From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 30 Jan 2006 14:54:07 +0000 (+0000)
Subject: Drop annotations onto alignment
X-Git-Tag: Root_VamJalview_2_07b+~206
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bb146716cea5dbc20e3dc1c5a5b288c979b30229;p=jalview.git

Drop annotations onto alignment
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bfdc40b..5685e42 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -34,6 +34,7 @@ import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.ws.*;
+import java.awt.dnd.*;
 
 
 /**
@@ -43,7 +44,7 @@ import jalview.ws.*;
  * @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)
     {
@@ -199,93 +201,6 @@ 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.getDatasetSequence().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);
@@ -1287,6 +1202,14 @@ public class AlignFrame
     new FontChooser(alignPanel);
   }
 
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+    viewport.antiAlias = smoothFont.isSelected();
+    alignPanel.annotationPanel.image = null;
+    alignPanel.repaint();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1558,6 +1481,12 @@ public class AlignFrame
     changeColour(new NucleotideColourScheme());
   }
 
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+    new AnnotationColourChooser(viewport, alignPanel);
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -2596,4 +2525,107 @@ 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)
+{
+  AnnotationReader ar = new AnnotationReader();
+
+  if (ar.readGroupsFile(alignPanel.seqPanel.seqCanvas.getFeatureRenderer(),
+                        viewport.alignment, file))
+  {
+    viewport.showSequenceFeatures = true;
+    alignPanel.repaint();
+    return true;
+  }
+  else
+    return false;
+}
+
+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)
+    {
+      AnnotationReader ar = new AnnotationReader();
+      try
+      {
+        for (int i = 0; i < files.size(); i++)
+        {
+          String file = files.get(i).toString();
+          if(! ar.readAnnotationFile(viewport.alignment, file) )
+            parseGroupsFile(file);
+          else
+          {
+
+          }
+        }
+
+        alignPanel.annotationPanel.adjustPanelHeight();
+        alignPanel.annotationScroller.validate();
+        alignPanel.repaint();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+}
+
 }