X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=6d70bf76256550ec1b903cb743be4d3c11c98280;hb=449001e7a8c9aad77117daa36567f3e8313646ea;hp=ee84bd38a2b9f463f7569f3349ceff5aa769980f;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ee84bd3..6d70bf7 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -153,6 +153,7 @@ public class AlignFrame extends Frame implements ActionListener,
       SequenceFeature sf;
       FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
       int lineNo = 0;
+      String featureGroup = null;
       while ( (line = in.readLine()) != null)
       {
         lineNo++;
@@ -160,8 +161,22 @@ 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 +199,6 @@ 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();
 
@@ -197,18 +210,24 @@ 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)
     {
+      ex.printStackTrace();
       System.out.println("Error parsing groups file: " + ex);
     }
   }
@@ -289,6 +308,10 @@ 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 +369,8 @@ 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)
@@ -817,6 +842,7 @@ public void itemStateChanged(ItemEvent evt)
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
+    alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.repaint();
     PaintRefresher.Refresh(null, viewport.alignment);
@@ -992,6 +1018,8 @@ public void itemStateChanged(ItemEvent evt)
     resetAllColourSchemes();
     if(alignPanel.overviewPanel!=null)
       alignPanel.overviewPanel.updateOverviewImage();
+
+    viewport.alignment.adjustSequenceAnnotations();
     alignPanel.repaint();
   }
 
@@ -1113,6 +1141,11 @@ 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)
@@ -1872,6 +1905,7 @@ public void itemStateChanged(ItemEvent evt)
         font.addActionListener(this);
         scaleAbove.setLabel("Scale Above");
         scaleAbove.setState(true);
+        scaleAbove.setEnabled(false);
         scaleAbove.addItemListener(this);
         scaleLeft.setEnabled(false);
         scaleLeft.setState(true);
@@ -1900,6 +1934,11 @@ 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);
@@ -1932,7 +1971,7 @@ 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);
@@ -1944,7 +1983,7 @@ 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();
@@ -2001,24 +2040,17 @@ public void itemStateChanged(ItemEvent evt)
     embeddedMenu.setBackground(Color.lightGray);
     embeddedMenu.setLayout(flowLayout1);
     embeddedEdit.setText("Edit");
-    embeddedEdit.setAlignment(Label.CENTER);
     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedSearch.setText("Search");
-    embeddedSearch.setAlignment(Label.CENTER);
     embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedView.setText("View");
-    embeddedView.setAlignment(Label.CENTER);
     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedColour.setText("Colour");
-    embeddedColour.setAlignment(Label.CENTER);
     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedFile.setAlignment(Label.CENTER);
     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedFile.setText("File");
-    embeddedHelp.setAlignment(Label.CENTER);
     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedHelp.setText("Help");
-    embeddedCalculate.setAlignment(Label.CENTER);
     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedCalculate.setText("Calculate");
     embeddedMenu.add(embeddedFile);
@@ -2029,7 +2061,7 @@ public void itemStateChanged(ItemEvent evt)
     embeddedMenu.add(embeddedCalculate);
     embeddedMenu.add(embeddedHelp);
     flowLayout1.setAlignment(FlowLayout.LEFT);
-    flowLayout1.setHgap(0);
+    flowLayout1.setHgap(2);
     flowLayout1.setVgap(0);
     embeddedFile.addMouseListener(this);
     embeddedEdit.addMouseListener(this);
@@ -2060,6 +2092,8 @@ 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)
   {