Drop annotations onto alignment

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bfdc40b..5685e42 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -34,6 +34,7 @@ import jalview.io.*;
 import jalview.jbgui.*;\r
 import jalview.schemes.*;\r
 import jalview.ws.*;\r
+import java.awt.dnd.*;\r
 \r
 \r
 /**\r
@@ -43,7 +44,7 @@ import jalview.ws.*;
  * @version $Revision$\r
  */\r
 public class AlignFrame\r
-    extends GAlignFrame implements ClipboardOwner\r
+    extends GAlignFrame implements ClipboardOwner, DropTargetListener\r
 {\r
   /** DOCUMENT ME!! */\r
   public static final int NEW_WINDOW_WIDTH = 700;\r
@@ -73,6 +74,7 @@ public class AlignFrame
     viewport = new AlignViewport(al);\r
     viewports.add(viewport);\r
 \r
+    this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
 \r
     if(viewport.vconsensus==null)\r
     {\r
@@ -199,93 +201,6 @@ public class AlignFrame
   }\r
 \r
 \r
-  /**\r
-   * DOCUMENT ME!\r
-   *\r
-   * @param String DOCUMENT ME!\r
-   */\r
-\r
-  public void parseGroupsFile(String file)\r
-  {\r
-    try\r
-    {\r
-      BufferedReader in = new BufferedReader(new FileReader(file));\r
-      SequenceI seq = null;\r
-      String line, type, desc, token;\r
-\r
-      int index, start, end;\r
-      StringTokenizer st;\r
-      SequenceFeature sf;\r
-      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
-      int lineNo = 0;\r
-      while ( (line = in.readLine()) != null)\r
-      {\r
-        lineNo++;\r
-        st = new StringTokenizer(line, "\t");\r
-        if (st.countTokens() == 2)\r
-        {\r
-          type = st.nextToken();\r
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
-          fr.setColour(type, ucs.findColour("A"));\r
-          continue;\r
-        }\r
-\r
-        while (st.hasMoreElements())\r
-        {\r
-          desc = st.nextToken();\r
-          token = st.nextToken();\r
-          if (!token.equals("ID_NOT_SPECIFIED"))\r
-          {\r
-            index = viewport.alignment.findIndex(viewport.alignment.findName(\r
-                token));\r
-            st.nextToken();\r
-          }\r
-          else\r
-          {\r
-            index = Integer.parseInt(st.nextToken());\r
-          }\r
-\r
-          start = Integer.parseInt(st.nextToken());\r
-          end = Integer.parseInt(st.nextToken());\r
-\r
-          seq = viewport.alignment.getSequenceAt(index);\r
-          start = seq.findIndex(start) - 1;\r
-          end = seq.findIndex(end) - 1;\r
-\r
-          type = st.nextToken();\r
-\r
-          if (fr.getColour(type) == null)\r
-          {\r
-            // Probably the old style groups file\r
-            UserColourScheme ucs = new UserColourScheme(type);\r
-            fr.setColour(type, ucs.findColour("A"));\r
-          }\r
-\r
-\r
-          sf = new SequenceFeature(type, desc, "", start, end);\r
-\r
-          seq.getDatasetSequence().addSequenceFeature(sf);\r
-\r
-\r
-         // sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
-         // sg.addSequence(seq, false);\r
-\r
-         // viewport.alignment.addGroup(sg);\r
-\r
-        }\r
-      }\r
-\r
-      viewport.showSequenceFeatures = true;\r
-\r
-      alignPanel.repaint();\r
-\r
-    }\r
-    catch (Exception ex)\r
-    {\r
-      System.out.println("Error parsing groups file: " + ex);\r
-    }\r
-  }\r
-\r
   public void fetchSequence_actionPerformed(ActionEvent e)\r
   {\r
     new SequenceFetcher(this);\r
@@ -1287,6 +1202,14 @@ public class AlignFrame
     new FontChooser(alignPanel);\r
   }\r
 \r
+  public void smoothFont_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.antiAlias = smoothFont.isSelected();\r
+    alignPanel.annotationPanel.image = null;\r
+    alignPanel.repaint();\r
+  }\r
+\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -1558,6 +1481,12 @@ public class AlignFrame
     changeColour(new NucleotideColourScheme());\r
   }\r
 \r
+  public void annotationColour_actionPerformed(ActionEvent e)\r
+  {\r
+    new AnnotationColourChooser(viewport, alignPanel);\r
+  }\r
+\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -2596,4 +2525,107 @@ public void showTranslation_actionPerformed(ActionEvent e)
   viewport = (AlignViewport)viewports.elementAt(index);\r
   alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
  }*/\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+public boolean parseGroupsFile(String file)\r
+{\r
+  AnnotationReader ar = new AnnotationReader();\r
+\r
+  if (ar.readGroupsFile(alignPanel.seqPanel.seqCanvas.getFeatureRenderer(),\r
+                        viewport.alignment, file))\r
+  {\r
+    viewport.showSequenceFeatures = true;\r
+    alignPanel.repaint();\r
+    return true;\r
+  }\r
+  else\r
+    return false;\r
+}\r
+\r
+public void dragEnter(DropTargetDragEvent evt)\r
+{}\r
+\r
+public void dragExit(DropTargetEvent evt)\r
+{}\r
+\r
+public void dragOver(DropTargetDragEvent evt)\r
+{}\r
+\r
+public void dropActionChanged(DropTargetDragEvent evt)\r
+{}\r
+\r
+public void drop(DropTargetDropEvent evt)\r
+{\r
+    Transferable t = evt.getTransferable();\r
+    java.util.List files = null;\r
+\r
+    try\r
+    {\r
+      DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");\r
+      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+      {\r
+        //Works on Windows and MacOSX\r
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+        files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
+      }\r
+      else if (t.isDataFlavorSupported(uriListFlavor))\r
+      {\r
+        // This is used by Unix drag system\r
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+        String data = (String) t.getTransferData(uriListFlavor);\r
+        files = new java.util.ArrayList(1);\r
+        for (java.util.StringTokenizer st = new java.util.StringTokenizer(\r
+            data,\r
+            "\r\n");\r
+             st.hasMoreTokens(); )\r
+        {\r
+          String s = st.nextToken();\r
+          if (s.startsWith("#"))\r
+          {\r
+            // the line is a comment (as per the RFC 2483)\r
+            continue;\r
+          }\r
+\r
+          java.net.URI uri = new java.net.URI(s);\r
+          java.io.File file = new java.io.File(uri);\r
+          files.add(file);\r
+        }\r
+      }\r
+    }\r
+    catch (Exception e)\r
+    {\r
+      e.printStackTrace();\r
+    }\r
+\r
+    if (files != null)\r
+    {\r
+      AnnotationReader ar = new AnnotationReader();\r
+      try\r
+      {\r
+        for (int i = 0; i < files.size(); i++)\r
+        {\r
+          String file = files.get(i).toString();\r
+          if(! ar.readAnnotationFile(viewport.alignment, file) )\r
+            parseGroupsFile(file);\r
+          else\r
+          {\r
+\r
+          }\r
+        }\r
+\r
+        alignPanel.annotationPanel.adjustPanelHeight();\r
+        alignPanel.annotationScroller.validate();\r
+        alignPanel.repaint();\r
+      }\r
+      catch (Exception ex)\r
+      {\r
+        ex.printStackTrace();\r
+      }\r
+    }\r
+}\r
+\r
 }\r