AAConWS is working

[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 5946e78..c995585 100644 (file)
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -25,6 +25,7 @@ import java.io.InputStreamReader;
 import java.io.OutputStream;\r
 import java.io.OutputStreamWriter;\r
 import java.util.ArrayList;\r
+import java.util.HashSet;\r
 import java.util.List;\r
 import java.util.Scanner;\r
 import java.util.logging.Level;\r
@@ -458,15 +459,14 @@ public final class SequenceUtil {
         * \r
         * @param results\r
         *            output file of AAConservation\r
-        * @return {@link MultiAnnotatedSequence}\r
+        * @return Map with keys {@link Method} -> float[]\r
         */\r
-       public static MultiAnnotatedSequence<Method> readResults(InputStream results) {\r
+       public static HashSet<Score> readAAConResults(InputStream results) {\r
                if (results == null) {\r
                        throw new NullPointerException(\r
                                        "InputStream with results must be provided");\r
                }\r
-               MultiAnnotatedSequence<Method> annotations = new MultiAnnotatedSequence<Method>(\r
-                               Method.class);\r
+               HashSet<Score> annotations = new HashSet<Score>();\r
                Scanner sc = new Scanner(results);\r
                sc.useDelimiter("#");\r
                while (sc.hasNext()) {\r
@@ -484,7 +484,7 @@ public final class SequenceUtil {
                                Double value = valuesScanner.nextDouble();\r
                                values.add(value.floatValue());\r
                        }\r
-                       annotations.addAnnotation(method, values);\r
+                       annotations.add(new Score(method, values));\r
                }\r
                return annotations;\r
        }\r