vamsasDemo new branch

[jalview.git] / src / jalview / appletgui / AlignFrame.java

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