X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FScaleRenderer.java;h=f3155c71960e2ccb3d27df0207f026cc696ed55c;hb=0c83c631f7d7db0baad3335805c15dd40c0aed59;hp=82536d4f53aed6280fe490e3044f61bb464e3e05;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index 82536d4..f3155c7 100644
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -34,12 +34,24 @@ import java.util.List;
  */
 public class ScaleRenderer
 {
+  /**
+   * Represents one major or minor scale mark
+   */
   public final class ScaleMark
   {
+    /**
+     * true for a major scale mark, false for minor
+     */
     public final boolean major;
 
+    /**
+     * visible column position (0..) e.g. 19
+     */
     public final int column;
 
+    /**
+     * text (if any) to show e.g. "20"
+     */
     public final String text;
 
     ScaleMark(boolean isMajor, int col, String txt)
@@ -68,17 +80,23 @@ public class ScaleRenderer
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = 0, refStartI = 0, refEndI = -1;
+    int refSp = 0;
+    int refStartI = 0;
+    int refEndI = -1;
     if (refSeq != null)
     {
-      // find bounds and set origin appopriately
+      // find bounds and set origin appropriately
       // locate first visible position for this sequence
-      int[] refbounds = av.getColumnSelection()
-              .locateVisibleBoundsOfSequence(refSeq);
+      refSp = av.getAlignment().getHiddenColumns()
+              .locateVisibleStartOfSequence(refSeq);
+
+      refStartI = refSeq.findIndex(refSeq.getStart()) - 1;
+
+      int seqlength = refSeq.getLength();
+      // get sequence position past the end of the sequence
+      int pastEndPos = refSeq.findPosition(seqlength + 1);
+      refEndI = refSeq.findIndex(pastEndPos - 1) - 1;
 
-      refSp = refbounds[0];
-      refStartI = refbounds[4];
-      refEndI = refbounds[5];
       scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
     }
 
@@ -86,7 +104,7 @@ public class ScaleRenderer
     {
       scalestartx += 5;
     }
-    List<ScaleMark> marks = new ArrayList<ScaleMark>();
+    List<ScaleMark> marks = new ArrayList<>();
     String string;
     int refN, iadj;
     // todo: add a 'reference origin column' to set column number relative to
@@ -96,12 +114,14 @@ public class ScaleRenderer
       {
         if (refSeq == null)
         {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
+          iadj = av.getAlignment().getHiddenColumns()
+                  .adjustForHiddenColumns(i - 1) + 1;
           string = String.valueOf(iadj);
         }
         else
         {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
+          iadj = av.getAlignment().getHiddenColumns()
+                  .adjustForHiddenColumns(i - 1);
           refN = refSeq.findPosition(iadj);
           // TODO show bounds if position is a gap
           // - ie L--R -> "1L|2R" for