X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=2b53d7672379948c423b3f0ca158c2fe8e183c4a;hb=7bc213bae5828287329a3490faba291706599b03;hp=c4c2c5bf13fe9d20e6a92efb6e9c2817405d031d;hpb=e30c8f0736f711e2dc7c32680ac57a28c77d567d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index c4c2c5b..2b53d76 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -40,12 +40,17 @@ public class AlignFrame extends Frame implements ActionListener,
   int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
 
+  String jalviewServletURL;
+
 
    public AlignFrame(AlignmentI al,
                      jalview.bin.JalviewLite applet,
                      String title,
                      boolean embedded)
   {
+
+    jalviewServletURL = applet.getParameter("APPLICATION_URL");
+
     try{
       jbInit();
     }catch(Exception ex)
@@ -59,6 +64,8 @@ public class AlignFrame extends Frame implements ActionListener,
 
     annotationPanelMenuItem.setState(viewport.showAnnotation);
 
+    seqLimits.setState(viewport.showJVSuffix);
+
     if(applet!=null)
     {
       String param = applet.getParameter("sortBy");
@@ -148,162 +155,35 @@ public class AlignFrame extends Frame implements ActionListener,
    * @param String DOCUMENT ME!
    */
 
-  public void parseFeaturesFile(String file)
+  public void parseFeaturesFile(String file, String type)
   {
-    String line = null;
-    try
-    {
-      BufferedReader in = null;
-      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
-      if (is != null)
-      {
-        in = new BufferedReader(new java.io.InputStreamReader(is));
-      }
-      else
-      {
-        URL url = new URL(file);
-        in = new BufferedReader(new InputStreamReader(url.openStream()));
-      }
-
-      SequenceI seq = null;
-      String type, desc, token;
-
-      int index, start, end;
-      StringTokenizer st;
-      SequenceFeature sf;
-      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
-      String featureGroup = null, groupLink = null;
-      Hashtable typeLink = new Hashtable();
-
-      while ( (line = in.readLine()) != null)
-      {
-        st = new StringTokenizer(line, "\t");
-        if(!st.hasMoreTokens())
-          continue;
-
-        if (st.countTokens() < 4)
-        {
-          type = st.nextToken();
-          if(type.equalsIgnoreCase("startgroup"))
-          {
-            featureGroup = st.nextToken();
-            if (st.hasMoreElements())
-            {
-              groupLink = st.nextToken();
-              fr.addFeatureLink(featureGroup, groupLink);
-            }
-          }
-          else if(type.equalsIgnoreCase("endgroup"))
-          {
-            //We should check whether this is the current group,
-            //but at present theres no way of showing more than 1 group
-            st.nextToken();
-            featureGroup = null;
-            groupLink = null;
-          }
-          else
-          {
-            UserColourScheme ucs = new UserColourScheme(st.nextToken());
-            fr.setColour(type, ucs.findColour("A"));
-            if (st.hasMoreElements())
-            {
-                String link = st.nextToken();
-                typeLink.put(type, link);
-                fr.addFeatureLink(type, link);
-            }
-
-          }
-          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);
-
-          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, 0f, featureGroup);
-          seq.addSequenceFeature(sf);
-
-          if(groupLink!=null)
-          {
-            sf.addLink(groupLink);
-            sf.description += "%LINK%";
-          }
-          if(typeLink.containsKey(type))
-          {
-            sf.addLink(typeLink.get(type).toString());
-            sf.description += "%LINK%";
-          }
-
-          parseDescriptionHTML(sf);
-        }
-      }
-
-      viewport.showSequenceFeatures = true;
-      sequenceFeatures.setState(true);
-
-      alignPanel.repaint();
-
+    Hashtable featureLinks = new Hashtable();
+    boolean featuresFile = false;
+    try{
+      featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
+                                         alignPanel.seqPanel.seqCanvas.
+                                         getFeatureRenderer().featureColours,
+                                         featureLinks,
+                                         true);
     }
-    catch (Exception ex)
+    catch(Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Error parsing groups file: " + ex +"\n"+line);
     }
-  }
 
-  void parseDescriptionHTML(SequenceFeature sf)
-  {
-    StringBuffer sb = new StringBuffer();
-    StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
-    String token,  link;
-    while(st.hasMoreElements())
+    if(featuresFile)
     {
-      token = st.nextToken("<>");
-      if(token.equalsIgnoreCase("html") || token.startsWith("/"))
-        continue;
-
-      if(token.startsWith("a href="))
-      {
-        link = token.substring(token.indexOf("\"")+1, token.length()-1);
-        String label = st.nextToken("<>");
-        sf.addLink(label+"|"+link);
-        sb.append(label+"%LINK%");
-      }
-      else if(token.equalsIgnoreCase("br"))
-        sb.append("\n");
-      else
-        sb.append(token);
+      if(featureLinks.size()>0)
+        alignPanel.seqPanel.seqCanvas
+            .getFeatureRenderer().featureLinks = featureLinks;
+      viewport.showSequenceFeatures = true;
+      sequenceFeatures.setState(true);
+      alignPanel.repaint();
     }
 
