DisEMBL and GlobProt web services further work

[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 754cf5f..3990f8f 100644 (file)
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -30,7 +30,6 @@ import java.util.HashSet;
 import java.util.List;\r
 import java.util.Map;\r
 import java.util.Scanner;\r
-import java.util.Set;\r
 import java.util.SortedSet;\r
 import java.util.TreeSet;\r
 import java.util.logging.Level;\r
@@ -365,7 +364,7 @@ public final class SequenceUtil {
                infasta.close();\r
                return seqs;\r
        }\r
-               \r
+\r
        private static float[] convertToNumber(String[] annotValues)\r
                        throws UnknownFileFormatException {\r
                float[] annotation = new float[annotValues.length];\r
@@ -431,7 +430,7 @@ public final class SequenceUtil {
         * @throws IOException\r
         * @throws UnknownFileFormatException\r
         */\r
-       public static Map<FastaSequence, Set<Score>> readDisembl(\r
+       public static HashMap<FastaSequence, HashSet<Score>> readDisembl(\r
                        final InputStream input) throws IOException,\r
                        UnknownFileFormatException {\r
                Scanner scan = new Scanner(input);\r
@@ -443,7 +442,7 @@ public final class SequenceUtil {
                                                        + " No such line was found!");\r
                }\r
 \r
-               Map<FastaSequence, Set<Score>> results = new HashMap<FastaSequence, Set<Score>>();\r
+               HashMap<FastaSequence, HashSet<Score>> results = new HashMap<FastaSequence, HashSet<Score>>();\r
                int seqCounter = 0;\r
                while (scan.hasNext()) {\r
                        seqCounter++;\r
@@ -478,7 +477,7 @@ public final class SequenceUtil {
                        }\r
                        FastaSequence fs = new FastaSequence(sequenceName,\r
                                        seqbuffer.toString());\r
-                       Set<Score> scores = new HashSet<Score>();\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
@@ -486,7 +485,7 @@ public final class SequenceUtil {
 \r
                        scansingle.close();\r
                }\r
-\r
+               scan.close();\r
                input.close();\r
                return results;\r
        }\r
@@ -506,10 +505,12 @@ public final class SequenceUtil {
         */\r
        private static SortedSet<Range> parseRanges(Enum resultType, String lines) {\r
                SortedSet<Range> ranges = new TreeSet<Range>();\r
+\r
                Scanner scan = new Scanner(lines);\r
 \r
                assert scan.hasNext();\r
-               assert "#".equals(scan.next()); // pass delimiter #\r
+               String del = scan.next();\r
+               assert "#".equals(del); // pass delimiter #\r
                String type = scan.next(); // pass enum name e.g. COILS\r
                assert resultType.toString().equalsIgnoreCase(type) : "Unknown result type: "\r
                                + resultType.toString();\r
@@ -525,10 +526,10 @@ public final class SequenceUtil {
                return ranges;\r
        }\r
 \r
-       public static Map<String, Set<Score>> removeSequences(\r
-                       Map<FastaSequence, Set<Score>> disemblResults) {\r
-               Map<String, Set<Score>> seqNameScores = new HashMap<String, Set<Score>>();\r
-               for (Map.Entry<FastaSequence, Set<Score>> dres : disemblResults\r
+       public static HashMap<String, HashSet<Score>> removeSequences(\r
+                       HashMap<FastaSequence, HashSet<Score>> disemblResults) {\r
+               HashMap<String, HashSet<Score>> seqNameScores = new HashMap<String, HashSet<Score>>();\r
+               for (Map.Entry<FastaSequence, HashSet<Score>> dres : disemblResults\r
                                .entrySet()) {\r
                        seqNameScores.put(dres.getKey().getId(), dres.getValue());\r
                }\r
@@ -559,7 +560,7 @@ public final class SequenceUtil {
         * @throws IOException\r
         * @throws UnknownFileFormatException\r
         */\r
-       public static Map<FastaSequence, Set<Score>> readGlobPlot(\r
+       public static HashMap<FastaSequence, HashSet<Score>> readGlobPlot(\r
                        final InputStream input) throws IOException,\r
                        UnknownFileFormatException {\r
                Scanner scan = new Scanner(input);\r
@@ -571,7 +572,7 @@ public final class SequenceUtil {
                                                        + " No such line was found!");\r
                }\r
 \r
-               Map<FastaSequence, Set<Score>> results = new HashMap<FastaSequence, Set<Score>>();\r
+               HashMap<FastaSequence, HashSet<Score>> results = new HashMap<FastaSequence, HashSet<Score>>();\r
                int seqCounter = 0;\r
                while (scan.hasNext()) {\r
                        seqCounter++;\r
@@ -604,7 +605,7 @@ public final class SequenceUtil {
                        }\r
                        FastaSequence fs = new FastaSequence(sequenceName,\r
                                        seqbuffer.toString());\r
-                       Set<Score> scores = new HashSet<Score>();\r
+                       HashSet<Score> scores = new HashSet<Score>();\r
                        scores.add(new Score(GlobProtResult.Disorder, disorderR));\r
                        scores.add(new Score(GlobProtResult.GlobDoms, domsR));\r
                        scores.add(new Score(GlobProtResult.Dydx, dydxScore));\r
@@ -614,7 +615,7 @@ public final class SequenceUtil {
 \r
                        scansingle.close();\r
                }\r
-\r
+               scan.close();\r
                input.close();\r
                return results;\r
        }\r