formatting
[jalview.git] / src / jalview / appletgui / AlignFrame.java
index 80b01d0..700c229 100644 (file)
@@ -1,37 +1,97 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ *\r
  * This file is part of Jalview.\r
- * \r
+ *\r
  * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
+ * modify it under the terms of the GNU General Public License\r
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ *\r
+ * Jalview is distributed in the hope that it will be useful, but\r
+ * WITHOUT ANY WARRANTY; without even the implied warranty\r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR\r
  * PURPOSE.  See the GNU General Public License for more details.\r
- * \r
+ *\r
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package jalview.appletgui;\r
 \r
-import java.net.*;\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
+import jalview.analysis.AAFrequency;\r
+import jalview.analysis.AlignmentSorter;\r
+import jalview.analysis.Conservation;\r
 import jalview.api.SequenceStructureBinding;\r
 import jalview.bin.JalviewLite;\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
+import jalview.commands.CommandI;\r
+import jalview.commands.EditCommand;\r
+import jalview.commands.OrderCommand;\r
+import jalview.commands.RemoveGapColCommand;\r
+import jalview.commands.RemoveGapsCommand;\r
+import jalview.commands.SlideSequencesCommand;\r
+import jalview.commands.TrimRegionCommand;\r
+import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.AlignmentOrder;\r
+import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceCollectionI;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.io.AnnotationFile;\r
+import jalview.io.AppletFormatAdapter;\r
+import jalview.io.FeaturesFile;\r
+import jalview.io.TCoffeeScoreFile;\r
+import jalview.schemes.Blosum62ColourScheme;\r
+import jalview.schemes.BuriedColourScheme;\r
+import jalview.schemes.ClustalxColourScheme;\r
+import jalview.schemes.ColourSchemeI;\r
+import jalview.schemes.HelixColourScheme;\r
+import jalview.schemes.HydrophobicColourScheme;\r
+import jalview.schemes.NucleotideColourScheme;\r
+import jalview.schemes.PIDColourScheme;\r
+import jalview.schemes.PurinePyrimidineColourScheme;\r
+import jalview.schemes.RNAHelicesColourChooser;\r
+import jalview.schemes.ResidueProperties;\r
+import jalview.schemes.StrandColourScheme;\r
+import jalview.schemes.TCoffeeColourScheme;\r
+import jalview.schemes.TaylorColourScheme;\r
+import jalview.schemes.TurnColourScheme;\r
+import jalview.schemes.ZappoColourScheme;\r
 import jalview.structure.StructureSelectionManager;\r
 \r
+import java.awt.BorderLayout;\r
+import java.awt.Canvas;\r
+import java.awt.CheckboxMenuItem;\r
+import java.awt.Color;\r
+import java.awt.Font;\r
+import java.awt.FontMetrics;\r
+import java.awt.Frame;\r
+import java.awt.Graphics;\r
+import java.awt.Label;\r
+import java.awt.Menu;\r
+import java.awt.MenuBar;\r
+import java.awt.MenuItem;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.FocusEvent;\r
+import java.awt.event.FocusListener;\r
+import java.awt.event.ItemEvent;\r
+import java.awt.event.ItemListener;\r
+import java.awt.event.KeyEvent;\r
+import java.awt.event.KeyListener;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.io.IOException;\r
+import java.io.InputStreamReader;\r
+import java.net.URL;\r
+import java.net.URLEncoder;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.List;\r
+import java.util.StringTokenizer;\r
+import java.util.Vector;\r
+\r
 public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
         ItemListener, KeyListener\r
 {\r
@@ -48,7 +108,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,\r
           String title, boolean embedded)\r
   {\r
-\r
     if (applet != null)\r
     {\r
       jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
@@ -69,12 +128,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.updateConsensus(alignPanel);\r
 \r
     annotationPanelMenuItem.setState(viewport.showAnnotation);\r
-    displayNonconservedMenuItem.setState(viewport.getShowunconserved());\r
+    displayNonconservedMenuItem.setState(viewport.getShowUnconserved());\r
     followMouseOverFlag.setState(viewport.getFollowHighlight());\r
-    showGroupConsensus.setState(viewport.showGroupConsensus);\r
