X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FScaleRenderer.java;h=d92608c2965f48b8f6a788d25e40a0fc22f35faa;hb=971707340a94a5ebf8fd8240700358d8274c31ba;hp=164c7c7edc99020f85c6428945248bcf3e2c17ee;hpb=f38aa05c9798d0dd2ddc70833001c55a3fd5b612;p=jalview.git

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index 164c7c7..d92608c 100644
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -34,12 +34,24 @@ import java.util.List;
  */
 public class ScaleRenderer
 {
-  public class ScaleMark
+  /**
+   * 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)
@@ -48,22 +60,30 @@ public class ScaleRenderer
       column = col;
       text = txt;
     }
+
+    /**
+     * String representation for inspection when debugging only
+     */
+    @Override
+    public String toString()
+    {
+      return String.format("%s:%d:%s", major ? "major" : "minor", column,
+              text);
+    }
   }
 
   /**
-   * calculate positions markers on the alignment ruler
+   * Calculates position markers on the alignment ruler
    * 
    * @param av
    * @param startx
-   *          left-most column in visible view
+   *          left-most column in visible view (0..)
    * @param endx
-   *          - right-most column in visible view
-   * @return List of ScaleMark holding boolean: true/false for major/minor mark,
-   *         marker position in alignment column coords, a String to be rendered
-   *         at the position (or null)
+   *          - right-most column in visible view (0..)
+   * @return
    */
-  public List<ScaleMark> calculateMarks(AlignViewportI av,
-          int startx, int endx)
+  public List<ScaleMark> calculateMarks(AlignViewportI av, int startx,
+          int endx)
   {
     int scalestartx = (startx / 10) * 10;
 
@@ -73,7 +93,7 @@ public class ScaleRenderer
     {
       // find bounds and set origin appopriately
       // locate first visible position for this sequence
-      int[] refbounds = av.getColumnSelection()
+      int[] refbounds = av.getAlignment().getHiddenColumns()
               .locateVisibleBoundsOfSequence(refSeq);
 
       refSp = refbounds[0];
@@ -87,39 +107,40 @@ public class ScaleRenderer
       scalestartx += 5;
     }
     List<ScaleMark> marks = new ArrayList<ScaleMark>();
-    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)
       {
+        String text;
         if (refSeq == null)
         {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
-          string = String.valueOf(iadj);
+          int iadj = av.getAlignment().getHiddenColumns()
+                  .adjustForHiddenColumns(i - 1) + 1;
+          text = String.valueOf(iadj);
         }
         else
         {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
-          refN = refSeq.findPosition(iadj);
+          int iadj = av.getAlignment().getHiddenColumns()
+                  .adjustForHiddenColumns(i - 1);
+          int 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);
+            text = String.valueOf(iadj - refStartI);
           }
           else if (iadj > refEndI)
           {
-            string = "+" + String.valueOf(iadj - refEndI);
+            text = "+" + String.valueOf(iadj - refEndI);
           }
           else
           {
-            string = String.valueOf(refN) + refSeq.getCharAt(iadj);
+            text = String.valueOf(refN) + refSeq.getCharAt(iadj);
           }
         }
-        marks.add(new ScaleMark(true, i - startx - 1, string));
+        marks.add(new ScaleMark(true, i - startx - 1, text));
       }
       else
       {