website/full_javadoc/index-files/index-4.html

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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/data/sequence/SMERFSConstraints.html#DEFAULT_COLUMN_SCORE"><B>DEFAULT_COLUMN_SCORE</B></A> - \r
  93 Static variable in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
  94 <DD>Default column scoring schema\r
  95 <DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD"><B>DEFAULT_GAP_THRESHOLD</B></A> - \r
  96 Static variable in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
  97 <DD>Default gap threshold value for SMERFS algorithm\r
  98 <DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE"><B>DEFAULT_WINDOW_SIZE</B></A> - \r
  99 Static variable in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
 100 <DD>Default window size value for SMERFS algorithm\r
 101 <DT><A HREF="../compbio/engine/Cleaner.html#deleteAllFiles(java.lang.String)"><B>deleteAllFiles(String)</B></A> - \r
 102 Static method in class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
 103 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 104 <DT><A HREF="../compbio/engine/Cleaner.html#deleteFiles(compbio.engine.client.ConfiguredExecutable)"><B>deleteFiles(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 105 Static method in class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
 106 <DD><B>Deprecated.</B>&nbsp;This method returns true if all files specified by List files were
 107  successfully removed or there was no files to remove (files list was
 108  empty)\r
 109 <DT><A HREF="../compbio/engine/conf/_Key.html#DELIM"><B>DELIM</B></A> - \r
 110 Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
 111 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 112 <DT><A HREF="../compbio/engine/conf/DirectoryManager.html#DELIM"><B>DELIM</B></A> - \r
 113 Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#DIGIT"><B>DIGIT</B></A> - \r
 116 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 117 <DD>A digit\r
 118 <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
 119 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
 120 <DD>&nbsp;\r
 121 <DT><A HREF="../compbio/engine/FilePuller.html#disconnect()"><B>disconnect()</B></A> - \r
 122 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 123 <DD>&nbsp;\r
 124 <DT><A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder"><B>Disembl</B></A> - Class in <A HREF="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A><DD>DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
 125  fold_rem465 sequence_file print
 126
 127  'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
 128
 129  This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
 130  capable of outputting raw values
 131
 132  The values of the parameters are hard coded in DisEMBL.py script.<DT><A HREF="../compbio/runner/disorder/Disembl.html#Disembl()"><B>Disembl()</B></A> - \r
 133 Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
 134 <DD>&nbsp;\r
 135 <DT><A HREF="../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server"><B>DisemblWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/DisemblWS.html#DisemblWS()"><B>DisemblWS()</B></A> - \r
 136 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</A>\r
 137 <DD>&nbsp;\r
 138 <DT><A HREF="../compbio/data/sequence/DisorderMethod.html" title="enum in compbio.data.sequence"><B>DisorderMethod</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>&nbsp;<DT><A HREF="../compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet"><B>DisplayStat</B></A> - Class in <A HREF="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</A><DD>&nbsp;<DT><A HREF="../compbio/stat/servlet/DisplayStat.html#DisplayStat()"><B>DisplayStat()</B></A> - \r
 139 Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet">DisplayStat</A>\r
 140 <DD>&nbsp;\r
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