-    showGroupConservation.setState(viewport.showGroupConservation);\r
-    showConsensusHistogram.setState(viewport.showConsensusHistogram);\r
-    showSequenceLogo.setState(viewport.showSequenceLogo);\r
+    showGroupConsensus.setState(viewport.isShowGroupConsensus());\r
+    showGroupConservation.setState(viewport.isShowGroupConservation());\r
+    showConsensusHistogram.setState(viewport.isShowConsensusHistogram());\r
+    showSequenceLogo.setState(viewport.isShowSequenceLogo());\r
+    normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());\r
 \r
     seqLimits.setState(viewport.showJVSuffix);\r
 \r
@@ -131,7 +191,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }\r
 \r
     }\r
-\r
+    if (viewport.getAlignment().isNucleotide())\r
+    {\r
+      viewport.updateStrucConsensus(alignPanel);\r
+      if (viewport.getAlignment().hasRNAStructure())\r
+      {\r
+        RNAHelixColour.setEnabled(true);\r
+      }\r
+      else\r
+      {\r
+        RNAHelixColour.setEnabled(false);\r
+      }\r
+    }\r
+    else\r
+    {\r
+      RNAHelixColour.setEnabled(false);\r
+      purinePyrimidineColour.setEnabled(false);\r
+    }\r
     // Some JVMS send keyevents to Top frame or lowest panel,\r
     // Havent worked out why yet. So add to both this frame and seqCanvas for\r
     // now\r
@@ -161,22 +237,46 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }\r
 \r
   /**\r
-   * DOCUMENT ME!\r
+   * Load a features file onto the alignment\r
    * \r
-   * @param String\r
-   *          DOCUMENT ME!\r
+   * @param file\r
+   *          file URL, content, or other resolvable path\r
+   * @param type\r
+   *          is protocol for accessing data referred to by file\r
    */\r
 \r
-  public void parseFeaturesFile(String file, String type)\r
+  public boolean parseFeaturesFile(String file, String type)\r
   {\r
+    return parseFeaturesFile(file, type, true);\r
+  }\r
+\r
+  /**\r
+   * Load a features file onto the alignment\r
+   * \r
+   * @param file\r
+   *          file URL, content, or other resolvable path\r
+   * @param type\r
+   *          is protocol for accessing data referred to by file\r
+   * @param autoenabledisplay\r
+   *          when true, display features flag will be automatically enabled if\r
+   *          features are loaded\r
+   * @return true if data parsed as a features file\r
+   */\r
+  public boolean parseFeaturesFile(String file, String type,\r
+          boolean autoenabledisplay)\r
+  {\r
+    // TODO: test if importing a features file onto an alignment which already\r
+    // has features with links overwrites the original links.\r
+\r
     Hashtable featureLinks = new Hashtable();\r
     boolean featuresFile = false;\r
     try\r
     {\r
       featuresFile = new jalview.io.FeaturesFile(file, type)\r
-              .parse(viewport.alignment,\r
-                      alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,\r
-                      featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));\r
+              .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas\r
+                      .getFeatureRenderer().featureColours, featureLinks,\r
+                      true, viewport.applet.getDefaultParameter(\r
+                              "relaxedidmatch", false));\r
     } catch (Exception ex)\r
     {\r
       ex.printStackTrace();\r
@@ -188,17 +288,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {\r
         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;\r
       }\r
-      viewport.showSequenceFeatures = true;\r
-      sequenceFeatures.setState(true);\r
+      if (autoenabledisplay)\r
+      {\r
+        viewport.showSequenceFeatures = true;\r
+        sequenceFeatures.setState(true);\r
+      }\r
       if (viewport.featureSettings != null)\r
       {\r
         viewport.featureSettings.refreshTable();\r
       }\r
       alignPanel.paintAlignment(true);\r
+      statusBar.setText("Successfully added features to alignment.");\r
     }\r
-\r
+    return featuresFile;\r
   }\r
 \r
+  @Override\r
   public void keyPressed(KeyEvent evt)\r
   {\r
     if (viewport.cursorMode\r
@@ -212,8 +317,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
     case 27: // escape key\r
       deselectAllSequenceMenuItem_actionPerformed();\r
