<commit_before><%@ page import="java.util.List" %>
<%@ page import="java.util.ArrayList" %>
<%@ page import="java.net.URLEncoder" %>
<%@ page import="com.google.common.base.Joiner" %>
<%@ page import="java.io.UnsupportedEncodingException" %>
<%@ page import="org.mskcc.portal.model.GeneWithScore" %>
<%@ page import="org.mskcc.portal.servlet.QueryBuilder" %>
<%@ page import="org.mskcc.portal.servlet.ServletXssUtil" %>
<%@ page import="org.mskcc.portal.util.GlobalProperties" %>
<%
	  // get URL to seg file used as parameter to IGV
	  String segFileURL = GlobalProperties.getSegfileUrl();

      // construct gene list parameter to IGV
      // use geneWithScoreList so we don't get any OQL
      List<String> onlyGenesList = new ArrayList<String>();
      for (GeneWithScore geneWithScore : geneWithScoreList) {
		  onlyGenesList.add(geneWithScore.getGene());
	  }
      String encodedGeneList = "";
      if (onlyGenesList.size() > 0) {
		  try {
			  encodedGeneList = URLEncoder.encode(Joiner.on(' ').join(onlyGenesList), "UTF-8");
		  }
		  catch(UnsupportedEncodingException e) {
			  // encode ourselves
			  encodedGeneList = Joiner.on('%20').join(onlyGenesList);
		  }
	  }
%>

<div class="section" id="igv_tab">
    <table>
        <tr>
            <td style="padding-right:25px; vertical-align:top;"><img src="images/IGVlogo.png" alt=""/></td>
            <td style="vertical-align:top">

                <p>
                    The <a href="http://www.broadinstitute.org/igv/home">Integrative Genomics
                    Viewer (IGV)</a> is a high-performance visualization tool for interactive exploration
                    of large, integrated datasets. It supports a wide variety of data types including
                    sequence alignments, microarrays, and genomic annotations.
                </p>

                <p>Clicking the launch button below will:</p>
<commit_msg>revert<commit_after><%@ page import="java.util.List" %>
<%@ page import="java.util.ArrayList" %>
<%@ page import="java.net.URLEncoder" %>
<%@ page import="com.google.common.base.Joiner" %>
<%@ page import="java.io.UnsupportedEncodingException" %>
<%@ page import="org.mskcc.portal.model.GeneWithScore" %>
<%@ page import="org.mskcc.portal.servlet.QueryBuilder" %>
<%@ page import="org.mskcc.portal.servlet.ServletXssUtil" %>
<%@ page import="org.mskcc.portal.util.GlobalProperties" %>
<%
	  // get URL to seg file used as parameter to IGV
	  String segFileURL = GlobalProperties.getSegfileUrl();

      // construct gene list parameter to IGV
      // use geneWithScoreList so we don't get any OQL
      List<String> onlyGenesList = new ArrayList<String>();
      for (GeneWithScore geneWithScore : geneWithScoreList) {
		  onlyGenesList.add(geneWithScore.getGene());
	  }
      String encodedGeneList = "";
      if (onlyGenesList.size() > 0) {
		  try {
			  encodedGeneList = URLEncoder.encode(Joiner.on(' ').join(onlyGenesList), "UTF-8");
		  }
		  catch(UnsupportedEncodingException e) {
		  }
	  }
%>

<div class="section" id="igv_tab">
    <table>
        <tr>
            <td style="padding-right:25px; vertical-align:top;"><img src="images/IGVlogo.png" alt=""/></td>
            <td style="vertical-align:top">

                <p>
                    The <a href="http://www.broadinstitute.org/igv/home">Integrative Genomics
                    Viewer (IGV)</a> is a high-performance visualization tool for interactive exploration
                    of large, integrated datasets. It supports a wide variety of data types including
                    sequence alignments, microarrays, and genomic annotations.
                </p>

                <p>Clicking the launch button below will:</p>

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{'dir': 'git-commits-cleaned', 'id': '4529266', 'n_tokens_mistral': 1228, 'n_tokens_neox': 1103, 'n_words': 244}