X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=6abee0882b7b8a31e230e64735c5c5ff549b4b1e;hb=9062c3dbd065631f01af61f47a8cbafabe9c6c8b;hp=909cbfbb52c6afa153dad69a4c1c613e06035ce3;hpb=d9cca7f68d28a41d0d62510ceaf14b430f76fb8b;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 909cbfb..6abee08 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -21,9 +21,15 @@
 package jalview.gui;
 
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -35,24 +41,25 @@ import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
+import java.util.List;
 
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * The panel containing the sequence ruler (when not in wrapped mode), and
+ * supports a range of mouse operations to select, hide or reveal columns.
  */
-public class ScalePanel extends JPanel implements MouseMotionListener,
-        MouseListener
+public class ScalePanel extends JPanel
+        implements MouseMotionListener, MouseListener, ViewportListenerI
 {
   protected int offy = 4;
 
-  /** DOCUMENT ME!! */
   public int width;
 
   protected AlignViewport av;
@@ -61,13 +68,26 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
   boolean stretchingGroup = false;
 
-  int min; // used by mouseDragged to see if user
+  /*
+   * min, max hold the extent of a mouse drag action
+   */
+  int min;
 
-  int max; // used by mouseDragged to see if user
+  int max;
 
   boolean mouseDragging = false;
 
-  // wants to delete columns
+  /*
+   * holds a hidden column range when the mouse is over an adjacent column
+   */
+  int[] reveal;
+
+  /**
+   * Constructor
+   * 
+   * @param av
+   * @param ap
+   */
   public ScalePanel(AlignViewport av, AlignmentPanel ap)
   {
     this.av = av;
@@ -75,6 +95,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     addMouseListener(this);
     addMouseMotionListener(this);
+
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   /**
@@ -86,12 +108,12 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int x = (evt.getX() / av.getCharWidth()) + av.getRanges().getStartRes();
     final int res;
 
     if (av.hasHiddenColumns())
     {
-      x = av.getColumnSelection().adjustForHiddenColumns(x);
+      x = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
     }
 
     if (x >= av.getAlignment().getWidth())
@@ -106,10 +128,19 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     min = res;
     max = res;
 
-    if (evt.isPopupTrigger())
+    if (evt.isPopupTrigger()) // Mac: mousePressed
     {
       rightMouseButtonPressed(evt, res);
     }
+    else if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
+    {
+      /*
+       * defer right-mouse click handling to mouse up on Windows
+       * (where isPopupTrigger() will answer true)
+       * but accept Cmd-click on Mac which passes isRightMouseButton
+       */
+      return;
+    }
     else
     {
       leftMouseButtonPressed(evt, res);
@@ -138,17 +169,13 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         {
           av.showColumn(reveal[0]);
           reveal = null;
-          ap.paintAlignment(true);
-          if (ap.overviewPanel != null)
-          {
-            ap.overviewPanel.updateOverviewImage();
-          }
+          ap.paintAlignment(true, true);
           av.sendSelection();
         }
       });
       pop.add(item);
 
-      if (av.getColumnSelection().hasHiddenColumns())
+      if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
       {
         item = new JMenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
@@ -158,11 +185,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
           {
             av.showAllHiddenColumns();
             reveal = null;
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
+            ap.paintAlignment(true, true);
             av.sendSelection();
           }
         });
@@ -180,18 +203,13 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         public void actionPerformed(ActionEvent e)
         {
           av.hideColumns(res, res);
-          if (av.getSelectionGroup() != null
-                  && av.getSelectionGroup().getSize() == av.getAlignment()
-                          .getHeight())
+          if (av.getSelectionGroup() != null && av.getSelectionGroup()
+                  .getSize() == av.getAlignment().getHeight())
           {
             av.setSelectionGroup(null);
           }
 
-          ap.paintAlignment(true);
-          if (ap.overviewPanel != null)
-          {
-            ap.overviewPanel.updateOverviewImage();
-          }
+          ap.paintAlignment(true, true);
           av.sendSelection();
         }
       });
@@ -208,7 +226,12 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
    */
   protected void leftMouseButtonPressed(MouseEvent evt, final int res)
   {
-    if (!evt.isControlDown() && !evt.isShiftDown())
+    /*
+     * Ctrl-click/Cmd-click adds to the selection
+     * Shift-click extends the selection
+     */
+    // TODO Problem: right-click on Windows not reported until mouseReleased?!?
+    if (!Platform.isControlDown(evt) && !evt.isShiftDown())
     {
       av.getColumnSelection().clear();
     }
@@ -238,7 +261,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       sg.setEndRes(max);
     }
     av.setSelectionGroup(sg);
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -253,11 +276,15 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   {
     mouseDragging = false;
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
+
+    int res = (xCords / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      res = av.getAlignment().getHiddenColumns()
+              .visibleToAbsoluteColumn(res);
     }
 
     if (res >= av.getAlignment().getWidth())
@@ -267,8 +294,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     if (!stretchingGroup)
     {
-      ap.paintAlignment(false);
-
+      if (evt.isPopupTrigger()) // Windows: mouseReleased
+      {
+        rightMouseButtonPressed(evt, res);
+      }
+      else
+      {
+        ap.paintAlignment(false, false);
+      }
       return;
     }
 