-      \r
-      alignPanel.alabels.cancelDrag(); \r
+\r
+      alignPanel.alabels.cancelDrag();\r
       break;\r
     case KeyEvent.VK_X:\r
       if (evt.isControlDown() || evt.isMetaDown())\r
@@ -473,8 +578,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       // Hide everything by the current selection - this is a hack - we do the\r
       // invert and then hide\r
       // first check that there will be visible columns after the invert.\r
-      if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel\r
-              .getSelected().size() > 0)\r
+      if ((viewport.getColumnSelection() != null\r
+              && viewport.getColumnSelection().getSelected() != null && viewport\r
+              .getColumnSelection().getSelected().size() > 0)\r
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg\r
                       .getEndRes()))\r
       {\r
@@ -497,12 +603,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
     if (toggleSeqs)\r
     {\r
-      if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
+      if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())\r
       {\r
         hide = true;\r
         viewport.hideAllSelectedSeqs();\r
       }\r
-      else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))\r
+      else if (!(toggleCols && viewport.getColumnSelection().getSelected()\r
+              .size() > 0))\r
       {\r
         viewport.showAllHiddenSeqs();\r
       }\r
@@ -510,12 +617,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
     if (toggleCols)\r
     {\r
-      if (viewport.colSel.getSelected().size() > 0)\r
+      if (viewport.getColumnSelection().getSelected().size() > 0)\r
       {\r
         viewport.hideSelectedColumns();\r
         if (!toggleSeqs)\r
         {\r
-          viewport.selectionGroup = sg;\r
+          viewport.setSelectionGroup(sg);\r
         }\r
       }\r
       else if (!hide)\r
@@ -525,14 +632,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }\r
   }\r
 \r
+  @Override\r
   public void keyReleased(KeyEvent evt)\r
   {\r
   }\r
 \r
+  @Override\r
   public void keyTyped(KeyEvent evt)\r
   {\r
   }\r
 \r
+  @Override\r
   public void itemStateChanged(ItemEvent evt)\r
   {\r
     if (evt.getSource() == displayNonconservedMenuItem)\r
@@ -599,7 +709,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }\r
     else if (evt.getSource() == autoCalculate)\r
     {\r
-      viewport.autocalculateConsensus = autoCalculate.getState();\r
+      viewport.autoCalculateConsensus = autoCalculate.getState();\r
+    }\r
+    else if (evt.getSource() == sortByTree)\r
+    {\r
+      viewport.sortByTree = sortByTree.getState();\r
     }\r
     else if (evt.getSource() == this.centreColumnLabelFlag)\r
     {\r
@@ -621,6 +735,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
       showSequenceLogo_actionPerformed();\r
     }\r
+    else if (evt.getSource() == normSequenceLogo)\r
+    {\r
+      normSequenceLogo_actionPerformed();\r
+    }\r
     else if (evt.getSource() == showConsensusHistogram)\r
     {\r
       showConsensusHistogram_actionPerformed();\r
@@ -645,6 +763,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     this.alignPanel.annotationPanel.repaint();\r
   }\r
 \r
+  @Override\r
   public void actionPerformed(ActionEvent evt)\r
   {\r
     Object source = evt.getSource();\r
@@ -830,6 +949,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
       showSequenceLogo_actionPerformed();\r
     }\r
+    else if (source == normSequenceLogo)\r
+    {\r
+      normSequenceLogo_actionPerformed();\r
+    }\r
     else if (source == showConsensusHistogram)\r
     {\r
       showConsensusHistogram_actionPerformed();\r
@@ -845,7 +968,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == alProperties)\r
     {\r
       StringBuffer contents = new jalview.io.AlignmentProperties(\r
-              viewport.alignment).formatAsString();\r
+              viewport.getAlignment()).formatAsString();\r
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
       cap.setText(contents.toString());\r
       Frame frame = new Frame();\r
@@ -864,9 +987,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == clustalColour)\r
     {\r
       abovePIDThreshold.setState(false);\r
-      changeColour(new ClustalxColourScheme(\r
