X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FScalePanel.java;h=4db8054a90477c832e2d862cce0df12df3c40316;hb=0eca27bca577e774acd5aefb165e7c6396a1995e;hp=f72ea7b7133a745f72a4c03ce661de207578305f;hpb=5cd5b6e7864fe435ceb3f5c2f339a436ea0aac93;p=jalview.git

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index f72ea7b..4db8054 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -38,7 +38,7 @@ public class ScalePanel
   int min; //used by mouseDragged to see if user
   int max; //used by mouseDragged to see if user
   boolean mouseDragging = false;
-  int [] reveal;
+  int[] reveal;
 
   public ScalePanel(AlignViewport av, AlignmentPanel ap)
   {
@@ -57,57 +57,60 @@ public class ScalePanel
     final int res;
 
     if (av.hasHiddenColumns)
+    {
       res = av.getColumnSelection().adjustForHiddenColumns(x);
+    }
     else
+    {
       res = x;
+    }
 
     min = res;
     max = res;
-    if (reveal != null
-        && (evt.getModifiers() & InputEvent.BUTTON3_MASK)
+    if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK)
         == InputEvent.BUTTON3_MASK)
     {
-
-      MenuItem item = new MenuItem("Reveal");
-      item.addActionListener(new ActionListener()
-      {
-        public void actionPerformed(ActionEvent e)
-        {
-          av.showColumn(reveal[0]);
-          reveal = null;
-          ap.repaint();
-          if (ap.overviewPanel != null)
-            ap.overviewPanel.updateOverviewImage();
-        }
-      });
       PopupMenu pop = new PopupMenu();
-      pop.add(item);
-
-      if (av.getColumnSelection().getHiddenColumns().size() > 1)
+      if (reveal != null)
       {
-        item = new MenuItem("Reveal All");
+        MenuItem item = new MenuItem("Reveal");
         item.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent e)
           {
-            av.showAllHiddenColumns();
+            av.showColumn(reveal[0]);
             reveal = null;
-            ap.repaint();
+            ap.paintAlignment(true);
             if (ap.overviewPanel != null)
+            {
               ap.overviewPanel.updateOverviewImage();
+            }
           }
         });
         pop.add(item);
-      }
-
-      this.add(pop);
-      pop.show(this, evt.getX(), evt.getY());
 
-    }
-    else if (av.getColumnSelection().contains(res))
-    {
-      if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK)
-          == InputEvent.BUTTON3_MASK)
+        if (av.getColumnSelection().getHiddenColumns().size() > 1)
+        {
+          item = new MenuItem("Reveal All");
+          item.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              av.showAllHiddenColumns();
+              reveal = null;
+              ap.paintAlignment(true);
+              if (ap.overviewPanel != null)
+              {
+                ap.overviewPanel.updateOverviewImage();
+              }
+            }
+          });
+          pop.add(item);
+        }
+        this.add(pop);
+        pop.show(this, evt.getX(), evt.getY());
+      }
+      else if (av.getColumnSelection().contains(res))
       {
         MenuItem item = new MenuItem("Hide Columns");
         item.addActionListener(new ActionListener()
@@ -115,27 +118,34 @@ public class ScalePanel
           public void actionPerformed(ActionEvent e)
           {
             av.hideColumns(res, res);
-            ap.repaint();
+            if (av.getSelectionGroup() != null
+                &&
+                av.getSelectionGroup().getSize() == av.alignment.getHeight())
+            {
+              av.setSelectionGroup(null);
+            }
+
+            ap.paintAlignment(true);
             if (ap.overviewPanel != null)
+            {
               ap.overviewPanel.updateOverviewImage();
+            }
           }
         });
-        PopupMenu pop = new PopupMenu();
         pop.add(item);
         this.add(pop);
         pop.show(this, evt.getX(), evt.getY());
       }
-      else
-      {
-        av.getColumnSelection().removeElement(res);
-        av.setSelectionGroup(null);
-      }
     }
-    else
+    else // LEFT MOUSE TO SELECT
     {
+      if (!evt.isControlDown() && !evt.isShiftDown())
+      {
+        av.getColumnSelection().clear();
+      }
+
       av.getColumnSelection().addElement(res);
       SequenceGroup sg = new SequenceGroup();
-
       for (int i = 0; i < av.alignment.getSequences().size(); i++)
       {
         sg.addSequence(av.alignment.getSequenceAt(i), false);
@@ -144,8 +154,21 @@ public class ScalePanel
       sg.setStartRes(res);
       sg.setEndRes(res);
       av.setSelectionGroup(sg);
+
+      if (evt.isShiftDown())
+      {
+        int min = Math.min(av.getColumnSelection().getMin(), res);
+        int max = Math.max(av.getColumnSelection().getMax(), res);
+        for (int i = min; i < max; i++)
+        {
+          av.getColumnSelection().addElement(i);
+        }
+        sg.setStartRes(min);
+        sg.setEndRes(max);
+      }
     }
-    ap.repaint();
+
+    ap.paintAlignment(true);
   }
 
   public void mouseReleased(MouseEvent evt)
@@ -154,34 +177,36 @@ public class ScalePanel
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    if(res> av.alignment.getWidth())
+    if (res > av.alignment.getWidth())
     {
-      res = av.alignment.getWidth()-1;
+      res = av.alignment.getWidth() - 1;
     }
 
-    if(av.hasHiddenColumns)
+    if (av.hasHiddenColumns)
+    {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
     if (!stretchingGroup)
     {
-        ap.repaint();
+      ap.paintAlignment(true);
 
