X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b714aea53cabf9b96dea336328ca497d1ca28d14;hb=366b11bb8e79ff5bb1a9e6c50b648c3d4101862c;hp=8c31ed0df7734b0f317e24409177a1455f4dc221;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8c31ed0..b714aea 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -34,7 +34,8 @@ import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.ws.*;
-import javax.swing.event.AncestorEvent;
+import java.awt.dnd.*;
+
 
 /**
  * DOCUMENT ME!
@@ -43,7 +44,7 @@ import javax.swing.event.AncestorEvent;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame implements ClipboardOwner
+    extends GAlignFrame implements ClipboardOwner, DropTargetListener
 {
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
@@ -73,6 +74,7 @@ public class AlignFrame
     viewport = new AlignViewport(al);
     viewports.add(viewport);
 
+    this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
     if(viewport.vconsensus==null)
     {
@@ -172,18 +174,13 @@ public class AlignFrame
   public void setGUINucleotide(boolean nucleotide)
   {
     showTranslation.setVisible( nucleotide );
-    sequenceFeatures.setVisible(!nucleotide );
-    featureSettings.setVisible( !nucleotide );
+    //sequenceFeatures.setVisible(!nucleotide );
+    //featureSettings.setVisible( !nucleotide );
     conservationMenuItem.setVisible( !nucleotide );
     modifyConservation.setVisible(   !nucleotide );
 
-    //Deal with separators
     //Remember AlignFrame always starts as protein
-    if(nucleotide)
-    {
-      viewMenu.remove(viewMenu.getItemCount()-2);
-    }
-    else
+    if(!nucleotide)
     {
       calculateMenu.remove(calculateMenu.getItemCount()-2);
     }
@@ -199,99 +196,10 @@ public class AlignFrame
   }
 
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param String DOCUMENT ME!
-   */
-
-  public void parseGroupsFile(String file)
-  {
-    try
-    {
-      BufferedReader in = new BufferedReader(new FileReader(file));
-      SequenceI seq = null;
-      String line, type, desc, token;
-
-      int index, start, end;
-      StringTokenizer st;
-      SequenceFeature sf;
-      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
-      int lineNo = 0;
-      while ( (line = in.readLine()) != null)
-      {
-        lineNo++;
-        st = new StringTokenizer(line, "\t");
-        if (st.countTokens() == 2)
-        {
-          type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          fr.setColour(type, ucs.findColour("A"));
-          continue;
-        }
-
-        while (st.hasMoreElements())
-        {
-          desc = st.nextToken();
-          token = st.nextToken();
-          if (!token.equals("ID_NOT_SPECIFIED"))
-          {
-            index = viewport.alignment.findIndex(viewport.alignment.findName(
-                token));
-            st.nextToken();
-          }
-          else
-          {
-            index = Integer.parseInt(st.nextToken());
-          }
-
-          start = Integer.parseInt(st.nextToken());
-          end = Integer.parseInt(st.nextToken());
-
-          seq = viewport.alignment.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
-
-          type = st.nextToken();
-
-          if (fr.getColour(type) == null)
-          {
-            // Probably the old style groups file
-            UserColourScheme ucs = new UserColourScheme(type);
-            fr.setColour(type, ucs.findColour("A"));
-          }
-
-
-          sf = new SequenceFeature(type, desc, "", start, end);
-
-          seq.addSequenceFeature(sf);
-
-
-         // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
-         // sg.addSequence(seq, false);
-
-         // viewport.alignment.addGroup(sg);
-
-        }
-      }
-
-      viewport.showSequenceFeatures = true;
-
-      alignPanel.repaint();
-
-    }
-    catch (Exception ex)
-    {
-      System.out.println("Error parsing groups file: " + ex);
-    }
-  }
-
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
   }
-
-
   /**
    * DOCUMENT ME!
    *
@@ -783,7 +691,7 @@ public class AlignFrame
       if(str.length()<1)
         return;
 
-      String format = IdentifyFile.Identify(str, "Paste");
+      String format = new IdentifyFile().Identify(str, "Paste");
       SequenceI[] sequences;
 
      if(Desktop.jalviewClipboard!=null)
@@ -844,7 +752,17 @@ public class AlignFrame
             newseq.setDatasetSequence(ds);
             viewport.alignment.getDataset().addSequence(ds);
           }
-
+          else
+          {
+            newseq.setDatasetSequence(sequences[i].getDatasetSequence());
+            if(sequences[i].getDatasetSequence().getAnnotation()!=null)
+            {
+              for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)
+              {
+                viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);
+              }
+            }
+          }
         }
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
@@ -853,6 +771,8 @@ public class AlignFrame
     }
     catch (Exception ex)
     {
+      ex.printStackTrace();
+        System.out.println("Exception whilst pasting: "+ex);
         // could be anything being pasted in here
     }
 
