X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FAAConClient.java;h=4619c602dd08b91d1f216bf9c5cd95d6f03f859a;hb=9d860c3793c6812f643caa01fc80a0036fa3fe2b;hp=57cf59f5019773ea41bbd41a8edc32717438f8a3;hpb=7e625752237ee07e815bfb28048bb0b1193b45c5;p=jabaws.git

diff --git a/webservices/compbio/ws/client/AAConClient.java b/webservices/compbio/ws/client/AAConClient.java
index 57cf59f..4619c60 100644
--- a/webservices/compbio/ws/client/AAConClient.java
+++ b/webservices/compbio/ws/client/AAConClient.java
@@ -33,10 +33,7 @@ import java.io.IOException;
 import java.io.OutputStream;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
-import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -46,7 +43,7 @@ import javax.xml.ws.WebServiceException;
 
 import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
 import compbio.metadata.JobSubmissionException;
@@ -115,7 +112,7 @@ public class AAConClient {
 			customOptions = MetadataHelper.processParameters(prms,
 					msaws.getRunnerOptions());
 		}
-		Map<String, HashSet<Score>> result = null;
+		ScoreManager result = null;
 		if (inputFile != null) {
 			System.out.println("Calculating conservation...");
 			result = analize(inputFile, msaws, preset, customOptions);
@@ -155,14 +152,9 @@ public class AAConClient {
 	 * @param result
 	 *            the AACon scores to output
 	 */
-	static void writeOut(OutputStream outStream,
-			Map<String, HashSet<Score>> result) {
+	static void writeOut(OutputStream outStream, ScoreManager result) {
 		try {
-			for (Map.Entry<String, ? extends Set<Score>> entry : result
-					.entrySet()) {
-				System.out.println(">" + entry.getKey());
-				Score.write(entry.getValue(), outStream);
-			}
+			result.writeOut(outStream);
 		} catch (IOException e) {
 			System.err
 					.println("Problems writing output file! Stack trace is below: ");
@@ -222,12 +214,11 @@ public class AAConClient {
 	 * @return Set<Score> the conservation scores
 	 * @throws UnknownFileFormatException
 	 */
-	static Map<String, HashSet<Score>> analize(File file,
-			SequenceAnnotation<AAConWS> wsproxy, Preset<AAConWS> preset,
-			List<Option<AAConWS>> customOptions) {
+	static ScoreManager analize(File file, SequenceAnnotation<AAConWS> wsproxy,
+			Preset<AAConWS> preset, List<Option<AAConWS>> customOptions) {
 
 		List<FastaSequence> fastalist = null;
-		Map<String, HashSet<Score>> scores = null;
+		ScoreManager scores = null;
 		try {
 			fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());