JAL-2491 Tidies and more refactoring

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 8619ad0..e545b8f 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -156,19 +156,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           int widthInRes = getSeqPanel().seqCanvas
                   .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-          vpRanges.setStartEndRes(vpRanges.getStartRes(),
-                  vpRanges.getStartRes() + widthInRes);
+          vpRanges.setViewportWidth(widthInRes);
         }
         else
         {
-          int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
-                  .getCharWidth()) - 1;
-          int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()) - 1;
+          int widthInRes = getSeqPanel().seqCanvas.getWidth()
+                  / av.getCharWidth();
+          int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+                  / av.getCharHeight();
           
-          vpRanges.setStartEndRes(vpRanges.getStartRes(),
-                  vpRanges.getStartRes() + widthInRes);
-          vpRanges.setStartEndSeq(vpRanges.getStartSeq(),
-                  vpRanges.getStartSeq() + heightInSeq);
+          vpRanges.setViewportWidth(widthInRes);
+          vpRanges.setViewportHeight(heightInSeq);
         }
       }
 
@@ -633,8 +631,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int widthInRes = getSeqPanel().seqCanvas
               .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-      vpRanges.setStartEndRes(vpRanges.getStartRes(),
-              vpRanges.getStartRes() + widthInRes - 1);
+      vpRanges.setViewportWidth(widthInRes);
     }
     else
     {
@@ -643,8 +640,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
               .getCharHeight()) - 1;
 
-      vpRanges.setStartEndRes(vpRanges.getStartRes(), widthInRes);
-      vpRanges.setStartEndSeq(vpRanges.getStartSeq(), heightInSeq);
+      vpRanges.setViewportWidth(widthInRes);
+      vpRanges.setViewportHeight(heightInSeq);
     }
 
     idSpaceFillerPanel1.setVisible(!wrap);
@@ -759,7 +756,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         }
         else if (offy > -1)
         {
-          vpRanges.setStartEndRes(offy * rowSize, (offy + 1) * rowSize - 1);
+          vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
         }
         else
         {
@@ -785,7 +782,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (evt.getSource() == hscroll)
       {
         int x = hscroll.getValue();
-        int width = (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth()) - 1;
+        int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
 
         // if we're scrolling to the position we're already at, stop
         // this prevents infinite recursion of events when the scroll/viewport
@@ -794,13 +791,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           return;
         }
-        vpRanges.setStartEndRes(x, x + width);
+        vpRanges.setViewportStartAndWidth(x, width);
       }
       else if (evt.getSource() == vscroll)
       {
         int y = vscroll.getValue();
-        int height = (getSeqPanel().seqCanvas.getHeight() / av
-                .getCharHeight()) - 1;
+        int height = getSeqPanel().seqCanvas.getHeight()
+                / av.getCharHeight();
 
         // if we're scrolling to the position we're already at, stop
         // this prevents infinite recursion of events when the scroll/viewport
@@ -809,7 +806,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           return;
         }
-        vpRanges.setStartEndSeq(y, y + height);
+        vpRanges.setViewportStartAndHeight(y, height);
       }
       if (!fastPaint)
       {

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index c14854b..f1e4d13 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -384,7 +384,6 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (av.getWrapAlignment())
     {
       av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
-      // ap.scrollToWrappedVisible(seqCanvas.cursorX);
     }
     else
     {

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 54bbfd8..0583a8d 100644 (file)
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -23,10 +23,10 @@ package jalview.viewmodel;
 import jalview.datamodel.AlignmentI;
 
 /**
- * Embryonic class which: Supplies and updates viewport properties relating to
- * position such as: start and end residues and sequences; ideally will serve
- * hidden columns/rows too. Intention also to support calculations for
- * positioning, scrolling etc. such as finding the middle of the viewport,
+ * Slightly less embryonic class which: Supplies and updates viewport properties
+ * relating to position such as: start and end residues and sequences; ideally
+ * will serve hidden columns/rows too. Intention also to support calculations
+ * for positioning, scrolling etc. such as finding the middle of the viewport,
  * checking for scrolls off screen
  */
 public class ViewportRanges extends ViewportProperties
@@ -90,26 +90,42 @@ public class ViewportRanges extends ViewportProperties
     setStartEndRes(res, res + width - 1);
   }
 
-  public void setStartEndRes(int startres, int endres)
+  /**
+   * Set start and end residues at the same time. This method only fires one
+   * event for the two changes, and should be used in preference to separate
+   * calls to setStartRes and setEndRes.
+   * 
+   * @param start
+   *          the start residue
+   * @param end
+   *          the end residue
+   */
+  public void setStartEndRes(int start, int end)
   {
     int oldres = this.startRes;
-    if (startres > al.getWidth() - 1)
+    if (start > al.getWidth() - 1)
     {
-      startres = al.getWidth() - 1;
+      startRes = al.getWidth() - 1;
     }
-    else if (startres < 0)
+    else if (start < 0)
     {
-      startres = 0;
+      startRes = 0;
+    }
+    else
+    {
+      startRes = start;
     }
-    this.startRes = startres;
 