@@ -286,83 +319,37 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       }
     }
     stretchingGroup = false;
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on dragging the mouse in the scale panel is to expand or shrink the
+   * selection group range (including any hidden columns that it spans)
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseDragged(MouseEvent evt)
   {
     mouseDragging = true;
+    ColumnSelection cs = av.getColumnSelection();
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    if (res < 0)
-    {
-      res = 0;
-    }
-
-    if (av.hasHiddenColumns())
-    {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
-    }
-
-    if (res >= av.getAlignment().getWidth())
-    {
-      res = av.getAlignment().getWidth() - 1;
-    }
-
-    if (res < min)
-    {
-      min = res;
-    }
-
-    if (res > max)
-    {
-      max = res;
-    }
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
+    res = Math.max(0, res);
+    res = hidden.visibleToAbsoluteColumn(res);
+    res = Math.min(res, av.getAlignment().getWidth() - 1);
+    min = Math.min(res, min);
+    max = Math.max(res, max);
 
     SequenceGroup sg = av.getSelectionGroup();
-
     if (sg != null)
     {
       stretchingGroup = true;
-
-      if (!av.getColumnSelection().contains(res))
-      {
-        av.getColumnSelection().addElement(res);
-      }
-
-      if (res > sg.getStartRes())
-      {
-        sg.setEndRes(res);
-      }
-      if (res < sg.getStartRes())
-      {
-        sg.setStartRes(res);
-      }
-
-      int col;
-      for (int i = min; i <= max; i++)
-      {
-        col = i; // av.getColumnSelection().adjustForHiddenColumns(i);
-
-        if ((col < sg.getStartRes()) || (col > sg.getEndRes()))
-        {
-          av.getColumnSelection().removeElement(col);
-        }
-        else
-        {
-          av.getColumnSelection().addElement(col);
-        }
-      }
-
-      ap.paintAlignment(false);
+      cs.stretchGroup(res, sg, min, max);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -389,42 +376,33 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   {
   }
 
+  /**
+   * Creates a tooltip when the mouse is over a hidden columns marker
+   */
   @Override
   public void mouseMoved(MouseEvent evt)
   {
+    this.setToolTipText(null);
+    reveal = null;
     if (!av.hasHiddenColumns())
     {
       return;
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
-    res = av.getColumnSelection().adjustForHiddenColumns(res);
+    reveal = av.getAlignment().getHiddenColumns()
+            .getRegionWithEdgeAtRes(res);
 
-    reveal = null;
-    if (av.getColumnSelection().getHiddenColumns() != null)
-    {
-      for (int[] region : av.getColumnSelection().getHiddenColumns())
-      {
-        if (res + 1 == region[0] || res - 1 == region[1])
-        {
-          reveal = region;
-          ToolTipManager.sharedInstance().registerComponent(this);
-          this.setToolTipText(MessageManager
-                  .getString("label.reveal_hidden_columns"));
-          break;
-        }
-        else
-        {
-          this.setToolTipText(null);
-        }
-      }
-    }
+    res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
+
+    ToolTipManager.sharedInstance().registerComponent(this);
+    this.setToolTipText(
+            MessageManager.getString("label.reveal_hidden_columns"));
     repaint();
   }
 
-  int[] reveal;
-
   /**
    * DOCUMENT ME!
    * 
@@ -434,7 +412,17 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   @Override
   public void paintComponent(Graphics g)
   {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
+    super.paintComponent(g);
+
+    /*
+     * shouldn't get called in wrapped mode as the scale above is
+     * drawn instead by SeqCanvas.drawNorthScale
+     */
+    if (!av.getWrapAlignment())
+    {
+      drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+              getWidth(), getHeight());
+    }
   }
 
   // scalewidth will normally be screenwidth,
@@ -457,9 +445,10 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
-    int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+    int avCharWidth = av.getCharWidth();
+    int avCharHeight = av.getCharHeight();
 
