X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=03c0db9d20c8814eaa106c75ce7c4fb57bc987ef;hb=4944c2f33bb34b4f262fd2f3ae40dcdc2a825557;hp=bd49198c38175d83fe6f964794faa1b42ec40a25;hpb=df1c58f9669c477db082016aa919d6c6cc9da071;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index bd49198..03c0db9 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -140,19 +140,30 @@ public class AlignFrame extends Frame implements ActionListener,
 
   public void parseFeaturesFile(String file)
   {
+    String line = null;
     try
     {
-      URL url = new URL(file);
+      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()));
+      }
 
-      BufferedReader in =  new BufferedReader(new InputStreamReader(url.openStream()));
       SequenceI seq = null;
-      String line, type, desc, token;
+      String type, desc, token;
 
       int index, start, end;
       StringTokenizer st;
       SequenceFeature sf;
       FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
       int lineNo = 0;
+      String featureGroup = null;
       while ( (line = in.readLine()) != null)
       {
         lineNo++;
@@ -160,8 +171,22 @@ public class AlignFrame extends Frame implements ActionListener,
         if (st.countTokens() == 2)
         {
           type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          fr.setColour(type, ucs.findColour("A"));
+          if(type.equalsIgnoreCase("startgroup"))
+          {
+            featureGroup = st.nextToken();
+          }
+          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;
+          }
+          else
+          {
+            UserColourScheme ucs = new UserColourScheme(st.nextToken());
+            fr.setColour(type, ucs.findColour("A"));
+          }
           continue;
         }
 
@@ -184,8 +209,6 @@ public class AlignFrame extends Frame implements ActionListener,
           end = Integer.parseInt(st.nextToken());
 
           seq = viewport.alignment.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
 
           type = st.nextToken();
 
@@ -197,19 +220,25 @@ public class AlignFrame extends Frame implements ActionListener,
           }
 
           sf = new SequenceFeature(type, desc, "", start, end);
+          sf.setFeatureGroup(featureGroup);
 
           seq.addSequenceFeature(sf);
         }
       }
 
       viewport.showSequenceFeatures = true;
+      viewMenu.addSeparator();
+      viewMenu.add(sequenceFeatures);
+      viewMenu.add(featureSettings);
+
 
       alignPanel.repaint();
 
     }
     catch (Exception ex)
     {
-      System.out.println("Error parsing groups file: " + ex);
+      ex.printStackTrace();
+      System.out.println("Error parsing groups file: " + ex +"\n"+line);
     }
   }
 
@@ -289,6 +318,10 @@ public void itemStateChanged(ItemEvent evt)
             renderGapsMenuItem_actionPerformed();
     else if(evt.getSource()==annotationPanelMenuItem)
             annotationPanelMenuItem_actionPerformed();
+      else if(evt.getSource()==sequenceFeatures)
+       {     viewport.showSequenceFeatures(sequenceFeatures.getState());
+            alignPanel.seqPanel.seqCanvas.repaint();
+        }
       else if(evt.getSource()==conservationMenuItem)
             conservationMenuItem_actionPerformed();
       else if(evt.getSource()==abovePIDThreshold)
@@ -346,6 +379,8 @@ public void itemStateChanged(ItemEvent evt)
             findMenuItem_actionPerformed();
     else if(evt.getSource()==font)
             font_actionPerformed();
+    else if(evt.getSource()==featureSettings)
+            featureSettings_actionPerformed();
     else if(evt.getSource()==overviewMenuItem)
             overviewMenuItem_actionPerformed();
     else if(evt.getSource()==noColourmenuItem)
@@ -1116,6 +1151,11 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
   }
 
+  public void featureSettings_actionPerformed()
+  {
+    new FeatureSettings(viewport, alignPanel);
+  }
+
   public void overviewMenuItem_actionPerformed()
   {
     if (alignPanel.overviewPanel != null)
@@ -1904,6 +1944,11 @@ public void itemStateChanged(ItemEvent evt)
           seqLimits.setState(true);
     seqLimits.setLabel("Show Sequence Limits");
     seqLimits.addItemListener(this);
+    featureSettings.setLabel("Feature Settings...");
+    featureSettings.addActionListener(this);
+    sequenceFeatures.setLabel("Sequence Features");
+    sequenceFeatures.addItemListener(this);
+    sequenceFeatures.setState(true);
 
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
@@ -1936,7 +1981,7 @@ public void itemStateChanged(ItemEvent evt)
         searchMenu.add(findMenuItem);
         viewMenu.add(font);
         viewMenu.addSeparator();
-        viewMenu.add(seqLimits);
+    viewMenu.add(seqLimits);
         viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
         viewMenu.add(scaleAbove);
@@ -1948,7 +1993,7 @@ public void itemStateChanged(ItemEvent evt)
         viewMenu.add(colourTextMenuItem);
         viewMenu.add(renderGapsMenuItem);
         viewMenu.add(annotationPanelMenuItem);
-        viewMenu.addSeparator();
+    viewMenu.addSeparator();
         viewMenu.add(overviewMenuItem);
         colourMenu.add(applyToAllGroups);
         colourMenu.addSeparator();
@@ -2057,6 +2102,8 @@ public void itemStateChanged(ItemEvent evt)
 
   PopupMenu filePopup, editPopup, searchPopup,
       viewPopup, colourPopup, calculatePopup, helpPopup;
+  MenuItem featureSettings = new MenuItem();
+  CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
 
   public void mousePressed(MouseEvent evt)
   {