X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=692c2fde137e81d89d6e25a2cbda80a00d0d7e4f;hb=a0d1b1826f8ab0792c589946746d52ad0316fc99;hp=ccf2bd21eeb011fa8703ddf77f37f3b7c9e83fce;hpb=d72c37ab022b3a8ff6f6cda1d3f09de5c5d004ab;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ccf2bd2..692c2fd 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 final int NEW_WINDOW_WIDTH = 700;
-  public static final int NEW_WINDOW_HEIGHT = 500;
+  public final AlignViewport viewport;
+  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);
@@ -48,38 +49,69 @@ public class AlignFrame
     add(alignPanel);
     alignPanel.validate();
 
-    String treeFile = applet.getParameter("treeFile");
-    if (treeFile != null)
+    if(applet!=null)
     {
-      try
+      String treeFile = applet.getParameter("treeFile");
+      if (treeFile != null)
       {
-        treeFile = treeFile;
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
-            getCodeBase() + treeFile, "URL");
-        fin.parse();
+        try
+        {
+          jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+              getCodeBase() + treeFile, "URL");
+          fin.parse();
 
-        if (fin.getTree() != null)
+          if (fin.getTree() != null)
+          {
+            TreePanel tp = null;
+            tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                               fin, "FromFile", applet.getCodeBase() + treeFile);
+            jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+            addTreeMenuItem(tp, treeFile);
+          }
+        }
+        catch (Exception ex)
         {
-          TreePanel tp = null;
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", applet.getCodeBase() + treeFile);
-          jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
-          addTreeMenuItem(tp, treeFile);
+          ex.printStackTrace();
         }
       }
-      catch (Exception ex)
+
+      String param = applet.getParameter("sortBy");
+      if (param != null)
       {
-        ex.printStackTrace();
+        if (param.equalsIgnoreCase("Id"))
+          sortIDMenuItem_actionPerformed(null);
+        else if (param.equalsIgnoreCase("Pairwise Identity"))
+          sortPairwiseMenuItem_actionPerformed(null);
       }
-    }
 
-    String param = applet.getParameter("sortBy");
-    if(param!=null)
-    {
-      if (param.equalsIgnoreCase("Id"))
-        sortIDMenuItem_actionPerformed(null);
-      else if (param.equalsIgnoreCase("Pairwise Identity"))
-        sortPairwiseMenuItem_actionPerformed(null);
+      param = applet.getParameter("wrap");
+      if (param != null)
+      {
+        if (param.equalsIgnoreCase("true"))
+        {
+          wrapMenuItem.setState(true);
+          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()
@@ -100,8 +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);
@@ -118,15 +240,17 @@ public class AlignFrame
     jalview.bin.JalviewLite.addFrame(frame,
                                      "Alignment output - " + e.getActionCommand(),
                                      600, 500);
-    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment().
-                                              getSequences()));
+    cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
+                                              viewport.getAlignment().getSequences(),
+                                                      viewport.showDBPrefix,
+                                                      viewport.showJVSuffix));
   }
 
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
     PaintRefresher.components.remove(viewport.alignment);
-    dispose();
+    if(PaintRefresher.components.size()==0 && applet==null)
+      System.exit(0);
   }
 
   Stack historyList = new Stack();
@@ -397,7 +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"))
         {
@@ -407,6 +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);
       }
@@ -623,30 +748,56 @@ public class AlignFrame
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
     }
     else
       seqs = viewport.alignment.getSequences();
 
-    for (int i = 0; i <seqs.size(); i++)
+    for (int i = 0; i < seqs.size(); i++)
     {
-      current = (SequenceI)seqs.elementAt(i);
+      current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
 
+      // Removing a range is much quicker than removing gaps
+      // one by one for long sequences
       int j = start;
+      int rangeStart=-1, rangeEnd=-1;
+
       do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
+          if(rangeStart==-1)
+           {
+             rangeStart = j;
+             rangeEnd = j+1;
+           }
+           else
+           {
+             rangeEnd++;
+           }
+           j++;
         }
-        j++;
+        else
+        {
+          if(rangeStart>-1)
+          {
+            current.deleteChars(rangeStart, rangeEnd);
+            j-=rangeEnd-rangeStart;
+            jSize-=rangeEnd-rangeStart;
+            rangeStart = -1;
+            rangeEnd = -1;
+          }
+          else
+            j++;
+        }
+      }
+      while (j < end && j < jSize);
+      if(rangeStart>-1)
+      {
+       current.deleteChars(rangeStart, rangeEnd);
       }
-      while(j < end && j < jSize) ;
     }
-
     viewport.setStartRes(seq.findIndex(startRes)-1);
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
@@ -704,25 +855,29 @@ public class AlignFrame
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    Finder finder = new Finder(alignPanel);
+    new Finder(alignPanel);
   }
 
   public void font_actionPerformed(ActionEvent e)
   {
-    Frame frame = new Frame();
-    FontChooser fc = new FontChooser(alignPanel, frame);
-    frame.add(fc);
-    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
+    new FontChooser(alignPanel);
+  }
 
+  public void dbref_actionPerformed(ItemEvent e)
+  {
+    viewport.showDBPrefix = dbref.getState();
+    alignPanel.fontChanged();
+    alignPanel.repaint();
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  public void seqLimits_itemStateChanged(ItemEvent e)
   {
-    viewport.setShowFullId(fullSeqId.getState());
+    viewport.setShowJVSuffix(seqLimits.getState());
     alignPanel.fontChanged();
     alignPanel.repaint();
   }
 
+
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.getState());
@@ -777,11 +932,6 @@ public class AlignFrame
 
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
-    {
-      annotationPanelMenuItem.setState(false);
-      return;
-    }
     viewport.setShowAnnotation(annotationPanelMenuItem.getState());
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
   }
@@ -1033,7 +1183,7 @@ 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)
@@ -1059,7 +1209,7 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
                                    HistoryItem.SORT));
-    AlignmentSorter.sortByID(viewport.getAlignment());
+    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
     alignPanel.repaint();
   }
 
@@ -1094,6 +1244,24 @@ public class AlignFrame
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
+    //are the sequences aligned?
+    if (!viewport.alignment.isAligned())
+    {
+      SequenceI current;
+      int Width = viewport.getAlignment().getWidth();
+
+      for (int i = 0; i < viewport.getAlignment().getSequences().size();
+           i++)
+      {
+        current = viewport.getAlignment().getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());
+        }
+      }
+      alignPanel.repaint();
+    }
 
     if ( (viewport.getSelectionGroup() != null &&
           viewport.getSelectionGroup().getSize() < 4 &&
@@ -1105,11 +1273,7 @@ public class AlignFrame
 
     try
     {
-      PCAPanel pcaPanel = new PCAPanel(viewport, null);
-      Frame frame = new Frame();
-      frame.add(pcaPanel);
-      jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
-                                       400, 400);
+      new PCAPanel(viewport);
     }
     catch (java.lang.OutOfMemoryError ex)
     {
@@ -1204,7 +1368,7 @@ 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)
@@ -1271,4 +1435,36 @@ 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();
+      }
+    }
+  }
+
 }