X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FScaleRenderer.java;h=9fec2565ba8eda9533914f2c1b6da3f73e3ee1dd;hb=954039bbfbde3648ac4c795277e788e49be5181b;hp=52778d5708f1fa7d351fd05d7b13496ba59e452b;hpb=fa7eb69d9da6df5ed78244d1968adbaa3b3b677c;p=jalview.git

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index 52778d5..9fec256 100644
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -34,18 +34,37 @@ import java.util.List;
  */
 public class ScaleRenderer
 {
+  public final class ScaleMark
+  {
+    public final boolean major;
+
+    public final int column;
+
+    public final String text;
+
+    ScaleMark(boolean isMajor, int col, String txt)
+    {
+      major = isMajor;
+      column = col;
+      text = txt;
+    }
+  }
+
   /**
    * calculate positions markers on the alignment ruler
    * 
-   * @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.
+   * @param av
+   * @param startx
+   *          left-most column in visible view
+   * @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)
    */
-  public static List<Object[]> calculateMarks(AlignViewportI av,
-          int startx, int endx)
+  public List<ScaleMark> calculateMarks(AlignViewportI av, int startx,
+          int endx)
   {
-    new ArrayList<Object[]>();
-
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
@@ -54,7 +73,7 @@ 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];
@@ -67,23 +86,24 @@ public class ScaleRenderer
     {
       scalestartx += 5;
     }
-    List<Object[]> marks = new ArrayList<Object[]>();
+    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)
     {
-      Object[] amark = new Object[3];
       if (((i - refSp) % 10) == 0)
       {
         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
@@ -101,18 +121,12 @@ public class ScaleRenderer
             string = String.valueOf(refN) + refSeq.getCharAt(iadj);
           }
         }
-        amark[0] = Boolean.TRUE;
-        amark[1] = Integer.valueOf(i - startx - 1);
-        amark[2] = string;
-
+        marks.add(new ScaleMark(true, i - startx - 1, string));
       }
       else
       {
-        amark[0] = Boolean.FALSE;
-        amark[1] = Integer.valueOf(i - startx - 1);
-        amark[2] = null;
+        marks.add(new ScaleMark(false, i - startx - 1, null));
       }
-      marks.add(amark);
     }
     return marks;
   }