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  75 <h2 class="title">I</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#id">id</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
  78 <dd>
  79 <div class="block">Sequence id</div>
  80 </dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html#id">id</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></dt>
  82 <dd>&nbsp;</dd>
  83 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#identify-java.lang.String-">identify(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
  84 <dd>&nbsp;</dd>
  85 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#identifyLine-java.lang.String-">identifyLine(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
  86 <dd>&nbsp;</dd>
  87 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#incomplete">incomplete</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>
  88 <dd>&nbsp;</dd>
  89 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#init--">init()</a></span> - Static method in class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
  90 <dd>&nbsp;</dd>
  91 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#init--">init()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
  92 <dd>&nbsp;</dd>
  93 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#init--">init()</a></span> - Static method in class compbio.engine.local.<a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></dt>
  94 <dd>&nbsp;</dd>
  95 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#init-java.util.List-">init(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
  96 <dd>&nbsp;</dd>
  97 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#init-java.util.List-">init(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
  98 <dd>&nbsp;</dd>
  99 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#init-java.util.List-">init(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
 100 <dd>&nbsp;</dd>
 101 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#init-java.util.List-">init(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
 102 <dd>&nbsp;</dd>
 103 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#init-java.util.List-">init(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
 104 <dd>&nbsp;</dd>
 105 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#init-java.util.List-">init(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 106 <dd>&nbsp;</dd>
 107 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#init-java.util.List-">init(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 108 <dd>&nbsp;</dd>
 109 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#init-java.util.List-">init(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 110 <dd>&nbsp;</dd>
 111 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#init--">init()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
 112 <dd>&nbsp;</dd>
 113 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#init-java.util.List-">init(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
 114 <dd>&nbsp;</dd>
 115 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#initBooleanValue-java.lang.String-">initBooleanValue(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 116 <dd>&nbsp;</dd>
 117 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#initClusterWorkDirectory--">initClusterWorkDirectory()</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 118 <dd>&nbsp;</dd>
 119 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#initLocalDirectory--">initLocalDirectory()</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 120 <dd>&nbsp;</dd>
 121 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#initPull--">initPull()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 122 <dd>&nbsp;</dd>
 123 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaReader.html#input">input</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></dt>
 124 <dd>&nbsp;</dd>
 125 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#input">input</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 126 <dd>
 127 <div class="block">Input</div>
 128 </dd>
 129 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 130 <dd>&nbsp;</dd>
 131 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#inputFile">inputFile</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 132 <dd>&nbsp;</dd>
 133 <dt><a href="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector"><span class="typeNameLink">InputFilter</span></a> - Class in <a href="../compbio/stat/collector/package-summary.html">compbio.stat.collector</a></dt>
 134 <dd>&nbsp;</dd>
 135 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/InputFilter.html#InputFilter--">InputFilter()</a></span> - Constructor for class compbio.stat.collector.<a href="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector">InputFilter</a></dt>
 136 <dd>&nbsp;</dd>
 137 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#inputkey">inputkey</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
 138 <dd>&nbsp;</dd>
 139 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#inputSize">inputSize</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 140 <dd>&nbsp;</dd>
 141 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#insertData-java.util.Set-">insertData(Set&lt;JobStat&gt;)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 142 <dd>&nbsp;</dd>
 143 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#INSTANCE">INSTANCE</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
 144 <dd>&nbsp;</dd>
 145 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#INSTANCE">INSTANCE</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></dt>
 146 <dd>&nbsp;</dd>
 147 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#io">io</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 148 <dd>&nbsp;</dd>
 149 <dt><a href="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><span class="typeNameLink">IOHelper</span></a> - Class in <a href="../compbio/ws/client/package-summary.html">compbio.ws.client</a></dt>
 150 <dd>&nbsp;</dd>
 151 <dt><span class="memberNameLink"><a href="../compbio/ws/client/IOHelper.html#IOHelper--">IOHelper()</a></span> - Constructor for class compbio.ws.client.<a href="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</a></dt>
 152 <dd>&nbsp;</dd>
 153 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#iow">iow</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 154 <dd>&nbsp;</dd>
 155 <dt><span class="memberNameLink"><a href="../compbio/engine/local/StreamGobbler.html#is">is</a></span> - Variable in class compbio.engine.local.<a href="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</a></dt>