-              viewport.alignment.getSequences(),\r
-              viewport.alignment.getWidth()));\r
+      changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));\r
     }\r
     else if (source == zappoColour)\r
     {\r
@@ -900,6 +1021,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
       changeColour(new NucleotideColourScheme());\r
     }\r
+    else if (source == purinePyrimidineColour)\r
+    {\r
+      changeColour(new PurinePyrimidineColourScheme());\r
+    }\r
+    else if (source == RNAHelixColour)\r
+    {\r
+      new RNAHelicesColourChooser(viewport, alignPanel);\r
+    }\r
     else if (source == modifyPID)\r
     {\r
       modifyPID_actionPerformed();\r
@@ -920,6 +1049,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
       changeColour(new Blosum62ColourScheme());\r
     }\r
+    else if (source == tcoffeeColour)\r
+    {\r
+      changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+    }\r
     else if (source == annotationColour)\r
     {\r
       new AnnotationColourChooser(viewport, alignPanel);\r
@@ -1002,7 +1135,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void loadAnnotations()\r
   {\r
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
-    cap.setText("Paste your features / annotations file here.");\r
+    cap.setText("Paste your features / annotations / T-coffee score file here.");\r
     cap.setAnnotationImport();\r
     Frame frame = new Frame();\r
     frame.add(cap);\r
@@ -1013,10 +1146,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public String outputAnnotations(boolean displayTextbox)\r
   {\r
     String annotation = new AnnotationFile().printAnnotations(\r
-            viewport.showAnnotation ? viewport.alignment\r
-                    .getAlignmentAnnotation() : null, viewport.alignment\r
-                    .getGroups(),\r
-            ((Alignment) viewport.alignment).alignmentProperties);\r
+            viewport.showAnnotation ? viewport.getAlignment()\r
+                    .getAlignmentAnnotation() : null, viewport\r
+                    .getAlignment().getGroups(), ((Alignment) viewport\r
+                    .getAlignment()).alignmentProperties);\r
 \r
     if (displayTextbox)\r
     {\r
@@ -1032,7 +1165,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
   private Hashtable getDisplayedFeatureCols()\r
   {\r
-    if (alignPanel.getFeatureRenderer() != null)\r
+    if (alignPanel.getFeatureRenderer() != null\r
+            && viewport.featuresDisplayed != null)\r
     {\r
       FeatureRenderer fr = alignPanel.getFeatureRenderer();\r
       Hashtable fcols = new Hashtable();\r
@@ -1052,26 +1186,40 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     String features;\r
     if (format.equalsIgnoreCase("Jalview"))\r
     {\r
-      features = new FeaturesFile().printJalviewFormat(\r
-              viewport.alignment.getSequencesArray(),\r
+      features = new FeaturesFile().printJalviewFormat(viewport\r
+              .getAlignment().getSequencesArray(),\r
               getDisplayedFeatureCols());\r
     }\r
     else\r
     {\r
-      features = new FeaturesFile().printGFFFormat(\r
-              viewport.alignment.getSequencesArray(),\r
-              getDisplayedFeatureCols());\r
+      features = new FeaturesFile().printGFFFormat(viewport.getAlignment()\r
+              .getSequencesArray(), getDisplayedFeatureCols());\r
     }\r
 \r
     if (displayTextbox)\r
     {\r
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+      boolean frimport = false;\r
+      if (features == null || features.equals("No Features Visible"))\r
+      {\r
+        features = "# No features visible - paste some and import them here.";\r
+        frimport = true;\r
+      }\r
+\r
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);\r
+      if (frimport)\r
+      {\r
+        cap.setAnnotationImport();\r
+      }\r
       Frame frame = new Frame();\r
       frame.add(cap);\r
       jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);\r
-\r
       cap.setText(features);\r
     }\r
+    else\r
+    {\r
+      if (features == null)\r
+        features = "";\r
+    }\r
 \r
     return features;\r
   }\r
@@ -1170,13 +1318,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void closeMenuItem_actionPerformed()\r
