--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+<title>SwingJS test Jalview</title>
+<meta charset="utf-8" />
+<script src="swingjs/swingjs2.js"></script>
+<script src="swingjs/JalviewApplet.js"></script>
+<script>
+if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
+JalviewInfo = {
+ code: null,
+ main: "jalview.bin.Jalview",
+ core: "NONE",
+ //core:"_jalview",
+ resourcePath: "examples",
+ readyFunction: null,
+ serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
+ j2sPath: 'swingjs/j2s',
+ console:'sysout',
+ startButton:'Start Jalview',
+ hideDesktop:true,
+ embedInternalFrames:false,
+ idPrefix:'%ID%',
+ allowjavascript: true
+}
+</script>
+</head>
+<body>
+<!-- content template start
+JalviewApplet.js will add divs such as these:
+<div id="jalview0-desktop-div" style="width:0px;display:none"></div>
+<div id="jalview0-alignment-div" style="width:0px;display:none"></div>
+ -->
+<p align="left">
+<h2>JalviewJS Button Examples</h2>
+Try out JalviewJS by pressing one of the buttons below.
+<a target="_blank" href="http://www.jalview.org/examples/applets.html">Original Java</a> (requires SeaMonkey browser)
+</p>
+<p> </p><div align="center">
+ <p align="center">
+ <h2>Ferredoxins, chloroplast precursor related UniRef50
+ cluster</h2>
+ <br /> (15 sequences x 150 residues)
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center">
+ <applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+ <param name="permissions" value="sandbox"/>
+ <param name="file" value="uniref50.fa"/>
+ <param name="treeFile" value="ferredoxin.nw"/>
+ <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+ <param name="sortByTree" value="True"/>
+ <param name="showSequenceLogo" value="true"/>
+ <param name="showGroupConsensus" value="true"/>
+ <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="EMBL-EBI Search"/>
+ <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
+ </applet>
+</td>
+ <td valign="center">User Defined Colours, loads an associated
+ Newick format tree file which is used to sort the alignment, and
+ group consensus and sequence logos are shown below the alignment.</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="features" value="exampleFeatures.txt"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="showFeatureSettings" value="true"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" 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="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">Displays a features file on the alignment</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="wrap" value="true"/>
+<param name="debug" value="true"/>
+<param name="showAnnotation" value="false"/>
+<param name="defaultColour" value="Strand Propensity"/>
+<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">Associates PDB file 1GAQ with sequence
+ FER1_MAIZE</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="jpred_msa.fasta"/>
+<param name="jnetfile" value="jpred_msa.seq.concise"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Clustal"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+ </td>
+ <td valign="middle">Displays a Multiple Sequence Alignment
+ Based JPred Prediction for a Sequence</td>
+ </tr>
+ </table>
+ <p>
+ <h2>RF00031 RFAM Alignment with per sequence secondary
+ structure</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="RF00031_folded.stk"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Purine/Pyrimidine"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">Displays an RFAM RNA fold family with
+ secondary structure annotation</td>
+ </tr>
+ </table>
+ <p>
+ <h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center">
+<applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file2" value="estrogenReceptorCdna_frag.fa"/>
+<param name="file" value="estrogenReceptorProtein_frag.fa"/>
+<param name="enableSplitFrame" value="true"/>
+<param name="scaleProteinAsCdna" value="true"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="300"/>
+<param name="windowWidth" value="800"/>
+<param name="showAnnotation" value="true"/>
+<param name="showSequenceLogo" value="true"/>
+<param name="defaultColourNuc" value="Purine/Pyrimidine"/>
+<param name="defaultColourProt" value="Clustal"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">Displays a split window view showing aligned protein
+ and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
+ href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
+ via the Jalview Desktop).<br />Data retrieved from Uniprot and
+ ENA, after Thornton, Need and Crews, <a
+ href="http://dx.doi.org/10.1126/science.1086185">Science 19
+ September 2003: 301 (5640), 1714-1717</a>
+ </td>
+ </tr>
+ </table>
+</div>
+<div id="sysout" style="width:500px;height:300px;background:yellow;overflow:auto"></div>
+
+</body>
+</html>
+<!--
+ * 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.
