<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.
+ -->
<header><title>BioJS viewer</title></header>
<body>
<!-- <script src="https://s3-eu-west-1.amazonaws.com/biojs/msa/latest/msa.js"></script> -->
<!-- <link type=text/css rel=stylesheet href=https://s3-eu-west-1.amazonaws.com/biojs/msa/latest/msa.css /> -->
- <img src="file:/Users/tcnofoegbu/Documents/workspace/java/dev/jalview/classes/images/Jalview_Logo.png" alt="Jalview Logo" title="This html page was generated from Jalview, to import the data back to Jalview, please drag the generated html file and drop it unto the Jalview workbench.
+ <img src="http://www.jalview.org/help/html/Jalview_Logo.png" alt="Jalview Logo" title="This html page was generated from Jalview, to import the data back to Jalview, please drag the generated html file and drop it unto the Jalview workbench.
Alternatively, you could copy the url from the address bar and use Jalview's url importer (main menu-> File-> Input Alignment-> from URL) to import back the alignment jalview." >
</br>
</br>
-<button onclick="javascipt:openJalviewUsingCurrentUrl();">Launch in Jalview</button>
<input type="button" name="divToggleButton" id="divToggleButton" onclick="javascipt:toggleMenuVisibility();" value="Show Menu"></input>
+<button onclick="javascipt:openJalviewUsingCurrentUrl();">Launch in Jalview</button>
</br>
</br>
<div id="yourDiv">press "Run with JS"</div>
-<input type='hidden' id='seqData' name='seqData' value='{"globalColorScheme":"zappo","seqs":[{"id":"1","start":1,"name":"FER_CAPAA/1-97","seq":"----------------------------------------------------------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-","features":[],"end":97},{"id":"2","start":1,"name":"FER_CAPAN/1-144","seq":"------MASVSATMISTSFMPRKPAVTSLKPIP-NVG-EALFGLKS---ANGGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-","features":[{"xEnd":22,"text":"feature_1","fillColor":"#8c25cd","xStart":2}],"end":144},{"id":"3","start":1,"name":"FER1_SOLLC/1-144","seq":"------MASISGTMISTSFLPRKPAVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA-","features":[],"end":144},{"id":"4","start":1,"name":"Q93XJ9_SOLTU/1-144","seq":"------MASISGTMISTSFLPRKPVVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA-","features":[],"end":144},{"id":"5","start":1,"name":"FER1_PEA/1-149","seq":"---MATTPALYGTAVSTSFLRTQPMPMSVTTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA-","features":[],"end":149},{"id":"6","start":1,"name":"Q7XA98_TRIPR/1-152","seq":"---MATTPALYGTAVSTSFMRRQPVPMSVATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA-","features":[],"end":152},{"id":"7","start":1,"name":"FER1_MESCR/1-148","seq":"--MAATTAALSGATMSTAFAPKT--PPMTAALPTNVG-RALFGLKS--SASRGRVTAMAAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA-","features":[],"end":148},{"id":"8","start":1,"name":"FER1_SPIOL/1-147","seq":"----MAATTTTMMGMATTFVPKPQAPPMMAALPSNTG-RSLFGLKT--GSRGGRMT-MAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA-","features":[],"end":147},{"id":"9","start":1,"name":"FER3_RAPSA/1-96","seq":"----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV--","features":[],"end":96},{"id":"10","start":1,"name":"FER1_ARATH/1-148","seq":"----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV--","features":[],"end":148},{"id":"11","start":1,"name":"FER_BRANA/1-96","seq":"----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV--","features":[],"end":96},{"id":"12","start":1,"name":"FER2_ARATH/1-148","seq":"----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM--","features":[],"end":148},{"id":"13","start":1,"name":"Q93Z60_ARATH/1-118","seq":"----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------------------","features":[],"end":118},{"id":"14","start":1,"name":"FER1_MAIZE/1-150","seq":"MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVG---IMGRSA---SSRRRLRAQATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA","features":[],"end":150},{"id":"15","start":1,"name":"O80429_MAIZE/1-140","seq":"---------MAATALSMSILRAPP-PCFSSPLRLRVAVAKPLAAPM----RRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL--","features":[],"end":140}]}'/>
