Alignment Annotation added

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d8131b4..248fb3d 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -22,10 +22,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   SeqPanel   seqPanel;\r
   IdPanel    idPanel;\r
   IdwidthAdjuster idwidthAdjuster;\r
-  SecondaryStructurePanel ssPanel;\r
   public AlignFrame alignFrame;\r
   ScalePanel scalePanel;\r
-  ScorePanel scorePanel;\r
+  AnnotationPanel annotationPanel;\r
+  AnnotationLabels alabels;\r
 \r
   public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
   {\r
@@ -35,22 +35,25 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     idPanel         = new IdPanel   (av, this);\r
 \r
     scalePanel = new ScalePanel(av, this);\r
-    scorePanel = new ScorePanel(av);\r
-    ssPanel = new SecondaryStructurePanel(av);\r
-\r
-    secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);\r
 \r
     idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
     idwidthAdjuster = new IdwidthAdjuster(this);\r
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
 \r
+    annotationPanel = new AnnotationPanel(this);\r
+    alabels = new AnnotationLabels(this);\r
+\r
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());\r
+    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
+    annotationScroller.setViewportView(annotationPanel);\r
+    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
+\r
     Dimension d = calculateIdWidth();\r
     d.setSize( d.width+4, d.height);\r
     idPanel.idCanvas.setPreferredSize( d );\r
     hscrollFillerPanel.setPreferredSize( d );\r
 \r
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
-    scorePanelHolder.add(scorePanel, BorderLayout.CENTER);\r
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
 \r
 \r
@@ -63,7 +66,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
          Dimension d = calculateIdWidth();\r
          d.setSize( d.width+4, d.height);\r
          idPanel.idCanvas.setPreferredSize( d );\r
-         hscrollFillerPanel.setPreferredSize( d );\r
          RefreshPanels();\r
        }\r
     });\r
@@ -92,15 +94,19 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
            RefreshPanels();\r
            break;\r
          case KeyEvent.VK_X:\r
+           if(evt.isControlDown())\r
            alignFrame.cut_actionPerformed(null);\r
            break;\r
          case KeyEvent.VK_C:\r
+         if(evt.isControlDown())\r
            alignFrame.copy_actionPerformed(null);\r
            break;\r
          case KeyEvent.VK_V:\r
+          if(evt.isControlDown())\r
            alignFrame.paste(true);\r
            break;\r
          case KeyEvent.VK_A:\r
+         if(evt.isControlDown())\r
            alignFrame.selectAllSequenceMenuItem_actionPerformed(null);\r
            break;\r
         case KeyEvent.VK_DOWN:\r
@@ -110,6 +116,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
           alignFrame.moveSelectedSequences(true);\r
           break;\r
         case KeyEvent.VK_F:\r
+         if(evt.isControlDown())\r
           alignFrame.findMenuItem_actionPerformed(null);\r
           break;\r
        }\r
@@ -176,32 +183,28 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
  }\r
 \r
 \r
-  public void setGraphPanelVisible(boolean b)\r
+  public void setAnnotationVisible(boolean b)\r
   {\r
-    idSpaceFillerPanel.setVisible(b);\r
-    scorePanelHolder.setVisible(b);\r
+    annotationSpaceFillerHolder.setVisible(b);\r
+    annotationScroller.setVisible(b);\r
+    javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+     {\r
+       public void run()\r
+       {\r
+         RefreshPanels();\r
+       }\r
+    });\r
 \r
-    RefreshPanels();\r
-    // bit annoying to call this twice, can you do better?\r
-    RefreshPanels();\r
   }\r
 \r
-  public void setSecondaryStructureVisible(boolean b)\r
-  {\r
-    secondaryPanelHolder.setVisible(b);\r
-    RefreshPanels();\r
-  }\r
 \r
   public void setWrapAlignment(boolean wrap)\r
   {\r
-    scorePanelHolder.setVisible(!wrap);\r
     scalePanelHolder.setVisible(!wrap);\r
-    secondaryPanelHolder.setVisible(!wrap);\r
-\r
     hscroll.setVisible(!wrap);\r
-\r
     idwidthAdjuster.setVisible(!wrap);\r
-    idSpaceFillerPanel.setVisible(!wrap);\r
+    annotationScroller.setVisible(!wrap);\r
+    annotationSpaceFillerHolder.setVisible(!wrap);\r
     idSpaceFillerPanel1.setVisible(!wrap);\r
 \r
     RefreshPanels();\r
@@ -232,35 +235,31 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     RefreshPanels();\r
   }\r
 \r
+\r
   public void RefreshPanels()\r
   {\r
+    requestFocus();\r
+    invalidate();\r
+\r
+    Dimension d = idPanel.idCanvas.getPreferredSize();\r
+    idPanelHolder.setPreferredSize(d);\r
+    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
 \r
-              requestFocus();\r
-              invalidate();\r
-              idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());\r
-              if(idPanel.idCanvas.getPreferredSize()!=null)\r
-                hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12));\r
-              idSpaceFillerPanel1.setPreferredSize(new Dimension(500,\r
-                  av.charHeight / 2 + 12));\r
-              scalePanelHolder.setPreferredSize(new Dimension(500,\r
-                  av.charHeight / 2 + 12));\r
-\r
-              if (av.getWrapAlignment())\r
-              {\r
-                int max = av.alignment.getWidth() /\r
-                    (seqPanel.seqCanvas.getWidth() / av.charWidth)+1 ;\r
-\r
-                vscroll.setValues(0, 1, 0, max);\r
-              }\r
-              else\r
-              {\r
-                av.getConsensus(true);\r
-                if (overviewPanel != null)\r
-                  overviewPanel.updateOverviewImage();\r
-                 setScrollValues(av.getStartRes(), av.getStartSeq());\r
-              }\r
-\r
-          repaint();\r
+    if (av.getWrapAlignment())\r
+    {\r
+      int max = av.alignment.getWidth() /\r
+          (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;\r
+      vscroll.setValues(0, 1, 0, max);\r
+    }\r
+    else\r
+    {\r
+      if (overviewPanel != null)\r
+        overviewPanel.updateOverviewImage();\r
+      setScrollValues(av.getStartRes(), av.getStartSeq());\r
+    }\r
+\r
+    validate();\r
+    repaint();\r
   }\r
 \r
   int hextent = 0;\r
@@ -329,8 +328,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
 \r
-    repaint();\r
-\r
   }\r
 \r
 \r
@@ -363,6 +360,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       overviewPanel.setBoxPosition();\r
 \r
     repaint();\r
+\r
   }\r
 \r
   public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r