X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9b3bd4a5ad9cbd57660a0af989b92fc490f10ab1;hb=b512e41cb378d9b7fb470db08bbb4d8ddbadce6f;hp=0edc57849ada3639a9322ac25e762225236ad05c;hpb=98f4db4c56ddbffb5690d9311b1e25bd9150f9c0;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0edc578..9b3bd4a 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!
  *
@@ -61,15 +60,14 @@ public class AlignFrame
   Stack redoList = new Stack();
   private int treeCount = 0;
 
-
   /**
-   * Creates a new AlignFrame object.
-   *
-   * @param al DOCUMENT ME!
+   * new alignment window with hidden columns
+   * @param al AlignmentI
+   * @param hiddenColumns ColumnSelection or null
    */
-  public AlignFrame(AlignmentI al)
-  {
-    viewport = new AlignViewport(al);
+  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {
+
+    viewport = new AlignViewport(al, hiddenColumns);
 
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
@@ -141,6 +139,17 @@ public class AlignFrame
 
   }
 
+
+  /**
+   * Creates a new AlignFrame object.
+   *
+   * @param al DOCUMENT ME!
+   */
+  public AlignFrame(AlignmentI al)
+  {
+    this(al, null);
+  }
+
   public AlignViewport getViewport()
   {
     return viewport;
@@ -203,8 +212,6 @@ public class AlignFrame
     {
       alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
       alignPanel.repaint();
-      if(featureSettings!=null)
-        featureSettings.setTableData();
     }
   }
 
@@ -352,16 +359,20 @@ 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)
       {
@@ -393,20 +404,31 @@ 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));
   }
 
@@ -464,6 +486,7 @@ public class AlignFrame
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
+
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(
@@ -670,16 +693,24 @@ public class AlignFrame
     }
 
     SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    String[] omitHidden = null;
 
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    if (viewport.hasHiddenColumns)
+    {
+      omitHidden = viewport.getViewAsString(true);
+    }
 
-    FastaFile ff = new FastaFile();
-    ff.addJVSuffix( viewport.showJVSuffix );
+    String output = new FormatAdapter().formatSequences(
+        "Fasta",
+        seqs,
+        omitHidden);
 
-    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)
+    if(viewport.hasHiddenColumns)
     {
       hiddenColumns =new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
@@ -692,6 +723,7 @@ public class AlignFrame
                           region[1]-hiddenOffset});
       }
     }
+
     Desktop.jalviewClipboard = new Object[]{ seqs,
         viewport.alignment.getDataset(),
         hiddenColumns};
@@ -743,6 +775,7 @@ 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
@@ -764,6 +797,7 @@ public class AlignFrame
            alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
         else
            alignment.setDataset( null );
+
       }
       else
       {
@@ -772,18 +806,23 @@ public class AlignFrame
         //!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++)
      {
@@ -818,15 +857,13 @@ public class AlignFrame
        AlignFrame af = new AlignFrame(alignment);
        String newtitle = new String("Copied sequences");
 
-       if(Desktop.jalviewClipboard[2]!=null)
+       if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
          {
            Vector hc = (Vector)Desktop.jalviewClipboard[2];
            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]);
            }
          }
 
@@ -1043,6 +1080,13 @@ public class AlignFrame
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+    viewport.invertColumnSelection();
+    alignPanel.repaint();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1376,6 +1420,46 @@ 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!
    *
@@ -1443,7 +1527,7 @@ public class AlignFrame
   }
 
 
-  FeatureSettings featureSettings;
+  public FeatureSettings featureSettings;
   public void featureSettings_actionPerformed(ActionEvent e)
   {
     if(featureSettings !=null )
@@ -2128,6 +2212,9 @@ public class AlignFrame
         return;
       }
 
+      if(viewport.alignment.getHeight()<2)
+        return;
+
       tp = new TreePanel(viewport, type, pwType);
     }
 
@@ -2216,27 +2303,28 @@ public class AlignFrame
    * or just the selected set will be submitted for multiple alignment.
    *
    */
-  private SequenceI[] gatherSequencesForAlignment()
+  private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
   {
     // Now, check we have enough sequences
-    SequenceI[] msa = null;
+    AlignmentView msa = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize(false) > 1))
     {
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
+      /*SequenceGroup seqs = viewport.getSelectionGroup();
       int sz;
       msa = new SequenceI[sz = seqs.getSize(false)];
 
       for (int i = 0; i < sz; i++)
       {
         msa[i] = (SequenceI) seqs.getSequenceAt(i);
-      }
+      } */
+      msa = viewport.getAlignmentView(true);
     }
     else
     {
-      Vector seqs = viewport.getAlignment().getSequences();
+      /*Vector seqs = viewport.getAlignment().getSequences();
 
       if (seqs.size() > 1)
       {
@@ -2246,7 +2334,8 @@ public class AlignFrame
         {
           msa[i] = (SequenceI) seqs.elementAt(i);
         }
-      }
+      }*/
+      msa = viewport.getAlignmentView(false);
     }
     return msa;
   }
@@ -2450,7 +2539,7 @@ public class AlignFrame
           {
             public void actionPerformed(ActionEvent e)
             {
-              SequenceI[] msa = gatherSequencesForAlignment();
+              AlignmentView msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
                   false, true, viewport.getAlignment().getDataset(), af);
 
@@ -2467,7 +2556,7 @@ public class AlignFrame
             {
               public void actionPerformed(ActionEvent e)
               {
-                SequenceI[] msa = gatherSequencesForAlignment();
+                AlignmentView msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
                     true, true, viewport.getAlignment().getDataset(), af);
 
@@ -2552,10 +2641,12 @@ 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;
@@ -2564,7 +2655,7 @@ 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;
 
@@ -2580,7 +2671,8 @@ 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());
   }
 
 
@@ -2778,16 +2870,8 @@ 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