X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=75729c330775e2b93ab5067126233e926b726e18;hb=8004878db16757b62ee2c35738506bc4509428cf;hp=d8131b4706c170a857f2e98f8848c79c0ea2990e;hpb=416b11342497ccc6f86cabfd5ae2a608f402ce9c;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d8131b4..75729c3 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -22,10 +22,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   SeqPanel   seqPanel;
   IdPanel    idPanel;
   IdwidthAdjuster idwidthAdjuster;
-  SecondaryStructurePanel ssPanel;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
-  ScorePanel scorePanel;
+  AnnotationPanel annotationPanel;
+  AnnotationLabels alabels;
+
+  // this value is set false when selection area being dragged
+  boolean fastPaint = true;
 
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
@@ -35,22 +38,25 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     idPanel         = new IdPanel   (av, this);
 
     scalePanel = new ScalePanel(av, this);
-    scorePanel = new ScorePanel(av);
-    ssPanel = new SecondaryStructurePanel(av);
-
-    secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
 
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idwidthAdjuster = new IdwidthAdjuster(this);
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
 
+    annotationPanel = new AnnotationPanel(this);
+    alabels = new AnnotationLabels(this);
+
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationScroller.setViewportView(annotationPanel);
+    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+
     Dimension d = calculateIdWidth();
     d.setSize( d.width+4, d.height);
     idPanel.idCanvas.setPreferredSize( d );
     hscrollFillerPanel.setPreferredSize( d );
 
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
 
@@ -63,7 +69,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
          Dimension d = calculateIdWidth();
          d.setSize( d.width+4, d.height);
          idPanel.idCanvas.setPreferredSize( d );
-         hscrollFillerPanel.setPreferredSize( d );
          RefreshPanels();
        }
     });
@@ -92,15 +97,19 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
            RefreshPanels();
            break;
          case KeyEvent.VK_X:
+           if(evt.isControlDown())
            alignFrame.cut_actionPerformed(null);
            break;
          case KeyEvent.VK_C:
+         if(evt.isControlDown())
            alignFrame.copy_actionPerformed(null);
            break;
          case KeyEvent.VK_V:
+          if(evt.isControlDown())
            alignFrame.paste(true);
            break;
          case KeyEvent.VK_A:
+         if(evt.isControlDown())
            alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
            break;
         case KeyEvent.VK_DOWN:
@@ -110,6 +119,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
           alignFrame.moveSelectedSequences(true);
           break;
         case KeyEvent.VK_F:
+         if(evt.isControlDown())
           alignFrame.findMenuItem_actionPerformed(null);
           break;
        }
@@ -176,32 +186,30 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
  }
 
 
-  public void setGraphPanelVisible(boolean b)
+  public void setAnnotationVisible(boolean b)
   {
-    idSpaceFillerPanel.setVisible(b);
-    scorePanelHolder.setVisible(b);
+    annotationSpaceFillerHolder.setVisible(b);
+    annotationScroller.setVisible(b);
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+     {
+       public void run()
+       {
+         RefreshPanels();
+       }
+    });
 
-    RefreshPanels();
-    // bit annoying to call this twice, can you do better?
-    RefreshPanels();
   }
 
-  public void setSecondaryStructureVisible(boolean b)
-  {
-    secondaryPanelHolder.setVisible(b);
-    RefreshPanels();
-  }
 
   public void setWrapAlignment(boolean wrap)
   {
-    scorePanelHolder.setVisible(!wrap);
     scalePanelHolder.setVisible(!wrap);
-    secondaryPanelHolder.setVisible(!wrap);
-
     hscroll.setVisible(!wrap);
-
     idwidthAdjuster.setVisible(!wrap);
-    idSpaceFillerPanel.setVisible(!wrap);
+
+    av.setShowAnnotation(!wrap);
+    annotationScroller.setVisible(!wrap);
+    annotationSpaceFillerHolder.setVisible(!wrap);
     idSpaceFillerPanel1.setVisible(!wrap);
 
     RefreshPanels();
@@ -232,35 +240,31 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     RefreshPanels();
   }
 
