apply version 2.7 copyright

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
old mode 100755 (executable)
new mode 100644 (file)
index efefeaf..b7028ac
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.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.
  * 
@@ -27,20 +27,22 @@ import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
 
 /**
  * DOCUMENT ME!
  * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.161 $
  */
 public class AlignmentPanel extends GAlignmentPanel implements
-        AdjustmentListener, Printable
+        AdjustmentListener, Printable, AlignmentViewPanel
 {
   public AlignViewport av;
 
@@ -223,10 +225,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Highlight the given results on the alignment.
    * 
-   * @param results
-   *          DOCUMENT ME!
    */
   public void highlightSearchResults(SearchResults results)
   {
@@ -271,12 +271,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         return false;
       }
       SequenceI seq = av.alignment.getSequenceAt(seqIndex);
-
-      int[] r = results.getResults(seq, 0, av.alignment.getWidth()); // results.getResults(seq,
-      // seq.getStart(),
-      // seq.getEnd());
-      // TODO: VAMSAS: fix hidden column issue where scroll to left from C
-      // terminus is not visible
+      
+      int[] r=results.getResults(seq, 0, av.alignment.getWidth());
       if (r == null)
       {
         return false;
@@ -293,6 +289,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         return false;
       }
+      if (av.hasHiddenColumns)
+      {
+        start = av.getColumnSelection().findColumnPosition(start);
+        end = av.getColumnSelection().findColumnPosition(end);
+        if (start==end)
+        {
+          if (!av.colSel.isVisible(r[0]))
+          {
+            // don't scroll - position isn't visible
+            return false;
+          }
+        }
+      }
       if (!av.wrapAlignment)
       {
         if ((startv = av.getStartRes()) >= start)
@@ -317,11 +326,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
         scrollToWrappedVisible(start);
       }
     }
-    if (!redrawOverview && overviewPanel != null)
+    if (redrawOverview && overviewPanel != null)
     {
       overviewPanel.setBoxPosition();
     }
-    paintAlignment(!redrawOverview);
+    paintAlignment(redrawOverview);
     return true;
   }
 
@@ -359,10 +368,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @param b
-   *          DOCUMENT ME!
+   * @param b Hide or show annotation panel
+   *          
    */
   public void setAnnotationVisible(boolean b)
   {
@@ -374,6 +382,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
     repaint();
   }
 
+  /**
+   * automatically adjust annotation panel height for new annotation
+   * whilst ensuring the alignment is still visible.
+   */
   public void adjustAnnotationHeight()
   {
     // TODO: display vertical annotation scrollbar if necessary
@@ -382,9 +394,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       System.out.println("NEEDS FIXING");
     }
-
+    validateAnnotationDimensions(true);
+    addNotify();
+    paintAlignment(true);
+  }
+  /**
+   * calculate the annotation dimensions and refresh slider values accordingly.
+   * need to do repaints/notifys afterwards. 
+   */
+  protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
     int height = annotationPanel.adjustPanelHeight();
-
+    
     if (hscroll.isVisible())
     {
       height += hscroll.getPreferredSize().height;
@@ -393,17 +413,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       height = alignFrame.getHeight() / 2;
     }
-
+    if (!adjustPanelHeight)
+    {
+      // maintain same window layout whilst updating sliders
+      height=annotationScroller.getSize().height;
+    }
     hscroll.addNotify();
-
+    
     annotationScroller.setPreferredSize(new Dimension(annotationScroller
             .getWidth(), height));
 
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), height));
     annotationScroller.validate();// repaint();
-    addNotify();
-    repaint();
+    annotationScroller.addNotify();
   }
 
   /**
@@ -501,12 +524,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Adjust row/column scrollers to show a visible position in the alignment.
    * 
-   * @param x
-   *          DOCUMENT ME!
-   * @param y
+   * @param x visible column to scroll to
    *          DOCUMENT ME!
+   * @param y visible row to scroll to
+   *          
    */
   public void setScrollValues(int x, int y)
   {
@@ -661,8 +684,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (updateOverview)
     {
-      jalview.structure.StructureSelectionManager
-              .getStructureSelectionManager().sequenceColoursChanged(this);
+      av.getStructureSelectionManager().sequenceColoursChanged(this);
 
       if (overviewPanel != null)
       {
@@ -1032,6 +1054,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (System.getProperty("java.awt.headless") != null
               && System.getProperty("java.awt.headless").equals("true"))
       {
+        // TODO: JAL-244
         width = alignFrame.getWidth() - vscroll.getPreferredSize().width
                 - alignFrame.getInsets().left
                 - alignFrame.getInsets().right;
@@ -1297,15 +1320,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void closePanel()
   {
-    jalview.structure.StructureSelectionManager ssm = jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager();
-    ssm.removeStructureViewerListener(seqPanel, null);
-    ssm.removeSelectionListener(seqPanel);
     PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
     PaintRefresher.RemoveComponent(idPanel.idCanvas);
     PaintRefresher.RemoveComponent(this);
     if (av != null)
     {
+      jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
+      ssm.removeStructureViewerListener(seqPanel, null);
+      ssm.removeSelectionListener(seqPanel);
       av.alignment = null;
       av = null;
     }
@@ -1391,4 +1413,41 @@ public class AlignmentPanel extends GAlignmentPanel implements
     oldrfs.clear();
     adjustAnnotationHeight();
   }
+
+  @Override
+  public AlignmentI getAlignment()
+  {
+    return av.alignment;
+  }
+
+  /**
+   * get the name for this view
+   * @return 
+   */
+  public String getViewName()
+  {
+    return av.viewName;
+  }
+
+  /**
+   * Make/Unmake this alignment panel the current input focus
+   * @param b
+   */
+  public void setSelected(boolean b)
+  {
+    try {
+      alignFrame.setSelected(b);
+      } catch (Exception ex) {};
+      
+    if (b)
+    {
+      alignFrame.setDisplayedView(this);
+    } 
+  }
+
+  @Override
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return av.getStructureSelectionManager();
+  }
 }