Merge branch 'releases/Release_2_10_4_Branch_merged_JAL-2759' into releases/Release_2...

[jalview.git] / src / jalview / viewmodel / ViewportRanges.java

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 9a1e13c..691e492 100644 (file)
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -544,18 +544,33 @@ public class ViewportRanges extends ViewportProperties
    * the startRes changed, else false.
    * 
    * @param res
-   *          residue position to scroll to
+   *          residue position to scroll to NB visible position not absolute
+   *          alignment position
    * @return
    */
   public boolean scrollToWrappedVisible(int res)
   {
-    int oldStartRes = startRes;
-    int width = getViewportWidth();
-
-    if (res >= oldStartRes && res < oldStartRes + width)
+    int newStartRes = calcWrappedStartResidue(res);
+    if (newStartRes == startRes)
     {
       return false;
     }
+    setStartRes(newStartRes);
+
+    return true;
+  }
+
+  /**
+   * Calculate wrapped start residue from visible start residue
+   * 
+   * @param res
+   *          visible start residue
+   * @return left column of panel res will be located in
+   */
+  private int calcWrappedStartResidue(int res)
+  {
+    int oldStartRes = startRes;
+    int width = getViewportWidth();
 
     boolean up = res < oldStartRes;
     int widthsToScroll = Math.abs((res - oldStartRes) / width);
@@ -571,19 +586,16 @@ public class ViewportRanges extends ViewportProperties
     {
       newStartRes = 0;
     }
-
-    setStartRes(newStartRes);
-
-    return true;
+    return newStartRes;
   }
 
   /**
    * Scroll so that (x,y) is visible. Fires a property change event.
    * 
    * @param x
-   *          x position in alignment
+   *          x position in alignment (absolute position)
    * @param y
-   *          y position in alignment
+   *          y position in alignment (absolute position)
    */
   public void scrollToVisible(int x, int y)
   {
@@ -597,14 +609,14 @@ public class ViewportRanges extends ViewportProperties
     }
     
     HiddenColumns hidden = al.getHiddenColumns();
-    while (x < hidden.adjustForHiddenColumns(startRes))
+    while (x < hidden.visibleToAbsoluteColumn(startRes))
     {
       if (!scrollRight(false))
       {
         break;
       }
     }
-    while (x > hidden.adjustForHiddenColumns(endRes))
+    while (x > hidden.visibleToAbsoluteColumn(endRes))
     {
       if (!scrollRight(true))
       {
@@ -617,30 +629,52 @@ public class ViewportRanges extends ViewportProperties
    * Set the viewport location so that a position is visible
    * 
    * @param x
-   *          column to be visible
+   *          column to be visible: absolute position in alignment
    * @param y
-   *          row to be visible
+   *          row to be visible: absolute position in alignment
    */
   public boolean setViewportLocation(int x, int y)
   {
-    // if (x,y) is already visible don't do anything
     boolean changedLocation = false;
-    if (startRes > x || x > endRes || startSeq > y && y > endSeq)
-    {
-      int width = getViewportWidth();
-      int[] oldresvalues = updateStartEndRes(x, x + width - 1);
 
-      int startseq = y;
-      int height = getViewportHeight();
-      if (startseq + height - 1 > getVisibleAlignmentHeight() - 1)
+    // convert the x,y location to visible coordinates
+    int visX = al.getHiddenColumns().absoluteToVisibleColumn(x);
+    int visY = al.getHiddenSequences().findIndexWithoutHiddenSeqs(y);
+
+    // if (vis_x,vis_y) is already visible don't do anything
+    if (startRes > visX || visX > endRes
+            || startSeq > visY && visY > endSeq)
+    {
+      int[] old = new int[] { startRes, startSeq };
+      int[] newresseq;
+      if (wrappedMode)
       {
-        startseq = getVisibleAlignmentHeight() - height;
+        int newstartres = calcWrappedStartResidue(visX);
+        setStartRes(newstartres);
+        newresseq = new int[] { startRes, startSeq };
       }
-      int[] oldseqvalues = updateStartEndSeq(startseq,
-              startseq + height - 1);
+      else
+      {
+        // set the viewport x location to contain vis_x
+        int newstartres = visX;
+        int width = getViewportWidth();
+        if (newstartres + width - 1 > getVisibleAlignmentWidth() - 1)
+        {
+          newstartres = getVisibleAlignmentWidth() - width;
+        }
+        updateStartEndRes(newstartres, newstartres + width - 1);
 
-      int[] old = new int[] { oldresvalues[0], oldseqvalues[0] };
-      int[] newresseq = new int[] { startRes, startSeq };
+        // set the viewport y location to contain vis_y
+        int newstartseq = visY;
+        int height = getViewportHeight();
+        if (newstartseq + height - 1 > getVisibleAlignmentHeight() - 1)
+        {
+          newstartseq = getVisibleAlignmentHeight() - height;
+        }
+        updateStartEndSeq(newstartseq, newstartseq + height - 1);
+
+        newresseq = new int[] { startRes, startSeq };
+      }
       changedLocation = true;
       changeSupport.firePropertyChange(MOVE_VIEWPORT, old, newresseq);
     }