From: amwaterhouse <Andrew Waterhouse>
Date: Sat, 16 Apr 2005 13:46:56 +0000 (+0000)
Subject: AlignPanel RefreshPanels put into paintComponent
X-Git-Tag: Release_2_0~401
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=79f4b175e12f4c16d598b4cb56ffe62532b592a1;p=jalview.git

AlignPanel RefreshPanels put into paintComponent
---

diff --git a/src/jalview/analysis/SequenceFeatureFetcher.java b/src/jalview/analysis/SequenceFeatureFetcher.java
index 667a2dd..2c0aaac 100755
--- a/src/jalview/analysis/SequenceFeatureFetcher.java
+++ b/src/jalview/analysis/SequenceFeatureFetcher.java
@@ -99,7 +99,7 @@ public class SequenceFeatureFetcher implements Runnable
     }
   }catch(Exception ex){ex.printStackTrace();}
 
-  ap.RefreshPanels();
+  ap.repaint();
   findMissingIds(align);
   if(sbuffer.length()>0)
   {
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3625e45..c12cf09 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -247,8 +247,7 @@ public class AlignFrame extends GAlignFrame
       viewport.setAlignment( new Alignment(seq) );
       updateEditMenuBar();
       viewport.updateConsensus();
-      alignPanel.RefreshPanels();
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
   }
 
   public void moveSelectedSequences(boolean up)
@@ -290,7 +289,7 @@ public class AlignFrame extends GAlignFrame
       }
     }
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
@@ -365,7 +364,7 @@ public class AlignFrame extends GAlignFrame
         viewport.alignment.getWidth();
         viewport.updateConservation();
         viewport.updateConsensus();
-        alignPanel.RefreshPanels();
+        alignPanel.repaint();
       }
 
     }catch(Exception ex){}// could be anything being pasted in here
@@ -408,7 +407,7 @@ public class AlignFrame extends GAlignFrame
      }catch(Exception ex){}
    viewport.updateConservation();
    viewport.updateConsensus();
-     alignPanel.RefreshPanels();
+     alignPanel.repaint();
 
   }
 
@@ -421,8 +420,8 @@ public class AlignFrame extends GAlignFrame
      viewport.setAlignment( new Alignment(seq) );
      updateEditMenuBar();
      viewport.updateConsensus();
-     alignPanel.RefreshPanels();
-     alignPanel.RefreshPanels();
+     alignPanel.repaint();
+     alignPanel.repaint();
   }
 
 
@@ -431,7 +430,7 @@ public class AlignFrame extends GAlignFrame
     viewport.alignment.deleteAllGroups();
     viewport.setSelectionGroup(null);
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
@@ -489,7 +488,7 @@ public class AlignFrame extends GAlignFrame
           viewport.alignment.deleteGroup(sg);
       }
 
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
     }
   }
 
@@ -514,7 +513,7 @@ public class AlignFrame extends GAlignFrame
 
 
 
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
     }
 
   }
@@ -525,7 +524,7 @@ public class AlignFrame extends GAlignFrame
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -547,7 +546,7 @@ public class AlignFrame extends GAlignFrame
     }
     viewport.updateConservation();
     viewport.updateConsensus();
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void setGapCharMenuItem_actionPerformed(ActionEvent e)
@@ -561,7 +560,7 @@ public class AlignFrame extends GAlignFrame
     }
     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
     viewport.setGapCharacter(thisChar);
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void findMenuItem_actionPerformed(ActionEvent e)
@@ -589,13 +588,13 @@ public class AlignFrame extends GAlignFrame
     viewport.setShowFullId( fullSeqId.isSelected() );
 