-    int s;
     if (cs != null)
     {
       gg.setColor(new Color(220, 0, 0));
@@ -471,9 +460,9 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
         if (av.hasHiddenColumns())
         {
-          if (cs.isVisible(sel))
+          if (hidden.isVisible(sel))
           {
-            sel = cs.findColumnPosition(sel);
+            sel = hidden.absoluteToVisibleColumn(sel);
           }
           else
           {
@@ -492,124 +481,85 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     int widthx = 1 + endx - startx;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = avCharHeight, yOf = fm.getDescent();
+    int y = avCharHeight;
+    int yOf = fm.getDescent();
     y -= yOf;
     if (av.hasHiddenColumns())
     {
       // draw any hidden column markers
       gg.setColor(Color.blue);
       int res;
-      if (av.getShowHiddenMarkers()
-              && av.getColumnSelection().getHiddenColumns() != null)
+
+      if (av.getShowHiddenMarkers())
       {
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
-                .size(); i++)
+        Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+                startx + widthx + 1);
+        while (it.hasNext())
         {
-          res = av.getColumnSelection().findHiddenRegionPosition(i)
-                  - startx;
-
-          if (res < 0 || res > widthx)
-          {
-            continue;
-          }
-
-          gg.fillPolygon(new int[] { res * avCharWidth - avCharHeight / 4,
-              res * avCharWidth + avCharHeight / 4, res * avCharWidth },
-                  new int[] { y - avCharHeight / 2, y - avCharHeight / 2,
-                      y + 8 }, 3);
-
+          res = it.next() - startx;
+
+          gg.fillPolygon(
+                  new int[]
+          { -1 + res * avCharWidth - avCharHeight / 4,
+              -1 + res * avCharWidth + avCharHeight / 4,
+              -1 + res * avCharWidth }, new int[]
+          { y, y, y + 2 * yOf }, 3);
         }
       }
     }
     // Draw the scale numbers
     gg.setColor(Color.black);
 
-    int scalestartx = (startx / 10) * 10;
+    int maxX = 0;
+    List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
+            endx);
 
-    SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
-    if (refSeq != null)
+    for (ScaleMark mark : marks)
     {
-      // find bounds and set origin appopriately
-      // locate first visible position for this sequence
-      int[] refbounds = av.getColumnSelection()
-              .locateVisibleBoundsOfSequence(refSeq);
-
-      refSp = refbounds[0];
-      refEp = refbounds[1];
-      refStart = refbounds[2];
-      refEnd = refbounds[3];
-      refStartI = refbounds[4];
-      refEndI = refbounds[5];
-      scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
-    }
-
-
-    if (refSeq == null && scalestartx % 10 == 0)
-    {
-      scalestartx += 5;
-    }
-
-    String string;
-    int maxX = 0, 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)
+      boolean major = mark.major;
+      int mpos = mark.column; // (i - startx - 1)
+      String mstring = mark.text;
+      if (mstring != null)
       {
-        if (refSeq == null)
+        if (mpos * avCharWidth > maxX)
         {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
-          string = String.valueOf(iadj);
+          gg.drawString(mstring, mpos * avCharWidth, y);
+          maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring);
         }
-        else
-        {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
-          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);
-          }
-          else if (iadj > refEndI)
-          {
-            string = "+" + String.valueOf(iadj - refEndI);
-          }
-          else
-          {
-            string = String.valueOf(refN) + refSeq.getCharAt(iadj);
-          }
-        }
-        if ((i - startx - 1) * avCharWidth > maxX)
-        {
-          gg.drawString(string, (i - startx - 1) * avCharWidth, y);
-          maxX = (i - startx + 1) * avCharWidth + fm.stringWidth(string);
-        }
-
-        gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
-                y + 2,
-                ((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
-                        + (yOf * 2));
+      }
+      if (major)
+      {
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
       }
       else
       {
-        gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
-                + yOf,
-                ((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
-                        + (yOf * 2));
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
       }
     }
+  }
 
-    if (av.hasHiddenColumns())
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    // Respond to viewport change events (e.g. alignment panel was scrolled)
+    // Both scrolling and resizing change viewport ranges: scrolling changes
+    // both start and end points, but resize only changes end values.
+    // Here we only want to fastpaint on a scroll, with resize using a normal
+    // paint, so scroll events are identified as changes to the horizontal or
+    // vertical start value.
+    if (evt.getPropertyName().equals(ViewportRanges.STARTRES)
+            || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)
+            || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
     {
-      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
-      {
-        gg.drawString(MessageManager.getString("label.reveal_columns"),
-                reveal[0] * avCharWidth, 0);
-      }
+      // scroll event, repaint panel
+    	
+  	// Call repaint on alignment panel so that repaints from other alignment
+    // panel components can be aggregated. Otherwise performance of the overview
+    // window and others may be adversely affected.
+      av.getAlignPanel().repaint();
     }
-
   }
+
 }