-    if (endres < 0)
+    if (end < 0)
     {
-      endres = 0;
+      endRes = 0;
+    }
+    else
+    {
+      endRes = end;
     }
-    this.endRes = endres;
 
-    changeSupport.firePropertyChange("startres", oldres, startres);
+    changeSupport.firePropertyChange("startres", oldres, start);
   }
 
   /**
@@ -136,29 +152,46 @@ public class ViewportRanges extends ViewportProperties
     setStartEndSeq(seq, seq + height - 1);
   }
 
-  public void setStartEndSeq(int startseq, int endseq)
+  /**
+   * Set start and end sequences at the same time. This method only fires one
+   * event for the two changes, and should be used in preference to separate
+   * calls to setStartSeq and setEndSeq.
+   * 
+   * @param start
+   *          the start sequence
+   * @param end
+   *          the end sequence
+   */
+  public void setStartEndSeq(int start, int end)
   {
     int oldseq = this.startSeq;
-    if (startseq > al.getHeight() - 1)
+    if (start > al.getHeight() - 1)
+    {
+      startSeq = al.getHeight() - 1;
+    }
+    else if (start < 0)
     {
-      startseq = al.getHeight() - 1;
+      startSeq = 0;
     }
-    else if (startseq < 0)
+    else
     {
-      startseq = 0;
+      startSeq = start;
     }
-    this.startSeq = startseq;
 
-    if (endseq >= al.getHeight())
+    if (end >= al.getHeight())
     {
-      endseq = al.getHeight() - 1;
+      endSeq = al.getHeight() - 1;
     }
-    else if (endseq < 0)
+    else if (end < 0)
     {
-      endseq = 0;
+      endSeq = 0;
     }
-    this.endSeq = endseq;
-    changeSupport.firePropertyChange("startseq", oldseq, startseq);
+    else
+    {
+      endSeq = end;
+    }
+
+    changeSupport.firePropertyChange("startseq", oldseq, start);
   }
 
   /**
@@ -206,13 +239,67 @@ public class ViewportRanges extends ViewportProperties
   }
 
   /**
+   * Set viewport width in residues, without changing startRes. Use in
+   * preference to calculating endRes from the width, to avoid out by one
+   * errors!
+   * 
+   * @param w
+   *          width in residues
+   */
+  public void setViewportWidth(int w)
+  {
+    setStartEndRes(startRes, startRes + w - 1);
+  }
+
+  /**
+   * Set viewport height in residues, without changing startSeq. Use in
+   * preference to calculating endSeq from the height, to avoid out by one
+   * errors!
+   * 
+   * @param h
+   *          height in sequences
+   */
+  public void setViewportHeight(int h)
+  {
+    setStartEndSeq(startSeq, startSeq + h - 1);
+  }
+
+  /**
+   * Set viewport horizontal start position and width. Use in preference to
+   * calculating endRes from the width, to avoid out by one errors!
+   * 
+   * @param start
+   *          start residue
+   * @param w
+   *          width in residues
+   */
+  public void setViewportStartAndWidth(int start, int w)
+  {
+    setStartEndRes(start, start + w - 1);
+  }
+
+  /**
+   * Set viewport vertical start position and height. Use in preference to
+   * calculating endSeq from the height, to avoid out by one errors!
+   * 
+   * @param start
+   *          start sequence
+   * @param h
+   *          height in sequences
+   */
+  public void setViewportStartAndHeight(int start, int h)
+  {
+    setStartEndSeq(start, start + h - 1);
+  }
+
+  /**
    * Get width of viewport in residues
    * 
    * @return width of viewport
    */
   public int getViewportWidth()
   {
-    return (endRes - startRes + 1); // TODO get for wrapped alignments too
+    return (endRes - startRes + 1);
   }
 
   /**
@@ -225,7 +312,14 @@ public class ViewportRanges extends ViewportProperties
     return (endSeq - startSeq + 1);
   }
 
-  // return value is true if the scroll is valid
+  /**
+   * Scroll the viewport range vertically
+   * 
+   * @param up
+   *          true if scrolling up, false if down
+   * 
+   * @return true if the scroll is valid
+   */
   public boolean scrollUp(boolean up)
   {
     if (up)
@@ -250,12 +344,12 @@ public class ViewportRanges extends ViewportProperties
   }
 
   /**
-   * DOCUMENT ME!
+   * Scroll the viewport range horizontally
    * 
    * @param right
-   *          DOCUMENT ME!
+   *          true if scrolling right, false if left
    * 
-   * @return DOCUMENT ME!
+   * @return true if the scroll is valid
    */
   public boolean scrollRight(boolean right)
   {
@@ -281,11 +375,18 @@ public class ViewportRanges extends ViewportProperties
     return true;
   }
 
+  /**
+   * Scroll a wrapped alignment so that the specified residue is visible
+   * 
+   * @param res
+   *          residue position to scroll to
+   */
   public void scrollToWrappedVisible(int res)
   {
     // get the start residue of the wrapped row which res is in
     // and set that as our start residue
-    setStartRes((res / getViewportWidth()) * getViewportWidth());
+    int width = getViewportWidth();
+    setStartRes((res / width) * width);
   }
 
 }