Mapping to PDB added

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

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 754d698..44370d4 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -22,10 +22,8 @@ package jalview.appletgui;
 import java.awt.*;\r
 import java.awt.event.*;\r
 \r
-import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
 import jalview.jbappletgui.*;\r
-import jalview.schemes.*;\r
 \r
 public class AlignmentPanel\r
     extends GAlignmentPanel implements AdjustmentListener\r
@@ -44,8 +42,13 @@ public class AlignmentPanel
   // this value is set false when selection area being dragged\r
   boolean fastPaint = true;\r
 \r
+  boolean MAC = false;\r
+\r
   public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
   {\r
+    if(System.getProperty("os.name").startsWith("Mac"))\r
+      MAC = true;\r
+\r
     alignFrame = af;\r
     this.av = av;\r
     seqPanel = new SeqPanel(av, this);\r
@@ -141,6 +144,11 @@ public class AlignmentPanel
             alignFrame.findMenuItem_actionPerformed(null);\r
           }\r
           break;\r
+        case KeyEvent.VK_BACK_SPACE:\r
+        case KeyEvent.VK_DELETE:\r
+          alignFrame.cut_actionPerformed(null);\r
+          break;\r
+\r
       }\r
     }\r
   }\r
@@ -162,6 +170,9 @@ public class AlignmentPanel
     hscrollFillerPanel.setSize(d);\r
 \r
     alignFrame.pack();\r
+\r
+    if(overviewPanel!=null)\r
+          overviewPanel.updateOverviewImage();\r
   }\r
 \r
   public void setIdWidth(int w, int h)\r
@@ -193,14 +204,7 @@ public class AlignmentPanel
     while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
     {\r
       SequenceI s = al.getSequenceAt(i);\r
-      if (av.getShowFullId())\r
-      {\r
-        id = s.getDisplayId();\r
-      }\r
-      else\r
-      {\r
-        id = s.getName();\r
-      }\r
+      id = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
 \r
       if (fm.stringWidth(id) > idWidth)\r
       {\r
@@ -261,21 +265,33 @@ public class AlignmentPanel
 \r
   public void setAnnotationVisible(boolean b)\r
   {\r
-    annotationSpaceFillerHolder.setVisible(b);\r
-    annotationScroller.setVisible(b);\r
+    if (!av.wrapAlignment)\r
+    {\r
+      annotationSpaceFillerHolder.setVisible(b);\r
+      annotationScroller.setVisible(b);\r
+    }\r
     validate();\r
     repaint();\r
   }\r
 \r
   public void setWrapAlignment(boolean wrap)\r
   {\r
+    av.startSeq = 0;\r
     scalePanelHolder.setVisible(!wrap);\r
     hscroll.setVisible(!wrap);\r
     idwidthAdjuster.setVisible(!wrap);\r
 \r
-    av.setShowAnnotation(!wrap);\r
-    annotationScroller.setVisible(!wrap);\r
-    annotationSpaceFillerHolder.setVisible(!wrap);\r
+    if (wrap)\r
+    {\r
+      annotationScroller.setVisible(false);\r
+      annotationSpaceFillerHolder.setVisible(false);\r
+    }\r
+    else if (av.showAnnotation)\r
+    {\r
+      annotationScroller.setVisible(true);\r
+      annotationSpaceFillerHolder.setVisible(true);\r
+    }\r
+\r
     idSpaceFillerPanel1.setVisible(!wrap);\r
 \r
     validate();\r
@@ -283,29 +299,6 @@ public class AlignmentPanel
 \r
   }\r
 \r
-  public void setColourScheme()\r
-  {\r
-    ColourSchemeI cs = av.getGlobalColourScheme();\r
-\r
-    if (av.getConservationSelected())\r
-    {\r
-\r
-      Alignment al = (Alignment) av.getAlignment();\r
-      Conservation c = new Conservation("All",\r
-                                        ResidueProperties.propHash, 3,\r
-                                        al.getSequences(), 0,\r
-                                        al.getWidth());\r
-\r
-      c.calculate();\r
-      c.verdict(false, av.ConsPercGaps);\r
-      ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
-\r
-      av.setGlobalColourScheme(ccs);\r
-\r
-    }\r
-\r
-    repaint();\r
-  }\r
 \r
   int hextent = 0;\r
   int vextent = 0;\r
@@ -447,7 +440,7 @@ public class AlignmentPanel
       overviewPanel.setBoxPosition();\r
     }\r
 \r
-    if (av.getWrapAlignment() || !fastPaint)\r
+    if (av.getWrapAlignment() || !fastPaint || MAC)\r
     {\r
       repaint();\r
     }\r
@@ -477,13 +470,8 @@ public class AlignmentPanel
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);\r
     annotationSpaceFillerHolder.setSize(d.width,\r
                                         annotationPanel.getSize().height);\r
-    alabels.setSize(d.width, annotationPanel.getSize().height);\r
 \r
-    alabels.repaint();\r
-    idPanel.idCanvas.repaint();\r
-    seqPanel.seqCanvas.repaint();\r
-    scalePanel.repaint();\r
-    annotationPanel.repaint();\r
+    alabels.setSize(d.width, annotationPanel.getSize().height);\r
 \r
     if (av.getWrapAlignment())\r
     {\r
@@ -499,5 +487,11 @@ public class AlignmentPanel
       setScrollValues(av.getStartRes(), av.getStartSeq());\r
     }\r
 \r
+    alabels.repaint();\r
+    idPanel.idCanvas.repaint();\r
+    seqPanel.seqCanvas.repaint();\r
+    scalePanel.repaint();\r
+    annotationPanel.repaint();\r
+\r
   }\r
 }\r