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82 <A NAME="_M_"><!-- --></A><H2>
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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> <DT><A HREF="../compbio/runner/msa/Mafft.html#Mafft()"><B>Mafft()</B></A> -
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86 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>
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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> <DT><A HREF="../compbio/ws/server/MafftWS.html#MafftWS()"><B>MafftWS()</B></A> -
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89 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>
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91 <DT><A HREF="../compbio/engine/cluster/drmaa/_DrmaaExample.html#main(java.lang.String[])"><B>main(String[])</B></A> -
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92 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/_DrmaaExample.html" title="class in compbio.engine.cluster.drmaa">_DrmaaExample</A>
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94 <DT><A HREF="../compbio/engine/cluster/drmaa/_JobStatus.html#main(java.lang.String[])"><B>main(String[])</B></A> -
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95 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/_JobStatus.html" title="class in compbio.engine.cluster.drmaa">_JobStatus</A>
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97 <DT><A HREF="../compbio/pipeline/_jpred/BlastParser.html#main(java.lang.String[])"><B>main(String[])</B></A> -
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98 Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A>
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99 <DD>args[0] is assumed to be the name of a Blast output file
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100 <DT><A HREF="../compbio/pipeline/_jpred/Pairwise.html#main(java.lang.String[])"><B>main(String[])</B></A> -
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101 Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A>
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103 <DT><A HREF="../compbio/runner/_impl/OB.html#main(java.lang.String[])"><B>main(String[])</B></A> -
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104 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>
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106 <DT><A HREF="../compbio/ws/client/Jws2Client.html#main(java.lang.String[])"><B>main(String[])</B></A> -
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107 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>
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108 <DD>Starts command line client, if no parameter are supported print help.
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109 <DT><A HREF="../compbio/ws/client/WSTester.html#main(java.lang.String[])"><B>main(String[])</B></A> -
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110 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>
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111 <DD>Test JWS2 web services
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112 <DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html#main(java.lang.String[])"><B>main(String[])</B></A> -
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113 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>
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115 <DT><A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html#MAX_MEMORY_LIMIT"><B>MAX_MEMORY_LIMIT</B></A> -
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116 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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118 <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> <DT><A HREF="../compbio/runner/_impl/Mcl.html#Mcl(java.lang.String)"><B>Mcl(String)</B></A> -
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119 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>
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121 <DT><A HREF="../compbio/engine/client/Util.html#mergeEnvVariables(java.util.Map, java.util.Map)"><B>mergeEnvVariables(Map<String, String>, Map<String, String>)</B></A> -
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122 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>
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124 <DT><A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><<A HREF="../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> - 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> <DT><A HREF="../compbio/runner/msa/Muscle.html#Muscle()"><B>Muscle()</B></A> -
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125 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>
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126 <DD>Default options are
128 -clwstrict - write output in clustal format
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129 <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> <DT><A HREF="../compbio/ws/server/MuscleWS.html#MuscleWS()"><B>MuscleWS()</B></A> -
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130 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>
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