import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.metadata.JobSubmissionException;\r
- if (service == Services.AAConWS) {\r
- Map<String, HashSet<Score>> result = analize(inputFile,\r
+ if (service.getServiceType() == SequenceAnnotation.class) {\r
+ ScoreManager result = analize(inputFile,\r
IOHelper.writeOut(outStream, result);\r
} else {\r
alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
customOptions);\r
IOHelper.writeOut(outStream, alignment);\r
}\r
IOHelper.writeOut(outStream, result);\r
} else {\r
alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
customOptions);\r
IOHelper.writeOut(outStream, alignment);\r
}\r
- <T> Map<String, HashSet<Score>> analize(File file,\r
- SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
- List<Option<T>> customOptions) {\r
+ <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,\r
+ Preset<T> preset, List<Option<T>> customOptions) {\r
} else if (preset != null) {\r
jobId = wsproxy.presetAnalize(fastalist, preset);\r
} else {\r
} else if (preset != null) {\r
jobId = wsproxy.presetAnalize(fastalist, preset);\r
} else {\r