 156 <dd>&nbsp;</dd>
 157 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#IS_CLUSTER_ENGINE_ENABLED">IS_CLUSTER_ENGINE_ENABLED</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 158 <dd>&nbsp;</dd>
 159 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#IS_GA_ENABLED">IS_GA_ENABLED</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></dt>
 160 <dd>&nbsp;</dd>
 161 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#IS_LOCAL_ENGINE_ENABLED">IS_LOCAL_ENGINE_ENABLED</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 162 <dd>&nbsp;</dd>
 163 <dt><span class="memberNameLink"><a href="../compbio/engine/client/PathValidator.html#isAbsolutePath-java.lang.String-">isAbsolutePath(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</a></dt>
 164 <dd>
 165 <div class="block">Whether a certain path is absolute or not is operation system dependent!</div>
 166 </dd>
 167 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/AnnualStat.html#isAdmin-javax.servlet.http.HttpServletRequest-">isAdmin(HttpServletRequest)</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet">AnnualStat</a></dt>
 168 <dd>&nbsp;</dd>
 169 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein-java.lang.String-">isAmbiguosProtein(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 170 <dd>
 171 <div class="block">Check whether the sequence confirms to amboguous protein sequence</div>
 172 </dd>
 173 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#isCancelled--">isCancelled()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
 174 <dd>&nbsp;</dd>
 175 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#isCancelled">isCancelled</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 176 <dd>&nbsp;</dd>
 177 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#isClusterJob--">isClusterJob()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 178 <dd>&nbsp;</dd>
 179 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#isCollected--">isCollected()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
 180 <dd>&nbsp;</dd>
 181 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#isCollected">isCollected</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 182 <dd>&nbsp;</dd>
 183 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#isCombinedValue-java.lang.String-">isCombinedValue(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 184 <dd>&nbsp;</dd>
 185 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#isComposite-java.lang.String-">isComposite(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 186 <dd>&nbsp;</dd>
 187 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#isDefault">isDefault</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 188 <dd>&nbsp;</dd>
 189 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#isDefault--">isDefault()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 190 <dd>&nbsp;</dd>
 191 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#isErrorSet">isErrorSet</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 192 <dd>&nbsp;</dd>
 193 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#isErrorSet--">isErrorSet()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 194 <dd>&nbsp;</dd>
 195 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#isExceeded-java.util.List-">isExceeded(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 196 <dd>
 197 <div class="block">Checks if the number of sequences or their average length in the dataset
 198  exceeds this limit.</div>
 199 </dd>
 200 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#isFileCreated--">isFileCreated()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 201 <dd>&nbsp;</dd>
 202 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#isFirst--">isFirst()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
 203 <dd>&nbsp;</dd>
 204 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#isGoogleAnalyticsEnabled--">isGoogleAnalyticsEnabled()</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></dt>
 205 <dd>&nbsp;</dd>
 206 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#isInputSet">isInputSet</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 207 <dd>&nbsp;</dd>
 208 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#isInputSet--">isInputSet()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 209 <dd>&nbsp;</dd>
 210 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#isJavaLibrary-java.lang.Class-">isJavaLibrary(Class&lt;?&gt;)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EngineUtil.html" title="class in compbio.engine.client">EngineUtil</a></dt>
 211 <dd>
 212 <div class="block">Returns true of executableName.jar.file property has some value in the
 213  Executable.properties file, false otherwise.</div>
 214 </dd>
 215 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#isJavaLibrary-java.lang.Class-">isJavaLibrary(Class&lt;?&gt;)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</a></dt>
 216 <dd>
 217 <div class="block">Returns true of executableName.jar.file property has some value in the
 218  Executable.properties file, false otherwise.</div>
 219 </dd>
 220 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#isLast--">isLast()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
 221 <dd>&nbsp;</dd>
 222 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#isLocal-java.lang.String-">isLocal(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 223 <dd>&nbsp;</dd>
 224 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#isMarked-java.lang.String-compbio.metadata.JobStatus-">isMarked(String, JobStatus)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EngineUtil.html" title="class in compbio.engine.client">EngineUtil</a></dt>
 225 <dd>&nbsp;</dd>
 226 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#isMarked-java.lang.String-compbio.metadata.JobStatus-">isMarked(String, JobStatus)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</a></dt>
 227 <dd>&nbsp;</dd>
 228 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence-java.lang.String-">isNonAmbNucleotideSequence(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 229 <dd>
 230 <div class="block">Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
 231  (!) - B char</div>
 232 </dd>
 233 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence-compbio.data.sequence.FastaSequence-">isNucleotideSequence(FastaSequence)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 234 <dd>&nbsp;</dd>
 235 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#isNumeric-java.lang.String-">isNumeric(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 236 <dd>&nbsp;</dd>
