X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=0b9af01ca9a08ee2b0b749eb09f40fe9cec2d190;hb=7e1770e6de8e4cb62329b5d40346c7403e92696c;hp=a20165a78123a2ffbe1ba0d85225a08d37e50f95;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index a20165a..0b9af01 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -27,6 +27,7 @@ import javax.swing.*;
 import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.structure.*;
 
 /**
  * DOCUMENT ME!
@@ -36,7 +37,7 @@ import jalview.schemes.*;
  */
 public class SeqPanel
     extends JPanel implements MouseListener,
-    MouseMotionListener, MouseWheelListener
+    MouseMotionListener, MouseWheelListener, SequenceListener
 
 {
   /** DOCUMENT ME!! */
@@ -76,6 +77,9 @@ public class SeqPanel
 
   EditCommand editCommand;
 
+  StructureSelectionManager ssm;
+
+
   /**
    * Creates a new SeqPanel object.
    *
@@ -102,6 +106,8 @@ public class SeqPanel
       addMouseMotionListener(this);
       addMouseListener(this);
       addMouseWheelListener(this);
+      ssm = StructureSelectionManager.getStructureSelectionManager();
+      ssm.addStructureViewerListener(this);
     }
   }
 
@@ -258,13 +264,13 @@ public class SeqPanel
 
   void setCursorRow()
   {
-    seqCanvas.cursorY = getKeyboardNo(keyboardNo1) - 1;
+    seqCanvas.cursorY = getKeyboardNo1() - 1;
     scrollToVisible();
   }
 
   void setCursorColumn()
   {
-    seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+    seqCanvas.cursorX = getKeyboardNo1() - 1;
     scrollToVisible();
   }
 
@@ -276,8 +282,8 @@ public class SeqPanel
     }
     else
     {
-      seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
-      seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
+      seqCanvas.cursorX = getKeyboardNo1() - 1;
+      seqCanvas.cursorY = getKeyboardNo2() - 1;
       scrollToVisible();
     }
   }
@@ -288,7 +294,7 @@ public class SeqPanel
         (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
     seqCanvas.cursorX = sequence.findIndex(
-        getKeyboardNo(keyboardNo1) - 1
+        getKeyboardNo1() - 1
         );
     scrollToVisible();
   }
@@ -449,7 +455,7 @@ public class SeqPanel
       av.setSelectionGroup(sg);
     }
 
-    ap.repaint();
+    ap.paintAlignment(false);
   }
 
   void insertGapAtCursor(boolean group)
@@ -457,7 +463,7 @@ public class SeqPanel
     groupEditing = group;
     startseq = seqCanvas.cursorY;
     lastres = seqCanvas.cursorX;
-    editSequence(true, seqCanvas.cursorX + getKeyboardNo(keyboardNo1));
+    editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
     endEditing();
   }
 
@@ -465,7 +471,7 @@ public class SeqPanel
   {
     groupEditing = group;
     startseq = seqCanvas.cursorY;
-    lastres = seqCanvas.cursorX + getKeyboardNo(keyboardNo1);
+    lastres = seqCanvas.cursorX + getKeyboardNo1();
     editSequence(false, seqCanvas.cursorX);
     endEditing();
   }
@@ -487,15 +493,27 @@ public class SeqPanel
     }
   }
 
-  int getKeyboardNo(StringBuffer kb)
+  int getKeyboardNo1()
   {
-    if (kb == null)
-    {
+    if (keyboardNo1 == null)
       return 1;
+    else
+    {
+      int value = Integer.parseInt(keyboardNo1.toString());
+      keyboardNo1 = null;
+      return value;
     }
+  }
+
+  int getKeyboardNo2()
+  {
+    if (keyboardNo2 == null)
+      return 1;
     else
     {
-      return Integer.parseInt(kb.toString());
+      int value = Integer.parseInt(keyboardNo2.toString());
+      keyboardNo2 = null;
+      return value;
     }
   }
 
@@ -517,7 +535,7 @@ public class SeqPanel
 
     endEditing();
 
-    ap.repaint();
+    ap.paintAlignment(true);
   }
 
   /**
@@ -573,6 +591,33 @@ public class SeqPanel
     return;
   }
 
+  String lastMessage;
+  public void mouseOverSequence(SequenceI sequence, int index)
+  {
+    String tmp = sequence.hashCode()+index+"";
+    if (lastMessage == null || !lastMessage.equals(tmp))
+      ssm.mouseOverSequence(sequence, index);
+
+    lastMessage = tmp;
+  }
+
+
+  public void highlightSequence(jalview.datamodel.SequenceI seq, int index)
+  {
+    if(av.alignment.findIndex(seq)>-1)
+    {
+      SearchResults highlight = new SearchResults();
+      highlight.addResult(seq,index,index);
+      seqCanvas.highlightSearchResults(highlight);
+    }
+  }
+
+  public void updateColours(SequenceI seq, int index)
+  {
+    System.out.println("update the seqPanel colours");
+    //repaint();
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -602,10 +647,8 @@ public class SeqPanel
       return;
     }
 
-    if (seqCanvas.pdbCanvas != null && sequence == seqCanvas.pdbCanvas.sequence)
-    {
-      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
-    }
+    if (ssm != null)
+      mouseOverSequence(sequence, sequence.findPosition(res));
 
     setStatusMessage(sequence, res, seq);
 
@@ -837,7 +880,7 @@ public class SeqPanel
           av.charWidth++;
         }
 
-        ap.repaint();
+        ap.paintAlignment(false);
       }
 
       FontMetrics fm = getFontMetrics(av.getFont());
@@ -881,9 +924,10 @@ public class SeqPanel
     {
       scrollThread.setEvent(evt);
     }
-
   }
 
+
+
   synchronized void editSequence(boolean insertGap, int startres)
   {
     int fixedLeft = -1;
@@ -1355,23 +1399,6 @@ public class SeqPanel
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-    /* if (mouseWheelPressed)
-     {
-       Font font = av.getFont();
-       int fontSize = font.getSize();
-       if (e.getWheelRotation() > 0 && fontSize < 51)
-         fontSize++;
-       else if (fontSize > 1)
-         fontSize--;
-
-
-
-       av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
-
-       ap.fontChanged();
-     }
-     else*/
-    {
       if (e.getWheelRotation() > 0)
       {
         ap.scrollUp(false);
@@ -1380,8 +1407,6 @@ public class SeqPanel
       {
         ap.scrollUp(true);
       }
-    }
-
   }
 
   /**
@@ -1575,6 +1600,7 @@ public class SeqPanel
     stretchGroup = null;
 
     PaintRefresher.Refresh(this, av.getSequenceSetId());
+    ap.paintAlignment(true);
   }
 
   /**