website/full_javadoc/index-files/index-22.html

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  83 <B>W</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/engine/FilePuller.html#waitForFile(long)"><B>waitForFile(long)</B></A> - \r
  86 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#waitForJob(java.lang.String)"><B>waitForJob(String)</B></A> - \r
  89 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#waitForJob(java.lang.String, long)"><B>waitForJob(String, long)</B></A> - \r
  92 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#waitForResult(compbio.engine.cluster.drmaa.ClusterSession, java.lang.String)"><B>waitForResult(ClusterSession, String)</B></A> - \r
  95 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
  96 <DD>&nbsp;\r
  97 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()"><B>waitForResult()</B></A> - \r
  98 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
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/engine/local/LocalRunner.html#waitForResult()"><B>waitForResult()</B></A> - \r
 101 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/engine/SyncExecutor.html#waitForResult()"><B>waitForResult()</B></A> - \r
 104 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 105 <DD>Call to this method block for as long as it is required for an executable to finish its job.\r
 106 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#wasAborted()"><B>wasAborted()</B></A> - \r
 107 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 108 <DD>&nbsp;\r
 109 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE"><B>WHITE_SPACE</B></A> - \r
 110 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 111 <DD>A whitespace character: [\t\n\x0B\f\r]\r
 112 <DT><A HREF="../compbio/data/sequence/Score.html#write(java.util.TreeSet, java.io.Writer)"><B>write(TreeSet&lt;Score&gt;, Writer)</B></A> - \r
 113 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
 114 <DD>Outputs the List of Score objects into the Output stream.\r
 115 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#write(compbio.engine.client.RunConfiguration)"><B>write(RunConfiguration)</B></A> - \r
 116 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 117 <DD>&nbsp;\r
 118 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#write(java.lang.Object, java.io.OutputStream)"><B>write(Object, OutputStream)</B></A> - \r
 119 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
 120 <DD>&nbsp;\r
 121 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#writeAndValidate(java.lang.Object, java.lang.String, java.io.OutputStream)"><B>writeAndValidate(Object, String, OutputStream)</B></A> - \r
 122 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
 123 <DD>&nbsp;\r
 124 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.Writer, compbio.data.sequence.Alignment)"><B>writeClustalAlignment(Writer, Alignment)</B></A> - \r
 125 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 126 <DD>Write Clustal formatted alignment Limitations: does not record the
 127  consensus.\r
 128 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)"><B>writeFasta(OutputStream, List&lt;FastaSequence&gt;, int)</B></A> - \r
 129 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 130 <DD>Writes list of FastaSequeces into the outstream formatting the sequence
 131  so that it contains width chars on each line\r
 132 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)"><B>writeFasta(OutputStream, List&lt;FastaSequence&gt;)</B></A> - \r
 133 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 134 <DD>Writes FastaSequence in the file, each sequence will take one line only\r
 135 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)"><B>writeFastaKeepTheStream(OutputStream, List&lt;FastaSequence&gt;, int)</B></A> - \r
 136 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 137 <DD>&nbsp;\r
 138 <DT><A HREF="../compbio/engine/client/Util.html#writeFile(java.lang.String, java.lang.String, java.lang.String, boolean)"><B>writeFile(String, String, String, boolean)</B></A> - \r
 139 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 140 <DD>&nbsp;\r
 141 <DT><A HREF="../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)"><B>writeInput(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 142 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
 143 <DD>&nbsp;\r
 144 <DT><A HREF="../compbio/engine/client/Util.html#writeMarker(java.lang.String, compbio.metadata.JobStatus)"><B>writeMarker(String, JobStatus)</B></A> - \r
 145 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 146 <DD>&nbsp;\r
 147 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#writeOut(java.io.Writer)"><B>writeOut(Writer)</B></A> - \r
 148 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
 149 <DD>&nbsp;\r
 150 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#writeOut(java.io.Writer)"><B>writeOut(Writer)</B></A> - \r
 151 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 152 <DD>&nbsp;\r
 153 <DT><A HREF="../compbio/engine/client/Util.html#writeStatFile(java.lang.String, java.lang.String)"><B>writeStatFile(String, String)</B></A> - \r
 154 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 155 <DD>&nbsp;\r
 156 <DT><A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>WrongParameterException is thrown wherever the <A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
 157  does not match the actual runnable or then attempting to set the value of
 158  <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)"><B>WrongParameterException(Option&lt;?&gt;)</B></A> - \r
 159 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
 160 <DD>&nbsp;\r
 161 <DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String)"><B>WrongParameterException(String)</B></A> - \r
 162 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
 163 <DD>&nbsp;\r
 164 <DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.Throwable)"><B>WrongParameterException(Throwable)</B></A> - \r
 165 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
 166 <DD>&nbsp;\r
 167 <DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String, java.lang.Throwable)"><B>WrongParameterException(String, Throwable)</B></A> - \r
 168 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
 169 <DD>&nbsp;\r
 170 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>WrongParameterExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#WrongParameterExceptionBean()"><B>WrongParameterExceptionBean()</B></A> - \r
 171 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
 172 <DD>&nbsp;\r
 173 <DT><A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>Class for testing web services<DT><A HREF="../compbio/ws/client/WSTester.html#WSTester(java.lang.String, java.io.PrintWriter)"><B>WSTester(String, PrintWriter)</B></A> - \r
 174 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
 175 <DD>Construct an instance of JABAWS tester\r
 176 <DT><A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server"><B>WSUtil</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/WSUtil.html#WSUtil()"><B>WSUtil()</B></A> - \r
 177 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 178 <DD>&nbsp;\r
 179 </DL>\r
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