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5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->
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10 <META NAME="date" CONTENT="2010-02-17">
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12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">
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15 function windowTitle()
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17 if (location.href.indexOf('is-external=true') == -1) {
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18 parent.document.title="S-Index";
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27 <BODY BGCOLOR="white" onload="windowTitle();">
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31 <!-- ========= START OF TOP NAVBAR ======= -->
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32 <A NAME="navbar_top"><!-- --></A>
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33 <A HREF="#skip-navbar_top" title="Skip navigation links"></A>
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34 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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37 <A NAME="navbar_top_firstrow"><!-- --></A>
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38 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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39 <TR ALIGN="center" VALIGN="top">
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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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45 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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46 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
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47 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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58 <A HREF="index-17.html"><B>PREV LETTER</B></A>
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63 <SCRIPT type="text/javascript">
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66 document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
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71 <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
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78 <A NAME="skip-navbar_top"></A>
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79 <!-- ========= END OF TOP NAVBAR ========= -->
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81 <A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>
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82 <A NAME="_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/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/jaxws/LimitExceededExceptionBean.html#setActualNumberofSequences(int)"><B>setActualNumberofSequences(int)</B></A> -
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92 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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94 <DT><A HREF="../compbio/metadata/Option.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> -
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95 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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96 <DD>Sets one of the values defined in optionList as default.
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97 <DT><A HREF="../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> -
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98 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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100 <DT><A HREF="../compbio/metadata/Option.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> -
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101 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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103 <DT><A HREF="../compbio/metadata/Preset.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> -
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104 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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106 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)"><B>setEmail(String)</B></A> -
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107 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>
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109 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setError(java.lang.String)"><B>setError(String)</B></A> -
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110 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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112 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)"><B>setError(String)</B></A> -
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113 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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115 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#setExecProvider(compbio.engine.client.Executable.ExecProvider)"><B>setExecProvider(Executable.ExecProvider)</B></A> -
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116 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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118 <DT><A HREF="../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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119 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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121 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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122 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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124 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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125 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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127 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setFirst(java.lang.String)"><B>setFirst(String)</B></A> -
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128 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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130 <DT><A HREF="../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)"><B>setFurtherDetails(URL)</B></A> -
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131 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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133 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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134 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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136 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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137 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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139 <DT><A HREF="../compbio/runner/msa/ClustalW.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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140 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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142 <DT><A HREF="../compbio/runner/msa/Mafft.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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143 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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145 <DT><A HREF="../compbio/runner/msa/Muscle.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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146 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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148 <DT><A HREF="../compbio/runner/msa/Probcons.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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149 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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151 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#setInput(java.lang.String)"><B>setInput(String)</B></A> -
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152 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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154 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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155 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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157 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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158 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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160 <DT><A HREF="../compbio/data/msa/jaxws/GetProgress.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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161 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws">GetProgress</A>
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163 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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164 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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166 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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167 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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169 <DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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170 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>
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172 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String)"><B>setLast(String)</B></A> -
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173 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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175 <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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176 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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178 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)"><B>setMax(String)</B></A> -
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179 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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181 <DT><A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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182 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobExecutionExceptionBean</A>
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184 <DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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185 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>
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187 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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188 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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190 <DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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191 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>
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193 <DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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194 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>
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196 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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197 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>
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199 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)"><B>setMin(String)</B></A> -
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200 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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202 <DT><A HREF="../compbio/metadata/Option.html#setName(java.lang.String)"><B>setName(String)</B></A> -
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203 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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205 <DT><A HREF="../compbio/metadata/Preset.html#setName(java.lang.String)"><B>setName(String)</B></A> -
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206 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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208 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)"><B>setName(String)</B></A> -
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209 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>
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211 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#setNCore(int)"><B>setNCore(int)</B></A> -
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212 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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214 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setNumberOfSequencesAllowed(int)"><B>setNumberOfSequencesAllowed(int)</B></A> -
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215 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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217 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionName(java.lang.String)"><B>setOptionName(String)</B></A> -
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218 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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220 <DT><A HREF="../compbio/metadata/Option.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> -
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221 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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223 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> -
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224 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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226 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)"><B>setOptions(List<Option>)</B></A> -
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227 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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229 <DT><A HREF="../compbio/metadata/Preset.html#setOptions(java.util.List)"><B>setOptions(List<String>)</B></A> -
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230 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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232 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)"><B>setOptions(List<Option<T>>)</B></A> -
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233 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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235 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
