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Make muscle executable compilation not static to fix problem on Macs
[jabaws.git] / website / dm_javadoc / index-files / index-6.html
diff --git a/website/dm_javadoc/index-files/index-6.html b/website/dm_javadoc/index-files/index-6.html
index 014bc6b..38104ad 100644 (file)
--- a/website/dm_javadoc/index-files/index-6.html
+++ b/website/dm_javadoc/index-files/index-6.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Thu Nov 18 15:38:37 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_21) on Tue Dec 21 18:32:59 GMT 2010 -->\r
 <TITLE>\r
 G-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-11-18">\r
+<META NAME="date" CONTENT="2010-12-21">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -88,6 +88,15 @@ Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence
 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/Annotation.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A>\r
+<DD>Return the result of the job.\r
+<DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html#getAnnotation()"><B>getAnnotation()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#getAnnotations()"><B>getAnnotations()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><B>getArgument(String)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 <DD>Returns the argument by its name if found, NULL otherwise.\r
@@ -143,26 +152,23 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title
 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getGapchar()"><B>getGapchar()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#getHost(java.lang.String[])"><B>getHost(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Extracts host name from the command line\r
 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getId()"><B>getId()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 <DD>Gets the value of id\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
 <DD>Return the status of the job.\r
 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getLength()"><B>getLength()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 <DD>Get a Limit for a preset.\r
 <DT><A HREF="../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)"><B>getLimitByName(String)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getLimits()"><B>getLimits()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 <DD>List Limits supported by a web service.\r
 <DT><A HREF="../compbio/metadata/LimitsManager.html#getLimits()"><B>getLimits()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
@@ -173,6 +179,12 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.htm
 <DT><A HREF="../compbio/data/sequence/Alignment.html#getMetadata()"><B>getMetadata()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ConservationMethod.html#getMethod(java.lang.String)"><B>getMethod(String)</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Score.html#getMethod()"><B>getMethod()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>Returns the ConservationMethod\r
 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getMin()"><B>getMin()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 <DD>&nbsp;\r
@@ -224,8 +236,8 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title=
 <DT><A HREF="../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)"><B>getPresetByName(String)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getPresets()"><B>getPresets()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 <DD>Get presets supported by a web service\r
 <DT><A HREF="../compbio/metadata/PresetManager.html#getPresets()"><B>getPresets()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
@@ -245,9 +257,12 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 <DD>Get options supported by a web service\r
+<DT><A HREF="../compbio/data/sequence/Score.html#getScores()"><B>getScores()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>The column scores for the alignment\r
 <DT><A HREF="../compbio/metadata/Limit.html#getSeqNumber()"><B>getSeqNumber()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 <DD>&nbsp;\r
@@ -266,15 +281,12 @@ Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignmen
 <DT><A HREF="../compbio/ws/client/Services.html#getService(java.lang.String)"><B>getService(String)</B></A> - \r
 Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Services.html#getService(java.lang.Class)"><B>getService(Class)</B></A> - \r
-Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#getServiceName(java.lang.String[])"><B>getServiceName(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Extracts service name from the command line\r
 <DT><A HREF="../compbio/data/sequence/Alignment.html#getSize()"><B>getSize()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#getSMERFSColumnScore(java.lang.String)"><B>getSMERFSColumnScore(String)</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getType()"><B>getType()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 <DD>&nbsp;\r