-    sf.description = sb.toString();
   }
 
+
   public void keyPressed(KeyEvent evt)
   {
     if (viewport.cursorMode
@@ -325,7 +205,7 @@ public class AlignFrame extends Frame implements ActionListener,
         }
         break;
       case KeyEvent.VK_C:
-        if (viewport.cursorMode)
+        if (viewport.cursorMode && !evt.isControlDown())
         {
           alignPanel.seqPanel.setCursorColumn();
         }
@@ -498,6 +378,8 @@ public void itemStateChanged(ItemEvent evt)
       inputText_actionPerformed();
     else if(evt.getSource()==loadTree)
       loadTree_actionPerformed();
+    else if(evt.getSource()==loadApplication)
+      launchFullApplication();
     else if(evt.getSource()==closeMenuItem)
       closeMenuItem_actionPerformed();
     else if(evt.getSource()==copy)
@@ -628,6 +510,63 @@ public void itemStateChanged(ItemEvent evt)
                                                       viewport.showJVSuffix));
   }
 
+  void launchFullApplication()
+  {
+    StringBuffer url = new StringBuffer(jalviewServletURL);
+
+    url.append("?open="+
+               appendProtocol( applet.getParameter("file") ) );
+
+    if(applet.getParameter("features")!=null)
+    {
+      url.append( "&features=" );
+      url.append( appendProtocol( applet.getParameter("features") ) );
+    }
+
+    if(applet.getParameter("defaultColour")!=null)
+    {
+      url.append("&colour=" +
+                 removeWhiteSpace(applet.getParameter("defaultColour"))
+          );
+    }
+
+    if(applet.getParameter("userDefinedColour")!=null)
+    {
+      url.append( "&colour=" +
+                 removeWhiteSpace( applet.getParameter("userDefinedColour") )
+         );
+    }
+
+    showURL(url.toString(), "FULL_APP");
+  }
+
+
+  String removeWhiteSpace(String colour)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < colour.length(); i++)
+    {
+      if (Character.isWhitespace(colour.charAt(i)))
+        sb.append("%20");
+      else
+        sb.append(colour.charAt(i));
+    }
+
+    return sb.toString();
+  }
+
+
+  String appendProtocol(String url)
+  {
+    try{
+       new URL(url);
+    }catch(java.net.MalformedURLException ex)
+    {
+      url = applet.getCodeBase()+url;
+    }
+    return url;
+  }
+
   public void closeMenuItem_actionPerformed()
   {
     PaintRefresher.components.remove(viewport.alignment);
@@ -713,13 +652,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = 1; i < viewport.alignment.getHeight(); i++)
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.sequences.contains(seq))
+        if (!sg.getSequences(false).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
-        if (sg.sequences.contains(temp))
+        if (sg.getSequences(false).contains(temp))
         {
           continue;
         }
@@ -733,13 +672,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.sequences.contains(seq))
+        if (!sg.getSequences(true).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
-        if (sg.sequences.contains(temp))
+        if (sg.getSequences(true).contains(temp))
         {
           continue;
         }
@@ -763,7 +702,7 @@ public void itemStateChanged(ItemEvent evt)
     SequenceGroup sg = viewport.getSelectionGroup();
     copiedSequences = new StringBuffer();
     Hashtable orderedSeqs = new Hashtable();
-    for (int i = 0; i < sg.getSize(); i++)
+    for (int i = 0; i < sg.getSize(false); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.alignment.findIndex(seq);
@@ -773,7 +712,7 @@ public void itemStateChanged(ItemEvent evt)
     int index = 0, startRes, endRes;
     char ch;
 
-    for (int i = 0; i < sg.getSize(); i++)
+    for (int i = 0; i < sg.getSize(false); i++)
     {
         SequenceI seq = null;
 
@@ -919,10 +858,10 @@ public void itemStateChanged(ItemEvent evt)
 
     SequenceGroup sg = viewport.getSelectionGroup();
     boolean allSequences = false;
-    if(sg.sequences.size()==viewport.alignment.getHeight())
+    if(sg.getSize(false)==viewport.alignment.getHeight())
           allSequences = true;
 
-    for (int i = 0; i < sg.sequences.size(); i++)
+    for (int i = 0; i < sg.getSize(false); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
@@ -1103,10 +1042,10 @@ public void itemStateChanged(ItemEvent evt)
     int start=0, end = viewport.alignment.getWidth();
 