+
   public void RefreshPanels()
   {
+    requestFocus();
+    invalidate();
 
-              requestFocus();
-              invalidate();
-              idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
-              if(idPanel.idCanvas.getPreferredSize()!=null)
-                hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12));
-              idSpaceFillerPanel1.setPreferredSize(new Dimension(500,
-                  av.charHeight / 2 + 12));
-              scalePanelHolder.setPreferredSize(new Dimension(500,
-                  av.charHeight / 2 + 12));
-
-              if (av.getWrapAlignment())
-              {
-                int max = av.alignment.getWidth() /
-                    (seqPanel.seqCanvas.getWidth() / av.charWidth)+1 ;
-
-                vscroll.setValues(0, 1, 0, max);
-              }
-              else
-              {
-                av.getConsensus(true);
-                if (overviewPanel != null)
-                  overviewPanel.updateOverviewImage();
-                 setScrollValues(av.getStartRes(), av.getStartSeq());
-              }
-
-          repaint();
+    Dimension d = idPanel.idCanvas.getPreferredSize();
+    idPanelHolder.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+
+    if (av.getWrapAlignment())
+    {
+      int max = av.alignment.getWidth() /
+          (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;
+      vscroll.setValues(0, 1, 0, max);
+    }
+    else
+    {
+      if (overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+      setScrollValues(av.getStartRes(), av.getStartSeq());
+    }
+
+    validate();
+    repaint();
   }
 
   int hextent = 0;
@@ -273,35 +277,40 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       if(vscroll.getValue()<1)
         return false;
+      fastPaint  = false;
       vscroll.setValue(vscroll.getValue() - 1);
     }
     else
     {
      if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
        return false;
+      fastPaint  = false;
       vscroll.setValue(vscroll.getValue() + 1);
     }
-
+    fastPaint = true;
     return true;
   }
 
   public boolean scrollRight(boolean right)
   {
-    if(right)
-   {
-     if(hscroll.getValue()<1)
-       return false;
-     hscroll.setValue(hscroll.getValue() - 1);
-   }
-   else
-   {
-    if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
-      return false;
-     hscroll.setValue(hscroll.getValue() + 1);
-   }
 
-   return true;
- }
+    if (right)
+    {
+      if (hscroll.getValue() < 1)
+        return false;
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() - 1);
+    }
+    else
+    {
+      if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+        return false;
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() + 1);
+    }
+    fastPaint = true;
+    return true;
+  }
 
 
   public void setScrollValues(int x, int y)
@@ -329,13 +338,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
 
-    repaint();
-
   }
 
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
+    int oldX = av.getStartRes();
+    int oldY = av.getStartSeq();
 
     if (evt.getSource() == hscroll)
     {
@@ -362,7 +371,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     if(overviewPanel!=null)
       overviewPanel.setBoxPosition();
 
-    repaint();
+    if(av.getWrapAlignment() || !fastPaint)
+      repaint();
+    else
+    {
+      seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
+                                   av.getStartSeq() - oldY);
+      idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
+      scalePanel.repaint();
+      if (av.getShowAnnotation())
+        annotationPanel.fastPaint(av.getStartRes() - oldX);
+    }
+
   }
 
   public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
@@ -452,9 +472,17 @@ 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);
 
+
+    if(av.getShowAnnotation())
+      {
+        pg.translate(-idWidth,(endSeq-startSeq)*av.charHeight);
+        alabels.drawComponent((Graphics2D)pg);
+        pg.translate(idWidth,0);
+        annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes+1);
+      }
+
     return Printable.PAGE_EXISTS;
   }
 
@@ -528,6 +556,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       height = (av.alignment.getHeight()+1) * av.charHeight + 30;
       width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
     }
+    if(av.getShowAnnotation())
+   {
+     height += annotationPanel.getPreferredSize().height;
+   }
 
     try
     {
@@ -571,7 +603,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
         width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
       }
 
+      if(av.getShowAnnotation())
+      {
+        height += annotationPanel.getPreferredSize().height;
+      }
+
 
+System.out.println(width +" "+height);
 
     try
     {