X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=aedb15790680f89c891aa79e49da177313936e54;hb=2303177fbc4c86e4a63c1e8efa8c8bc50516b6a5;hp=3ab681cc18b8ac9fab1565ddc9d539e20b3c7cec;hpb=69bab27e77ceaca6d12e0de49f8fc62e01678f53;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 3ab681c..aedb157 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -492,25 +492,67 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     gg.setColor(Color.black);
 
     int scalestartx = (startx / 10) * 10;
+
+    SequenceI refSeq = av.getAlignment().getSeqrep();
+    int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
+    if (refSeq != null)
+    {
+      // find bounds and set origin appopriately
+      // locate first visible position for this sequence
+      int[] refbounds = av.getColumnSelection()
+              .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;
+    }
+
+
     int widthx = 1 + endx - startx;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
     int y = avCharHeight - fm.getDescent();
 
-    if ((scalestartx % 10) == 0)
+    if (refSeq == null && scalestartx % 10 == 0)
     {
       scalestartx += 5;
     }
 
     String string;
-    int maxX = 0;
-
+    int maxX = 0, refN, iadj;
+    // todo: add a 'reference origin column' to set column number relative to
     for (int i = scalestartx; i < endx; i += 5)
     {
-      if ((i % 10) == 0)
+      if (((i - refSp) % 10) == 0)
       {
-        string = String.valueOf(av.getColumnSelection()
-                .adjustForHiddenColumns(i));
+        iadj = av.getColumnSelection().adjustForHiddenColumns(i) - 1;
+        if (refSeq == null)
+        {
+          string = String.valueOf(iadj + 1);
+        }
+        else
+        {
+          refN = refSeq.findPosition(iadj);
+          // TODO show bounds if position is a gap
+          // - ie L--R -> "1L|2R" for
+          // marker
+          if (iadj < refStartI)
+          {
+            string = String.valueOf(iadj - refStartI);
+          }
+          else if (iadj > refEndI)
+          {
+            string = "+" + String.valueOf(iadj - refEndI);
+          }
+          else
+          {
+            string = String.valueOf(refN) + refSeq.getCharAt(iadj);
+          }
+        }
         if ((i - startx - 1) * avCharWidth > maxX)
         {
           gg.drawString(string, (i - startx - 1) * avCharWidth, y);