Added OverviewPanel

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
new file mode 100755 (executable)
index 0000000..2c67388
--- /dev/null
+++ b/src/jalview/gui/OverviewPanel.java
@@ -0,0 +1,168 @@
+package jalview.gui;\r
+\r
+import javax.swing.*;\r
+import java.awt.event.*;\r
+import java.awt.image.*;\r
+import java.awt.*;\r
+\r
+public class OverviewPanel extends JPanel\r
+{\r
+  BufferedImage miniMe;\r
+  AlignViewport av;\r
+  AlignmentPanel ap;\r
+  float scalew = 1f;\r
+  float scaleh = 1f;\r
+\r
+  int sequencesWidth=400, sequencesHeight=150;\r
+  int graphHeight=30;\r
+  int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;\r
+\r
+  public OverviewPanel(AlignmentPanel ap, AlignViewport av)\r
+  {\r
+    this.av = av;\r
+    this.ap = ap;\r
+    setSize(sequencesWidth, sequencesHeight+graphHeight);\r
+    setLayout(null);\r
+\r
+    updateOverviewImage();\r
+\r
+    addComponentListener(new ComponentAdapter()\r
+   {\r
+\r
+       public void componentResized(ComponentEvent evt)\r
+       {\r
+         if( getWidth()!=sequencesWidth || getHeight()!=sequencesHeight+graphHeight)\r
+           updateOverviewImage();\r
+       }\r
+   });\r
+\r
+\r
+    addMouseMotionListener(new MouseMotionAdapter()\r
+           {\r
+             public void mouseDragged(MouseEvent evt)\r
+             { doMouseDragged(evt);}\r
+           });\r
+\r
+    addMouseListener(new MouseAdapter()\r
+    {\r
+      public void mousePressed(MouseEvent evt)\r
+      { doMousePressed(evt);}\r
+      public void mouseReleased(MouseEvent evt)\r
+      { doMouseReleased(evt);}\r
+    });\r
+\r
+  }\r
+\r
+  public void doMousePressed(MouseEvent evt)\r
+  {\r
+    checkValid(evt.getX(), evt.getY());\r
+    repaint();\r
+  }\r
+\r
+  public void doMouseReleased(MouseEvent evt)\r
+  {\r
+    int x = evt.getX();\r
+    int y = evt.getY();\r
+    checkValid(x, y);\r
+    ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) );\r
+  }\r
+\r
+  public void doMouseDragged(MouseEvent evt)\r
+  {\r
+    int x = evt.getX();\r
+    int y = evt.getY();\r
+    checkValid(x, y);\r
+    ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) );\r
+    repaint();\r
+  }\r
+\r
+  void checkValid(int x, int y)\r
+  {\r
+\r
+    if (y < 0)\r
+      y = 0;\r
+    if (y > sequencesHeight - boxHeight)\r
+      y = sequencesHeight- boxHeight;\r
+\r
+\r
+    if (x < 0)\r
+      x = 0;\r
+\r
+    if (x > sequencesWidth - boxWidth)\r
+      x = sequencesWidth - boxWidth;\r
+\r
+    boxX = x;\r
+    boxY = y;\r
+  }\r
+\r
+  public void updateOverviewImage()\r
+  {\r
+   miniMe = null;\r
+   setPreferredSize (new Dimension(sequencesWidth, sequencesHeight+graphHeight));\r
+   sequencesWidth=getWidth();\r
+   sequencesHeight=this.getHeight()-graphHeight;\r
+\r
+\r
+    int fullsizeWidth = (int)(av.getAlignment().getWidth()*av.getCharWidth());\r
+    int fullsizeHeight = av.getAlignment().getHeight()*av.getCharHeight();\r
+\r
+\r
+    BufferedImage fullSize = new BufferedImage(fullsizeWidth,\r
+                                               fullsizeHeight,\r
+                                               BufferedImage.TYPE_INT_RGB);\r
+\r
+    BufferedImage consensus = new BufferedImage(fullsizeWidth,\r
+                                               80,\r
+                                               BufferedImage.TYPE_INT_RGB);\r
+\r
+\r
+    Graphics g = fullSize.getGraphics();\r
+    ap.seqPanel.seqCanvas.drawPanel(g,0,av.getAlignment().getWidth(),0,av.getAlignment().getHeight(),0,0,0);\r
+\r
+    g = consensus.getGraphics();\r
+    ap.scorePanel.drawScorePanel(g, fullsizeWidth, 0, av.getAlignment().getWidth());\r
+\r
+    try{\r
+      miniMe = new BufferedImage(sequencesWidth, sequencesHeight + graphHeight,\r
+                                 BufferedImage.TYPE_INT_RGB);\r
+      Graphics mg = miniMe.getGraphics();\r
+\r
+      mg.drawImage(fullSize, 0, 0, sequencesWidth, sequencesHeight, 0, 0,\r
+                   fullsizeWidth, fullsizeHeight, this);\r
+      mg.drawImage(consensus, 0, sequencesHeight, sequencesWidth,\r
+                   sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
+\r
+      scalew = (float) sequencesWidth / (float) fullsizeWidth;\r
+      scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
+\r
+      setBoxPosition();\r
+    }catch(Exception ex)\r
+    {// most likely the frame size is zero\r
+      miniMe = null;\r
+    }\r
+\r
+  }\r
+\r
+  public void setBoxPosition()\r
+  {\r
+      boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
+      boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
+      boxWidth = (int) (av.getEndRes() * av.getCharWidth() * scalew) - boxX;\r
+      boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;\r
+      repaint();\r
+\r
+  }\r
+\r
+\r
+  public void paintComponent(Graphics g)\r
+  {\r
+    if(miniMe!=null)\r
+      g.drawImage(miniMe, 0,0,this);\r
+\r
+    g.setColor(Color.red);\r
+\r
+    g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
+    g.drawRect(boxX+1, boxY+1, boxWidth-2, boxHeight-2);\r
+  }\r
+\r
+}\r