import java.net.MalformedURLException;\r
import java.net.URL;\r
import java.util.Arrays;\r
+import java.util.HashSet;\r
import java.util.List;\r
-import java.util.Set;\r
+import java.util.Map;\r
import java.util.logging.Level;\r
import java.util.logging.Logger;\r
\r
import javax.xml.ws.Service;\r
import javax.xml.ws.WebServiceException;\r
\r
-import compbio.data.msa.Annotation;\r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.Metadata;\r
import compbio.data.msa.MsaWS;\r
+import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.data.sequence.Score;\r
outStream = System.out;\r
}\r
if (service == Services.AAConWS) {\r
- Set<Score> result = analize(inputFile, ((Annotation<T>) msaws),\r
- preset, customOptions);\r
+ Map<String, HashSet<Score>> result = analize(inputFile,\r
+ ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
IOHelper.writeOut(outStream, result);\r
} else {\r
alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
* @return Set<Score> the conservation scores\r
* @throws UnknownFileFormatException\r
*/\r
- <T> Set<Score> analize(File file, Annotation<T> wsproxy, Preset<T> preset,\r
+ <T> Map<String, HashSet<Score>> analize(File file,\r
+ SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
List<Option<T>> customOptions) {\r
\r
List<FastaSequence> fastalist = null;\r
- Set<Score> scores = null;\r
+ Map<String, HashSet<Score>> scores = null;\r
try {\r
fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
\r