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+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
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<p> </p>
+ <strong>Using the <a href="jalviewLiteJs.html">JalviewLite API</a> to fill out forms using data from JalviewLite<br></strong>
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>
+ View the source in your browser to see how it has been done. <br>
+ <a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
<applet code="jalview.bin.JalviewLite" width="140" height="35"
archive="jalviewApplet.jar" name="Jalview">
<param name="file" value="plantfdx.fa">
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>
+
+<!-- InstanceEndEditable --></td>
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git://source.jalview.org / jalview.git / blobdiff