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  75 <h2 class="title">D</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#DATE_TIME">DATE_TIME</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#deepClean--">deepClean()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
  80 <dd>&nbsp;</dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#deepClean--">deepClean()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
  82 <dd>&nbsp;</dd>
  83 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#deepCleanSequence-java.lang.String-">deepCleanSequence(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
  84 <dd>
  85 <div class="block">Removes all special characters and digits as well as whitespace chars
  86  from the sequence</div>
  87 </dd>
  88 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_COLUMN_SCORE">DEFAULT_COLUMN_SCORE</a></span> - Static variable in enum compbio.data.sequence.<a href="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></dt>
  89 <dd>
  90 <div class="block">Default column scoring schema</div>
  91 </dd>
  92 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</a></span> - Static variable in enum compbio.data.sequence.<a href="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></dt>
  93 <dd>
  94 <div class="block">Default gap threshold value for SMERFS algorithm</div>
  95 </dd>
  96 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</a></span> - Static variable in enum compbio.data.sequence.<a href="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></dt>
  97 <dd>
  98 <div class="block">Default window size value for SMERFS algorithm</div>
  99 </dd>
 100 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#defaultDelay">defaultDelay</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 101 <dd>&nbsp;</dd>
 102 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#defaultValue">defaultValue</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 103 <dd>&nbsp;</dd>
 104 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#delay">delay</a></span> - Variable in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 105 <dd>&nbsp;</dd>
 106 <dt><span class="memberNameLink"><a href="../compbio/engine/Cleaner.html#deleteAllFiles-java.lang.String-">deleteAllFiles(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</a></dt>
 107 <dd>&nbsp;</dd>
 108 <dt><span class="memberNameLink"><a href="../compbio/engine/Cleaner.html#deleteDirectory-java.lang.String-">deleteDirectory(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</a></dt>
 109 <dd>&nbsp;</dd>
 110 <dt><span class="memberNameLink"><a href="../compbio/engine/Cleaner.html#deleteFiles-compbio.engine.client.ConfiguredExecutable-">deleteFiles(ConfiguredExecutable&lt;?&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</a></dt>
 111 <dd>
 112 <div class="block">This method returns true if all files specified by List files were
 113  successfully removed or there was no files to remove (files list was
 114  empty)</div>
 115 </dd>
 116 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaReader.html#DELIM">DELIM</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></dt>
 117 <dd>
 118 <div class="block">Delimiter for the scanner</div>
 119 </dd>
 120 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/DirectoryManager.html#DELIM">DELIM</a></span> - Static variable in class compbio.engine.conf.<a href="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</a></dt>
 121 <dd>&nbsp;</dd>
 122 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#description">description</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 123 <dd>&nbsp;</dd>
 124 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#description">description</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 125 <dd>&nbsp;</dd>
 126 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#details">details</a></span> - Variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
 127 <dd>&nbsp;</dd>
 128 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/ExecutionStatCollector.html#DF">DF</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</a></dt>
 129 <dd>&nbsp;</dd>
 130 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#DIGIT">DIGIT</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 131 <dd>
 132 <div class="block">A digit</div>
 133 </dd>
 134 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html#dir">dir</a></span> - Variable in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html" title="class in compbio.engine.conf">RunnerConfigMarshaller.MySchemaOutputResolver</a></dt>
 135 <dd>&nbsp;</dd>
 136 <dt><a href="../compbio/stat/collector/DirCleaner.html" title="class in compbio.stat.collector"><span class="typeNameLink">DirCleaner</span></a> - Class in <a href="../compbio/stat/collector/package-summary.html">compbio.stat.collector</a></dt>