@@ -883,24 +803,50 @@ public class AlignFrame
       return;
     }
 
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
 
     SequenceGroup sg = viewport.getSelectionGroup();
-    boolean allSequences = false;
-    if (sg.sequences.size() == viewport.alignment.getHeight())
+
+
+
+    //Jalview no longer allows deletion of residues.
+    //Check here whether any residues are in selection area
+    if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
     {
-      allSequences = true;
+      for (int i = 0; i < sg.sequences.size(); i++)
+      {
+        SequenceI seq = sg.getSequenceAt(i);
+        int j = sg.getStartRes();
+        do
+        {
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+          {
+            JOptionPane.showInternalMessageDialog(
+                Desktop.desktop, "Cannot delete residues from alignment!\n"
+                + "Try hiding columns instead.",
+                "Deletion of residues not permitted",
+                JOptionPane.WARNING_MESSAGE);
+
+            return;
+          }
+          j++;
+        }while(j<=sg.getEndRes());
+      }
     }
 
+
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                                   HistoryItem.HIDE));
+
+
     for (int i = 0; i < sg.sequences.size(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
+
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
       // If the cut affects all sequences, remove highlighted columns
-      if (allSequences)
+      if (sg.sequences.size() == viewport.alignment.getHeight())
       {
         viewport.getColumnSelection().removeElements(sg.getStartRes(),
             sg.getEndRes() + 1);
@@ -979,7 +925,7 @@ public class AlignFrame
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.annotationPanel.activeRes = null;
+    alignPanel.idPanel.idCanvas.searchResults = null;
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
@@ -1206,6 +1152,8 @@ public class AlignFrame
    if(alignPanel.overviewPanel!=null)
      alignPanel.overviewPanel.updateOverviewImage();
 
+   viewport.alignment.adjustSequenceAnnotations();
+
    alignPanel.repaint();
  }
 
@@ -1257,22 +1205,8 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
-
-    SequenceI current;
-    int Width = viewport.getAlignment().getWidth();
-
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
-    {
-      current = viewport.getAlignment().getSequenceAt(i);
-
-      if (current.getLength() < Width)
-      {
-        current.insertCharAt(Width - 1, viewport.getGapCharacter());
-      }
-    }
-
-    alignmentChanged();
+    if (viewport.getAlignment().padGaps())
+      alignmentChanged();
   }
 
   /**
@@ -1285,8 +1219,8 @@ public class AlignFrame
     JInternalFrame frame = new JInternalFrame();
     Finder finder = new Finder(viewport, alignPanel, frame);
     frame.setContentPane(finder);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Find", 340, 110);
   }
 
   /**
@@ -1299,6 +1233,14 @@ public class AlignFrame
     new FontChooser(alignPanel);
   }
 
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+    viewport.antiAlias = smoothFont.isSelected();
+    alignPanel.annotationPanel.image = null;
+    alignPanel.repaint();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1405,25 +1347,37 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
+  {
+    if (!viewport.alignment.isNucleotide())
+    {
+      new SequenceFeatureFetcher(viewport.
+                                 alignment,
+                                 alignPanel);
+      viewport.setShowSequenceFeatures(true);
+      showSeqFeatures.setSelected(true);
+    }
+  }
+
+
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+    new FeatureSettings(viewport, alignPanel);
+  }
+
   /**
    * DOCUMENT ME!
    *
    * @param evt DOCUMENT ME!
    */
-  public void sequenceFeatures_actionPerformed(ActionEvent evt)
+  public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
-    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
-
-    if (viewport.showSequenceFeatures)
+    viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
+    alignPanel.repaint();
+    if (alignPanel.getOverviewPanel() != null)
     {
-      new SequenceFeatureFetcher(viewport.
-         alignment,
-          alignPanel);
+      alignPanel.getOverviewPanel().updateOverviewImage();
     }
-
-    featureSettings.setEnabled(true);
-
-    alignPanel.repaint();
   }
 
   /**
@@ -1570,6 +1524,12 @@ public class AlignFrame
     changeColour(new NucleotideColourScheme());
   }
 
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+    new AnnotationColourChooser(viewport, alignPanel);
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -2495,10 +2455,7 @@ public class AlignFrame
     }
   }*/
 
-  public void featureSettings_actionPerformed(ActionEvent e)
-  {
-    new FeatureSettings(viewport, alignPanel);
-  }
+
 
 
 
