X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRotatableCanvas.java;h=c5ae3399f374bb51b8df0f9131f0c5091b14f84e;hb=82de3ff949ae61b771136fbdb49baacc20e652fd;hp=1c38c56f7088c6081b453527668ef6ca59e173ae;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git

diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 1c38c56..c5ae339 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -1,32 +1,46 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
 import jalview.api.RotatableCanvasI;
-import jalview.datamodel.*;
-import jalview.math.*;
-import jalview.util.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
 
 public class RotatableCanvas extends Panel implements MouseListener,
         MouseMotionListener, KeyListener, RotatableCanvasI
@@ -73,7 +87,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
   int npoint;
 
-  Vector points;
+  Vector<SequencePoint> points;
 
   float[][] orig;
 
@@ -97,11 +111,11 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
   float scalefactor = 1;
 
-  AlignViewport av;
+  AlignmentViewport av;
 
   boolean showLabels = false;
 
-  public RotatableCanvas(AlignViewport av)
+  public RotatableCanvas(AlignmentViewport av)
   {
     this.av = av;
   }
@@ -112,6 +126,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void setPoints(Vector points, int npoint)
   {
     this.points = points;
@@ -216,7 +231,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     {
       for (int j = 0; j < npoint; j++)
       {
-        SequencePoint sp = (SequencePoint) points.elementAt(j);
+        SequencePoint sp = points.elementAt(j);
         if (sp.coord[i] >= max[i])
         {
           max[i] = sp.coord[i];
@@ -273,7 +288,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
       dim = height;
     }
 
-    return (float) (dim * scalefactor / (2 * maxwidth));
+    return dim * scalefactor / (2 * maxwidth);
   }
 
   public void findCentre()
@@ -290,6 +305,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     // System.out.println("Centre z " + centre[2]);
   }
 
+  @Override
   public Dimension getPreferredSize()
   {
     if (prefsize != null)
@@ -302,22 +318,27 @@ public class RotatableCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public Dimension getMinimumSize()
   {
     return getPreferredSize();
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     if (points == null)
     {
       g.setFont(new Font("Verdana", Font.PLAIN, 18));
-      g.drawString(MessageManager.getString("label.calculating_pca") + "....", 20, getSize().height / 2);
+      g.drawString(
+              MessageManager.getString("label.calculating_pca") + "....",
+              20, getSize().height / 2);
     }
     else
     {
@@ -381,25 +402,26 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
-      int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+      SequencePoint sp = points.elementAt(i);
+      int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
+      int y = (int) ((sp.coord[1] - centre[1]) * scale)
               + halfheight;
       float z = sp.coord[1] - centre[2];
 
-      if (av.getSequenceColour(sp.sequence) == Color.black)
+      SequenceI sequence = sp.getSequence();
+      if (av.getSequenceColour(sequence) == Color.black)
       {
         g.setColor(Color.white);
       }
       else
       {
-        g.setColor(av.getSequenceColour(sp.sequence));
+        g.setColor(av.getSequenceColour(sequence));
       }
 
       if (av.getSelectionGroup() != null)
       {
         if (av.getSelectionGroup().getSequences(null)
-                .contains(((SequencePoint) points.elementAt(i)).sequence))
+                .contains(sequence))
         {
           g.setColor(Color.gray);
         }
@@ -413,9 +435,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
       if (showLabels)
       {
         g.setColor(Color.red);
-        g.drawString(
-                ((SequencePoint) points.elementAt(i)).sequence.getName(),
-                x - 3, y - 4);
+        g.drawString(sequence.getName(), x - 3, y - 4);
       }
     }
   }
@@ -430,14 +450,17 @@ public class RotatableCanvas extends Panel implements MouseListener,
     return prefsize;
   }
 
+  @Override
   public void keyTyped(KeyEvent evt)
   {
   }
 
+  @Override
   public void keyReleased(KeyEvent evt)
   {
   }
 
+  @Override
   public void keyPressed(KeyEvent evt)
   {
     if (evt.getKeyCode() == KeyEvent.VK_UP)
@@ -466,7 +489,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
   {
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      SequencePoint sp = points.elementAt(i);
       Format.print(System.out, "%5d ", i);
       for (int j = 0; j < 3; j++)
       {
@@ -476,22 +499,27 @@ public class RotatableCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     int x = evt.getX();
@@ -536,6 +564,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     SequenceI found = findPoint(evt.getX(), evt.getY());
@@ -552,6 +581,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     mx = evt.getX();
@@ -559,12 +589,12 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
     rotmat.setIdentity();
 
-    rotmat.rotate((float) (my - omy), 'x');
-    rotmat.rotate((float) (mx - omx), 'y');
+    rotmat.rotate(my - omy, 'x');
+    rotmat.rotate(mx - omx, 'y');
 
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      SequencePoint sp = points.elementAt(i);
       sp.coord[0] -= centre[0];
       sp.coord[1] -= centre[1];
       sp.coord[2] -= centre[2];
@@ -593,18 +623,21 @@ public class RotatableCanvas extends Panel implements MouseListener,
     // boolean changedSel = false;
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale + (float) getSize().width / 2.0);
-      int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale + (float) getSize().height / 2.0);
+      SequencePoint sp = points.elementAt(i);
+      int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale
+              + getSize().width / 2.0);
+      int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale
+              + getSize().height / 2.0);
 
+      SequenceI sequence = sp.getSequence();
       if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
       {
         if (av != null)
         {
           if (!av.getSelectionGroup().getSequences(null)
-                  .contains(sp.sequence))
+                  .contains(sequence))
           {
-            av.getSelectionGroup().addSequence(sp.sequence, true);
+            av.getSelectionGroup().addSequence(sequence, true);
           }
         }
       }
@@ -622,10 +655,10 @@ public class RotatableCanvas extends Panel implements MouseListener,
     for (int i = 0; i < npoint; i++)
     {
 
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+      SequencePoint sp = points.elementAt(i);
+      int px = (int) ((sp.coord[0] - centre[0]) * scale)
               + halfwidth;
-      int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+      int py = (int) ((sp.coord[1] - centre[1]) * scale)
               + halfheight;
 
       if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
@@ -635,7 +668,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     }
     if (found != -1)
     {
-      return ((SequencePoint) points.elementAt(found)).sequence;
+      return points.elementAt(found).getSequence();
     }
     else
     {