X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FSequenceUtil.java;h=14dedf4214b4d8dfe4f5e0264b0a31b59ae949d2;hb=94faa6031ae916e4f7f7e61494e36278adcab7e0;hp=16b65f241c43b2b7a31fcd55abfe76ee977609c1;hpb=96ab3a201572c3ed7f9a27682bd0b6ca7edb34c7;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java
index 16b65f2..14dedf4 100644
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -290,7 +290,7 @@ public final class SequenceUtil {
 	 * Read IUPred output
 	 * 
 	 * @param result
-	 * @return
+	 * @return Map key->sequence name, value->Score
 	 * @throws IOException
 	 * @throws UnknownFileFormatException
 	 */
@@ -427,7 +427,7 @@ public final class SequenceUtil {
 	 * 
 	 * @param inStream
 	 *            the InputStream connected to the JRonn output file
-	 * @return List of {@link AnnotatedSequence} objects
+	 * @return Map key=sequence name value=Score
 	 * @throws IOException
 	 *             is thrown if the inStream has problems accessing the data
 	 * @throws UnknownFileFormatException
@@ -533,7 +533,8 @@ public final class SequenceUtil {
 	 * 
 	 * 
 	 * @param input
-	 * @return
+	 *            the InputStream
+	 * @return Map key=sequence name, value=set of score
 	 * @throws IOException
 	 * @throws UnknownFileFormatException
 	 */
@@ -588,8 +589,8 @@ public final class SequenceUtil {
 			 */
 			HashSet<Score> scores = new HashSet<Score>();
 			scores.add(new Score(DisemblResult.COILS, coils, coilsR));
-			scores.add(new Score(DisemblResult.HOTLOOPS, hotloops, rem465R));
-			scores.add(new Score(DisemblResult.REM465, rem, loopsR));
+			scores.add(new Score(DisemblResult.REM465, rem, rem465R));
+			scores.add(new Score(DisemblResult.HOTLOOPS, hotloops, loopsR));
 			results.put(sequenceName, scores);
 
 			scansingle.close();
@@ -655,7 +656,7 @@ public final class SequenceUtil {
 	 * 
 	 * 
 	 * @param input
-	 * @return
+	 * @return Map key=sequence name, value=set of score
 	 * @throws IOException
 	 * @throws UnknownFileFormatException
 	 */