+<input type='hidden' id='seqData' name='seqData' value='{"globalColorScheme":"zappo","seqs":[{"id":"1","start":1,"name":"FER_CAPAA/1-97","seq":"----------------------------------------------------------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-","features":[],"end":97},{"id":"2","start":1,"name":"FER_CAPAN/1-144","seq":"------MASVSATMISTSFMPRKPAVTSLKPIP-NVG-EALFGLKS---ANGGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-","features":[{"text":"feature_1","xEnd":46,"fillColor":"#8c25cd","xStart":16}],"end":144},{"id":"3","start":1,"name":"FER1_SOLLC/1-144","seq":"------MASISGTMISTSFLPRKPAVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA-","features":[],"end":144},{"id":"4","start":1,"name":"Q93XJ9_SOLTU/1-144","seq":"------MASISGTMISTSFLPRKPVVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA-","features":[],"end":144},{"id":"5","start":1,"name":"FER1_PEA/1-149","seq":"---MATTPALYGTAVSTSFLRTQPMPMSVTTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA-","features":[],"end":149},{"id":"6","start":1,"name":"Q7XA98_TRIPR/1-152","seq":"---MATTPALYGTAVSTSFMRRQPVPMSVATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA-","features":[{"text":"feature_2","xEnd":24,"fillColor":"#0000cc","xStart":8}],"end":152},{"id":"7","start":1,"name":"FER1_MESCR/1-148","seq":"--MAATTAALSGATMSTAFAPKT--PPMTAALPTNVG-RALFGLKS--SASRGRVTAMAAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA-","features":[],"end":148},{"id":"8","start":1,"name":"FER1_SPIOL/1-147","seq":"----MAATTTTMMGMATTFVPKPQAPPMMAALPSNTG-RSLFGLKT--GSRGGRMT-MAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA-","features":[],"end":147},{"id":"9","start":1,"name":"FER3_RAPSA/1-96","seq":"----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV--","features":[],"end":96},{"id":"10","start":1,"name":"FER1_ARATH/1-148","seq":"----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV--","features":[],"end":148},{"id":"11","start":1,"name":"FER_BRANA/1-96","seq":"----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV--","features":[],"end":96},{"id":"12","start":1,"name":"FER2_ARATH/1-148","seq":"----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM--","features":[{"text":"feature_3","xEnd":32,"fillColor":"#ffff00","xStart":4}],"end":148},{"id":"13","start":1,"name":"Q93Z60_ARATH/1-118","seq":"----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------------------","features":[],"end":118},{"id":"14","start":1,"name":"FER1_MAIZE/1-150","seq":"MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVG---IMGRSA---SSRRRLRAQATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA","features":[],"end":150},{"id":"15","start":1,"name":"O80429_MAIZE/1-140","seq":"---------MAATALSMSILRAPP-PCFSSPLRLRVAVAKPLAAPM----RRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL--","features":[],"end":140}],"webStartUrl":"http://www.jalview.org/services/launchApp","jalviewVersion":"Test"}'/>
</body>
</html>
<script>
function toggleMenuVisibility(){
- //alert("toggleMenuVisibility called!");
-
var menu = document.getElementsByClassName("biojs_msa_menubar");
var divToggleButton = document.getElementById("divToggleButton");
if(menu[0].style.display == 'block'){
divToggleButton.value="Hide Menu";
}
}
-function openJalviewUsingCurrentUrl2(){
-var jnpl = "<!--"+
-"Hi!"+
-"If you have downloaded this file after pressing \"Launch Full Application\" from Jalview on a web page and you don't know what to do with this file, you must install Java from http://www.java.sun.com then try opening this file again."+
-" \n"+
-" JNLP generated by /jalviewServlet/services/launchAppDev"+
-" JNLP generated from http://www.jalview.org/builds/develop/webstart/jalview.jnlp"+
-"Available servlet parameters (please URLEncode):"+
-" open=<alignment file URL>"+
