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  82 <A NAME="_I_"><!-- --></A><H2>\r
  83 <B>I</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/engine/FilePuller.html#initPull()"><B>initPull()</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/Configurator.html#IS_CLUSTER_ENGINE_ENABLED"><B>IS_CLUSTER_ENGINE_ENABLED</B></A> - \r
  89 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/engine/Configurator.html#IS_LOCAL_ENGINE_ENABLED"><B>IS_LOCAL_ENGINE_ENABLED</B></A> - \r
  92 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/engine/client/PathValidator.html#isAbsolutePath(java.lang.String)"><B>isAbsolutePath(String)</B></A> - \r
  95 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
  96 <DD>Whether a certain path is absolute or not is operation system dependent!\r
  97 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> - \r
  98 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
  99 <DD>Check whether the sequence confirms to amboguous protein sequence\r
 100 <DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> - \r
 101 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List&lt;FastaSequence&gt;)</B></A> - \r
 104 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 105 <DD>Checks if the number of sequences or their average length in the dataset
 106  exceeds limits the values defined by this Limit\r
 107 <DT><A HREF="../compbio/engine/FilePuller.html#isFileCreated()"><B>isFileCreated()</B></A> - \r
 108 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 109 <DD>&nbsp;\r
 110 <DT><A HREF="../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)"><B>isMarked(String, JobStatus)</B></A> - \r
 111 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 112 <DD>&nbsp;\r
 113 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> - \r
 114 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 115 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
 116  (!) - B char\r
 117 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> - \r
 118 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 119 <DD>&nbsp;\r
 120 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> - \r
 121 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 122 <DD>&nbsp;\r
 123 <DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> - \r
 124 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 125 <DD>Flag that indicated that this option must be specified in the command
 126  line for an executable to run\r
 127 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#isReturn()"><B>isReturn()</B></A> - \r
 128 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
 129 <DD>&nbsp;\r
 130 <DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#isShutdown()"><B>isShutdown()</B></A> - \r
 131 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
 132 <DD>&nbsp;\r
 133 <DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#isTerminated()"><B>isTerminated()</B></A> - \r
 134 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
 135 <DD>&nbsp;\r
 136 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> - \r
 137 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 138 <DD>&nbsp;\r
 139 <DT><A HREF="../compbio/engine/client/PathValidator.html#isValidDirectory(java.lang.String)"><B>isValidDirectory(String)</B></A> - \r
 140 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
 141 <DD>&nbsp;\r
 142 <DT><A HREF="../compbio/engine/client/PathValidator.html#isValidExecutable(java.lang.String)"><B>isValidExecutable(String)</B></A> - \r
 143 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
 144 <DD>&nbsp;\r
 145 <DT><A HREF="../compbio/engine/client/Util.html#isValidJobId(java.lang.String)"><B>isValidJobId(String)</B></A> - \r
 146 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 147 <DD>&nbsp;\r
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