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<HTML>\r
<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:04 BST 2011 -->\r
<TITLE>\r
G-Index\r
</TITLE>\r
\r
-<META NAME="date" CONTENT="2010-11-24">\r
+<META NAME="date" CONTENT="2011-08-12">\r
\r
<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
\r
<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar"><B>gapchar</B></A> - \r
Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
<DD>Dash char to be used as gap char in the alignments\r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD> \r
<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> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotation</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#GetAnnotation()"><B>GetAnnotation()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
+<DD>Return the result of the job.\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence(java.lang.String)"><B>getAnnotationForSequence(String)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotationResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#GetAnnotationResponse()"><B>GetAnnotationResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#getArg0()"><B>getArg0()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#getArg0()"><B>getArg0()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#getArg0()"><B>getArg0()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/TestService.html#getArg0()"><B>getArg0()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>\r
+<DD> \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
<DT><A HREF="../compbio/metadata/Preset.html#getDescription()"><B>getDescription()</B></A> - \r
Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/Align.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/Analize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
+<DD> \r
<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)"><B>getFormatedSequence(int)</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>Format sequence per width letter in one string.\r
<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> \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/jaxws/CancelJob.html#getJobId()"><B>getJobId()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#getJobId()"><B>getJobId()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#getJobId()"><B>getJobId()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#getJobId()"><B>getJobId()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getJobId()"><B>getJobId()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatus</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#GetJobStatus()"><B>GetJobStatus()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
+<DD> \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/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatusResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#GetJobStatusResponse()"><B>GetJobStatusResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws"><B>GetLastTested</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#GetLastTested()"><B>GetLastTested()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#getLastTested(compbio.ws.client.Services)"><B>getLastTested(Services)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>Number of seconds since the last test.\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOn</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#GetLastTestedOn()"><B>GetLastTestedOn()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#getLastTestedOn(compbio.ws.client.Services)"><B>getLastTestedOn(Services)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>The date and time the service has been verified to work last time\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOnResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#GetLastTestedOnResponse()"><B>GetLastTestedOnResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#GetLastTestedResponse()"><B>GetLastTestedResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
+<DD> \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> \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/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws"><B>GetLimit</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#GetLimit()"><B>GetLimit()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
+<DD> \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> \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/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#GetLimitResponse()"><B>GetLimitResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><B>GetLimits</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html#GetLimits()"><B>GetLimits()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws">GetLimits</A>\r
+<DD> \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
<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#GetLimitsResponse()"><B>GetLimitsResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
+<DD> \r
<DT><A HREF="../compbio/metadata/ValueConstrain.html#getMax()"><B>getMax()</B></A> - \r
Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
+<DD> \r
<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> \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> \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> \r
<DT><A HREF="../compbio/metadata/ChunkHolder.html#getNextPosition()"><B>getNextPosition()</B></A> - \r
Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
<DD> \r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getNumberOfScores()"><B>getNumberOfScores()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#getNumberOfSeq()"><B>getNumberOfSeq()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD> \r
<DT><A HREF="../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
<DD> \r
<DT><A HREF="../compbio/metadata/Option.html#getOptionNames()"><B>getOptionNames()</B></A> - \r
Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getOptions()"><B>getOptions()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#getOptions()"><B>getOptions()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
+<DD> \r
<DT><A HREF="../compbio/metadata/Preset.html#getOptions()"><B>getOptions()</B></A> - \r
Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
<DD> \r
<DT><A HREF="../compbio/metadata/RunnerConfig.html#getParameters()"><B>getParameters()</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 list of parameters supported executable of type T.\r
+<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getPosition()"><B>getPosition()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
+<DD> \r
<DT><A HREF="../compbio/metadata/Argument.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
<DD> \r
<DT><A HREF="../compbio/metadata/Parameter.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
<DD>List is more convenient to work with\r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getPreset()"><B>getPreset()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#getPreset()"><B>getPreset()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
+<DD> \r
<DT><A HREF="../compbio/metadata/Limit.html#getPreset()"><B>getPreset()</B></A> - \r
Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
<DD> \r
<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> \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/jaxws/GetLimit.html#getPresetName()"><B>getPresetName()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><B>GetPresets</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html#GetPresets()"><B>GetPresets()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws">GetPresets</A>\r
+<DD> \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
<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetPresetsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#GetPresetsResponse()"><B>GetPresetsResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
+<DD> \r
<DT><A HREF="../compbio/metadata/RunnerConfig.html#getPrmSeparator()"><B>getPrmSeparator()</B></A> - \r
Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
<DD> \r
<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getProgram()"><B>getProgram()</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> \r
+<DT><A HREF="../compbio/data/sequence/Score.html#getRanges()"><B>getRanges()</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>Return Ranges if any Collections.EMPTY_SET otherwise\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws"><B>GetResult</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#GetResult()"><B>GetResult()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
+<DD> \r
<DT><A HREF="../compbio/data/msa/MsaWS.html#getResult(java.lang.String)"><B>getResult(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
<DD>Return the result of the job.\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws"><B>GetResultResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#GetResultResponse()"><B>GetResultResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/ws/client/ServicesUtil.html#getRunnerByJobDirectory(java.io.File)"><B>getRunnerByJobDirectory(File)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
+<DD> \r
<DT><A HREF="../compbio/metadata/PresetManager.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
<DD> \r
<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> \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/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptions</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html#GetRunnerOptions()"><B>GetRunnerOptions()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws">GetRunnerOptions</A>\r
+<DD> \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/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptionsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#GetRunnerOptionsResponse()"><B>GetRunnerOptionsResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.Enum)"><B>getScoreByMethod(Enum<?>)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.String)"><B>getScoreByMethod(String)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
+<DD> \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> \r
<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getSequence()"><B>getSequence()</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 sequence\r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD> \r
<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
<DD> \r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD> \r
<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
<DD> \r
<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> \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
+<DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceByJobDirectory(java.io.File)"><B>getServiceByJobDirectory(File)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
+<DD> \r
+<DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceByRunner(java.lang.Class)"><B>getServiceByRunner(Class<Executable<?>>)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
<DD> \r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#getServiceName(java.lang.String[])"><B>getServiceName(String[])</B></A> - \r
+<DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceImpl(compbio.ws.client.Services)"><B>getServiceImpl(Services)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
+<DD> \r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html#getServices(java.lang.String)"><B>getServices(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
+<DD> \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> \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> \r
+<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServices</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html#GetSupportedServices()"><B>GetSupportedServices()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws">GetSupportedServices</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#getSupportedServices()"><B>getSupportedServices()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>List of services that are functioning on the server.\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServicesResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#GetSupportedServicesResponse()"><B>GetSupportedServicesResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
+<DD> \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> \r
git://source.jalview.org / jabaws.git / blobdiff