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10 <META NAME="date" CONTENT="2010-02-17">
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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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82 <A NAME="_P_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred"><B>Pairwise</B></A> - Class in <A HREF="../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A><DD> <DT><A HREF="../compbio/pipeline/_jpred/Pairwise.html#Pairwise(java.util.List)"><B>Pairwise(List<FastaSequence>)</B></A> -
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86 Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A>
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88 <DT><A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A><<A HREF="../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A single value containing option supported by the web service e.g.<DT><A HREF="../compbio/metadata/Parameter.html#Parameter(java.lang.String, java.lang.String)"><B>Parameter(String, String)</B></A> -
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89 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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91 <DT><A HREF="../compbio/runner/OptionCombinator.html#parametersToCommandString(java.util.List, java.util.Map)"><B>parametersToCommandString(List<Parameter<?>>, Map<Parameter<?>, String>)</B></A> -
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92 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>
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94 <DT><A HREF="../compbio/engine/conf/_Key.html#parse(java.lang.String)"><B>parse(String)</B></A> -
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95 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>
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97 <DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#PATH"><B>PATH</B></A> -
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98 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>
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99 <DD>Special variable keys Absolute path(s) will be merged with the content of
100 the system PATH variable
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101 <DT><A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client"><B>PathValidator</B></A> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD> <DT><A HREF="../compbio/engine/client/PathValidator.html#PathValidator()"><B>PathValidator()</B></A> -
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102 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>
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104 <DT><A HREF="../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><B>PipedExecutable</B></A><<A HREF="../compbio/engine/client/PipedExecutable.html" title="type parameter in PipedExecutable">T</A>> - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>This is a marker interface to indicate that the output of the process must be
105 captured.<DT><A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A><<A HREF="../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Collection of Options and Parameters with their values<DT><A HREF="../compbio/metadata/Preset.html#Preset()"><B>Preset()</B></A> -
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106 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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108 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws"><B>PresetAlign</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#PresetAlign()"><B>PresetAlign()</B></A> -
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109 Constructor for 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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111 <DT><A HREF="../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List<FastaSequence>, Preset<T>)</B></A> -
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112 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>
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113 <DD>Align a list of sequences with preset.
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114 <DT><A HREF="../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List<FastaSequence>, Preset<ClustalW>)</B></A> -
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115 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>
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117 <DT><A HREF="../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List<FastaSequence>, Preset<Mafft>)</B></A> -
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118 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>
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120 <DT><A HREF="../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List<FastaSequence>, Preset<Muscle>)</B></A> -
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121 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>
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123 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List<FastaSequence>, Preset<Probcons>)</B></A> -
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124 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>
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126 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List<FastaSequence>, Preset<Tcoffee>)</B></A> -
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127 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>
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129 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>PresetAlignResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#PresetAlignResponse()"><B>PresetAlignResponse()</B></A> -
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130 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>
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132 <DT><A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A><<A HREF="../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Collection of presets and methods to manipulate them @see <A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A><DT><A HREF="../compbio/metadata/PresetManager.html#PresetManager()"><B>PresetManager()</B></A> -
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133 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
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135 <DT><A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>Probcons</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD> <DT><A HREF="../compbio/runner/msa/Probcons.html#Probcons()"><B>Probcons()</B></A> -
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136 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>
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138 <DT><A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server"><B>ProbconsWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD> <DT><A HREF="../compbio/ws/server/ProbconsWS.html#ProbconsWS()"><B>ProbconsWS()</B></A> -
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139 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>
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141 <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE"><B>PROC_ERR_FILE</B></A> -
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142 Static variable in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>
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144 <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE"><B>PROC_OUT_FILE</B></A> -
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145 Static variable in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>
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147 <DT><A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>Program</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Programmes that can produce alignments<DT><A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine"><B>ProgressGetter</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD> <DT><A HREF="../compbio/engine/ProgressGetter.html#ProgressGetter()"><B>ProgressGetter()</B></A> -
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148 Constructor for class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>
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150 <DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf"><B>PropertyHelperManager</B></A> - Class in <A HREF="../compbio/engine/conf/package-summary.html">compbio.engine.conf</A><DD> <DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#PropertyHelperManager()"><B>PropertyHelperManager()</B></A> -
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151 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>
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153 <DT><A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred"><B>PScore</B></A> - Class in <A HREF="../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A><DD> <DT><A HREF="../compbio/pipeline/_jpred/PScore.html#PScore()"><B>PScore()</B></A> -
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154 Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>
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156 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><B>PSIBlast</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD> <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#PSIBlast(java.lang.String)"><B>PSIBlast(String)</B></A> -
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157 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>
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159 <DT><A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast"><B>PsiBlast</B></A> - Class in <A HREF="../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A><DD> <DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#PsiBlast()"><B>PsiBlast()</B></A> -
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160 Constructor for class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>
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162 <DT><A HREF="../compbio/engine/FilePuller.html#pull(long)"><B>pull(long)</B></A> -
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163 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>
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165 <DT><A HREF="../compbio/engine/ProgressGetter.html#pull(java.lang.String, long)"><B>pull(String, long)</B></A> -
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166 Static method in class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>
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168 <DT><A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine"><B>PulledFileCache</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD> <DT><A HREF="../compbio/engine/PulledFileCache.html#PulledFileCache()"><B>PulledFileCache()</B></A> -
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169 Constructor for class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>
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171 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws"><B>PullExecStatistics</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#PullExecStatistics()"><B>PullExecStatistics()</B></A> -
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172 Constructor for 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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174 <DT><A HREF="../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> -
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175 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>
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176 <DD>Reads 1kb chunk from the statistics file which is specific to a given web
177 service from the position.
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178 <DT><A HREF="../compbio/ws/server/ClustalWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> -
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179 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>
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181 <DT><A HREF="../compbio/ws/server/MafftWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> -
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182 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>
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184 <DT><A HREF="../compbio/ws/server/MuscleWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> -
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185 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>
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187 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> -
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188 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>
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190 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> -
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191 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>
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193 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws"><B>PullExecStatisticsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#PullExecStatisticsResponse()"><B>PullExecStatisticsResponse()</B></A> -
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194 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>
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196 <DT><A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws"><B>PullFile</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#PullFile()"><B>PullFile()</B></A> -
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197 Constructor for 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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199 <DT><A HREF="../compbio/ws/server/WSUtil.html#pullFile(java.lang.String, long)"><B>pullFile(String, long)</B></A> -
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200 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>
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202 <DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws"><B>PullFileResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html#PullFileResponse()"><B>PullFileResponse()</B></A> -
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203 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws">PullFileResponse</A>
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205 <DT><A HREF="../compbio/engine/PulledFileCache.html#put(compbio.engine.FilePuller)"><B>put(FilePuller)</B></A> -
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206 Static method in class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>
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207 <DD>This method allows duplicates to be added.
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212 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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213 <A NAME="navbar_bottom"><!-- --></A>
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214 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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215 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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217 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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218 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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219 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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220 <TR ALIGN="center" VALIGN="top">
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221 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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222 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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223 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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224 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
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225 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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226 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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227 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
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228 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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232 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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238 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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239 <A HREF="index-15.html"><B>PREV LETTER</B></A>
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240 <A HREF="index-17.html"><B>NEXT LETTER</B></A></FONT></TD>
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241 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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242 <A HREF="../index.html?index-filesindex-16.html" target="_top"><B>FRAMES</B></A>
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243 <A HREF="index-16.html" target="_top"><B>NO FRAMES</B></A>
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244 <SCRIPT type="text/javascript">
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247 document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
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