X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=4fc6208a753a374ae5d785396aefc6bd8fc843dd;hb=6e21be7d86ab4ac3936e1e7691b31ebcf9080cdf;hp=bda314d9c4b34785b7b11b52c0510e0b4ea98966;hpb=ee53965807b83bf93a21cbc341cee9a9e005b2cb;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index bda314d..4fc6208 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -29,18 +29,19 @@ import java.awt.event.*;
 import java.util.*;
 import java.io.InputStreamReader;
 import java.io.BufferedReader;
+import java.net.URL;
 
 public class AlignFrame
     extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
-  public static int NEW_WINDOW_WIDTH = 700;
-  public static int NEW_WINDOW_HEIGHT = 500;
+  int NEW_WINDOW_WIDTH = 700;
+  int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
 
 
-  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
+  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)
   {
     this.applet = applet;
     viewport = new AlignViewport(al, applet);
@@ -55,7 +56,6 @@ public class AlignFrame
       {
         try
         {
-          treeFile = treeFile;
           jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
               getCodeBase() + treeFile, "URL");
           fin.parse();
@@ -93,6 +93,25 @@ public class AlignFrame
           wrapMenuItem_actionPerformed(null);
         }
       }
+
+      try
+      {
+        param = applet.getParameter("windowWidth");
+        if (param != null)
+        {
+          int width = Integer.parseInt(param);
+          NEW_WINDOW_WIDTH = width;
+        }
+        param = applet.getParameter("windowHeight");
+        if (param != null)
+        {
+          int height = Integer.parseInt(param);
+          NEW_WINDOW_HEIGHT = height;
+        }
+      }
+      catch (Exception ex)
+      {}
+
     }
 
     this.addWindowListener(new WindowAdapter()
@@ -113,8 +132,98 @@ public class AlignFrame
        }
      }
    });
+
+   jalview.bin.JalviewLite.addFrame(this, title,
+                                    NEW_WINDOW_WIDTH,
+                                    NEW_WINDOW_HEIGHT);
+
+
   }
 
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param String DOCUMENT ME!
+   */
+
+  public void parseFeaturesFile(String file)
+  {
+    try
+    {
+      URL url = new URL(file);
+
+      BufferedReader in =  new BufferedReader(new InputStreamReader(url.openStream()));
+      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);
+        }
+      }
+
+      viewport.showSequenceFeatures = true;
+      ((Alignment)viewport.alignment).featuresAdded = true;
+
+      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);
@@ -131,7 +240,7 @@ 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()));
   }
@@ -412,7 +521,6 @@ public class AlignFrame
           newSeqs[i] = (SequenceI) seqs.elementAt(i);
         }
 
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
         String newtitle = new String("Copied sequences");
         if (getTitle().startsWith("Copied sequences"))
         {
@@ -422,6 +530,8 @@ public class AlignFrame
         {
           newtitle = newtitle.concat("- from " + getTitle());
         }
+        AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
+
         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
                                          NEW_WINDOW_HEIGHT);
       }
@@ -745,7 +855,7 @@ public class AlignFrame
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    Finder finder = new Finder(alignPanel);
+    new Finder(alignPanel);
   }
 
   public void font_actionPerformed(ActionEvent e)
@@ -755,7 +865,7 @@ public class AlignFrame
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
   {
-    viewport.setShowFullId(fullSeqId.getState());
+    viewport.setShowJVSuffix(fullSeqId.getState());
     alignPanel.fontChanged();
     alignPanel.repaint();
   }
@@ -1065,7 +1175,7 @@ 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)
@@ -1250,7 +1360,7 @@ public class AlignFrame
 
   protected void documentation_actionPerformed(ActionEvent e)
   {
-    jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
+    showURL("http://www.jalview.org/help.html");
   }
 
   protected void about_actionPerformed(ActionEvent e)
@@ -1317,4 +1427,36 @@ public class AlignFrame
     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
 
   }
+
+  /**
+   * Displays the given URL in a new browser window
+   *
+   * @param url URL to display in browser window.
+   * <br>New window will be named "HELP_WINDOW"
+   */
+  public void showURL(String url)
+  {
+    showURL(url, "HELP");
+  }
+
+  public void showURL(String url, String target)
+  {
+    if (applet == null)
+    {
+      System.out.println("Not running as applet - no browser available.");
+    }
+    else
+    {
+      try
+      {
+        applet.getAppletContext().showDocument(new java.net.URL(url),
+                                               target);
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+  }
+
 }