@@ -2515,6 +2472,8 @@ public void showTranslation_actionPerformed(ActionEvent e)
     protein = new StringBuffer();
     seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
     resSize = seq.length();
+    resSize -= resSize%3;
+
     for(res = 0; res < resSize; res+=3)
     {
       String codon = seq.substring(res, res+3);
@@ -2608,4 +2567,205 @@ public void showTranslation_actionPerformed(ActionEvent e)
   viewport = (AlignViewport)viewports.elementAt(index);
   alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
  }*/
+
+/**
+ * DOCUMENT ME!
+ *
+ * @param String DOCUMENT ME!
+ */
+public boolean parseGroupsFile(String file)
+{
+    try
+    {
+      BufferedReader in = new BufferedReader(new FileReader(file));
+      SequenceI seq = null;
+      String line, type, desc, token;
+
+      int index, start, end;
+      StringTokenizer st;
+      SequenceFeature sf;
+      int lineNo = 0;
+      String featureGroup = null;
+      while ( (line = in.readLine()) != null)
+      {
+        lineNo++;
+        st = new StringTokenizer(line, "\t");
+        if (st.countTokens() == 2)
+        {
+          type = st.nextToken();
+          if (type.equalsIgnoreCase("startgroup"))
+          {
+            featureGroup = st.nextToken();
+          }
+          else if (type.equalsIgnoreCase("endgroup"))
+          {
+            //We should check whether this is the current group,
+            //but at present theres no way of showing more than 1 group
+            st.nextToken();
+            featureGroup = null;
+          }
+          else
+          {
+            UserColourScheme ucs = new UserColourScheme(st.nextToken());
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type,
+                ucs.findColour("A"));
+          }
+          continue;
+        }
+
+        while (st.hasMoreElements())
+        {
+          desc = st.nextToken();
+          token = st.nextToken();
+          if (!token.equals("ID_NOT_SPECIFIED"))
+          {
+            index = viewport.alignment.findIndex(viewport.alignment.findName(token));
+            st.nextToken();
+          }
+          else
+          {
+            index = Integer.parseInt(st.nextToken());
+          }
+
+          start = Integer.parseInt(st.nextToken());
+          end = Integer.parseInt(st.nextToken());
+
+          seq = viewport.alignment.getSequenceAt(index);
+
+          type = st.nextToken();
+
+          if (alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type) == null)
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
+          }
+
+          sf = new SequenceFeature(type, desc, "", start, end);
+          sf.setFeatureGroup(featureGroup);
+
+          seq.getDatasetSequence().addSequenceFeature(sf);
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+      System.out.println("Error parsing groups file: " + ex);
+      return false;
+    }
+
+    viewport.showSequenceFeatures = true;
+    showSeqFeatures.setSelected(true);
+    alignPanel.repaint();
+    return true;
+}
+
+public void dragEnter(DropTargetDragEvent evt)
+{}
+
+public void dragExit(DropTargetEvent evt)
+{}
+
+public void dragOver(DropTargetDragEvent evt)
+{}
+
+public void dropActionChanged(DropTargetDragEvent evt)
+{}
+
+public void drop(DropTargetDropEvent evt)
+{
+    Transferable t = evt.getTransferable();
+    java.util.List files = null;
+
+    try
+    {
+      DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+      {
+        //Works on Windows and MacOSX
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+      }
+      else if (t.isDataFlavorSupported(uriListFlavor))
+      {
+        // This is used by Unix drag system
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        String data = (String) t.getTransferData(uriListFlavor);
+        files = new java.util.ArrayList(1);
+        for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+            data,
+            "\r\n");
+             st.hasMoreTokens(); )
+        {
+          String s = st.nextToken();
+          if (s.startsWith("#"))
+          {
+            // the line is a comment (as per the RFC 2483)
+            continue;
+          }
+
+          java.net.URI uri = new java.net.URI(s);
+          java.io.File file = new java.io.File(uri);
+          files.add(file);
+        }
+      }
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    if (files != null)
+    {
+      try
+      {
+        boolean isAnnotation = false;
+
+        for (int i = 0; i < files.size(); i++)
+        {
+          String file = files.get(i).toString();
+
+          isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);
+
+          if( !isAnnotation )
+          {
+            boolean isGroupsFile = parseGroupsFile(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)), this);
+
+              this.paste(false);
+
+            }
+          }
+        }
+
+        if(isAnnotation)
+        {
+          int height = alignPanel.annotationPanel.adjustPanelHeight();
+          alignPanel.annotationScroller.setPreferredSize(
+              new Dimension(alignPanel.annotationScroller.getWidth(),
+                            height));
+
+          alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+              alignPanel.annotationSpaceFillerHolder.getWidth(),
+              height));
+
+          alignPanel.addNotify();
+        }
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+}
+
 }