import java.io.ByteArrayInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
+import java.util.HashSet;\r
import java.util.List;\r
-import java.util.Set;\r
+import java.util.Map;\r
\r
-import compbio.data.msa.Annotation;\r
+import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.data.sequence.Score;\r
import compbio.data.sequence.SequenceUtil;\r
/*\r
* Annotation interface for AAConWS web service instance\r
*/\r
- Annotation<AACon> client = (Annotation<AACon>) Jws2Client.connect(\r
- "http://www.compbio.dundee.ac.uk/aacon", Services.AAConWS);\r
+ SequenceAnnotation<AACon> client = (SequenceAnnotation<AACon>) Jws2Client\r
+ .connect("http://www.compbio.dundee.ac.uk/aacon",\r
+ Services.AAConWS);\r
\r
/* Get the list of available presets */\r
PresetManager presetman = client.getPresets();\r
String jobId = client.presetAnalize(fastalist, preset);\r
\r
/* This method will block for the duration of the calculation */\r
- Set<Score> result = client.getAnnotation(jobId);\r
+ Map<String, HashSet<Score>> result = client.getAnnotation(jobId);\r
\r
/*\r
* This is a better way of obtaining results, it does not involve\r
// }\r
\r
/* Output the alignment to standard out */\r
- Score.write(result, System.out);\r
+ IOHelper.writeOut(System.out, result);\r
+ // Score.write(result, System.out);\r
\r
/* Alternatively, you can record retrieved alignment into the file */\r
// FileOutputStream out = new FileOutputStream("result.txt");\r