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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>\r
  82 <A NAME="_P_"><!-- --></A><H2>\r
  83 <B>P</B></H2>\r
  84 <DL>\r
  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>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/Pairwise.html#Pairwise(java.util.List)"><B>Pairwise(List&lt;FastaSequence&gt;)</B></A> - \r
  86 Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A>&lt;<A HREF="../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt; - 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> - \r
  89 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/runner/OptionCombinator.html#parametersToCommandString(java.util.List, java.util.Map)"><B>parametersToCommandString(List&lt;Parameter&lt;?&gt;&gt;, Map&lt;Parameter&lt;?&gt;, String&gt;)</B></A> - \r
  92 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/engine/conf/_Key.html#parse(java.lang.String)"><B>parse(String)</B></A> - \r
  95 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
  96 <DD>&nbsp;\r
  97 <DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#PATH"><B>PATH</B></A> - \r
  98 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
  99 <DD>Special variable keys Absolute path(s) will be merged with the content of
 100  the system PATH variable\r
 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>&nbsp;<DT><A HREF="../compbio/engine/client/PathValidator.html#PathValidator()"><B>PathValidator()</B></A> - \r
 102 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
 103 <DD>&nbsp;\r
 104 <DT><A HREF="../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><B>PipedExecutable</B></A>&lt;<A HREF="../compbio/engine/client/PipedExecutable.html" title="type parameter in PipedExecutable">T</A>&gt; - 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>&lt;<A HREF="../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt; - 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> - \r
 106 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 107 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#PresetAlign()"><B>PresetAlign()</B></A> - \r
 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>\r
 110 <DD>&nbsp;\r
 111 <DT><A HREF="../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;T&gt;)</B></A> - \r
 112 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
 113 <DD>Align a list of sequences with preset.\r
 114 <DT><A HREF="../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;ClustalW&gt;)</B></A> - \r
 115 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 116 <DD>&nbsp;\r
 117 <DT><A HREF="../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Mafft&gt;)</B></A> - \r
 118 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 119 <DD>&nbsp;\r
 120 <DT><A HREF="../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Muscle&gt;)</B></A> - \r
 121 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 122 <DD>&nbsp;\r
 123 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Probcons&gt;)</B></A> - \r
 124 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 125 <DD>&nbsp;\r
 126 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Tcoffee&gt;)</B></A> - \r
 127 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 128 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#PresetAlignResponse()"><B>PresetAlignResponse()</B></A> - \r
 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>\r
 131 <DD>&nbsp;\r
 132 <DT><A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A>&lt;<A HREF="../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt; - 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> - \r
 133 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 134 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/runner/msa/Probcons.html#Probcons()"><B>Probcons()</B></A> - \r
 136 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
 137 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/ws/server/ProbconsWS.html#ProbconsWS()"><B>ProbconsWS()</B></A> - \r
 139 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 140 <DD>&nbsp;\r
 141 <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE"><B>PROC_ERR_FILE</B></A> - \r
 142 Static variable in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
 143 <DD>&nbsp;\r
 144 <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE"><B>PROC_OUT_FILE</B></A> - \r
 145 Static variable in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
 146 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/engine/ProgressGetter.html#ProgressGetter()"><B>ProgressGetter()</B></A> - \r
 148 Constructor for class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
 149 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#PropertyHelperManager()"><B>PropertyHelperManager()</B></A> - \r
 151 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
 152 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/PScore.html#PScore()"><B>PScore()</B></A> - \r
 154 Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
 155 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#PSIBlast(java.lang.String)"><B>PSIBlast(String)</B></A> - \r
 157 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 158 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#PsiBlast()"><B>PsiBlast()</B></A> - \r
 160 Constructor for class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
 161 <DD>&nbsp;\r
 162 <DT><A HREF="../compbio/engine/FilePuller.html#pull(long)"><B>pull(long)</B></A> - \r
 163 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 164 <DD>&nbsp;\r
 165 <DT><A HREF="../compbio/engine/ProgressGetter.html#pull(java.lang.String, long)"><B>pull(String, long)</B></A> - \r
 166 Static method in class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
 167 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/engine/PulledFileCache.html#PulledFileCache()"><B>PulledFileCache()</B></A> - \r
 169 Constructor for class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
 170 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#PullExecStatistics()"><B>PullExecStatistics()</B></A> - \r
 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>\r
 173 <DD>&nbsp;\r
 174 <DT><A HREF="../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
 175 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
 176 <DD>Reads 1kb chunk from the statistics file which is specific to a given web
 177  service from the position.\r
 178 <DT><A HREF="../compbio/ws/server/ClustalWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
 179 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 180 <DD>&nbsp;\r
 181 <DT><A HREF="../compbio/ws/server/MafftWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
 182 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 183 <DD>&nbsp;\r
 184 <DT><A HREF="../compbio/ws/server/MuscleWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
 185 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 186 <DD>&nbsp;\r
 187 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
 188 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 189 <DD>&nbsp;\r
 190 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
 191 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 192 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#PullExecStatisticsResponse()"><B>PullExecStatisticsResponse()</B></A> - \r
 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>\r
 195 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#PullFile()"><B>PullFile()</B></A> - \r
 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>\r
 198 <DD>&nbsp;\r
 199 <DT><A HREF="../compbio/ws/server/WSUtil.html#pullFile(java.lang.String, long)"><B>pullFile(String, long)</B></A> - \r
 200 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 201 <DD>&nbsp;\r
 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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html#PullFileResponse()"><B>PullFileResponse()</B></A> - \r
 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>\r
 204 <DD>&nbsp;\r
 205 <DT><A HREF="../compbio/engine/PulledFileCache.html#put(compbio.engine.FilePuller)"><B>put(FilePuller)</B></A> - \r
 206 Static method in class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
 207 <DD>This method allows duplicates to be added.\r
 208 </DL>\r
 209 <HR>\r
 210 \r
 211 \r
 212 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 213 <A NAME="navbar_bottom"><!-- --></A>\r
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 246   if(window==top) {\r
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