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10 <META NAME="date" CONTENT="2011-12-07">
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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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43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
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82 <A NAME="_S_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#saveRunConfiguration()"><B>saveRunConfiguration()</B></A> -
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86 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>
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88 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration()"><B>saveRunConfiguration()</B></A> -
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89 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>
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91 <DT><A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>Score</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>A value class for AACon annotation results storage.<DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList)"><B>Score(Enum<?>, ArrayList<Float>)</B></A> -
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92 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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93 <DD>Instantiate the Score
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94 <DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)"><B>Score(Enum<?>, ArrayList<Float>, TreeSet<Range>)</B></A> -
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95 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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97 <DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.TreeSet)"><B>Score(Enum<?>, TreeSet<Range>)</B></A> -
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98 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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100 <DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, float[])"><B>Score(Enum<?>, float[])</B></A> -
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101 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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103 <DT><A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence"><B>ScoreManager</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><B>ScoreManager.ScoreHolder</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#scores"><B>scores</B></A> -
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104 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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106 <DT><A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa"><B>SequenceAnnotation</B></A><<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Interface for tools that results to one or more annotation to sequence(s)
108 Single, multiple sequences their groups or alignments can be annotated<DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server"><B>SequenceAnnotationService</B></A><<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>Common methods for all SequenceAnnotation web services<DT><A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Utility class for operations on sequences<DT><A HREF="../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE"><B>SERVICE_NAMESPACE</B></A> -
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109 Static variable in interface compbio.data.msa.<A HREF="../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>
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111 <DT><A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A> - Enum in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>List of web services currently supported by JABAWS version 2<DT><A HREF="../compbio/stat/servlet/ServiceStatus.html" title="class in compbio.stat.servlet"><B>ServiceStatus</B></A> - Class in <A HREF="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</A><DD>Use cases:
113 Test web services and display results on the web page
114 <DT><A HREF="../compbio/stat/servlet/ServiceStatus.html#ServiceStatus()"><B>ServiceStatus()</B></A> -
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115 Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceStatus.html" title="class in compbio.stat.servlet">ServiceStatus</A>
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117 <DT><A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client"><B>ServicesUtil</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD> <DT><A HREF="../compbio/ws/client/ServicesUtil.html#ServicesUtil()"><B>ServicesUtil()</B></A> -
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118 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>
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120 <DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet"><B>ServiceTestResult</B></A> - Class in <A HREF="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</A><DD>Value class for test results.<DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html#ServiceTestResult(compbio.ws.client.Services)"><B>ServiceTestResult(Services)</B></A> -
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121 Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</A>
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123 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setActualNumberofSequences(int)"><B>setActualNumberofSequences(int)</B></A> -
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124 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
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126 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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127 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>
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129 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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130 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>
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132 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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133 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</A>
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135 <DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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136 Method in 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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138 <DT><A HREF="../compbio/data/msa/jaxws/TestService.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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139 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>
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141 <DT><A HREF="../compbio/metadata/Option.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> -
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142 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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143 <DD>Sets one of the values defined in optionList as default.
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144 <DT><A HREF="../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> -
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145 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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147 <DT><A HREF="../compbio/metadata/Option.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> -
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148 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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150 <DT><A HREF="../compbio/metadata/Preset.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> -
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151 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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153 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)"><B>setEmail(String)</B></A> -
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154 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>
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155 <DD><B>Deprecated.</B>
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156 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setError(java.lang.String)"><B>setError(String)</B></A> -
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157 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>
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159 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)"><B>setError(String)</B></A> -
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160 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
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162 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#setExecProvider(compbio.engine.client.Executable.ExecProvider)"><B>setExecProvider(Executable.ExecProvider)</B></A> -
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163 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>
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165 <DT><A HREF="../compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server"><B>SetExecutableFlag</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>Run setexecflag.sh script if executable flag is not set<DT><A HREF="../compbio/ws/server/SetExecutableFlag.html#SetExecutableFlag()"><B>SetExecutableFlag()</B></A> -
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166 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server">SetExecutableFlag</A>
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168 <DT><A HREF="../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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169 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>
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171 <DT><A HREF="../compbio/data/msa/jaxws/Analize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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172 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>
