JAL-2110 JAL-2131 JAL-1765 remove reference to jalview.datamodel.Alignment from Align...

[jalview.git] / src / jalview / renderer / ScaleRenderer.java

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index d91ea74..7f1e074 100644 (file)
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -37,6 +37,11 @@ public class ScaleRenderer
   /**
    * calculate positions markers on the alignment ruler
    * 
+   * @param av
+   * @param startx
+   *          left-most column in visible view
+   * @param endx
+   *          - right-most column in visible view
    * @return List { Object { .. } } Boolean: true/false for major/minor mark,
    *         Integer: marker position in alignment column coords, String: null
    *         or a String to be rendered at the position.
@@ -49,7 +54,7 @@ public class ScaleRenderer
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
+    int refSp = 0, refStartI = 0, refEndI = -1;
     if (refSeq != null)
     {
       // find bounds and set origin appopriately
@@ -58,9 +63,6 @@ public class ScaleRenderer
               .locateVisibleBoundsOfSequence(refSeq);
 
       refSp = refbounds[0];
-      refEp = refbounds[1];
-      refStart = refbounds[2];
-      refEnd = refbounds[3];
       refStartI = refbounds[4];
       refEndI = refbounds[5];
       scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
@@ -72,7 +74,7 @@ public class ScaleRenderer
     }
     List<Object[]> marks = new ArrayList<Object[]>();
     String string;
-    int maxX = 0, refN, iadj;
+    int refN, iadj;
     // todo: add a 'reference origin column' to set column number relative to
     for (int i = scalestartx; i < endx; i += 5)
     {