   {\r
     PaintRefresher.RemoveComponent(alignPanel);\r
-    PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
-    PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+    if (alignPanel.seqPanel != null\r
+            && alignPanel.seqPanel.seqCanvas != null)\r
+    {\r
+      PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+    }\r
+    if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)\r
+    {\r
+      PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+    }\r
 \r
     if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
     {\r
       System.exit(0);\r
-    } else {\r
+    }\r
+    else\r
+    {\r
     }\r
     viewport = null;\r
     alignPanel = null;\r
@@ -1184,7 +1341,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }\r
 \r
   /**\r
-   * DOCUMENT ME!\r
+   * TODO: JAL-1104\r
    */\r
   void updateEditMenuBar()\r
   {\r
@@ -1215,6 +1372,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }\r
   }\r
 \r
+  /**\r
+   * TODO: JAL-1104\r
+   */\r
   public void addHistoryItem(CommandI command)\r
   {\r
     if (command.getSize() > 0)\r
@@ -1222,12 +1382,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewport.historyList.push(command);\r
       viewport.redoList.removeAllElements();\r
       updateEditMenuBar();\r
-      viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+      viewport.updateHiddenColumns();\r
     }\r
   }\r
 \r
   /**\r
-   * DOCUMENT ME!\r
+   * TODO: JAL-1104 DOCUMENT ME!\r
    * \r
    * @param e\r
    *          DOCUMENT ME!\r
@@ -1244,15 +1404,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     command.undoCommand(null);\r
 \r
     AlignViewport originalSource = getOriginatingSource(command);\r
-\r
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+    // JBPNote Test\r
+    if (originalSource != viewport)\r
+    {\r
+      System.err\r
+              .println("Warning: Viewport object mismatch whilst undoing");\r
+    }\r
+    originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =\r
+                                          // viewport.getColumnSelection().getHiddenColumns()\r
+                                          // != null;\r
     updateEditMenuBar();\r
-    originalSource.firePropertyChange("alignment", null,\r
-            originalSource.alignment.getSequences());\r
+    originalSource.firePropertyChange("alignment", null, originalSource\r
+            .getAlignment().getSequences());\r
   }\r
 \r
   /**\r
-   * DOCUMENT ME!\r
+   * TODO: JAL-1104 DOCUMENT ME!\r
    * \r
    * @param e\r
    *          DOCUMENT ME!\r
@@ -1269,11 +1436,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     command.doCommand(null);\r
 \r
     AlignViewport originalSource = getOriginatingSource(command);\r
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+    // JBPNote Test\r
+    if (originalSource != viewport)\r
+    {\r
+      System.err\r
+              .println("Warning: Viewport object mismatch whilst re-doing");\r
+    }\r
+    originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =\r
+                                          // viewport.getColumnSelection().getHiddenColumns()\r
+                                          // != null;\r
 \r
     updateEditMenuBar();\r
-    originalSource.firePropertyChange("alignment", null,\r
-            originalSource.alignment.getSequences());\r
+    originalSource.firePropertyChange("alignment", null, originalSource\r
+            .getAlignment().getSequences());\r
   }\r
 \r
   AlignViewport getOriginatingSource(CommandI command)\r
@@ -1293,7 +1468,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {\r
         if (comps.elementAt(i) instanceof AlignmentPanel)\r
         {\r
-          if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)\r
+          if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())\r
           {\r
             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;\r
             break;\r
@@ -1308,7 +1483,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       // the current view against the closed view first\r
       if (al != null)\r
       {\r
-        PaintRefresher.validateSequences(al, viewport.alignment);\r
+        PaintRefresher.validateSequences(al, viewport.getAlignment());\r