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174 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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175 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>
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177 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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178 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>
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180 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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181 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>
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183 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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184 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>
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186 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setFirst(java.lang.String)"><B>setFirst(String)</B></A> -
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187 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
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189 <DT><A HREF="../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)"><B>setFurtherDetails(URL)</B></A> -
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190 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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192 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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193 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>
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195 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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196 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
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198 <DT><A HREF="../compbio/runner/conservation/AACon.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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199 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>
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201 <DT><A HREF="../compbio/runner/disorder/Disembl.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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202 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>
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204 <DT><A HREF="../compbio/runner/disorder/GlobPlot.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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205 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>
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207 <DT><A HREF="../compbio/runner/disorder/IUPred.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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208 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>
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210 <DT><A HREF="../compbio/runner/disorder/Jronn.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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211 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>
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213 <DT><A HREF="../compbio/runner/msa/ClustalO.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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214 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>
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216 <DT><A HREF="../compbio/runner/msa/ClustalW.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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217 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>
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219 <DT><A HREF="../compbio/runner/msa/Mafft.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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220 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>
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222 <DT><A HREF="../compbio/runner/msa/Muscle.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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223 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>
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225 <DT><A HREF="../compbio/runner/msa/Probcons.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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226 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>
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228 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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229 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>
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231 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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232 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>
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234 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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235 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>
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237 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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238 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>
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240 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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241 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>
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243 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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244 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>
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246 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String)"><B>setLast(String)</B></A> -
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247 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
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249 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String, java.lang.String)"><B>setLast(String, String)</B></A> -
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250 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
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252 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)"><B>setMax(String)</B></A> -
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253 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
\r
255 <DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
\r
256 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>
\r
258 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
\r
259 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
\r
261 <DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
\r
262 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>
\r
264 <DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
\r
265 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>
\r
267 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
\r
268 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>
\r
270 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)"><B>setMin(String)</B></A> -
\r
271 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
\r
273 <DT><A HREF="../compbio/metadata/Option.html#setName(java.lang.String)"><B>setName(String)</B></A> -
\r
274 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
\r
276 <DT><A HREF="../compbio/metadata/Preset.html#setName(java.lang.String)"><B>setName(String)</B></A> -
\r
277 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
\r
279 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)"><B>setName(String)</B></A> -
\r
280 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>
\r
281 <DD><B>Deprecated.</B>
\r
282 <DT><A HREF="../compbio/runner/conservation/AACon.html#setNCore(int)"><B>setNCore(int)</B></A> -
\r
283 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>
\r
285 <DT><A HREF="../compbio/runner/disorder/Jronn.html#setNCore(int)"><B>setNCore(int)</B></A> -
\r
286 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>
\r
288 <DT><A HREF="../compbio/runner/msa/ClustalO.html#setNCore(int)"><B>setNCore(int)</B></A> -
\r
289 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>
\r
291 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#setNCore(int)"><B>setNCore(int)</B></A> -
\r
292 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>
\r
294 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setNumberOfSequencesAllowed(int)"><B>setNumberOfSequencesAllowed(int)</B></A> -
\r
295 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
\r
297 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionName(java.lang.String)"><B>setOptionName(String)</B></A> -
\r
298 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
\r
300 <DT><A HREF="../compbio/metadata/Option.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> -
\r
301 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
\r
303 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> -
\r
304 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
\r
306 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)"><B>setOptions(List<Option>)</B></A> -
\r
307 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>
\r
309 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#setOptions(java.util.List)"><B>setOptions(List<Option>)</B></A> -
\r
310 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>
\r
312 <DT><A HREF="../compbio/metadata/Preset.html#setOptions(java.util.List)"><B>setOptions(List<String>)</B></A> -
\r
313 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
\r
315 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)"><B>setOptions(List<Option<T>>)</B></A> -
\r
316 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
\r
317 <DD>Adds the list of options or parameters to the internal list of options
\r
318 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
\r
319 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>
\r
