JAL-2827 release notes

[jalview.git] / src / jalview / renderer / ScaleRenderer.java

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index 52778d5..d92608c 100644 (file)
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -35,17 +35,56 @@ import java.util.List;
 public class ScaleRenderer
 {
   /**
-   * 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.
+   * Represents one major or minor scale mark
    */
-  public static List<Object[]> calculateMarks(AlignViewportI av,
-          int startx, int endx)
+  public final class ScaleMark
   {
-    new ArrayList<Object[]>();
+    /**
+     * 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)
+    {
+      major = isMajor;
+      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);
+    }
+  }
+
+  /**
+   * Calculates position markers on the alignment ruler
+   * 
+   * @param av
+   * @param startx
+   *          left-most column in visible view (0..)
+   * @param endx
+   *          - right-most column in visible view (0..)
+   * @return
+   */
+  public List<ScaleMark> calculateMarks(AlignViewportI av, int startx,
+          int endx)
+  {
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
@@ -54,7 +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];
@@ -67,52 +106,46 @@ public class ScaleRenderer
     {
       scalestartx += 5;
     }
-    List<Object[]> marks = new ArrayList<Object[]>();
-    String string;
-    int refN, iadj;
+    List<ScaleMark> marks = new ArrayList<ScaleMark>();
     // 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)
     {
-      Object[] amark = new Object[3];
       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);
           }
         }
-        amark[0] = Boolean.TRUE;
-        amark[1] = Integer.valueOf(i - startx - 1);
-        amark[2] = string;
-
+        marks.add(new ScaleMark(true, i - startx - 1, text));
       }
       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;
   }