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-<TITLE>JalviewLite Applet API and Form Complete Example</TITLE>
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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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- <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>
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- history</a></td>
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- Code</a></td>
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- Mailing List</a></td>
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- 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>
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- <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)
+<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#formComplete"> here</a> to view decorated page</b></div>
-// 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)
+<!-- boiler plate link to alternate demopage -->
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
-// 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
+</div>
+</div>
-</pre> <!-- InstanceEndEditable --></td>
- </tr>
- </table>
+<!-- content template start -->
+<h2><a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite API</a> Demo</h2>
+<p>Using the Javascript API to fill out forms using data from JalviewLite
+<br/>Click the Javascript buttons below to interact with the Applet
+instance on the page.</p>
+ <a href="view-source:http://www.jalview.org/builds/develop/examples/formComplete.html" target="_blank">View the source here to see how it has been done</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/formComplete.html">this page</a> and viewing the page source manually).<br/>
+<a name="api">View the full <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite API documentation</a>.</a>
+<applet code="jalview.bin.JalviewLite" width="0" height="0"
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.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="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="Expasy">
+ <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>
</div>
-</body>
-<!-- InstanceEnd --></html>
+<!-- content template end -->
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