JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 55138e7..6828202 100755 (executable)
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -59,7 +59,7 @@ public class JnetAnnotationMaker
     // in the future we could search for the query
     // sequence in the alignment before calling this function.
     SequenceI seqRef = al.getSequenceAt(firstSeq);
-    int width = preds[0].getSequence().length;
+    int width = preds[0].getLength();
     int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
     if ((delMap != null && delMap.length > width)
             || (delMap == null && gapmap.length != width))
@@ -148,7 +148,7 @@ public class JnetAnnotationMaker
             {
               for (int j = 0; j < width; j++)
               {
-                float value = new Float(preds[i].getCharAt(j) + "")
+                float value = Float.valueOf(preds[i].getCharAt(j) + "")
                         .floatValue();
                 annotations[gapmap[j]] = new Annotation(
                         preds[i].getCharAt(j) + "", "",
@@ -159,7 +159,7 @@ public class JnetAnnotationMaker
             {
               for (int j = 0; j < width; j++)
               {
-                float value = new Float(preds[i].getCharAt(j) + "")
+                float value = Float.valueOf(preds[i].getCharAt(j) + "")
                         .floatValue();
                 annotations[gapmap[delMap[j]]] = new Annotation(
                         preds[i].getCharAt(j) + "", "",