Commit 9ccee026 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

html, js: references to '.vidjil' instead of '.data'

parent 102b2e6e
......@@ -75,13 +75,13 @@
<h2>Vidjil <span class='logo'>(beta)</span> &ndash; V(D)J repertoire browsing and analysis</h2>
Data file (.data):<br/>
Data file (.vidjil):<br/>
<input id="upload_json" type="file" name="json" /></br>
<p class='help'>The data file stores a set of clones on several points.</p>
<p class='help'>The .vidjil file stores a set of clones on several points.</p>
Analysis file (.analysis, optional):<br/>
<input id="upload_pref" type="file" name="pref" /></br>
<p class='help'>The analysis file stores all parameters set by the user (tags, colors, manual clusters).</p>
<p class='help'>The .analysis file stores all parameters set by the user (tags, colors, manual clusters).</p>
<button onclick="document.getElementById('file_menu').style.display='none';
m.load('upload_json','upload_pref', 200)">start</button>
......@@ -91,7 +91,7 @@
<span class="closeButton" onclick="cancel();">X</span>
<h2>analysis menu</h2>
Analysis file :<br/>
Analysis file:<br/>
<input id="upload_analysis" type="file" name="analysis" /></br></br>
<button onclick="document.getElementById('analysis_menu').style.display='none';
......
......@@ -33,11 +33,11 @@ function Com(flash_id, log_id, popup_id, data_id) {
this.msg = {
"align_error": "Error &ndash; connection to align server ("+return_URL_CGI()+") failed" + "</br> Please check your internet connection and retry." + "</br></br> <div class='center' > <button onclick='myConsole.closePopupMsg()'>ok</button></div>",
"file_error": "Error &ndash; incorrect data file" + "</br> Please check you use a .data file generated by Vidjil." + "</br></br> <div class='center' > <button onclick='myConsole.closePopupMsg()'>ok</button></div>",
"file_error": "Error &ndash; incorrect .vidjil file" + "</br> Please check you use a .vidjil file generated by a compatible program." + "</br></br> <div class='center' > <button onclick='myConsole.closePopupMsg()'>ok</button></div>",
"json_not_found":"Error &ndash; editDistanceFile.json not found" + "</br> Please to check the specified repository in the c++ program, or to run Vidjil program with the specified datas." + "</br></br> <div class='center'><button onclick='myConsole.closePopupMsg()'>ok</button></div>",
"version_error": "Error &ndash; data file too old (version " + VIDJIL_JSON_VERSION + " required)" + "</br> This data file was generated by a too old version of Vidjil. " + "</br> Please regenerate a newer data file. " + "</br></br> <div class='center' > <button onclick='myConsole.closePopupMsg()'>ok</button></div>",
"version_error": "Error &ndash; .vidjil file too old (version " + VIDJIL_JSON_VERSION + " required)" + "</br> This .vidjil file was generated by a too old program. " + "</br> Please regenerate a newer .vidjil file. " + "</br></br> <div class='center' > <button onclick='myConsole.closePopupMsg()'>ok</button></div>",
"welcome": " <h2>Vidjil <span class='logo'>(beta)</span></h2>" + "(c) 2011-2014, the Vidjil team" + "<br />Marc Duez, Mathieu Giraud and Mikaël Salson" + " &ndash; <a href='http://www.vidjil.org'>http://www.vidjil.org/</a>" + "</br>" + "</br>Vidjil is developed by the <a href='http://www.lifl.fr/bonsai'>Bonsai bioinformatics team</a> (LIFL, CNRS, U. Lille 1, Inria Lille), in collaboration with the <a href='http://biologiepathologie.chru-lille.fr/organisation-fbp/91210.html'>department of Hematology</a> of CHRU Lille"
+ " the <a href='http://www.ircl.org/plate-forme-genomique.html'>Functional and Structural Genomic Platform</a> (U. Lille 2, IFR-114, IRCL)" + " and the <a href='http://www.euroclonality.org/'>EuroClonality-NGS</a> working group." + "<br/>" + "<br>Vidjil is free software, and you are welcome to redistribute it under <a href='http://git.vidjil.org/blob/master/doc/LICENSE'>certain conditions</a>. This software is for research use only and comes with no warranty." + "<br>" + "Please cite <a href='http://www.biomedcentral.com/1471-2164/15/409'>BMC Genomics 2014, 15:409</a> if you use Vidjil for your research." +"<br><br> <div class='center' > <button onclick='myConsole.myConsole.closePopupMsg()'>start</button></div>",
......@@ -139,4 +139,4 @@ Com.prototype = {
.innerHTML = "";
},
}
\ No newline at end of file
}
......@@ -133,8 +133,8 @@ Model.prototype = {
this.segment = segment;
},
/* load the selected data/analysis file in the model
* @id : id of the form (html element) linking to the data file
/* load the selected vidjil/analysis file in the model
* @id : id of the form (html element) linking to the vidjil file
* @analysis : id of the form (html element) linking to the analysis file
* impossible to use direct path to input files, need a fakepath from input form
* @limit : minimum top value to keep a clone*/
......@@ -192,7 +192,7 @@ Model.prototype = {
loadAnalysisUrl: function (url) {
var self = this;
var url2 = url.replace(".data",".analysis");
var url2 = url.replace(".vidjil",".analysis");
var url_split = url2.split('/')
......@@ -234,7 +234,7 @@ Model.prototype = {
}
self.reset();
//copy .data file in model
//copy .vidjil file in model
for (var key in data){
if (key != "clusters") self[key] = data[key]
}
......@@ -369,7 +369,7 @@ Model.prototype = {
}
self.initClones();
}else{
myConsole.flash("invalid json version for analysis file", 1)
myConsole.flash("invalid version for this .analysis file", 1)
}
},
......
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