X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FScaleRenderer.java;h=dc3272ff84decd7d8a0a499230a2850cbe870d58;hb=refs%2Fheads%2Ffeature%2FJAL-3364splitFrameImage;hp=f3155c71960e2ccb3d27df0207f026cc696ed55c;hpb=0c83c631f7d7db0baad3335805c15dd40c0aed59;p=jalview.git

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index f3155c7..dc3272f 100644
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -21,9 +21,11 @@
 package jalview.renderer;
 
 import jalview.api.AlignViewportI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 
 /**
@@ -83,12 +85,16 @@ public class ScaleRenderer
     int refSp = 0;
     int refStartI = 0;
     int refEndI = -1;
+
+    HiddenColumns hc = av.getAlignment().getHiddenColumns();
+
     if (refSeq != null)
     {
       // find bounds and set origin appropriately
-      // locate first visible position for this sequence
-      refSp = av.getAlignment().getHiddenColumns()
-              .locateVisibleStartOfSequence(refSeq);
+      // locate first residue in sequence which is not hidden
+      Iterator<int[]> it = hc.iterator();
+      int index = refSeq.firstResidueOutsideIterator(it);
+      refSp = hc.absoluteToVisibleColumn(index);
 
       refStartI = refSeq.findIndex(refSeq.getStart()) - 1;
 
@@ -108,20 +114,18 @@ public class ScaleRenderer
     String string;
     int refN, iadj;
     // todo: add a 'reference origin column' to set column number relative to
-    for (int i = scalestartx; i < endx; i += 5)
+    for (int i = scalestartx; i <= endx; i += 5)
     {
       if (((i - refSp) % 10) == 0)
       {
         if (refSeq == null)
         {
-          iadj = av.getAlignment().getHiddenColumns()
-                  .adjustForHiddenColumns(i - 1) + 1;
+          iadj = hc.visibleToAbsoluteColumn(i - 1) + 1;
           string = String.valueOf(iadj);
         }
         else
         {
-          iadj = av.getAlignment().getHiddenColumns()
-                  .adjustForHiddenColumns(i - 1);
+          iadj = hc.visibleToAbsoluteColumn(i - 1);
           refN = refSeq.findPosition(iadj);
           // TODO show bounds if position is a gap
           // - ie L--R -> "1L|2R" for