X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FScaleRenderer.java;h=dc3272ff84decd7d8a0a499230a2850cbe870d58;hb=d8720fc191cba996c440171ef8e07462ef9f7035;hp=d92608c2965f48b8f6a788d25e40a0fc22f35faa;hpb=af891ca5a64368cff67d242bbac4eda9dd43a42a;p=jalview.git

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index d92608c..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;
 
 /**
@@ -60,27 +62,19 @@ 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);
-    }
   }
 
   /**
-   * Calculates position markers on the alignment ruler
+   * calculate positions markers on the alignment ruler
    * 
    * @param av
    * @param startx
-   *          left-most column in visible view (0..)
+   *          left-most column in visible view
    * @param endx
-   *          - right-most column in visible view (0..)
-   * @return
+   *          - 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 List<ScaleMark> calculateMarks(AlignViewportI av, int startx,
           int endx)
@@ -88,17 +82,27 @@ public class ScaleRenderer
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = 0, refStartI = 0, refEndI = -1;
+    int refSp = 0;
+    int refStartI = 0;
+    int refEndI = -1;
+
+    HiddenColumns hc = av.getAlignment().getHiddenColumns();
+
     if (refSeq != null)
     {
-      // find bounds and set origin appopriately
-      // locate first visible position for this sequence
-      int[] refbounds = av.getAlignment().getHiddenColumns()
-              .locateVisibleBoundsOfSequence(refSeq);
+      // find bounds and set origin appropriately
+      // 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;
+
+      int seqlength = refSeq.getLength();
+      // get sequence position past the end of the sequence
+      int pastEndPos = refSeq.findPosition(seqlength + 1);
+      refEndI = refSeq.findIndex(pastEndPos - 1) - 1;
 
-      refSp = refbounds[0];
-      refStartI = refbounds[4];
-      refEndI = refbounds[5];
       scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
     }
 
@@ -106,41 +110,40 @@ public class ScaleRenderer
     {
       scalestartx += 5;
     }
-    List<ScaleMark> marks = new ArrayList<ScaleMark>();
+    List<ScaleMark> marks = new ArrayList<>();
+    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)
     {
       if (((i - refSp) % 10) == 0)
       {
-        String text;
         if (refSeq == null)
         {
-          int iadj = av.getAlignment().getHiddenColumns()
-                  .adjustForHiddenColumns(i - 1) + 1;
-          text = String.valueOf(iadj);
+          iadj = hc.visibleToAbsoluteColumn(i - 1) + 1;
+          string = String.valueOf(iadj);
         }
         else
         {
-          int iadj = av.getAlignment().getHiddenColumns()
-                  .adjustForHiddenColumns(i - 1);
-          int refN = refSeq.findPosition(iadj);
+          iadj = hc.visibleToAbsoluteColumn(i - 1);
+          refN = refSeq.findPosition(iadj);
           // TODO show bounds if position is a gap
           // - ie L--R -> "1L|2R" for
           // marker
           if (iadj < refStartI)
           {
-            text = String.valueOf(iadj - refStartI);
+            string = String.valueOf(iadj - refStartI);
           }
           else if (iadj > refEndI)
           {
-            text = "+" + String.valueOf(iadj - refEndI);
+            string = "+" + String.valueOf(iadj - refEndI);
           }
           else
           {
-            text = String.valueOf(refN) + refSeq.getCharAt(iadj);
+            string = String.valueOf(refN) + refSeq.getCharAt(iadj);
           }
         }
-        marks.add(new ScaleMark(true, i - startx - 1, text));
+        marks.add(new ScaleMark(true, i - startx - 1, string));
       }
       else
       {