">JalviewLite Javascript Library</a> and the <a href="#api">public methods on the JalviewLite applet</a>.
- <p>The best way to learn how to use the API is to see it in action on the demonstration pages below:</p>
- <ul>
- <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
- <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other.</a></li>
- <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page (EXPERIMENTAL! please provide feedback!).</a></li>
- <li><a href="javascriptLaunch.html">launch JalviewLite from a javascript button</a></li>
-
- </ul>
- <h4>Notes</h4>
+
+
+
+<div id="view_decorated" name="view_decorated" style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#jalviewLiteJs"> here</a> to view decorated page</b></div>
+
+<!-- content start -->
+<p>The jalviewLite applet's application programming interface (API) includes two components. A <a href="javascript/jalview.js">JalviewLite Javascript Library</a> and the <a href="#api">public methods on the JalviewLite applet</a>.
+</p>
+ <h3>Notes</h3>
<ul>
<li>Unfortunately Javascript - Java communication is not possible
using Internet Explorer or Opera on Macs. Please use Safari or
</li>
</ul>
<a name="api">
- <h4>JalviewLite's Java API</h4></a>
+ <h1>JalviewLite's Javascript API</h1></a>
<p>The following public methods on the jalviewLite applet are available to be called from javascript:</p>
<pre>//get list of IDs of selected sequences
public String getSelectedSequences()
public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
// add the given features or annotation to the current alignment
+// if features are loaded, feature display is automatically enabled
public void loadAnnotation(String annotation)
// add the given features or annotation to the given alignment view
+// if features are loaded, feature display is automatically enabled
public void loadAnnotationFrom(AlignFrame alf, String annotation)
+// parse the given string as a jalview or GFF features file and optionally enable feature display on the current alignment
+// (v2.8)
+public abstract void loadFeatures(String features, boolean autoenabledisplay)
+
+// parse the given string as a jalview or GFF features file and optionally enable feature display on the given alignment
+// (v2.8)
+public abstract void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
+
// get the sequence features in the given format (Jalview or GFF)
public String getFeatures(String format)
public AlignFrame newViewFrom(AlignFrame alf, String name)
// load a new alignment
+// remember to store the AlignFrame object reference
+// if you want to manipulate the new alignment view.
public AlignFrame loadAlignment(String text, String title)
// the given location the top left hand corner for given current view (v2.7)
public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn)
+// adjust horizontal scroll in alf to the make
+// the given location the left hand corner for given current view (v2.7)
+public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
+
+// adjust horizontal/vertical scroll in alf to the make
+// the given location the top row for given current view (v2.7)
+public void scrollViewToRowIn(AlignFrame alf, String topRow)
+
// return separator separated list of feature groups
// on the current alignment
// debug flag - controls output to standard out
public static boolean debug
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