Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 20c44bc..6af0cdf 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -140,8 +140,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @return true if features were added
    */
   public boolean parse(AlignmentI align,
-          Map<String, FeatureColourI> colours,
-          boolean removeHTML)
+          Map<String, FeatureColourI> colours, boolean removeHTML)
   {
     return parse(align, colours, removeHTML, false);
   }
@@ -178,8 +177,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @return true if features were added
    */
   public boolean parse(AlignmentI align,
-          Map<String, FeatureColourI> colours,
-          boolean removeHTML, boolean relaxedIdmatching)
+          Map<String, FeatureColourI> colours, boolean removeHTML,
+          boolean relaxedIdmatching)
   {
     Map<String, String> gffProps = new HashMap<String, String>();
     /*
@@ -589,7 +588,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         {
           for (SequenceFeature sequenceFeature : features)
           {
-            isnonpos = sequenceFeature.begin == 0 && sequenceFeature.end == 0;
+            isnonpos = sequenceFeature.begin == 0
+                    && sequenceFeature.end == 0;
             if ((!nonpos && isnonpos)
                     || (!isnonpos && visOnly && !visible
                             .containsKey(sequenceFeature.type)))
@@ -712,7 +712,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       dataset = new Alignment(new SequenceI[] {});
     }
 
-    boolean parseResult = parse(dataset, null, false, true);
+    Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
+    boolean parseResult = parse(dataset, featureColours, false, true);
     if (!parseResult)
     {
       // pass error up somehow