-" jvm-max-heap=heap size in M or G"+
-" features maps to '-features'"+
-" treeFile maps to '-tree'"+
-" tree maps to '-tree'"+
-" annotations maps to '-annotations'"+
-" colour maps to '-colour'"+
-" "+
-"-->"+
-"<?xml version=\"1.0\" encoding=\"UTF-8\"?><jnlp spec=\"1.0+\" codebase=\"http://www.jalview.org/builds/develop/webstart\"> <information> <title>Jalview</title> <vendor>The Barton Group</vendor> <homepage href=\"http://www.jalview.org\"/> <description>Jalview Multiple Alignment Editor</description> <description kind=\"short\">Jalview</description> <icon href=\"JalviewLogo_big.png\"/> <offline-allowed/> </information> <security> <all-permissions/> </security> <resources> <j2se version=\"1.7+\" initial-heap-size=\"10M\" max-heap-size=\"2G\"/> <jar href=\"jalview.jar\"/> <jar href=\"JGoogleAnalytics_0.3.jar\"/> <jar href=\"Jmol-12.2.4.jar\"/> <jar href=\"VARNAv3-91.jar\"/> <jar href=\"activation.jar\"/> <jar href=\"apache-mime4j-0.6.jar\"/> <jar href=\"axis.jar\"/> <jar href=\"castor-1.1-cycle-xml.jar\"/> <jar href=\"commons-codec-1.3.jar\"/> <jar href=\"commons-discovery.jar\"/> <jar href=\"commons-logging-1.1.1.jar\"/> <jar href=\"groovy-all-1.8.2.jar\"/> <jar href=\"httpclient-4.0.3.jar\"/> <jar href=\"httpcore-4.0.1.jar\"/> <jar href=\"httpmime-4.0.3.jar\"/> <jar href=\"jalview_jnlp_vm.jar\"/> <jar href=\"jaxrpc.jar\"/> <jar href=\"jdas-1.0.4.jar\"/> <jar href=\"jhall.jar\"/> <jar href=\"json_simple-1.1.jar\"/> <jar href=\"jsoup-1.8.1.jar\"/> <jar href=\"jswingreader-0.3.jar\"/> <jar href=\"log4j-to-slf4j-2.0-rc2.jar\"/> <jar href=\"mail.jar\"/> <jar href=\"miglayout-4.0-swing.jar\"/> <jar href=\"min-jabaws-client-2.1.0.jar\"/> <jar href=\"regex.jar\"/> <jar href=\"saaj.jar\"/> <jar href=\"slf4j-api-1.7.7.jar\"/> <jar href=\"slf4j-log4j12-1.7.7.jar\"/> <jar href=\"spring-core-3.0.5.RELEASE.jar\"/> <jar href=\"spring-web-3.0.5.RELEASE.jar\"/> <jar href=\"vamsas-client.jar\"/> <jar href=\"wsdl4j.jar\"/> <jar href=\"xercesImpl.jar\"/> <jar href=\"xml-apis.jar\"/> <property name=\"jalview.version\" value=\"Development Branch Build\"/> </resources>"+
-"<application-desc main-class=\"jalview.bin.Jalview\">"+
-"<argument>-open</argument>"+
-"<argument>file:///Users/tcnofoegbu/Documents/workspace/java/dev/jalview/examples/example_biojs.html</argument>"+
-"</application-desc>"+
-" <security>"+
-" <all-permissions/>"+
-" </security>"+
-"</jnlp>"
-
-var encodedUri = encodeURI(jnpl);
-window.open(encodedUri)
-//alert(jnpl)
-}
+
function openJalviewUsingCurrentUrl(){
- var url = "http://webservices.compbio.dundee.ac.uk:38080/jalviewServlet/services/launchAppDev";
+ var jalviewData = JSON.parse(document.getElementById("seqData").value)
+ var jalviewVersion = jalviewData['jalviewVersion'];
+ var url = jalviewData['webStartUrl'];
var myForm = document.createElement("form");
myForm.action = url;
- var myInput = document.createElement("input") ;
- myInput.setAttribute("name", "jvm-max-heap") ;
- myInput.setAttribute("value", "2G");
- myForm.appendChild(myInput) ;
+ var heap = document.createElement("input") ;
+ heap.setAttribute("name", "jvm-max-heap") ;
+ heap.setAttribute("value", "2G");
+ myForm.appendChild(heap) ;
- var myInput1 = document.createElement("input") ;
- myInput1.setAttribute("name", "open") ;
- myInput1.setAttribute("value", document.URL);
- myForm.appendChild(myInput1) ;
+ var target = document.createElement("input") ;
+ target.setAttribute("name", "open") ;
+ target.setAttribute("value", document.URL);
+ myForm.appendChild(target) ;
+
+ var jvVersion = document.createElement("input") ;
+ jvVersion.setAttribute("name", "version") ;
+ jvVersion.setAttribute("value", jalviewVersion);
+ myForm.appendChild(jvVersion) ;
-
document.body.appendChild(myForm) ;
myForm.submit() ;
document.body.removeChild(myForm) ;
// call render at the end to display the whole MSA
m.render();
-
toggleMenuVisibility();
toggleMenuVisibility();
});
git://source.jalview.org / jalview.git / blobdiff