- addParameters(Arrays.asList("-output=clustalw"));\r
- setInput(super.inputFile);\r
- }\r
-\r
- @Override\r
- public Tcoffee setInput(String inFile) {\r
- super.setInput(inFile);\r
- cbuilder.setParam("-seq", inFile);\r
- return this;\r
- }\r
-\r
- @SuppressWarnings("unchecked")\r
- @Override\r
- public Alignment getResults(String workDirectory)\r
- throws ResultNotAvailableException {\r
- try {\r
- return Util.readClustalFile(workDirectory, getOutput());\r
- } catch (FileNotFoundException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (IOException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (UnknownFileFormatException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (NullPointerException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- }\r
- }\r