X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cc57961160589c5068f7df08939f9a45573cb9ef;hb=e3eb93bc131a0f088312fddde91b728dbebe40d4;hp=2ce8f06b68fd17074cb50c97b62a8a32614828fd;hpb=ef6555067c63693c06f0b6335a1c9f5761d712c6;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2ce8f06..cc57961 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -37,7 +37,6 @@ import jalview.ws.*;
 import java.awt.dnd.*;
 import org.biojava.dasobert.eventmodel.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -69,6 +68,7 @@ public class AlignFrame
    */
   public AlignFrame(AlignmentI al)
   {
+
     viewport = new AlignViewport(al);
 
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
@@ -479,6 +479,7 @@ public class AlignFrame
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
+
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(
@@ -767,6 +768,7 @@ public class AlignFrame
       String format = new IdentifyFile().Identify(str, "Paste");
       SequenceI[] sequences;
 
+
      if(Desktop.jalviewClipboard!=null)
      {
        // The clipboard was filled from within Jalview, we must use the sequences
@@ -782,32 +784,40 @@ public class AlignFrame
 
       if (newAlignment)
       {
+        System.out.println(format +" 2");
         alignment = new Alignment(sequences);
 
         if(Desktop.jalviewClipboard!=null)
            alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
         else
            alignment.setDataset( null );
+
       }
       else
       {
+        System.out.println(format +" 24");
         alignment = viewport.getAlignment();
 
         //!newAlignment
         for (int i = 0; i < sequences.length; i++)
         {
-
           Sequence newseq = new Sequence(sequences[i].getName(),
               sequences[i].getSequence(), sequences[i].getStart(),
               sequences[i].getEnd());
 
           alignment.addSequence(newseq);
         }
+
+
         viewport.setEndSeq(alignment.getHeight());
         alignment.getWidth();
         viewport.firePropertyChange("alignment", null, alignment.getSequences());
       }
 
+
+
+
+
       // Add any annotations attached to sequences
       for (int i = 0; i < sequences.length; i++)
      {
@@ -848,7 +858,7 @@ public class AlignFrame
            for(int i=0; i<hc.size(); i++)
            {
              int [] region = (int[]) hc.elementAt(i);
-             af.viewport.hideColumns(region[0], region[1]+1);
+             af.viewport.hideColumns(region[0], region[1]);
            }
          }
 
@@ -1406,7 +1416,7 @@ public class AlignFrame
 
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
-    viewport.getColumnSelection().revealAllHiddenColumns(viewport);
+    viewport.showAllHiddenColumns();
   }
 
   public void hideSelSequences_actionPerformed(ActionEvent e)
@@ -1422,13 +1432,14 @@ public class AlignFrame
     {
       viewport.hideSequence(seqs[i]);
     }
-    repaint();
+
+    alignPanel.repaint();
   }
 
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
-    repaint();
+    alignPanel.repaint();
   }
 
   public void hiddenMarkers_actionPerformed(ActionEvent e)
@@ -2842,16 +2853,8 @@ public void drop(DropTargetDropEvent evt)
                                                 AppletFormatAdapter.FILE);
         if (!isGroupsFile)
         {
-          String protocol = "File";
-          String format = new IdentifyFile().Identify(file, protocol);
-          SequenceI[] sequences = new FormatAdapter().readFile(file, protocol,
-              format);
-
-          FastaFile ff = new FastaFile();
-          Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-          c.setContents(new StringSelection(ff.print(sequences)), Desktop.instance);
-
-          this.paste(false);
+          String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);
+          new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);
         }
       }
       else