 237 <dt><a href="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">IsOperating</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 238 <dd>&nbsp;</dd>
 239 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/IsOperating.html#IsOperating--">IsOperating()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</a></dt>
 240 <dd>&nbsp;</dd>
 241 <dt><span class="memberNameLink"><a href="../compbio/data/msa/RegistryWS.html#isOperating-compbio.ws.client.Services-">isOperating(Services)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</a></dt>
 242 <dd>
 243 <div class="block">Check whether a particular web service is working on this server</div>
 244 </dd>
 245 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#isOperating-compbio.ws.client.Services-">isOperating(Services)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
 246 <dd>&nbsp;</dd>
 247 <dt><a href="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">IsOperatingResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 248 <dd>&nbsp;</dd>
 249 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/IsOperatingResponse.html#IsOperatingResponse--">IsOperatingResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</a></dt>
 250 <dd>&nbsp;</dd>
 251 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#isOutputSet">isOutputSet</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 252 <dd>&nbsp;</dd>
 253 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#isOutputSet--">isOutputSet()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 254 <dd>&nbsp;</dd>
 255 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#isParameter-java.lang.String-">isParameter(String)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 256 <dd>&nbsp;</dd>
 257 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#isProteinSequence-java.lang.String-">isProteinSequence(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 258 <dd>&nbsp;</dd>
 259 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#isRequired">isRequired</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 260 <dd>&nbsp;</dd>
 261 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#isRequired--">isRequired()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 262 <dd>
 263 <div class="block">Flag that indicated that this option must be specified in the command
 264  line for an executable to run</div>
 265 </dd>
 266 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CancelJobResponse.html#isReturn--">isReturn()</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</a></dt>
 267 <dd>&nbsp;</dd>
 268 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/IsOperatingResponse.html#isReturn--">isReturn()</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</a></dt>
 269 <dd>&nbsp;</dd>
 270 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#isTargetedForLocalExecution-compbio.engine.client.ConfiguredExecutable-">isTargetedForLocalExecution(ConfiguredExecutable&lt;?&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 271 <dd>&nbsp;</dd>
 272 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile-java.io.InputStream-">isValidClustalFile(InputStream)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></dt>
 273 <dd>
 274 <div class="block">Please note this method closes the input stream provided as a parameter</div>
 275 </dd>
 276 <dt><span class="memberNameLink"><a href="../compbio/engine/client/PathValidator.html#isValidDirectory-java.lang.String-">isValidDirectory(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</a></dt>
 277 <dd>&nbsp;</dd>
 278 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#isValidEnvVariableProperty-java.lang.String-">isValidEnvVariableProperty(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
 279 <dd>&nbsp;</dd>
 280 <dt><span class="memberNameLink"><a href="../compbio/engine/client/PathValidator.html#isValidExecutable-java.lang.String-">isValidExecutable(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</a></dt>
 281 <dd>&nbsp;</dd>
 282 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#isValidJobId-java.lang.String-">isValidJobId(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EngineUtil.html" title="class in compbio.engine.client">EngineUtil</a></dt>
 283 <dd>&nbsp;</dd>
 284 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#isValidJobId-java.lang.String-">isValidJobId(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</a></dt>
 285 <dd>&nbsp;</dd>
 286 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#isValidValue-java.lang.String-">isValidValue(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 287 <dd>&nbsp;</dd>
 288 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#isWhiteSpaceSeparator--">isWhiteSpaceSeparator()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 289 <dd>&nbsp;</dd>
 290 <dt><a href="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder"><span class="typeNameLink">IUPred</span></a> - Class in <a href="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</a></dt>
 291 <dd>
 292 <div class="block">iupred sequenceFile <short long glob >
 293
 294  Maximum sequence length is 40000 chars.</div>
 295 </dd>
 296 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#IUPred--">IUPred()</a></span> - Constructor for class compbio.runner.disorder.<a href="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a></dt>
 297 <dd>&nbsp;</dd>
 298 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#IUPRED_INFO">IUPRED_INFO</a></span> - Static variable in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 299 <dd>&nbsp;</dd>
 300 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#iupred_path">iupred_path</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>
 301 <dd>&nbsp;</dd>
 302 <dt><a href="../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence"><span class="typeNameLink">IUPredResult</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 303 <dd>&nbsp;</dd>
 304 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/IUPredResult.html#IUPredResult--">IUPredResult()</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a></dt>
 305 <dd>&nbsp;</dd>
 306 <dt><a href="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server"><span class="typeNameLink">IUPredWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 307 <dd>&nbsp;</dd>
 308 <dt><span class="memberNameLink"><a href="../compbio/ws/server/IUPredWS.html#IUPredWS--">IUPredWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</a></dt>
 309 <dd>&nbsp;</dd>
 310 </dl>
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