     if (viewport.getSelectionGroup() != null
-        && viewport.getSelectionGroup().sequences != null
-        && viewport.getSelectionGroup().sequences.size()>0)
+        && viewport.getSelectionGroup().getSequences(false) != null
+        && viewport.getSelectionGroup().getSize(false)>0)
     {
-      seqs = viewport.getSelectionGroup().sequences;
+      seqs = viewport.getSelectionGroup().getSequences(true);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes()+1;
     }
@@ -1212,7 +1151,8 @@ public void itemStateChanged(ItemEvent evt)
       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+        ((ClustalxColourScheme)sg.cs).resetClustalX(
+            sg.getSequences(true), sg.getWidth());
       }
       sg.recalcConservation();
     }
@@ -1448,7 +1388,7 @@ public void itemStateChanged(ItemEvent evt)
         }
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+          sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
         }
         else
         {
@@ -1468,7 +1408,7 @@ public void itemStateChanged(ItemEvent evt)
             || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
         }
         else
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
@@ -1477,7 +1417,7 @@ public void itemStateChanged(ItemEvent evt)
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.sequences, 0,
+                                            sg.getSequences(true), 0,
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
@@ -1590,17 +1530,12 @@ public void itemStateChanged(ItemEvent evt)
 
   public void removeRedundancyMenuItem_actionPerformed()
   {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel);
-    Frame frame = new Frame();
-    frame.add(sp);
-    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
-                                     400, 120);
-
+     new RedundancyPanel(alignPanel);
   }
 
   public void pairwiseAlignmentMenuItem_actionPerformed()
   {
-    if (viewport.getSelectionGroup().getSize() > 1)
+    if (viewport.getSelectionGroup().getSize(false) > 1)
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(alignPanel));
@@ -1630,8 +1565,8 @@ public void itemStateChanged(ItemEvent evt)
     }
 
     if ( (viewport.getSelectionGroup() != null &&
-          viewport.getSelectionGroup().getSize() < 4 &&
-          viewport.getSelectionGroup().getSize() > 0)
+          viewport.getSelectionGroup().getSize(false) < 4 &&
+          viewport.getSelectionGroup().getSize(false) > 0)
         || viewport.getAlignment().getHeight() < 4)
     {
       return;
@@ -1689,19 +1624,9 @@ public void itemStateChanged(ItemEvent evt)
 
     }
 
-    final TreePanel tp;
-    if (viewport.getSelectionGroup() != null &&
-        viewport.getSelectionGroup().getSize() > 3)
-    {
-      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
-                         pwType,
-                         0, viewport.alignment.getWidth());
-    }
-    else
-    {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, 0, viewport.alignment.getWidth());
-    }
+    final TreePanel tp = new TreePanel(viewport,
+                         type,
+                         pwType);
 
     addTreeMenuItem(tp, title);
 
@@ -1710,8 +1635,6 @@ public void itemStateChanged(ItemEvent evt)
 
   void loadTree_actionPerformed()
   {
-    TreePanel tp = null;
-
       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
       cap.setText("Paste your Newick tree file here.");
       cap.treeImport = true;
@@ -1723,8 +1646,9 @@ public void itemStateChanged(ItemEvent evt)
   public void loadTree(jalview.io.NewickFile tree, String treeFile)
   {
     TreePanel tp = new TreePanel(viewport,
-                      viewport.getAlignment().getSequences(),
-                      tree, "From File - ", treeFile);
+                                 treeFile,
+                                 "From File - ",
+                                 tree);
     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
     addTreeMenuItem(tp, treeFile);
   }
@@ -1833,6 +1757,7 @@ public void itemStateChanged(ItemEvent evt)
     {
       try
       {
+        System.out.println("Show url: "+url);
         applet.getAppletContext().showDocument(new java.net.URL(url),
                                                target);
       }
@@ -1849,6 +1774,7 @@ public void itemStateChanged(ItemEvent evt)
 
     protected MenuBar alignFrameMenuBar = new MenuBar();
     protected Menu fileMenu = new Menu("File");
+    protected MenuItem loadApplication = new MenuItem("View in Full Application");
     protected MenuItem loadTree = new MenuItem("Load Associated Tree");
     protected MenuItem closeMenuItem = new MenuItem("Close");
     protected Menu editMenu = new Menu("Edit");
@@ -1959,6 +1885,7 @@ public void itemStateChanged(ItemEvent evt)
         outputTextboxMenu.add(item);
       }
         closeMenuItem.addActionListener(this);
+        loadApplication.addActionListener(this);
 
         loadTree.addActionListener(this);
         selectAllSequenceMenuItem.addActionListener(this);
@@ -2124,6 +2051,8 @@ public void itemStateChanged(ItemEvent evt)
         alignFrameMenuBar.add(helpMenu);
         fileMenu.add(inputText);
         fileMenu.add(outputTextboxMenu);
+        if(jalviewServletURL!=null)
+          fileMenu.add(loadApplication);
         fileMenu.addSeparator();
         fileMenu.add(loadTree);
         fileMenu.add(closeMenuItem);
@@ -2254,7 +2183,7 @@ public void itemStateChanged(ItemEvent evt)
 
    // setVisible(false);
     fileMenu.remove(closeMenuItem);
-    fileMenu.remove(2); // Seperator
+    fileMenu.remove(3); // Seperator
 
     applet.setLayout(new BorderLayout());
     applet.add(embeddedMenu, BorderLayout.NORTH);