X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=9d6467a05ac5b2dede3fd9101bedc1d8a0294c75;hb=e83f899e879e04af8f9baa9a495e2918a67f6a4f;hp=33b86651dde4deced7d41e611158f823453d46a2;hpb=4679c58949f642fd64e9726ec5bf2c3f338a0861;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 33b8665..9d6467a 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,11 +1,12 @@
 package jalview.gui;
 
 import jalview.jbgui.GAlignmentPanel;
+import jalview.schemes.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
 import java.awt.*;
-import java.awt.image.*;
 import java.awt.event.*;
 import java.awt.print.*;
-import javax.swing.*;
 
 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
 {
@@ -14,19 +15,22 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   OverviewPanel overviewPanel;
   SeqPanel   seqPanel;
   IdPanel    idPanel;
+  SecondaryStructurePanel ssPanel;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
   ScorePanel scorePanel;
 
-  public AlignmentPanel(AlignFrame af, AlignViewport av)
+  public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     alignFrame = af;
     this.av         = av;
     seqPanel        = new SeqPanel  (av, this);
     idPanel         = new IdPanel   (av, this);
-    scalePanel = new ScalePanel(av);
+    scalePanel = new ScalePanel(av, this);
     scorePanel = new ScorePanel(av);
+    ssPanel = new SecondaryStructurePanel(av);
 
+    secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idPanel.addNotify();
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
@@ -44,6 +48,24 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
           RefreshPanels();
      }
    });
+
+   hscroll.setFocusable(false);
+   vscroll.setFocusable(false);
+   setFocusable(true);
+
+   addKeyListener(new KeyAdapter()
+   {
+     public void keyPressed(KeyEvent evt)
+     {
+       if(evt.getKeyCode()==27)
+       {
+         av.setRubberbandGroup(null);
+         RefreshPanels();
+       }
+     }
+   });
+
+
   }
 
  public void highlightSearchResults(int [] results)
@@ -74,8 +96,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setGraphPanelVisible(boolean b)
   {
-    scorePanelHolder.setVisible(b);
     idSpaceFillerPanel.setVisible(b);
+    scorePanelHolder.setVisible(b);
+
+    RefreshPanels();
+    // bit annoying to call this twice, can you do better?
+    RefreshPanels();
+  }
+
+  public void setSecondaryStructureVisible(boolean b)
+  {
+    secondaryPanelHolder.setVisible(b);
     RefreshPanels();
   }
 
@@ -90,27 +121,44 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   }
 
 
-  public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
+  public void setColourScheme()
   {
-    seqPanel.setColourScheme(cs, conservation);
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
-  }
+    ColourSchemeI cs = av.getGlobalColourScheme();
 
+    if(av.getConservationSelected())
+    {
+
+       Alignment al = (Alignment)av.getAlignment();
+       Conservation c = new Conservation("All",
+                            ResidueProperties.propHash, 3, al.getSequences(), 0,
+                            al.getWidth() );
+
+       c.calculate();
+       c.verdict(false, 100);
+       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+
+       av.setGlobalColourScheme( ccs );
+
+    }
+
+    RefreshPanels();
+  }
 
   public void RefreshPanels()
   {
+    requestFocus();
     invalidate();
     seqPanel.seqCanvas.paintFlag = true;
     idPanel.idCanvas.paintFlag = true;
     idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
     setScrollValues(av.getStartRes(), av.getStartSeq());
     av.getConsensus(true);
-    repaint();
-    validate();
     if(overviewPanel!=null)
       overviewPanel.updateOverviewImage();
 
+    validate();
+    repaint();
+
   }
 
   int hextent = 0;
@@ -118,7 +166,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setScrollValues(int x, int y)
   {
-    hextent = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth());
+    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
     vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
 
     if(hextent+x  >  av.getAlignment().getWidth())
@@ -135,6 +183,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+
+
     repaint();
 
   }
@@ -147,7 +197,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1));
+      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
     }
 
     if (evt.getSource() == vscroll)
@@ -175,15 +225,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     int pheight = (int)pf.getImageableHeight();
     int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
 
-    //BufferedImage printImage = new BufferedImage(pwidth,pheight,BufferedImage.TYPE_INT_RGB);
-   // Graphics pg = printImage.getGraphics();
     pg.setColor(Color.white);
     pg.fillRect(0,0,pwidth, pheight);
     pg.setFont( av.getFont() );
 
     ////////////////////////////////////
     /// How many sequences and residues can we fit on a printable page?
-    int totalRes = (int)((pwidth - idWidth)/av.getCharWidth());
+    int totalRes = (pwidth - idWidth)/av.getCharWidth();
     int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
     int pagesWide = av.getAlignment().getWidth() / totalRes +1;
     int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
@@ -230,7 +278,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
       pg.setColor(currentColor);
       pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
-                              getWidth(),
+                              idWidth,
                               av.getCharHeight());
 
       pg.setColor(currentTextColor);
@@ -242,9 +290,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     // draw main sequence panel
     pg.translate(idWidth,0);
+    pg.setClip(0,0,pwidth-idWidth, pheight);
     seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
 
     return Printable.PAGE_EXISTS;
   }
+
 }
 
+
+