       }\r
 \r
       originalSource = viewport;\r
@@ -1324,65 +1499,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
       return;\r
     }\r
-\r
-    if (up)\r
-    {\r
-      for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
-      {\r
-        SequenceI seq = viewport.alignment.getSequenceAt(i);\r
-        if (!sg.getSequences(null).contains(seq))\r
-        {\r
-          continue;\r
-        }\r
-\r
-        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
-        if (sg.getSequences(null).contains(temp))\r
-        {\r
-          continue;\r
-        }\r
-\r
-        viewport.alignment.getSequences().setElementAt(temp, i);\r
-        viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
-      }\r
-    }\r
-    else\r
-    {\r
-      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
-      {\r
-        SequenceI seq = viewport.alignment.getSequenceAt(i);\r
-        if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
-        {\r
-          continue;\r
-        }\r
-\r
-        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
-        if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
-        {\r
-          continue;\r
-        }\r
-\r
-        viewport.alignment.getSequences().setElementAt(temp, i);\r
-        viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
-      }\r
-    }\r
-\r
+    viewport.getAlignment().moveSelectedSequencesByOne(sg,\r
+            up ? null : viewport.getHiddenRepSequences(), up);\r
     alignPanel.paintAlignment(true);\r
   }\r
 \r
   synchronized void slideSequences(boolean right, int size)\r
   {\r
-    Vector sg = new Vector();\r
+    List<SequenceI> sg = new Vector<SequenceI>();\r
     if (viewport.cursorMode)\r
     {\r
-      sg.addElement(viewport.alignment\r
-              .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));\r
+      sg.add(viewport.getAlignment().getSequenceAt(\r
+              alignPanel.seqPanel.seqCanvas.cursorY));\r
     }\r
     else if (viewport.getSelectionGroup() != null\r
-            && viewport.getSelectionGroup().getSize() != viewport.alignment\r
-                    .getHeight())\r
+            && viewport.getSelectionGroup().getSize() != viewport\r
+                    .getAlignment().getHeight())\r
     {\r
       sg = viewport.getSelectionGroup().getSequences(\r
-              viewport.hiddenRepSequences);\r
+              viewport.getHiddenRepSequences());\r
     }\r
 \r
     if (sg.size() < 1)\r
@@ -1390,21 +1525,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       return;\r
     }\r
 \r
-    Vector invertGroup = new Vector();\r
+    Vector<SequenceI> invertGroup = new Vector();\r
 \r
-    for (int i = 0; i < viewport.alignment.getHeight(); i++)\r
+    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
     {\r
-      if (!sg.contains(viewport.alignment.getSequenceAt(i)))\r
-        invertGroup.addElement(viewport.alignment.getSequenceAt(i));\r
+      if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))\r
+        invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));\r
     }\r
 \r
-    SequenceI[] seqs1 = new SequenceI[sg.size()];\r
-    for (int i = 0; i < sg.size(); i++)\r
-      seqs1[i] = (SequenceI) sg.elementAt(i);\r
+    SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);\r
 \r
-    SequenceI[] seqs2 = new SequenceI[invertGroup.size()];\r
+    SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup\r
+            .size()]);\r
     for (int i = 0; i < invertGroup.size(); i++)\r
-      seqs2[i] = (SequenceI) invertGroup.elementAt(i);\r
+      seqs2[i] = invertGroup.elementAt(i);\r
 \r
     SlideSequencesCommand ssc;\r
     if (right)\r
@@ -1470,14 +1604,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     for (int i = 0; i < sg.getSize(); i++)\r
     {\r
       SequenceI seq = sg.getSequenceAt(i);\r
-      int index = viewport.alignment.findIndex(seq);\r
+      int index = viewport.getAlignment().findIndex(seq);\r
       orderedSeqs.put(index + "", seq);\r
     }\r
 \r
     int index = 0, startRes, endRes;\r
     char ch;\r
 \r
-    if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
+    if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)\r
     {\r
       copiedHiddenColumns = new Vector();\r
