X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cc57961160589c5068f7df08939f9a45573cb9ef;hb=e3eb93bc131a0f088312fddde91b728dbebe40d4;hp=05ba50cb09a3e88ce75cafea9baf0797e15eeb3b;hpb=7c05496d1da22f21ce5ae1a199afb9b16c8777ea;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 05ba50c..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));
@@ -352,15 +352,20 @@ public class AlignFrame
 
       if (viewport.hasHiddenColumns)
       {
-        System.out.println("PROMPT USER HERE");
-        omitHidden = viewport.getSelectionAsString();
+        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+            "The Alignment contains hidden columns."
+            + "\nDo you want to save only the visible alignment?",
+            "Save / Omit Hidden Columns",
+            JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+        if (reply == JOptionPane.YES_OPTION)
+          omitHidden = viewport.getViewAsString(false);
       }
 
       String output = new FormatAdapter().formatSequences(
           format,
-          viewport.getSelectionAsNewSequence(),
-          omitHidden) ;
-
+          viewport.alignment.getSequencesArray(),
+          omitHidden);
 
       if (output == null)
       {
@@ -392,20 +397,31 @@ public class AlignFrame
    */
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-
-
     String [] omitHidden = null;
 
     if(viewport.hasHiddenColumns)
     {
-      System.out.println("PROMPT USER HERE");
-      omitHidden = viewport.getSelectionAsString();
+      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          "The Alignment contains hidden columns."
+      +"\nDo you want to output only the visible alignment?",
+      "Save / Omit Hidden Columns",
+      JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+      if(reply==JOptionPane.YES_OPTION)
+      {
+        omitHidden = viewport.getViewAsString(false);
+      }
     }
 
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
+
+
     cap.setText(new FormatAdapter().formatSequences(
         e.getActionCommand(),
-        viewport.getSelectionAsNewSequence(),
+        viewport.alignment.getSequencesArray(),
         omitHidden));
   }
 
@@ -463,6 +479,7 @@ public class AlignFrame
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
+
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(
@@ -667,22 +684,23 @@ public class AlignFrame
     {
       return;
     }
-    SequenceI [] seqs;
-    if(viewport.getSelectionGroup()==null)
-    {
-      seqs = viewport.alignment.getSequencesArray();
-    }
-    else
+
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    String[] omitHidden = null;
+
+    if (viewport.hasHiddenColumns)
     {
-      seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.alignment);
+      omitHidden = viewport.getViewAsString(true);
     }
 
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    String output = new FormatAdapter().formatSequences(
+        "Fasta",
+        seqs,
+        omitHidden);
 
-    FastaFile ff = new FastaFile();
-    ff.addJVSuffix( viewport.showJVSuffix );
 
-    c.setContents(new StringSelection(ff.print(seqs)), Desktop.instance);
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+        .setContents(new StringSelection(output), Desktop.instance);
 
     Vector hiddenColumns = null;
     if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)
@@ -698,6 +716,7 @@ public class AlignFrame
                           region[1]-hiddenOffset});
       }
     }
+
     Desktop.jalviewClipboard = new Object[]{ seqs,
         viewport.alignment.getDataset(),
         hiddenColumns};
@@ -749,6 +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
@@ -764,32 +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++)
      {
@@ -830,9 +858,7 @@ public class AlignFrame
            for(int i=0; i<hc.size(); i++)
            {
              int [] region = (int[]) hc.elementAt(i);
-             for(int j=region[0]; j<region[1]+1; j++)
-               af.viewport.getColumnSelection().addElement(j);
-             af.viewport.getColumnSelection().hideColumns(region[0], af.viewport);
+             af.viewport.hideColumns(region[0], region[1]);
            }
          }
 
@@ -1382,6 +1408,46 @@ public class AlignFrame
     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
   }
 
+  public void showAllSeqs_actionPerformed(ActionEvent e)
+  {
+    viewport.showAllHiddenSeqs();
+    repaint();
+  }
+
+  public void showAllColumns_actionPerformed(ActionEvent e)
+  {
+    viewport.showAllHiddenColumns();
+  }
+
+  public void hideSelSequences_actionPerformed(ActionEvent e)
+  {
+    if(viewport.getSelectionGroup()==null)
+      return;
+
+    SequenceI [] seqs = viewport.getSelectionGroup().getSequencesInOrder(
+        viewport.alignment
+          );
+
+    for(int i=0; i<seqs.length; i++)
+    {
+      viewport.hideSequence(seqs[i]);
+    }
+
+    alignPanel.repaint();
+  }
+
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
+    viewport.hideSelectedColumns();
+    alignPanel.repaint();
+  }
+
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
+    repaint();
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -2385,9 +2451,9 @@ public class AlignFrame
       if (nf.getTree() != null)
       {
         tp = new TreePanel(viewport,
-                           nf,
                            "FromFile",
-                           title);
+                           title,
+                           nf);
 
         tp.setSize(w,h);
 
@@ -2558,10 +2624,12 @@ public class AlignFrame
 
 
 
-
 public void showTranslation_actionPerformed(ActionEvent e)
 {
-  int s, sSize = viewport.alignment.getHeight();
+  SequenceI [] selection = viewport.getSelectionAsNewSequence();
+  String [] seqstring = viewport.getViewAsString(true);
+
+  int s, sSize = selection.length;
   SequenceI [] newSeq = new SequenceI[sSize];
 
   int res, resSize;
@@ -2570,7 +2638,7 @@ public void showTranslation_actionPerformed(ActionEvent e)
   for(s=0; s<sSize; s++)
   {
     protein = new StringBuffer();
-    seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
+    seq = AlignSeq.extractGaps("-. ", seqstring[s]);
     resSize = seq.length();
     resSize -= resSize%3;
 
@@ -2586,7 +2654,8 @@ public void showTranslation_actionPerformed(ActionEvent e)
       else
         protein.append( aa );
     }
-    newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
+    newSeq[s] = new Sequence(selection[s].getName(),
+                             protein.toString());
   }
 
 
@@ -2784,16 +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