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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/data/sequence/ScoreManager.ScoreHolder.html#id"><B>id</B></A> - \r
  86 Variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/engine/FilePuller.html#initPull()"><B>initPull()</B></A> - \r
  89 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#INPUT"><B>INPUT</B></A> - \r
  92 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><B>IOHelper</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>&nbsp;<DT><A HREF="../compbio/ws/client/IOHelper.html#IOHelper()"><B>IOHelper()</B></A> - \r
  95 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A>\r
  96 <DD>&nbsp;\r
  97 <DT><A HREF="../compbio/engine/Configurator.html#IS_CLUSTER_ENGINE_ENABLED"><B>IS_CLUSTER_ENGINE_ENABLED</B></A> - \r
  98 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/engine/Configurator.html#IS_LOCAL_ENGINE_ENABLED"><B>IS_LOCAL_ENGINE_ENABLED</B></A> - \r
 101 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/engine/client/PathValidator.html#isAbsolutePath(java.lang.String)"><B>isAbsolutePath(String)</B></A> - \r
 104 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
 105 <DD>Whether a certain path is absolute or not is operation system dependent!\r
 106 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> - \r
 107 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 108 <DD>Check whether the sequence confirms to amboguous protein sequence\r
 109 <DT><A HREF="../compbio/stat/collector/JobStat.html#isClusterJob()"><B>isClusterJob()</B></A> - \r
 110 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 111 <DD>&nbsp;\r
 112 <DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> - \r
 113 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List&lt;FastaSequence&gt;)</B></A> - \r
 116 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 117 <DD>Checks if the number of sequences or their average length in the dataset
 118  exceeds this limit.\r
 119 <DT><A HREF="../compbio/engine/FilePuller.html#isFileCreated()"><B>isFileCreated()</B></A> - \r
 120 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 121 <DD>&nbsp;\r
 122 <DT><A HREF="../compbio/engine/client/Util.html#isJavaLibrary(java.lang.Class)"><B>isJavaLibrary(Class&lt;?&gt;)</B></A> - \r
 123 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 124 <DD>Returns true of executableName.jar.file property has some value in the
 125  Executable.properties file, false otherwise.\r
 126 <DT><A HREF="../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)"><B>isMarked(String, JobStatus)</B></A> - \r
 127 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 128 <DD>&nbsp;\r
 129 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> - \r
 130 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 131 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
 132  (!) - B char\r
 133 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> - \r
 134 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 135 <DD>&nbsp;\r
 136 <DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws"><B>IsOperating</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#IsOperating()"><B>IsOperating()</B></A> - \r
 137 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>\r
 138 <DD>&nbsp;\r
 139 <DT><A HREF="../compbio/data/msa/RegistryWS.html#isOperating(compbio.ws.client.Services)"><B>isOperating(Services)</B></A> - \r
 140 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
 141 <DD>Check whether a particular web service is working on this server\r
 142 <DT><A HREF="../compbio/ws/server/RegistryWS.html#isOperating(compbio.ws.client.Services)"><B>isOperating(Services)</B></A> - \r
 143 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
 144 <DD>&nbsp;\r
 145 <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws"><B>IsOperatingResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#IsOperatingResponse()"><B>IsOperatingResponse()</B></A> - \r
 146 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>\r
 147 <DD>&nbsp;\r
 148 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> - \r
 149 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 150 <DD>&nbsp;\r
 151 <DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> - \r
 152 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 153 <DD>Flag that indicated that this option must be specified in the command
 154  line for an executable to run\r
 155 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#isReturn()"><B>isReturn()</B></A> - \r
 156 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
 157 <DD>&nbsp;\r
 158 <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#isReturn()"><B>isReturn()</B></A> - \r
 159 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>\r
 160 <DD>&nbsp;\r
 161 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> - \r
 162 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 163 <DD>Please note this method closes the input stream provided as a parameter\r
 164 <DT><A HREF="../compbio/engine/client/PathValidator.html#isValidDirectory(java.lang.String)"><B>isValidDirectory(String)</B></A> - \r
 165 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
 166 <DD>&nbsp;\r
 167 <DT><A HREF="../compbio/engine/client/PathValidator.html#isValidExecutable(java.lang.String)"><B>isValidExecutable(String)</B></A> - \r
 168 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
 169 <DD>&nbsp;\r
 170 <DT><A HREF="../compbio/engine/client/Util.html#isValidJobId(java.lang.String)"><B>isValidJobId(String)</B></A> - \r
 171 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 172 <DD>&nbsp;\r
 173 <DT><A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder"><B>IUPred</B></A> - Class in <A HREF="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A><DD>iupred sequenceFile <short long glob >
 174
 175  Maximum sequence length is 40000 chars.<DT><A HREF="../compbio/runner/disorder/IUPred.html#IUPred()"><B>IUPred()</B></A> - \r
 176 Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
 177 <DD>&nbsp;\r
 178 <DT><A HREF="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server"><B>IUPredWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/IUPredWS.html#IUPredWS()"><B>IUPredWS()</B></A> - \r
 179 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</A>\r
 180 <DD>&nbsp;\r
 181 </DL>\r
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