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| -Packages that use Alignment | -|
|---|---|
| compbio.data.msa | -Web Service interfaces for JAva Bioinformatics Analysis Web Services. | -
| compbio.data.msa.jaxws | -- |
| compbio.data.sequence | -A data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. | -
| compbio.runner | -Utilities commonly used by all runners. | -
| compbio.runner.msa | -Wrappers for native executables for multiple sequence alignment (msa) | -
| compbio.ws.server | -- |
| -Uses of Alignment in compbio.data.msa | -
|---|
- -
| Methods in compbio.data.msa that return Alignment | -|
|---|---|
- Alignment |
-MsaWS.getResult(String jobId)
-
-- Return the result of the job. |
-
| -Uses of Alignment in compbio.data.msa.jaxws | -
|---|
- -
| Methods in compbio.data.msa.jaxws that return Alignment | -|
|---|---|
- Alignment |
-GetResultResponse.getReturn()
-
-- |
-
- -
| Methods in compbio.data.msa.jaxws with parameters of type Alignment | -|
|---|---|
- void |
-GetResultResponse.setReturn(Alignment _return)
-
-- |
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| -Uses of Alignment in compbio.data.sequence | -
|---|
- -
| Methods in compbio.data.sequence that return Alignment | -|
|---|---|
-static Alignment |
-ClustalAlignmentUtil.readClustalFile(File file)
-
-- |
-
-static Alignment |
-ClustalAlignmentUtil.readClustalFile(InputStream instream)
-
-- Read Clustal formatted alignment. |
-
- -
| Methods in compbio.data.sequence with parameters of type Alignment | -|
|---|---|
-static void |
-ClustalAlignmentUtil.writeClustalAlignment(Writer out,
- Alignment alignment)
-
-- Write Clustal formatted alignment Limitations: does not record the - consensus. |
-
| -Uses of Alignment in compbio.runner | -
|---|
- -
| Methods in compbio.runner that return Alignment | -|
|---|---|
-static Alignment |
-Util.readClustalFile(String workDirectory,
- String clustFile)
-
-- |
-
| -Uses of Alignment in compbio.runner.msa | -
|---|
- -
| Methods in compbio.runner.msa that return Alignment | -|
|---|---|
- Alignment |
-Mafft.getResults(String workDirectory)
-
-- |
-
- Alignment |
-ClustalW.getResults(String workDirectory)
-
-- |
-
- Alignment |
-Tcoffee.getResults(String workDirectory)
-
-- |
-
- Alignment |
-Muscle.getResults(String workDirectory)
-
-- |
-
- Alignment |
-ClustalO.getResults(String workDirectory)
-
-- |
-
- Alignment |
-Probcons.getResults(String workDirectory)
-
-- |
-
| -Uses of Alignment in compbio.ws.server | -
|---|
- -
| Methods in compbio.ws.server that return Alignment | -|
|---|---|
- Alignment |
-ClustalWS.getResult(String jobId)
-
-- |
-
- Alignment |
-_MsaService.getResult(String jobId)
-
-- |
-
- Alignment |
-MuscleWS.getResult(String jobId)
-
-- |
-
- Alignment |
-MafftWS.getResult(String jobId)
-
-- |
-
- Alignment |
-TcoffeeWS.getResult(String jobId)
-
-- |
-
- Alignment |
-ProbconsWS.getResult(String jobId)
-
-- |
-
- Alignment |
-ClustalOWS.getResult(String jobId)
-
-- |
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