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  82 <A NAME="_P_"><!-- --></A><H2>\r
  83 <B>P</B></H2>\r
  84 <DL>\r
  85 <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 an 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
  86 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
  87 <DD>&nbsp;\r
  88 <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
  89 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
  90 <DD>&nbsp;\r
  91 <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
  92 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
  93 <DD>&nbsp;\r
  94 <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
  95 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
  96 <DD>Align a list of sequences with preset.\r
  97 <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
  98 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
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws"><B>PresetAnalize</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/PresetAnalize.html#PresetAnalize()"><B>PresetAnalize()</B></A> - \r
 101 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)"><B>presetAnalize(List&lt;FastaSequence&gt;, Preset&lt;T&gt;)</B></A> - \r
 104 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
 105 <DD>Analyse the sequences according to the preset settings.\r
 106 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>PresetAnalizeResponse</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/PresetAnalizeResponse.html#PresetAnalizeResponse()"><B>PresetAnalizeResponse()</B></A> - \r
 107 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>\r
 108 <DD>&nbsp;\r
 109 <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
 110 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 111 <DD>&nbsp;\r
 112 <DT><A HREF="../compbio/ws/client/Services.html#PROBCONS_INFO"><B>PROBCONS_INFO</B></A> - \r
 113 Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
 114 <DD>&nbsp;\r
 115 <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>The list of programmes that can produce alignments<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
 116 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
 117 <DD>&nbsp;\r
 118 <DT><A HREF="../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
 119 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
 120 <DD>Reads 1kb chunk from the statistics file which is specific to a given web
 121  service from the <code>position</code>.\r
 122 <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
 123 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
 124 <DD>&nbsp;\r
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