     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
       viewport.setColourText( colourTextMenuItem.isSelected() );
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
   }
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
@@ -605,7 +604,7 @@ public class AlignFrame extends GAlignFrame
     scaleAbove.setVisible( wrapMenuItem.isSelected() );
     scaleLeft.setVisible( wrapMenuItem.isSelected() );
     scaleRight.setVisible( wrapMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   protected void scaleAbove_actionPerformed(ActionEvent e)
@@ -631,20 +630,20 @@ public class AlignFrame extends GAlignFrame
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText( viewTextMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sequenceFeatures_actionPerformed(ActionEvent evt)
@@ -655,7 +654,7 @@ public class AlignFrame extends GAlignFrame
          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
          ((Alignment)viewport.alignment).featuresAdded = true;
     }
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
@@ -870,7 +869,7 @@ public class AlignFrame extends GAlignFrame
 
 
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
@@ -952,14 +951,14 @@ public class AlignFrame extends GAlignFrame
   {
     addHistoryItem("sort");
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("sort");
     AlignmentSorter.sortByID( viewport.getAlignment() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
@@ -967,7 +966,7 @@ public class AlignFrame extends GAlignFrame
     addHistoryItem("sort");
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
@@ -1078,7 +1077,7 @@ public class AlignFrame extends GAlignFrame
       {
         addHistoryItem("sort");
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
-        alignPanel.RefreshPanels();
+        alignPanel.repaint();
       }
     });
 
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 0cbdfbe..98eb180 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -59,19 +59,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-     {
-       public void run()
-       {
-         invalidate();
-         setScrollValues(0,0);
-         Dimension d = calculateIdWidth();
-         d.setSize( d.width+4, d.height);
-         idPanel.idCanvas.setPreferredSize( d );
-         RefreshPanels();
-       }
-    });
-
+    setScrollValues(0, 0);
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
@@ -80,7 +68,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    {
      public void componentResized(ComponentEvent evt)
      {
-          RefreshPanels();
+          repaint();
      }
    });
 
@@ -93,7 +81,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
        {
          case  27: // escape key
            av.setSelectionGroup(null);
-           RefreshPanels();
+           repaint();
            break;
          case KeyEvent.VK_X:
            if(evt.isControlDown())
@@ -203,14 +191,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   {
     annotationSpaceFillerHolder.setVisible(b);
     annotationScroller.setVisible(b);
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-     {
-       public void run()
-       {
-         RefreshPanels();
-       }
-    });
-
   }
 
 
@@ -224,13 +204,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     annotationScroller.setVisible(!wrap);
     annotationSpaceFillerHolder.setVisible(!wrap);
     idSpaceFillerPanel1.setVisible(!wrap);
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-     {
-       public void run()
-       {
-         RefreshPanels();
-       }
-    });
+
+    repaint();
 
   }
 
@@ -255,30 +230,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     }
 
-    RefreshPanels();
-  }
-
-
-  public void RefreshPanels()
-  {
-
-    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.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-      vscroll.setValues(0, 1, 0, max);
-    }
-    else
-    {
-      if (overviewPanel != null)
-        overviewPanel.updateOverviewImage();
-      setScrollValues(av.getStartRes(), av.getStartSeq());
-    }
-
-    validate();
     repaint();
   }
 
@@ -403,6 +354,31 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   }
 
+  public void paintComponent(Graphics g)
+  {
+    invalidate();
+
+    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.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+      vscroll.setMaximum(max);
+      vscroll.setUnitIncrement(1);
+    }
+    else
+    {
+      if (overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+      setScrollValues(av.getStartRes(), av.getStartSeq());
+    }
+
+    validate();
+
+  }
+
   public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
   {
     pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 3332f08..26cba7a 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -84,7 +84,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, MouseMoti
    }
 
    ap.annotationPanel.adjustPanelHeight();
-   ap.RefreshPanels();
+   ap.repaint();
 
