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/************************************************
 *WordCloud methods below are modifications of wordcloud by yoah.bardavid@gmail.com and razbarvaz@gmail.com 
 *wordcloud is part of the following project: http://visapi-gadgets.googlecode.com
 *The visapi-gadgets project is licensed under Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
 *Modifications include: 
 *  inclusion of a some sort of a log scale
 *  exclusion of single letter words
 *  exclusion of excludedTerms
 *  exclusion of numbers
 *  attempt to merge plural and singular

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makeSearchCommand({
//to subscribe to the command ,go to: <http://gist.github.com/13700>
//project: <http://code.google.com/p/tl-ubiquity-commands/>
  author: {name: "Thomas Lemberger", email: "thomas.lemberger@gmail.com"},
  license: "GPL",
  name: "pubmed",
  help: "Search selected terms or directly typed in the input line. The number of records to be displayed can be specified by adding '#number' somewhere in the query (eg. #3 will show only 3 records, default is 5, maximum is 15).",
  url: "http://www.ncbi.nlm.nih.gov/pubmed?term={QUERY}",
  icon: "http://www.ncbi.nlm.nih.gov/favicon.ico",
  description: "Searches <a href='http://www.ncbi.nlm.nih.gov/pubmed'>PubMed</a>.",

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CmdUtils.CreateCommand({  
    names: ["rewrap"],
    arguments: [{role: "object",
               nountype: noun_arb_text,
               label: "input"}], 
    help: "removes unnecessary carriage returns and strings of spaces",
    execute: function(arguments) {
      var selectedText=arguments.text;
      selectedText=selectedText.replace(/[\r\n]{2}/g,"§#!");
      selectedText=selectedText.replace(/[\r\n]+/g," ");

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function HTMLescape(string)  {  
      var LT = new RegExp("<", "g");  
      var GT = new RegExp(">", "g");  
      var AMP = new RegExp("&", "g");  
      var TAB = new RegExp("\t", "g");  
      return  string.replace(AMP,"&amp;").replace(LT, "&lt;").replace(GT, "&gt;").replace(TAB, "...");
}  

CmdUtils.CreateCommand({  
    name: "whatizit",  

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CmdUtils.CreateCommand({  
//to subscribe to the command, go to http://gist.github.com/15544
//code maintained at http://code.google.com/p/tl-ubiquity-commands/
    author: {name: "thomas lemberger", email: "thomas.lemberger@embo.org"},
    license: "GPL",
    name: "more-like-this",  
    takes: {"selected text": noun_arb_text},  
    help: "The command is based on Jane (http://www.biosemantics.org/jane/, Schuemie & Kors (2008) Bioinformatics.24:727). It lists PubMed records related to the selected text (typically an abstract).", 
    execute: function(directObj) {
      var selectedText=directObj.text;

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CmdUtils.CreateCommand({
//to install this command, visit http://gist.github.com/21865
//code is part of http://code.google.com/p/tl-ubiquity-commands/
  name: "open-doi",
  takes: {"selected text": noun_arb_text},
  preview: function(pblock, directObject){
    if (directObject.text){
      var m = directObject.text.match(/(doi:)?.*?\b(10\.\d{4}\/\S+)/i);
      if (!m){pblock.innerHTML="The selection <pre>"+directObject.text+"</pre> does not include a recognized doi !";}
      else {pblock.innerHTML="press Return to go to the document associated with <i>"+m[2]+"</i>.";}