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236 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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238 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
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239 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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241 <DT><A HREF="../compbio/runner/msa/ClustalW.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
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242 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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244 <DT><A HREF="../compbio/runner/msa/Muscle.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> -
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245 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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247 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String)"><B>setParam(String)</B></A> -
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248 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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250 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String, java.lang.String)"><B>setParam(String, String)</B></A> -
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251 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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253 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)"><B>setParameter(String)</B></A> -
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254 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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256 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)"><B>setParameters(CommandBuilder<?>)</B></A> -
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257 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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259 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)"><B>setParameters(List<Parameter<T>>)</B></A> -
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260 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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262 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParams(java.util.List)"><B>setParams(List<String>)</B></A> -
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263 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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265 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setPosition(long)"><B>setPosition(long)</B></A> -
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266 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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268 <DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#setPosition(long)"><B>setPosition(long)</B></A> -
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269 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>
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271 <DT><A HREF="../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)"><B>setPossibleValues(Set<String>)</B></A> -
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272 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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274 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> -
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275 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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277 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#setPresetName(java.lang.String)"><B>setPresetName(String)</B></A> -
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278 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>
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280 <DT><A HREF="../compbio/metadata/PresetManager.html#setPresets(java.util.List)"><B>setPresets(List<Preset<T>>)</B></A> -
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281 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
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283 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)"><B>setPrmSeparator(String)</B></A> -
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284 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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286 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setQueue(java.lang.String)"><B>setQueue(String)</B></A> -
\r
287 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>
\r
289 <DT><A HREF="../compbio/metadata/Option.html#setRequired(boolean)"><B>setRequired(boolean)</B></A> -
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290 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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292 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setRequiredMemory(int)"><B>setRequiredMemory(int)</B></A> -
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293 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>
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295 <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
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296 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>
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298 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#setReturn(boolean)"><B>setReturn(boolean)</B></A> -
\r
299 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
301 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
302 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
304 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn(compbio.metadata.JobStatus)"><B>setReturn(JobStatus)</B></A> -
\r
305 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>
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307 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn(compbio.metadata.Limit)"><B>setReturn(Limit)</B></A> -
\r
308 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
310 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#setReturn(compbio.metadata.LimitsManager)"><B>setReturn(LimitsManager)</B></A> -
\r
311 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
313 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn(compbio.metadata.PresetManager)"><B>setReturn(PresetManager)</B></A> -
\r
314 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
316 <DT><A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html#setReturn(byte)"><B>setReturn(byte)</B></A> -
\r
317 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws">GetProgressResponse</A>
\r
319 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)"><B>setReturn(Alignment)</B></A> -
\r
320 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
322 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)"><B>setReturn(RunnerConfig)</B></A> -
\r
323 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
325 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
326 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
328 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> -
\r
329 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
331 <DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> -
\r
332 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws">PullFileResponse</A>
\r
334 <DT><A HREF="../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> -
\r
335 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
\r
337 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> -
\r
338 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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340 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtActual(int)"><B>setSequenceLenghtActual(int)</B></A> -
\r
341 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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343 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtAllowed(int)"><B>setSequenceLenghtAllowed(int)</B></A> -
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344 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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346 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)"><B>setType(ValueConstrain.Type)</B></A> -
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347 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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349 <DT><A HREF="../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)"><B>setValidValue(ValueConstrain)</B></A> -
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350 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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352 <DT><A HREF="../compbio/metadata/Argument.html#setValue(java.lang.String)"><B>setValue(String)</B></A> -
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353 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>
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354 <DD>Set default values for the parameter or an option
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355 <DT><A HREF="../compbio/metadata/Option.html#setValue(java.lang.String)"><B>setValue(String)</B></A> -
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356 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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358 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> -
\r
359 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>
\r
361 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> -
\r
362 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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364 <DT><A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html#SHORT_TIME_LIMIT"><B>SHORT_TIME_LIMIT</B></A> -
\r
365 Static variable in class compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A>
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367 <DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#shutdown()"><B>shutdown()</B></A> -
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368 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>
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370 <DT><A HREF="../compbio/engine/local/LocalExecutorService.html#shutDown()"><B>shutDown()</B></A> -
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371 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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372 <DD>This stops all executing processes via interruption.
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373 <DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#shutdownNow()"><B>shutdownNow()</B></A> -
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374 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>
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376 <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>This class publish a web service.<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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377 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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379 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#size()"><B>size()</B></A> -
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380 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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382 <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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383 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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385 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)"><B>SkeletalExecutable(String)</B></A> -
\r
386 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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388 <DT><A HREF="../compbio/runner/Util.html#SPACE"><B>SPACE</B></A> -
\r
389 Static variable in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>
\r
391 <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> -
\r
392 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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394 <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/local/_TrackingExecutor.html#submit(java.util.concurrent.Callable)"><B>submit(Callable<T>)</B></A> -
\r
395 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>
\r
397 <DT><A HREF="../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable<?>)</B></A> -
\r
398 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>
\r
399 <DD>Submits job for the execution
400 Immediate execution is not guaranteed, this method puts the job in the queue.
\r
401 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable<?>)</B></A> -
\r
402 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>
\r
404 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable<?>)</B></A> -
\r
405 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>
\r
407 <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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411 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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412 <A NAME="navbar_bottom"><!-- --></A>
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413 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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414 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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419 <TR ALIGN="center" VALIGN="top">
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420 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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421 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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422 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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423 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
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425 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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426 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
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427 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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431 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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437 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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438 <A HREF="index-17.html"><B>PREV LETTER</B></A>
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446 document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
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