X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FAlignment.html;h=ac64d26e8881561a79859560d03d2c0462c0b992;hb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;hp=af197d7c6b66c85d9f09086ffd7d0cac604a3c89;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html index af197d7..ac64d26 100644 --- a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html +++ b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html @@ -2,12 +2,12 @@ - + Uses of Class compbio.data.sequence.Alignment - + @@ -91,7 +91,7 @@ Packages that use compbio.data.msa -   +Web Service interfaces for JAva Bioinformatics Analysis Web Services.  compbio.data.msa.jaxws @@ -99,8 +99,8 @@ Packages that use compbio.data.sequence -A data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project.  +A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.  compbio.runner @@ -134,7 +134,7 @@ Uses of  Alignment -MsaWS.getResult(java.lang.String jobId) +MsaWS.getResult(String jobId)
          Return the result of the job. @@ -200,7 +200,7 @@ Uses of static Alignment -ClustalAlignmentUtil.readClustalFile(java.io.File file) +ClustalAlignmentUtil.readClustalFile(File file)
            @@ -208,7 +208,7 @@ Uses of static Alignment -ClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) +ClustalAlignmentUtil.readClustalFile(InputStream instream)
          Read Clustal formatted alignment. @@ -224,7 +224,7 @@ Uses of static void -ClustalAlignmentUtil.writeClustalAlignment(java.io.OutputStream outStream, +ClustalAlignmentUtil.writeClustalAlignment(Writer out, Alignment alignment)
@@ -251,8 +251,8 @@ Uses of static Alignment -Util.readClustalFile(java.lang.String workDirectory, - java.lang.String clustFile) +Util.readClustalFile(String workDirectory, + String clustFile)
            @@ -277,7 +277,7 @@ Uses of  Alignment -Tcoffee.getResults(java.lang.String workDirectory) +Mafft.getResults(String workDirectory)
            @@ -285,7 +285,7 @@ Uses of  Alignment -ClustalW.getResults(java.lang.String workDirectory) +ClustalW.getResults(String workDirectory)
            @@ -293,7 +293,7 @@ Uses of  Alignment -Probcons.getResults(java.lang.String workDirectory) +Tcoffee.getResults(String workDirectory)
            @@ -301,7 +301,7 @@ Uses of  Alignment -Muscle.getResults(java.lang.String workDirectory) +Muscle.getResults(String workDirectory)
            @@ -309,7 +309,15 @@ Uses of  Alignment -Mafft.getResults(java.lang.String workDirectory) +ClustalO.getResults(String workDirectory) + +
+            + + + + Alignment +Probcons.getResults(String workDirectory)
            @@ -334,7 +342,23 @@ Uses of  Alignment -TcoffeeWS.getResult(java.lang.String jobId) +ClustalWS.getResult(String jobId) + +
+            + + + + Alignment +_MsaService.getResult(String jobId) + +
+            + + + + Alignment +MuscleWS.getResult(String jobId)
            @@ -342,7 +366,7 @@ Uses of  Alignment -ProbconsWS.getResult(java.lang.String jobId) +MafftWS.getResult(String jobId)
            @@ -350,7 +374,7 @@ Uses of  Alignment -MuscleWS.getResult(java.lang.String jobId) +TcoffeeWS.getResult(String jobId)
            @@ -358,7 +382,7 @@ Uses of  Alignment -MafftWS.getResult(java.lang.String jobId) +ProbconsWS.getResult(String jobId)
            @@ -366,7 +390,7 @@ Uses of  Alignment -ClustalWS.getResult(java.lang.String jobId) +ClustalOWS.getResult(String jobId)