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  82 <A NAME="_D_"><!-- --></A><H2>\r
  83 <B>D</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#deepClean()"><B>deepClean()</B></A> - \r
  86 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)"><B>deepCleanSequence(String)</B></A> - \r
  89 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
  90 <DD>Removes all special characters and digits as well as whitespace chars
  91  from the sequence\r
  92 <DT><A HREF="../compbio/engine/Cleaner.html#deleteAllFiles(java.lang.String)"><B>deleteAllFiles(String)</B></A> - \r
  93 Static method in class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
  94 <DD>&nbsp;\r
  95 <DT><A HREF="../compbio/engine/Cleaner.html#deleteFiles(compbio.engine.client.ConfiguredExecutable)"><B>deleteFiles(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
  96 Static method in class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
  97 <DD>This method returns true if all files specified by List files were
  98  successfully removed or there was no files to remove (files list was
  99  empty)\r
 100 <DT><A HREF="../compbio/engine/conf/_Key.html#DELIM"><B>DELIM</B></A> - \r
 101 Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/engine/conf/DirectoryManager.html#DELIM"><B>DELIM</B></A> - \r
 104 Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#DIGIT"><B>DIGIT</B></A> - \r
 107 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 108 <DD>A digit\r
 109 <DT><A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf"><B>DirectoryManager</B></A> - Class in <A HREF="../compbio/engine/conf/package-summary.html">compbio.engine.conf</A><DD>&nbsp;<DT><A HREF="../compbio/engine/conf/DirectoryManager.html#DirectoryManager()"><B>DirectoryManager()</B></A> - \r
 110 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
 111 <DD>&nbsp;\r
 112 <DT><A HREF="../compbio/engine/FilePuller.html#disconnect()"><B>disconnect()</B></A> - \r
 113 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><B>Disembl</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/Disembl.html#Disembl(java.lang.String)"><B>Disembl(String)</B></A> - \r
 116 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
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