+-->
+
+++ /dev/null
-Jalview = {}
-
-
-$(document).ready(function() {
- Jalview.processAllAppletElements();
-});
-
-
-var currentPage = "applets";
-
-Jalview.processAllAppletElements = function() {
- var apps = document.getElementsByTagName("applet");
- for (var i = apps.length; --i >= 0;) {
- processAppletElement(apps[i]);
- }
-}
-
-Jalview.jvid = 0;
-
-Jalview.doStartJalview = function(e) {
- var element = e.target.appletElement;
- var text = element.outerHTML;
-
- var Info = self.JalviewInfo || {
-code: null,
-main: "jalview.bin.Jalview",
-core: "NONE",
- width: 850,
- height: 550,
- readyFunction: null,
- serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
- j2sPath: 'swingjs/j2s',
- console:'sysoutdiv',
- allowjavascript: true
- }
-
-var addParam = function(key,value) {
- args.push("name=\"" + key + "\" value=\"" + value + "\"");
-}
-
-var id = "JVApplet" + jvid++;
-var args = text.replace(/[\n\t]/g, " ").split("<param ");
-Info.j2sAppletID = i;
-Info.j2sAppletID = id;
-Info.jalview_SCREEN_X= 10,
-Info.jalview_SCREEN_Y= 10;
-//Info.jalview_EMBEDDED= true;
-
-
-Info.jalview_SCREEN_WIDTH = 400;
-Info.jalview_SCREEN_HEIGHT = 100;
-for (var i in Info) {
- var v = ("" + Info[i] || "null").replace(/\"/g,"'");
- addParam(args, "Info." + i, v);
-}
- Info.args = args;
- SwingJS.getApplet(id, Info);
- document.title = id;
- e.target.style.visibility="hidden";
-}
-
-Jalview.processAppletElement = function(element) {
-var code = element.getAttribute("code");
-var parent = element.parentElement;
-if (code == "jalview.bin.JalviewLite") {
- var text = element.outerHTML;
- console.log(text);
- var btn = document.createElement("button");
- btn.innerHTML = "Start Jalview";
- var a = element.getAttribute("width");
- btn.style.width = (a || 140) + "px";
- a = element.getAttribute("height");
- btn.style.height = (a || 25) + "px";
- btn.appletElement = element;
- parent.replaceChild(btn, element);
- $(btn).click(doStartJalview)
-} else {
- parent.removeElement(element);
-}
-}
-
-
- /**
- * Generate an applet tag
- *
- * @param code
- * @param name
- * @param archive
- * @param width
- * @param height
- * @param params
- * @returns a DOM APPLET element
- */
-
-Jalview.createAppletTag = function(code, name, archive, width, height, params){
- var app = document.createElement('applet');
- app.code= code;
- app.width = width;
- app.height = height;
- app.archive = archive;
-
- var arrayLength = params.length;
- for (var i = 0; i < arrayLength; i++) {
- //console.log('name : '+ params[i][0] + ' code : '+ params[i][1]);
- var param = document.createElement('param');
- param.name = params[i][0];
- param.value = params[i][1];
- app.appendChild(param);
- }
- return app;
-}
-
Jalview.processAllAppletElements = function(PageInfo) {
- var applets = document.getElementsByTagName("applet");
+ var applets = document.getElementsByTagName("applet") || document.getElementsByTagName("jvapplet");
var apps=[];
for (var i = 0; i < applets.length; i++)
apps[i] = applets[i];
Jalview.processAppletElement = function(element, UserInfo) {
+ // This code is specifically for processing the <applet> or <jvapplet> tag.
+
+ // To set Jalview application tags, use Info.args="......."
+
+ // To set preferences, use "jalview_" prefix with all-upper-case names:
+
+ //Info.jalview_SCREEN_X= 10,Info.jalview_SCREEN_Y= 10;
+ //Info.jalview_EMBEDDED= true;
+ //Info.jalview_SCREEN_WIDTH = 400;
+ //Info.jalview_SCREEN_HEIGHT = 100;
+
+var text = element.outerHTML;
var code = element.getAttribute("code");
var parent = element.parentElement;
-if (code != "jalview.bin.JalviewLite") {
+if (code != "jalview.bin.JalviewLite" && text.indexOf("<applet") == 0) {
return;
}
allowjavascript: true
}
-var text = element.outerHTML;
-var args = Info.args = text.replace(/[\n\t]/g, " ").split("<param ");
+ var args = Info.args = text.replace(/[\n\t]/g, " ").replace("<jvapplet","<applet").split("<param ");
-// overwrite default parameters with UserInfo (global JalviewInfo):
+ // overwrite default parameters with UserInfo (global JalviewInfo):
if (UserInfo) {
-for (var i in UserInfo) {
- Info[i] = UserInfo[i];
-}
+ for (var i in UserInfo) {
+ Info[i] = UserInfo[i];
+ }
}
-// generate name/value pairs for parameters in Applet tag
+ // generate name/value pairs for parameters in Applet tag
Info.j2sAppletID = Info.j2sAppletID
|| element.getAttribute("name")
|| element.getAttribute("id")
|| Info.idPrefix.replace(/%ID%/g, "jalview" + ++Jalview.jvid);
-//Info.jalview_SCREEN_X= 10,Info.jalview_SCREEN_Y= 10;
-//Info.jalview_EMBEDDED= true;
-//Info.jalview_SCREEN_WIDTH = 400;
-//Info.jalview_SCREEN_HEIGHT = 100;
-
-var addParam = function(key,value) {
- args.push("name=\"" + key + "\" value=\"" + value + "\"");
-}
-
-
-for (var i in Info) {
- var v = ("" + Info[i] || "null").replace(/\"/g,"'");
- addParam("Info." + i, v);
-}
+ var addParam = function(key,value) {
+ args.push("name=\"" + key + "\" value=\"" + value + "\"");
+ }
-
+ for (var i in Info) {
+ var v = ("" + Info[i] || "null").replace(/\"/g,"'");
+ addParam("Info." + i, v);
+ }
+
+
+
element.JalviewInfo = Info;
var btn = document.createElement("button");
-btn.appletElement = element;
+ btn.appletElement = element;
var a = element.getAttribute("width");
btn.style.width = (a || 140) + "px";
a = element.getAttribute("height");
btn.jvparent = parent;
if (Info.startButton) {
btn.innerHTML = Info.startButton;
-parent.replaceChild(btn, element);
-$(btn).click(Jalview.doStartJalview);
-} else {
- parent.removeElement(element);
- Jalview.doStartJalview({target:btn});
-}
+ parent.replaceChild(btn, element);
+ $(btn).click(Jalview.doStartJalview);
+ } else {
+ parent.removeElement(element);
+ Jalview.doStartJalview({target:btn});
+ }
}
git://source.jalview.org / jalview.git / commitdiff