apply version 2.7 copyright

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

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
old mode 100755 (executable)
new mode 100644 (file)
index 24f4786..b0de2ae
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -25,6 +25,7 @@ import java.awt.event.*;
 import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.structure.SelectionSource;
 import jalview.structure.SequenceListener;
 import jalview.structure.StructureSelectionManager;
 
@@ -90,7 +91,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     seqCanvas.addMouseMotionListener(this);
     seqCanvas.addMouseListener(this);
-    ssm = StructureSelectionManager.getStructureSelectionManager();
+    ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
     ssm.addStructureViewerListener(this);
 
     seqCanvas.repaint();
@@ -302,8 +303,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
     }
-
     ap.paintAlignment(false);
+    av.sendSelection();
   }
 
   void insertGapAtCursor(boolean group)
@@ -631,18 +632,22 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     String tmp = sequence.hashCode() + index + "";
     if (lastMessage == null || !lastMessage.equals(tmp))
-      ssm.mouseOverSequence(sequence, index, pos);
+      ssm.mouseOverSequence(sequence, index, pos, av);
 
     lastMessage = tmp;
   }
 
   public void highlightSequence(SearchResults results)
   {
-    seqCanvas.highlightSearchResults(results);
     if (av.followHighlight)
     {
-      ap.scrollToPosition(results);
+      if (ap.scrollToPosition(results, true))
+      {
+        ap.alignFrame.repaint();
+      }
     }
+    seqCanvas.highlightSearchResults(results);
+
   }
 
   public void updateColours(SequenceI seq, int index)
@@ -1448,6 +1453,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     stretchGroup = null;
     PaintRefresher.Refresh(ap, av.getSequenceSetId());
     ap.paintAlignment(true);
+    av.sendSelection();
   }
 
   public void doMouseDraggedDefineMode(MouseEvent evt)
@@ -1682,4 +1688,128 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
   }
 
+  /**
+   * modify current selection according to a received message.
+   */
+  public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+          SelectionSource source)
+  {
+    // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+    // handles selection messages...
+    // TODO: extend config options to allow user to control if selections may be
+    // shared between viewports.
+    if (av != null
+            && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignViewport) source)
+                    .getSequenceSetId().equals(av.getSequenceSetId()))))
+    {
+      return;
+    }
+    // do we want to thread this ? (contention with seqsel and colsel locks, I
+    // suspect)
+    // rules are: colsel is copied if there is a real intersection between
+    // sequence selection
+    boolean repaint = false, copycolsel = true;
+    if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+    {
+      SequenceGroup sgroup = null;
+      if (seqsel != null && seqsel.getSize()>0)
+      {
+        if (av.alignment == null)
+        {
+          System.out
+                  .println("Selection message: alignviewport av SeqSetId="
+                          + av.getSequenceSetId() + " ViewId="
+                          + av.getViewId()
+                          + " 's alignment is NULL! returning immediatly.");
+          return;
+        }
+        sgroup = seqsel.intersect(av.alignment,
+                (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+        if ((sgroup == null || sgroup.getSize() == 0)
+                && (colsel == null || colsel.size() == 0))
+        {
+          // don't copy columns if the region didn't intersect.
+          copycolsel = false;
+        }
+      }
+      if (sgroup != null && sgroup.getSize() > 0)
+      {
+        av.setSelectionGroup(sgroup);
+      }
+      else
+      {
+        av.setSelectionGroup(null);
+      }
+      repaint = av.isSelectionGroupChanged();
+    }
+    if (copycolsel && (av.colSel == null || !av.isColSelChanged()))
+    {
+      // the current selection is unset or from a previous message
+      // so import the new colsel.
+      if (colsel == null || colsel.size() == 0)
+      {
+        if (av.colSel != null)
+        {
+          av.colSel.clear();
+        }
+      }
+      else
+      {
+        // TODO: shift colSel according to the intersecting sequences
+        if (av.colSel == null)
+        {
+          av.colSel = new ColumnSelection(colsel);
+        }
+        else
+        {
+          av.colSel.setElementsFrom(colsel);
+        }
+      }
+      repaint |= av.isColSelChanged();
+    }
+    if (copycolsel && av.hasHiddenColumns
+            && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+    {
+      System.err.println("Bad things");
+    }
+    if (repaint)
+    {
+      ap.scalePanelHolder.repaint();
+      ap.repaint();
+    }
+  }
+
+  /**
+   * scroll to the given row/column - or nearest visible location
+   * @param row
+   * @param column
+   */
+  public void scrollTo(int row, int column)
+  {
+    
+    row = row<0 ? ap.av.startSeq : row;
+    column = column<0 ? ap.av.startRes : column;
+    ap.scrollTo(row, row, column, true, true);
+  }
+  /**
+   * scroll to the given row - or nearest visible location
+   * @param row
+   */
+  public void scrollToRow(int row)
+  {
+    
+    row = row<0 ? ap.av.startSeq : row;
+    ap.scrollTo(row, row, ap.av.startRes, true, true);
+  }
+  /**
+   * scroll to the given column - or nearest visible location
+   * @param column
+   */
+  public void scrollToColumn(int column)
+  {
+    
+    column = column<0 ? ap.av.startRes : column;
+    ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true);
+  }
+
 }