Merge branch 'bug/JAL-3141_backupfiles_prefs_widget_disable_bug' into merge/develop_b...

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 00476d6..86b4402 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -274,7 +274,7 @@ public class AnnotationFile
           if (row.graphGroup > -1)
           {
             graphGroupSeen.set(row.graphGroup);
-            Integer key = new Integer(row.graphGroup);
+            Integer key = Integer.valueOf(row.graphGroup);
             if (graphGroup.containsKey(key))
             {
               graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
@@ -762,7 +762,7 @@ public class AnnotationFile
                       autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
                               (aa[aai].groupRef == null ? null
                                       : aa[aai].groupRef.getName())),
-                      new Integer(1));
+                      Integer.valueOf(1));
             }
           }
         }
@@ -968,7 +968,7 @@ public class AnnotationFile
             else
             {
               // consider deferring this till after the file has been parsed ?
-              hidden.hideInsertionsFor(sr);
+              hidden.hideList(sr.getInsertions());
             }
           }
           modified = true;
@@ -1271,7 +1271,7 @@ public class AnnotationFile
         {
           displayChar = token;
           // foo
-          value = new Float(token).floatValue();
+          value = Float.valueOf(token).floatValue();
           parsedValue = true;
           continue;
         } catch (NumberFormatException ex)
@@ -1617,8 +1617,10 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("colour"))
         {
+          // TODO need to notify colourscheme of view reference once it is
+          // available
           sg.cs.setColourScheme(
-                  ColourSchemeProperty.getColourScheme(al, value));
+                  ColourSchemeProperty.getColourScheme(null, al, value));
         }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {