X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=b6324423a0f9384364fd178391440860bf2e22b1;hb=783520af519c958e10a2af29f1d4242e1ab890a3;hp=0f275dee19c4984385b8be614b2566e1d7caeee6;hpb=04b6d995eb9395cb4107b28119fff413d8bacafd;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0f275de..b632442 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -29,6 +29,7 @@ import java.awt.event.*;
 import java.util.*;
 import java.io.InputStreamReader;
 import java.io.BufferedReader;
+import java.io.FileReader;
 
 public class AlignFrame
     extends GAlignFrame
@@ -55,7 +56,6 @@ public class AlignFrame
       {
         try
         {
-          treeFile = treeFile;
           jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
               getCodeBase() + treeFile, "URL");
           fin.parse();
@@ -140,6 +140,78 @@ 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, text, token;
+      UserColourScheme ucs;
+      int index, start, end;
+      StringTokenizer st;
+      SequenceGroup sg;
+      int lineNo = 0;
+      while ( (line = in.readLine()) != null)
+      {
+        lineNo++;
+        st = new StringTokenizer(line, "\t");
+        if (st.countTokens() != 6)
+        {
+          System.out.println("Groups file " + file +
+                             " is invalid. Read help file.\nLine: \n"
+              +lineNo +": "+line);
+          break;
+        }
+
+        while (st.hasMoreElements())
+        {
+          text = 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());
+          ucs = new UserColourScheme(st.nextToken());
+
+          seq = viewport.alignment.getSequenceAt(index);
+          start = seq.findIndex(start) - 1;
+          end = seq.findIndex(end) - 1;
+
+          sg = new SequenceGroup(text, ucs, true, true, false, start, end);
+          sg.addSequence(seq, false);
+
+          viewport.alignment.addGroup(sg);
+
+        }
+      }
+
+      alignPanel.repaint();
+
+    }
+    catch (Exception ex)
+    {
+      System.out.println("Error parsing groups file: " + ex);
+    }
+  }
+
+
   public void inputText_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
@@ -156,7 +228,7 @@ public class AlignFrame
     jalview.bin.JalviewLite.addFrame(frame,
                                      "Alignment output - " + e.getActionCommand(),
                                      600, 500);
-    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+    cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
                                               viewport.getAlignment().
                                               getSequences()));
   }
@@ -771,7 +843,7 @@ public class AlignFrame
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    Finder finder = new Finder(alignPanel);
+    new Finder(alignPanel);
   }
 
   public void font_actionPerformed(ActionEvent e)
@@ -1091,7 +1163,7 @@ public class AlignFrame
 
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
+    new UserDefinedColours(alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)