321 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
\r
322 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
\r
324 <DT><A HREF="../compbio/runner/conservation/AACon.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
\r
325 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>
\r
327 <DT><A HREF="../compbio/runner/disorder/IUPred.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
\r
328 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>
\r
330 <DT><A HREF="../compbio/runner/disorder/Jronn.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
\r
331 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>
\r
333 <DT><A HREF="../compbio/runner/msa/ClustalO.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
\r
334 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>
\r
336 <DT><A HREF="../compbio/runner/msa/ClustalW.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
\r
337 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>
\r
339 <DT><A HREF="../compbio/runner/msa/Muscle.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
\r
340 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>
\r
342 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String)"><B>setParam(String)</B></A> -
\r
343 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
\r
345 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String, java.lang.String)"><B>setParam(String, String)</B></A> -
\r
346 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
\r
348 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)"><B>setParameter(String)</B></A> -
\r
349 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
\r
351 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)"><B>setParameters(CommandBuilder<?>)</B></A> -
\r
352 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>
\r
354 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)"><B>setParameters(List<Parameter<T>>)</B></A> -
\r
355 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
\r
356 <DD>Sets the list of parameters as internal list
\r
357 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParams(java.util.List)"><B>setParams(List<String>)</B></A> -
\r
358 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
\r
360 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setPosition(long)"><B>setPosition(long)</B></A> -
\r
361 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>
\r
363 <DT><A HREF="../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)"><B>setPossibleValues(Set<String>)</B></A> -
\r
364 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
\r
366 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> -
\r
367 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>
\r
369 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> -
\r
370 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>
\r
372 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#setPresetName(java.lang.String)"><B>setPresetName(String)</B></A> -
\r
373 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>
\r
375 <DT><A HREF="../compbio/metadata/PresetManager.html#setPresets(java.util.List)"><B>setPresets(List<Preset<T>>)</B></A> -
\r
376 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
\r
378 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)"><B>setPrmSeparator(String)</B></A> -
\r
379 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
\r
380 <DD>Sets name value separator character
\r
381 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setQueue(java.lang.String)"><B>setQueue(String)</B></A> -
\r
382 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>
\r
383 <DD><B>Deprecated.</B>
\r
384 <DT><A HREF="../compbio/data/sequence/Score.html#setRanges(java.util.TreeSet)"><B>setRanges(TreeSet<Range>)</B></A> -
\r
385 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
\r
387 <DT><A HREF="../compbio/metadata/Option.html#setRequired(boolean)"><B>setRequired(boolean)</B></A> -
\r
388 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
\r
390 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setRequiredMemory(int)"><B>setRequiredMemory(int)</B></A> -
\r
391 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>
\r
392 <DD><B>Deprecated.</B>
\r
393 <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
394 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>
\r
396 <DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
397 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>
\r
399 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#setReturn(boolean)"><B>setReturn(boolean)</B></A> -
\r
400 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
402 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
403 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>
\r
405 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
406 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>
\r
408 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#setReturn(compbio.data.sequence.ScoreManager)"><B>setReturn(ScoreManager)</B></A> -
\r
409 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>
\r
411 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn(compbio.metadata.JobStatus)"><B>setReturn(JobStatus)</B></A> -
\r
412 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>
\r
414 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#setReturn(java.util.Date)"><B>setReturn(Date)</B></A> -
\r
415 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>
\r
417 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#setReturn(int)"><B>setReturn(int)</B></A> -
\r
418 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>
\r
420 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn(compbio.metadata.Limit)"><B>setReturn(Limit)</B></A> -
\r
421 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>
\r
423 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#setReturn(compbio.metadata.LimitsManager)"><B>setReturn(LimitsManager)</B></A> -
\r
424 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>
\r
426 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn(compbio.metadata.PresetManager)"><B>setReturn(PresetManager)</B></A> -
\r
427 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>
\r
429 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)"><B>setReturn(Alignment)</B></A> -
\r
430 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>
\r
432 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)"><B>setReturn(RunnerConfig)</B></A> -
\r
433 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>
\r
435 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#setReturn(java.util.Set)"><B>setReturn(Set<Category>)</B></A> -
\r
436 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</A>
\r
438 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
439 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</A>
\r
441 <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#setReturn(java.util.Set)"><B>setReturn(Set<Services>)</B></A> -
\r
442 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>
\r
444 <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#setReturn(boolean)"><B>setReturn(boolean)</B></A> -
\r
445 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
447 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
448 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>
\r
450 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
451 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>
\r
453 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> -
\r
454 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>
\r
456 <DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
457 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>
\r
459 <DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
460 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>
\r
462 <DT><A HREF="../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> -
\r
463 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
\r
465 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> -
\r
466 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
\r
467 <DD>Set the name of a runner class
\r
468 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtActual(int)"><B>setSequenceLenghtActual(int)</B></A> -
\r
469 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
\r
471 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtAllowed(int)"><B>setSequenceLenghtAllowed(int)</B></A> -
\r
472 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
\r
474 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)"><B>setType(ValueConstrain.Type)</B></A> -
\r
475 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
\r
477 <DT><A HREF="../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)"><B>setValidValue(ValueConstrain)</B></A> -
\r
478 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
\r
480 <DT><A HREF="../compbio/metadata/Argument.html#setValue(java.lang.String)"><B>setValue(String)</B></A> -
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481 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>
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482 <DD>Set default values for the parameter or an option
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483 <DT><A HREF="../compbio/metadata/Option.html#setValue(java.lang.String)"><B>setValue(String)</B></A> -
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484 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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486 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> -
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487 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>
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489 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> -
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490 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>
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492 <DT><A HREF="../compbio/engine/local/LocalExecutorService.html#shutDown()"><B>shutDown()</B></A> -
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493 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>
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494 <DD>This stops all executing processes via interruption.
