- Map<String, Set<Score>> results= null; \r
- try {\r
- inStream = new FileInputStream(new File(workDirectory,\r
- getOutput()));\r
- results = SequenceUtil.removeSequences(SequenceUtil.readDisembl(inStream));\r
- inStream.close();\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
+ ScoreManager results = null;\r
+\r
+ try {\r
+ inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
+ results = ScoreManager.newInstance(SequenceUtil\r
+ .readDisembl(inStream));\r
+ inStream.close();\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
+ log.trace("DRESULTS: " + results);\r