website/docs/full_javadoc/index-files/index-6.html

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  75 <h2 class="title">F</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#failed">failed</a></span> - Variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#failed">failed</a></span> - Variable in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</a></dt>
  80 <dd>&nbsp;</dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#FAILED">FAILED</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
  82 <dd>
  83 <div class="block">Status strings</div>
  84 </dd>
  85 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#fasta4mafft">fasta4mafft</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
  86 <dd>&nbsp;</dd>
  87 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#fastaAlignment">fastaAlignment</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
  88 <dd>&nbsp;</dd>
  89 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#fastaInput1record">fastaInput1record</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
  90 <dd>&nbsp;</dd>
  91 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#fastaInput2records">fastaInput2records</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
  92 <dd>
  93 <div class="block">Test sequences to be used as input for WS</div>
  94 </dd>
  95 <dt><a href="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence"><span class="typeNameLink">FastaReader</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
  96 <dd>
  97 <div class="block">Reads files with FASTA formatted sequences.</div>
  98 </dd>
  99 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaReader.html#FastaReader-java.lang.String-">FastaReader(String)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></dt>
 100 <dd>
 101 <div class="block">Header data can contain non-ASCII symbols and read in UTF8</div>
 102 </dd>
 103 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaReader.html#FastaReader-java.io.InputStream-">FastaReader(InputStream)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></dt>
 104 <dd>
 105 <div class="block">This class will not close the incoming stream! So the client should do
 106  so.</div>
 107 </dd>
 108 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#fastaRNAAlignment">fastaRNAAlignment</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
 109 <dd>&nbsp;</dd>
 110 <dt><a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><span class="typeNameLink">FastaSequence</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 111 <dd>
 112 <div class="block">A FASTA formatted sequence.</div>
 113 </dd>
 114 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#FastaSequence--">FastaSequence()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
 115 <dd>&nbsp;</dd>
 116 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#FastaSequence-java.lang.String-java.lang.String-">FastaSequence(String, String)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
 117 <dd>
 118 <div class="block">Upon construction the any whitespace characters are removed from the
 119  sequence</div>
 120 </dd>
 121 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Align.html#fastaSequences">fastaSequences</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</a></dt>
 122 <dd>&nbsp;</dd>
 123 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Analize.html#fastaSequences">fastaSequences</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</a></dt>
 124 <dd>&nbsp;</dd>
 125 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlign.html#fastaSequences">fastaSequences</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</a></dt>
 126 <dd>&nbsp;</dd>
 127 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalize.html#fastaSequences">fastaSequences</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</a></dt>
 128 <dd>&nbsp;</dd>
 129 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlign.html#fastaSequences">fastaSequences</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</a></dt>
 130 <dd>&nbsp;</dd>
 131 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalize.html#fastaSequences">fastaSequences</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</a></dt>
 132 <dd>&nbsp;</dd>
 133 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/UnknownFileFormatException.html#file">file</a></span> - Variable in exception compbio.data.sequence.<a href="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></dt>
 134 <dd>&nbsp;</dd>
 135 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#file">file</a></span> - Variable in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 136 <dd>&nbsp;</dd>
 137 <dt><a href="../compbio/engine/FilePuller.html" title="class in compbio.engine"><span class="typeNameLink">FilePuller</span></a> - Class in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
 138 <dd>&nbsp;</dd>
 139 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#FilePuller-java.lang.String-int-">FilePuller(String, int)</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 140 <dd>&nbsp;</dd>
 141 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#FilePuller-java.lang.String-">FilePuller(String)</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 142 <dd>&nbsp;</dd>
 143 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#files">files</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
 144 <dd>&nbsp;</dd>
 145 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#finish">finish</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 146 <dd>&nbsp;</dd>
 147 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#FIRST">FIRST</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
 148 <dd>&nbsp;</dd>
 149 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#floatP">floatP</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 150 <dd>&nbsp;</dd>
 151 <dt><a href="../compbio/data/msa/jaxws/Fold.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">Fold</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 152 <dd>&nbsp;</dd>
 153 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Fold.html#Fold--">Fold()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/Fold.html" title="class in compbio.data.msa.jaxws">Fold</a></dt>
 154 <dd>&nbsp;</dd>
 155 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#fold-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">fold(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, String, Limit&lt;T&gt;)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 156 <dd>&nbsp;</dd>
 157 <dt><a href="../compbio/data/msa/jaxws/FoldResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">FoldResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 158 <dd>&nbsp;</dd>
 159 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/FoldResponse.html#FoldResponse--">FoldResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/FoldResponse.html" title="class in compbio.data.msa.jaxws">FoldResponse</a></dt>
 160 <dd>&nbsp;</dd>
 161 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#formatTime-java.lang.String-">formatTime(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 162 <dd>
 163 <div class="block">Convert grid engine time format End time: 1250701672.0000 to a readable
 164  time representation as defined in Util.dataf</div>
 165 </dd>
 166 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#freeEnergyP">freeEnergyP</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 167 <dd>&nbsp;</dd>
 168 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#freqP">freqP</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 169 <dd>&nbsp;</dd>
 170 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Range.html#from">from</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a></dt>
 171 <dd>&nbsp;</dd>
 172 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#furtherDetails">furtherDetails</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 173 <dd>&nbsp;</dd>
 174 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalRunner.html#future">future</a></span> - Variable in class compbio.engine.local.<a href="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</a></dt>
 175 <dd>&nbsp;</dd>
 176 </dl>
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