X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColour.java;h=62b457998deb64e37adb48977153cdfeb38e2544;hb=refs%2Fheads%2Fpatch%2FJAL-4110_stdout_for_tests;hp=dbc9c03dd6ac5b3ab9c265f915eaa1997a45a1e7;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index dbc9c03..62b4579 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -45,7 +46,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * Maps sequence positions to the RNA helix they belong to. Key: position,
    * Value: helix TODO: Revise or drop in favour of annotation position numbers
    */
-  public Hashtable<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
+  public Hashtable<Integer, String> positionsToHelix = new Hashtable<>();
 
   /**
    * Number of helices in the RNA secondary structure
@@ -132,7 +133,7 @@ public class RNAHelicesColour extends ResidueColourScheme
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();
       numHelix = 0;
-      positionsToHelix = new Hashtable<Integer, String>();
+      positionsToHelix = new Hashtable<>();
 
       // Figure out number of helices
       // Length of rnasecstr is the number of pairs of positions that base pair
@@ -141,10 +142,10 @@ public class RNAHelicesColour extends ResidueColourScheme
       {
 
         /*
-         * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+         * jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
          * this.annotation._rnasecstr[x].getBegin());
          */
-        // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+        // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
 
         positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
                 this.annotation._rnasecstr[x].getFeatureGroup());
@@ -206,8 +207,8 @@ public class RNAHelicesColour extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg)
   {
     return new RNAHelicesColour(sg);
   }