 137 <dd>
 138 <div class="block">Number of runs of each WS = number of folders with name
 139
 140  Number of successful runs = all runs with no result file
 141
 142  Per period of time = limit per file creating time Runtime (avg/max) =
 143
 144  started time - finished time
 145
 146  Task & result size = result.size
 147
 148  Abandoned runs - not collected runs
 149
 150  Cancelled runs - cancelled
 151
 152  Cluster vs local runs
 153
 154  Reasons for failure = look in the err out?
 155
 156  Metadata required:
 157
 158  work directory for local and cluster tasks = from Helper or cmd parameter.</div>
 159 </dd>
 160 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/DirCleaner.html#DirCleaner-java.lang.String-int-">DirCleaner(String, int)</a></span> - Constructor for class compbio.stat.collector.<a href="../compbio/stat/collector/DirCleaner.html" title="class in compbio.stat.collector">DirCleaner</a></dt>
 161 <dd>&nbsp;</dd>
 162 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/DirCleaner.html#directories">directories</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/DirCleaner.html" title="class in compbio.stat.collector">DirCleaner</a></dt>
 163 <dd>&nbsp;</dd>
 164 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/ExecutionStatCollector.html#directories">directories</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</a></dt>
 165 <dd>&nbsp;</dd>
 166 <dt><a href="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf"><span class="typeNameLink">DirectoryManager</span></a> - Class in <a href="../compbio/engine/conf/package-summary.html">compbio.engine.conf</a></dt>
 167 <dd>&nbsp;</dd>
 168 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/DirectoryManager.html#DirectoryManager--">DirectoryManager()</a></span> - Constructor for class compbio.engine.conf.<a href="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</a></dt>
 169 <dd>&nbsp;</dd>
 170 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#disconnect--">disconnect()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 171 <dd>&nbsp;</dd>
 172 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#disconnected--">disconnected()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 173 <dd>&nbsp;</dd>
 174 <dt><a href="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder"><span class="typeNameLink">Disembl</span></a> - Class in <a href="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</a></dt>
 175 <dd>
 176 <div class="block">DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
 177  fold_rem465 sequence_file print
 178
 179  'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
 180
 181  This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
 182  capable of outputting raw values
 183
 184  The values of the parameters are hard coded in DisEMBL.py script.</div>
 185 </dd>
 186 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Disembl.html#Disembl--">Disembl()</a></span> - Constructor for class compbio.runner.disorder.<a href="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a></dt>
 187 <dd>&nbsp;</dd>
 188 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#DISEMBL_INFO">DISEMBL_INFO</a></span> - Static variable in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 189 <dd>&nbsp;</dd>
 190 <dt><a href="../compbio/data/sequence/DisemblResult.html" title="enum in compbio.data.sequence"><span class="typeNameLink">DisemblResult</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 191 <dd>&nbsp;</dd>
 192 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/DisemblResult.html#DisemblResult--">DisemblResult()</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/DisemblResult.html" title="enum in compbio.data.sequence">DisemblResult</a></dt>
 193 <dd>&nbsp;</dd>
 194 <dt><a href="../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server"><span class="typeNameLink">DisemblWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 195 <dd>&nbsp;</dd>
 196 <dt><span class="memberNameLink"><a href="../compbio/ws/server/DisemblWS.html#DisemblWS--">DisemblWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</a></dt>
 197 <dd>&nbsp;</dd>
 198 <dt><a href="../compbio/data/sequence/DisorderMethod.html" title="enum in compbio.data.sequence"><span class="typeNameLink">DisorderMethod</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 199 <dd>&nbsp;</dd>
 200 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/DisorderMethod.html#DisorderMethod--">DisorderMethod()</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/DisorderMethod.html" title="enum in compbio.data.sequence">DisorderMethod</a></dt>
 201 <dd>&nbsp;</dd>
 202 <dt><a href="../compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet"><span class="typeNameLink">DisplayStat</span></a> - Class in <a href="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</a></dt>
 203 <dd>&nbsp;</dd>
 204 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/DisplayStat.html#DisplayStat--">DisplayStat()</a></span> - Constructor for class compbio.stat.servlet.<a href="../compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet">DisplayStat</a></dt>
 205 <dd>&nbsp;</dd>
 206 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/DirCleaner.html#doCleaning--">doCleaning()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/DirCleaner.html" title="class in compbio.stat.collector">DirCleaner</a></dt>
 207 <dd>&nbsp;</dd>
 208 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/AnnualStat.html#doGet-javax.servlet.http.HttpServletRequest-javax.servlet.http.HttpServletResponse-">doGet(HttpServletRequest, HttpServletResponse)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet">AnnualStat</a></dt>
 209 <dd>&nbsp;</dd>
 210 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/DisplayStat.html#doGet-javax.servlet.http.HttpServletRequest-javax.servlet.http.HttpServletResponse-">doGet(HttpServletRequest, HttpServletResponse)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet">DisplayStat</a></dt>
 211 <dd>&nbsp;</dd>
 212 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/DownloadRedirector.html#doGet-javax.servlet.http.HttpServletRequest-javax.servlet.http.HttpServletResponse-">doGet(HttpServletRequest, HttpServletResponse)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/DownloadRedirector.html" title="class in compbio.stat.servlet">DownloadRedirector</a></dt>
 213 <dd>&nbsp;</dd>
 214 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/HttpCodeResponseServiceStatus.html#doGet-javax.servlet.http.HttpServletRequest-javax.servlet.http.HttpServletResponse-">doGet(HttpServletRequest, HttpServletResponse)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/HttpCodeResponseServiceStatus.html" title="class in compbio.stat.servlet">HttpCodeResponseServiceStatus</a></dt>
 215 <dd>&nbsp;</dd>
 216 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/Joblist.html#doGet-javax.servlet.http.HttpServletRequest-javax.servlet.http.HttpServletResponse-">doGet(HttpServletRequest, HttpServletResponse)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</a></dt>
 217 <dd>
 218 <div class="block">Input:
 219
 220  ws=${ws.key}
 221
 222  where=everywhere cluster local
 223
 224  type=cancelled all incomplete
 225
 226  from=${startDate}
 227
 228  to=${stopDate}</div>
 229 </dd>
 230 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceStatus.html#doGet-javax.servlet.http.HttpServletRequest-javax.servlet.http.HttpServletResponse-">doGet(HttpServletRequest, HttpServletResponse)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceStatus.html" title="class in compbio.stat.servlet">ServiceStatus</a></dt>
 231 <dd>&nbsp;</dd>
 232 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/HttpCodeResponseServiceStatus.html#doHead-javax.servlet.http.HttpServletRequest-javax.servlet.http.HttpServletResponse-">doHead(HttpServletRequest, HttpServletResponse)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/HttpCodeResponseServiceStatus.html" title="class in compbio.stat.servlet">HttpCodeResponseServiceStatus</a></dt>
 233 <dd>&nbsp;</dd>
 234 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/DownloadRedirector.html#doPost-javax.servlet.http.HttpServletRequest-javax.servlet.http.HttpServletResponse-">doPost(HttpServletRequest, HttpServletResponse)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/DownloadRedirector.html" title="class in compbio.stat.servlet">DownloadRedirector</a></dt>
 235 <dd>&nbsp;</dd>
 236 <dt><a href="../compbio/stat/servlet/DownloadRedirector.html" title="class in compbio.stat.servlet"><span class="typeNameLink">DownloadRedirector</span></a> - Class in <a href="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</a></dt>
 237 <dd>&nbsp;</dd>
 238 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/DownloadRedirector.html#DownloadRedirector--">DownloadRedirector()</a></span> - Constructor for class compbio.stat.servlet.<a href="../compbio/stat/servlet/DownloadRedirector.html" title="class in compbio.stat.servlet">DownloadRedirector</a></dt>
 239 <dd>&nbsp;</dd>
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