patch fixes JWS-35

[jabaws.git] / datamodel / compbio / data / sequence / SequenceUtil.java

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