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  82 <A NAME="_M_"><!-- --></A><H2>\r
  83 <B>M</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>Mafft</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Mafft.html#Mafft()"><B>Mafft()</B></A> - \r
  86 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>MafftWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/MafftWS.html#MafftWS()"><B>MafftWS()</B></A> - \r
  89 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/pipeline/_jpred/BlastBlastComparator.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
  92 Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/BlastBlastComparator.html" title="class in compbio.pipeline._jpred">BlastBlastComparator</A>\r
  93 <DD>args[0] is assumed to be the name of a Blast output file\r
  94 <DT><A HREF="../compbio/pipeline/_jpred/BlastHmmerComparator.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
  95 Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/BlastHmmerComparator.html" title="class in compbio.pipeline._jpred">BlastHmmerComparator</A>\r
  96 <DD>args[0] is assumed to be the name of a Blast output file\r
  97 <DT><A HREF="../compbio/pipeline/_jpred/BlastParser.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
  98 Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A>\r
  99 <DD>args[0] is assumed to be the name of a Blast output file\r
 100 <DT><A HREF="../compbio/pipeline/_jpred/JackHmmerHitParser.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
 101 Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred">JackHmmerHitParser</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/pipeline/_jpred/Pairwise.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
 104 Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/runner/_impl/OB.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
 107 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
 108 <DD>&nbsp;\r
 109 <DT><A HREF="../compbio/stat/collector/ExecutionStatCollector.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
 110 Static method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</A>\r
 111 <DD>Not in use\r
 112 <DT><A HREF="../compbio/stat/collector/StatDB.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
 113 Static method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/ws/client/AAConClient.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
 116 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</A>\r
 117 <DD>Starts command line client, if no parameters are supplied prints help.\r
 118 <DT><A HREF="../compbio/ws/client/Jws2Client.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
 119 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
 120 <DD>Starts command line client, if no parameter are supported print help.\r
 121 <DT><A HREF="../compbio/ws/client/WSTester.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
 122 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
 123 <DD>Test JWS2 web services\r
 124 <DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
 125 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>\r
 126 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 127 <DT><A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>Mcl</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/Mcl.html#Mcl(java.lang.String)"><B>Mcl(String)</B></A> - \r
 128 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 129 <DD>&nbsp;\r
 130 <DT><A HREF="../compbio/engine/client/Util.html#mergeEnvVariables(java.util.Map, java.util.Map)"><B>mergeEnvVariables(Map&lt;String, String&gt;, Map&lt;String, String&gt;)</B></A> - \r
 131 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 132 <DD>&nbsp;\r
 133 <DT><A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>Metadata</B></A>&lt;<A HREF="../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>&gt; - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>&nbsp;<DT><A HREF="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>MetadataHelper</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>&nbsp;<DT><A HREF="../compbio/ws/client/MetadataHelper.html#MetadataHelper()"><B>MetadataHelper()</B></A> - \r
 134 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</A>\r
 135 <DD>&nbsp;\r
 136 <DT><A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A>&lt;<A HREF="../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt; - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Multiple Sequence Alignment (MSA) Web Services Interface<DT><A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>Muscle</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Muscle.html#Muscle()"><B>Muscle()</B></A> - \r
 137 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
 138 <DD>Default options are
 139
 140  -clwstrict - write output in clustal format\r
 141 <DT><A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><B>MuscleWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/MuscleWS.html#MuscleWS()"><B>MuscleWS()</B></A> - \r
 142 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 143 <DD>&nbsp;\r
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