getSelectionAsNewSequence added

[jalview.git] / src / jalview / io / JnetAnnotationMaker.java

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 9a397d7..60c0a68 100755 (executable)
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -22,6 +22,8 @@ public class JnetAnnotationMaker
   {\r
     int i = 0;\r
     SequenceI[] preds = prediction.getSeqsAsArray();\r
+    // in the future we could search for the query\r
+    // sequence in the alignment before calling this function.\r
     SequenceI seqRef = al.getSequenceAt(FirstSeq);\r
     int width = preds[0].getSequence().length();\r
     int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
@@ -61,8 +63,8 @@ public class JnetAnnotationMaker
         {\r
           for (int j = 0; j < width; j++)\r
           {\r
-            float value = Float.parseFloat(preds[i].getCharAt(\r
-                j) + "");\r
+            float value = new Float(preds[i].getCharAt(\r
+                j) + "").floatValue();\r
             annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
                 j) + "", "", preds[i].getCharAt(j),\r
                 value);\r