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495 <DT><A HREF="../compbio/stat/collector/StatDB.html#shutdownDBServer()"><B>shutdownDBServer()</B></A> -
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496 Static method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>
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498 <DT><A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server"><B>ShutdownEngines</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>Switch off engines if JABAWS web application is undeployed, or web server is
499 shutdown<DT><A HREF="../compbio/ws/server/ShutdownEngines.html#ShutdownEngines()"><B>ShutdownEngines()</B></A> -
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500 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server">ShutdownEngines</A>
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502 <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#shutdownService()"><B>shutdownService()</B></A> -
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503 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>
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504 <DD>Stops internal executor service which captures streams of native
506 <DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><B>SimpleWSPublisher</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD><B>Deprecated.</B> <DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html#SimpleWSPublisher(java.lang.Object, java.lang.String)"><B>SimpleWSPublisher(Object, String)</B></A> -
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507 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>
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508 <DD><B>Deprecated.</B>
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509 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY"><B>SINGLE_ENTRY_KEY</B></A> -
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510 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>
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512 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#size()"><B>size()</B></A> -
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513 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
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515 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>SkeletalExecutable</B></A><<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD> <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable()"><B>SkeletalExecutable()</B></A> -
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516 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
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518 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)"><B>SkeletalExecutable(String)</B></A> -
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519 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
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521 <DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence"><B>SMERFSConstraints</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Enumeration defining two constraints for SMERFS columns score calculation.<DT><A HREF="../compbio/stat/collector/StatProcessor.html#sortByResultSize()"><B>sortByResultSize()</B></A> -
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522 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>
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524 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#sortByRuntime()"><B>sortByRuntime()</B></A> -
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525 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>
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527 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#sortByStartTime()"><B>sortByStartTime()</B></A> -
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528 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>
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530 <DT><A HREF="../compbio/runner/Util.html#SPACE"><B>SPACE</B></A> -
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531 Static variable in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>
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533 <DT><A HREF="../compbio/runner/conservation/AACon.html#STAT_FILE"><B>STAT_FILE</B></A> -
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534 Static variable in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>
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536 <DT><A HREF="../compbio/runner/disorder/Jronn.html#STAT_FILE"><B>STAT_FILE</B></A> -
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537 Static variable in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>
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539 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util"><B>StatCollection</B></A> - Class in <A HREF="../compbio/stat/servlet/util/package-summary.html">compbio.stat.servlet.util</A><DD> <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#StatCollection()"><B>StatCollection()</B></A> -
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540 Constructor for class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>
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542 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.Stattype.html" title="enum in compbio.stat.servlet.util"><B>StatCollection.Stattype</B></A> - Enum in <A HREF="../compbio/stat/servlet/util/package-summary.html">compbio.stat.servlet.util</A><DD>Total number of requests
544 incomplete abandoned cancelled<DT><A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector"><B>StatDB</B></A> - Class in <A HREF="../compbio/stat/collector/package-summary.html">compbio.stat.collector</A><DD>The database must be stored in the application root directory and called
545 "ExecutionStatistic"<DT><A HREF="../compbio/stat/collector/StatDB.html#StatDB()"><B>StatDB()</B></A> -
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546 Constructor for class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>
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548 <DT><A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet"><B>StatisticCollector</B></A> - Class in <A HREF="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</A><DD> <DT><A HREF="../compbio/stat/servlet/StatisticCollector.html#StatisticCollector()"><B>StatisticCollector()</B></A> -
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549 Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</A>
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551 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa"><B>StatisticManager</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD> <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#StatisticManager(org.ggf.drmaa.JobInfo)"><B>StatisticManager(JobInfo)</B></A> -
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552 Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>
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554 <DT><A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector"><B>StatProcessor</B></A> - Class in <A HREF="../compbio/stat/collector/package-summary.html">compbio.stat.collector</A><DD> <DT><A HREF="../compbio/stat/collector/StatProcessor.html#StatProcessor(java.util.List)"><B>StatProcessor(List<JobStat>)</B></A> -
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555 Constructor for class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>
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557 <DT><A HREF="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local"><B>StreamGobbler</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD> <DT><A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine"><B>SubmissionManager</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>Submit jobs for execution<DT><A HREF="../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable<?>)</B></A> -
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558 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>
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559 <DD>Submits job for the execution
560 Immediate execution is not guaranteed, this method puts the job in the queue.
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561 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable<?>)</B></A> -
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562 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>
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564 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable<?>)</B></A> -
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565 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>
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567 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#sumOfTotals(java.util.Map)"><B>sumOfTotals(Map<Date, Totals>)</B></A> -
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568 Static method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>
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570 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#sumStats(java.util.Map)"><B>sumStats(Map<Services, StatProcessor>)</B></A> -
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571 Static method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>
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573 <DT><A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine"><B>SyncExecutor</B></A> - Interface in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>Synchronous executor, is an engine to run the Executable synchronously.</DL>
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577 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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578 <A NAME="navbar_bottom"><!-- --></A>
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