   }
 
@@ -156,7 +156,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, MouseMoti
       ap.annotationScroller.setPreferredSize(new Dimension(d.width,d.height - dif));
       d = ap.annotationSpaceFillerHolder.getPreferredSize();
       ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,d.height - dif));
-      ap.RefreshPanels();
+      ap.repaint();
     }
     ap.addNotify();
   }
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index 3edbdb6..e04c177 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -52,7 +52,7 @@ public class FontChooser extends GFontChooser
   protected void cancel_actionPerformed(ActionEvent e)
   {
     ap.av.setFont(oldFont);
-    ap.RefreshPanels();
+    ap.repaint();
     fontName.setSelectedItem(oldFont.getName());
     fontSize.setSelectedItem(oldFont.getSize()+"");
     fontStyle.setSelectedIndex(oldFont.getStyle());
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 81e9da7..6872136 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -38,8 +38,7 @@ public class IdwidthAdjuster extends JPanel implements MouseListener, MouseMotio
     if(d.width+dif>20 || dif>0)
     {
       ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,d.height));
-      ap.invalidate();
-      ap.RefreshPanels();
+      ap.repaint();
     }
 
     oldX = evt.getX();
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index b04530c..b07dce8 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -546,7 +546,7 @@ public class PopupMenu extends JPopupMenu
     if(s!=null)
     {
       sequence.setName(s);
-      ap.RefreshPanels();
+      ap.repaint();
     }
 
   }
@@ -556,7 +556,7 @@ public class PopupMenu extends JPopupMenu
      SequenceGroup sg = ap.av.getSelectionGroup();
      ap.av.alignment.deleteGroup(sg);
      ap.av.setSelectionGroup(null);
-     ap.RefreshPanels();
+     ap.repaint();
   }
 
   void pdbMenuItem_actionPerformed(ActionEvent e)
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 3eec476..93ffd9c 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -76,7 +76,7 @@ public class RedundancyPanel extends GSliderPanel
            }
          }
 
-         ap.RefreshPanels();
+         ap.repaint();
 
   }
 
@@ -85,7 +85,7 @@ public class RedundancyPanel extends GSliderPanel
       undoButton.setEnabled(false);
       ap.av.setAlignment( new Alignment(oldAlignment) );
       oldAlignment = null;
-      ap.RefreshPanels();
+      ap.repaint();
   }
 
 
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 01ba119..e49eb17 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -65,7 +65,7 @@ public class ScalePanel extends JPanel
       ap.annotationPanel.addEditableColumn(res);
     }
     av.setSelectionGroup(sg);
-    ap.RefreshPanels();
+    ap.repaint();
   }
 
   public void doMouseReleased(MouseEvent evt)
@@ -87,7 +87,7 @@ public class ScalePanel extends JPanel
      sg.setStartRes(res);
 
    stretchingGroup = false;
-   ap.RefreshPanels();
+   ap.repaint();
   }
 
   public void doMouseDragged(MouseEvent evt)
@@ -105,7 +105,7 @@ public class ScalePanel extends JPanel
         sg.setStartRes(res);
 
        ap.annotationPanel.addEditableColumn(res);
-      ap.RefreshPanels();
+      ap.repaint();
     }
   }
 
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 6dc2acd..c243a2e 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -133,11 +133,19 @@ public void fastPaint(int horizontal, int vertical)
 
     else if (vertical > 0) // scroll down
     {
-      transY = imgHeight - vertical * av.charHeight;
       ss = es - vertical;
+      if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time
+        ss = av.startSeq;
+      else
+        transY = imgHeight - vertical * av.charHeight;
     }
     else if (vertical < 0)
+    {
       es = ss - vertical;
+      if(es > av.endSeq)
+        es = av.endSeq;
+    }
+
 
     gg.translate(transX, transY);
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 0fa6d17..0b84fa5 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -115,8 +115,7 @@ public class SeqPanel extends JPanel
 
     seqEditOccurred = -1;
 
-    ap.RefreshPanels();
-    repaint();
+    ap.repaint();
 
   }
 
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 05edac5..25820c9 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -119,7 +119,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
     else
       ap.av.setGlobalColourScheme(ucs);
 
-    ap.RefreshPanels();
+    ap.repaint();
   }
 
   protected void loadbutton_actionPerformed(ActionEvent e)
@@ -200,7 +200,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
     else
       ap.av.setGlobalColourScheme(ucs);
 
-    ap.RefreshPanels();
+    ap.repaint();
 
   }