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40 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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81 <A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>
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82 <A NAME="_I_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#id"><B>id</B></A> -
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86 Variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>
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88 <DT><A HREF="../compbio/engine/FilePuller.html#initPull()"><B>initPull()</B></A> -
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89 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>
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91 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#INPUT"><B>INPUT</B></A> -
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92 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
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94 <DT><A HREF="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector"><B>InputFilter</B></A> - Class in <A HREF="../compbio/stat/collector/package-summary.html">compbio.stat.collector</A><DD> <DT><A HREF="../compbio/stat/collector/InputFilter.html#InputFilter()"><B>InputFilter()</B></A> -
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95 Constructor for class compbio.stat.collector.<A HREF="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector">InputFilter</A>
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97 <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> <DT><A HREF="../compbio/ws/client/IOHelper.html#IOHelper()"><B>IOHelper()</B></A> -
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98 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A>
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100 <DT><A HREF="../compbio/engine/Configurator.html#IS_CLUSTER_ENGINE_ENABLED"><B>IS_CLUSTER_ENGINE_ENABLED</B></A> -
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101 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>
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103 <DT><A HREF="../compbio/engine/Configurator.html#IS_LOCAL_ENGINE_ENABLED"><B>IS_LOCAL_ENGINE_ENABLED</B></A> -
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104 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>
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106 <DT><A HREF="../compbio/engine/client/PathValidator.html#isAbsolutePath(java.lang.String)"><B>isAbsolutePath(String)</B></A> -
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107 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>
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108 <DD>Whether a certain path is absolute or not is operation system dependent!
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109 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> -
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110 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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111 <DD>Check whether the sequence confirms to amboguous protein sequence
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112 <DT><A HREF="../compbio/stat/collector/JobStat.html#isClusterJob()"><B>isClusterJob()</B></A> -
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113 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>
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115 <DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> -
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116 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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118 <DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List<FastaSequence>)</B></A> -
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119 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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120 <DD>Checks if the number of sequences or their average length in the dataset
121 exceeds this limit.
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122 <DT><A HREF="../compbio/engine/FilePuller.html#isFileCreated()"><B>isFileCreated()</B></A> -
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123 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>
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125 <DT><A HREF="../compbio/engine/client/Util.html#isJavaLibrary(java.lang.Class)"><B>isJavaLibrary(Class<?>)</B></A> -
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126 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>
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127 <DD>Returns true of executableName.jar.file property has some value in the
128 Executable.properties file, false otherwise.
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129 <DT><A HREF="../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)"><B>isMarked(String, JobStatus)</B></A> -
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130 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>
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132 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> -
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133 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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134 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
136 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> -
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137 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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139 <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> <DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#IsOperating()"><B>IsOperating()</B></A> -
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140 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>
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142 <DT><A HREF="../compbio/data/msa/RegistryWS.html#isOperating(compbio.ws.client.Services)"><B>isOperating(Services)</B></A> -
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143 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>
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144 <DD>Check whether a particular web service is working on this server
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145 <DT><A HREF="../compbio/ws/server/RegistryWS.html#isOperating(compbio.ws.client.Services)"><B>isOperating(Services)</B></A> -
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146 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>
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148 <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> <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#IsOperatingResponse()"><B>IsOperatingResponse()</B></A> -
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149 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>
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151 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> -
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152 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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154 <DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> -
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155 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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156 <DD>Flag that indicated that this option must be specified in the command
157 line for an executable to run
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158 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#isReturn()"><B>isReturn()</B></A> -
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159 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>
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161 <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#isReturn()"><B>isReturn()</B></A> -
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162 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>
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164 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> -
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165 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>
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166 <DD>Please note this method closes the input stream provided as a parameter
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167 <DT><A HREF="../compbio/engine/client/PathValidator.html#isValidDirectory(java.lang.String)"><B>isValidDirectory(String)</B></A> -
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168 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>
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170 <DT><A HREF="../compbio/engine/client/PathValidator.html#isValidExecutable(java.lang.String)"><B>isValidExecutable(String)</B></A> -
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171 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>
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173 <DT><A HREF="../compbio/engine/client/Util.html#isValidJobId(java.lang.String)"><B>isValidJobId(String)</B></A> -
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174 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>
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176 <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 >
178 Maximum sequence length is 40000 chars.<DT><A HREF="../compbio/runner/disorder/IUPred.html#IUPred()"><B>IUPred()</B></A> -
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179 Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>
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181 <DT><A HREF="../compbio/ws/client/Services.html#IUPRED_INFO"><B>IUPRED_INFO</B></A> -
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182 Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>
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184 <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> <DT><A HREF="../compbio/ws/server/IUPredWS.html#IUPredWS()"><B>IUPredWS()</B></A> -
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185 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</A>
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191 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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