-        return;
+      return;
     }
 
     SequenceGroup sg = av.getSelectionGroup();
 
     if (res > sg.getStartRes())
     {
-        sg.setEndRes(res);
+      sg.setEndRes(res);
     }
     else if (res < sg.getStartRes())
     {
-        sg.setStartRes(res);
+      sg.setStartRes(res);
     }
 
     stretchingGroup = false;
-    ap.repaint();
+    ap.paintAlignment(true);
   }
 
   public void mouseDragged(MouseEvent evt)
@@ -190,10 +215,14 @@ public class ScalePanel
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
     if (res < 0)
+    {
       res = 0;
+    }
 
     if (av.hasHiddenColumns)
+    {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
     if (res > av.alignment.getWidth())
     {
@@ -230,33 +259,39 @@ public class ScalePanel
         sg.setStartRes(res);
       }
 
+      int col;
       for (int i = min; i <= max; i++)
       {
-        if ( (i < sg.getStartRes()) || (i > sg.getEndRes()))
+        col = av.getColumnSelection().adjustForHiddenColumns(i);
+
+        if ( (col < sg.getStartRes()) || (col > sg.getEndRes()))
         {
-          av.getColumnSelection().removeElement(i);
+          av.getColumnSelection().removeElement(col);
         }
         else
         {
-          av.getColumnSelection().addElement(i);
+          av.getColumnSelection().addElement(col);
         }
       }
 
-      ap.repaint();
+      ap.paintAlignment(true);
     }
   }
 
-
   public void mouseEntered(MouseEvent evt)
   {
     if (mouseDragging)
+    {
       ap.seqPanel.scrollCanvas(null);
+    }
   }
 
   public void mouseExited(MouseEvent evt)
   {
     if (mouseDragging)
+    {
       ap.seqPanel.scrollCanvas(evt);
+    }
   }
 
   public void mouseClicked(MouseEvent evt)
@@ -267,7 +302,9 @@ public class ScalePanel
   public void mouseMoved(MouseEvent evt)
   {
     if (!av.hasHiddenColumns)
+    {
       return;
+    }
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
@@ -305,7 +342,6 @@ public class ScalePanel
   {
     gg.setFont(av.getFont());
 
-
     //Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, width, height);
@@ -317,16 +353,17 @@ public class ScalePanel
 
     for (int i = 0; i < cs.size(); i++)
     {
-        int sel = cs.columnAt(i);
-        if(av.hasHiddenColumns)
-          sel = av.getColumnSelection().findColumnPosition(sel);
-
+      int sel = cs.columnAt(i);
+      if (av.hasHiddenColumns)
+      {
+        sel = av.getColumnSelection().findColumnPosition(sel);
+      }
 
-        if ((sel >= startx) && (sel <= endx))
-        {
-            gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
-                getSize().height);
-        }
+      if ( (sel >= startx) && (sel <= endx))
+      {
+        gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,
+                    getSize().height);
+      }
     }
 
     // Draw the scale numbers
@@ -337,47 +374,48 @@ public class ScalePanel
     FontMetrics fm = gg.getFontMetrics(av.getFont());
     int y = av.charHeight - fm.getDescent();
 
-    if ((scalestartx % 10) == 0)
+    if ( (scalestartx % 10) == 0)
     {
-        scalestartx += 5;
+      scalestartx += 5;
     }
 
     String string;
-    int maxX=0;
+    int maxX = 0;
 
     for (int i = scalestartx; i < endx; i += 5)
     {
-        if ((i % 10) == 0)
+      if ( (i % 10) == 0)
+      {
+        string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(
+            i));
+        if ( (i - startx - 1) * av.charWidth > maxX)
         {
-            string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(i));
-            if ( (i - startx - 1) * av.charWidth > maxX)
-            {
-              gg.drawString(string,
-                            (i - startx - 1) * av.charWidth, y);
-              maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
-            }
+          gg.drawString(string,
+                        (i - startx - 1) * av.charWidth, y);
+          maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
+        }
 
-            gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
-                                (av.charWidth / 2)), y + 2,
-                        (int) ( ( (i - startx - 1) * av.charWidth) +
-                               (av.charWidth / 2)),
-                        y + (fm.getDescent() * 2));
+        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
+                            (av.charWidth / 2)), y + 2,
+                    (int) ( ( (i - startx - 1) * av.charWidth) +
+                           (av.charWidth / 2)),
+                    y + (fm.getDescent() * 2));
 
-        }
-        else
-        {
-            gg.drawLine((int) (((i - startx - 1) * av.charWidth) +
-                (av.charWidth / 2)), y + fm.getDescent(),
-                (int) (((i - startx - 1) * av.charWidth) +
-                (av.charWidth / 2)), y + (fm.getDescent() * 2));
-        }
+      }
+      else
+      {
+        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
+                            (av.charWidth / 2)), y + fm.getDescent(),
+                    (int) ( ( (i - startx - 1) * av.charWidth) +
+                           (av.charWidth / 2)), y + (fm.getDescent() * 2));
+      }
     }
 
     if (av.hasHiddenColumns)
     {
       gg.setColor(Color.blue);
       int res;
-      if(av.getShowHiddenMarkers())
+      if (av.getShowHiddenMarkers())
       {
         for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
              i++)
@@ -386,8 +424,10 @@ public class ScalePanel
           res = av.getColumnSelection().findHiddenRegionPosition(i) -
               startx;
 
-          if(res < 0 || res > endx-scalestartx)
+          if (res < 0 || res > endx - scalestartx)
+          {
             continue;
+          }
 
           gg.fillPolygon(new int[]
                          {res * av.charWidth - av.charHeight / 4,