JAL-192 need visible and actual sequence limits for scale

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 624e083..e3a8472 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1082,10 +1082,12 @@ public class ColumnSelection
   /**
    * Locate the first and last position visible for this sequence. if seq isn't
    * visible then return the position of the left and right of the hidden
-   * boundary region
+   * boundary region, and the corresponding alignment column indices for the
+   * extent of the sequence
    * 
    * @param seq
-   * @return int[] { visible start, visible end, first seqpos, last seqpos }
+   * @return int[] { visible start, visible end, first seqpos, last seqpos,
+   *         alignment index for seq start, alignment index for seq end }
    */
   public int[] locateVisibleBoundsOfSequence(SequenceI seq)
   {
@@ -1094,9 +1096,8 @@ public class ColumnSelection
     
     if (hiddenColumns == null || hiddenColumns.size() == 0)
     {
-      return new int[] { seq.findIndex(fpos) - 1, seq.findIndex(lpos) - 1,
-          fpos,
-          lpos };
+      int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
+      return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
     }
 
     // Simply walk along the sequence whilst watching for hidden column
@@ -1104,13 +1105,20 @@ public class ColumnSelection
     List<int[]> regions = getHiddenColumns();
     int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq
             .getLength(), hideEnd = -1;
-    int visPrev = 0, visNext = 0;
+    int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
     boolean foundStart = false;
     for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
             && p < pLen; p++)
     {
       if (!Comparison.isGap(seq.getCharAt(p)))
       {
+        // keep track of first/last column
+        // containing sequence data regardless of visibility
+        if (firstP == -1)
+        {
+          firstP = p;
+        }
+        lastP = p;
         // update hidden region start/end
         while (hideEnd < p && rcount < regions.size())
         {
@@ -1143,10 +1151,10 @@ public class ColumnSelection
     if (foundStart)
     {
       return new int[] { findColumnPosition(start),
-          findColumnPosition(lastvispos), fpos, lpos };
+          findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
     }
     // otherwise, sequence was completely hidden
-    return new int[] { visPrev, visNext, 0, 0 };
+    return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
   }
 
   /**

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index f266d36..aedb157 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -494,7 +494,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = 0, refEp = -1;
+    int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
     if (refSeq != null)
     {
       // find bounds and set origin appopriately
@@ -504,6 +504,10 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
       refSp = refbounds[0];
       refEp = refbounds[1];
+      refStart = refbounds[2];
+      refEnd = refbounds[3];
+      refStartI = refbounds[4];
+      refEndI = refbounds[5];
       scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
     }
 
@@ -536,13 +540,13 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
           // TODO show bounds if position is a gap
           // - ie L--R -> "1L|2R" for
           // marker
-          if (iadj < refSp)
+          if (iadj < refStartI)
           {
-            string = String.valueOf(iadj - refSp);
+            string = String.valueOf(iadj - refStartI);
           }
-          else if (iadj > refEp)
+          else if (iadj > refEndI)
           {
-            string = "+" + String.valueOf(iadj - refEp);
+            string = "+" + String.valueOf(iadj - refEndI);
           }
           else
           {

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 36932d1..63f80b2 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -107,7 +107,8 @@ public class ColumnSelectionTest
     assertEquals(
             Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
                 seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
-                seq.getEnd() }),
+                seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
             Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
 
     // hidden column on gap after end of sequence - should not affect bounds
@@ -115,7 +116,8 @@ public class ColumnSelectionTest
     assertEquals(
             Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
                 seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
-                seq.getEnd() }),
+                seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
             Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
 
     cs.revealAllHiddenColumns();
@@ -125,7 +127,8 @@ public class ColumnSelectionTest
     assertEquals(
             Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
                 seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
-                seq.getEnd() }),
+                seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
             Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
 
     cs.revealAllHiddenColumns();
@@ -134,14 +137,20 @@ public class ColumnSelectionTest
     cs.hideColumns(6, 11);
     assertEquals("-D",
             cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]);
-    assertEquals(Arrays.toString(new int[] { 1, 1, 3, 3 }),
+    assertEquals(
+            Arrays.toString(new int[] { 1, 1, 3, 3,
+                seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
             Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
     cs.revealAllHiddenColumns();
 
     // hide whole sequence - should just get location of hidden region
     // containing sequence
     cs.hideColumns(1, 11);
-    assertEquals(Arrays.toString(new int[] { 0, 1, 0, 0 }),
+    assertEquals(
+            Arrays.toString(new int[] { 0, 1, 0, 0,
+                seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
             Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
 
   }