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
@@ -1624,17 +1758,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {\r
     for (int i = 0; i < seqs.length; i++)\r
     {\r
-      viewport.alignment.addSequence(seqs[i]);\r
+      viewport.getAlignment().addSequence(seqs[i]);\r
     }\r
 \r
     // !newAlignment\r
     addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,\r
-            seqs, 0, viewport.alignment.getWidth(), viewport.alignment));\r
+            seqs, 0, viewport.getAlignment().getWidth(),\r
+            viewport.getAlignment()));\r
 \r
-    viewport.setEndSeq(viewport.alignment.getHeight());\r
-    viewport.alignment.getWidth();\r
-    viewport.firePropertyChange("alignment", null,\r
-            viewport.alignment.getSequences());\r
+    viewport.setEndSeq(viewport.getAlignment().getHeight());\r
+    viewport.getAlignment().getWidth();\r
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+            .getSequences());\r
 \r
   }\r
 \r
@@ -1662,7 +1797,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }\r
 \r
     // If the cut affects all sequences, remove highlighted columns\r
-    if (sg.getSize() == viewport.alignment.getHeight())\r
+    if (sg.getSize() == viewport.getAlignment().getHeight())\r
     {\r
       viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
               sg.getEndRes() + 1);\r
@@ -1679,10 +1814,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
      */\r
     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,\r
             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,\r
-            viewport.alignment));\r
+            viewport.getAlignment()));\r
 \r
     viewport.setSelectionGroup(null);\r
-    viewport.alignment.deleteGroup(sg);\r
+    viewport.getAlignment().deleteGroup(sg);\r
 \r
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
             .getSequences());\r
@@ -1726,6 +1861,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());\r
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
   }\r
+\r
   /*\r
    * (non-Javadoc)\r
    * \r
@@ -1739,6 +1875,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
   }\r
 \r
+  protected void normSequenceLogo_actionPerformed()\r
+  {\r
+    showSequenceLogo.setState(true);\r
+    viewport.setShowSequenceLogo(true);\r
+    viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());\r
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+  }\r
+\r
   protected void applyAutoAnnotationSettings_actionPerformed()\r
   {\r
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
@@ -1751,9 +1895,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(\r
               viewport.getSequenceSelection(),\r
               viewport.getAlignmentView(true).getSequenceStrings(\r
-                      viewport.getGapCharacter()),\r
-              viewport.alignment.getGroups());\r
-      viewport.alignment.deleteAllGroups();\r
+                      viewport.getGapCharacter()), viewport.getAlignment()\r
+                      .getGroups());\r
+      viewport.getAlignment().deleteAllGroups();\r
       viewport.sequenceColours = null;\r
       viewport.setSelectionGroup(null);\r
       // set view properties for each group\r
@@ -1761,14 +1905,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {\r
         // gps[g].setShowunconserved(viewport.getShowUnconserved());\r
         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());\r
-        viewport.alignment.addGroup(gps[g]);\r
+        viewport.getAlignment().addGroup(gps[g]);\r
         Color col = new Color((int) (Math.random() * 255),\r
                 (int) (Math.random() * 255), (int) (Math.random() * 255));\r
         col = col.brighter();\r
-        for (Enumeration sq = gps[g].getSequences(null).elements(); sq\r
-                .hasMoreElements(); viewport.setSequenceColour(\r
-                (SequenceI) sq.nextElement(), col))\r
-          ;\r
+        for (SequenceI sq : gps[g].getSequences(null))\r
+          viewport.setSequenceColour(sq, col);\r
       }\r
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
       alignPanel.updateAnnotation();\r
@@ -1778,7 +1920,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
   protected void deleteGroups_actionPerformed()\r
   {\r
-    viewport.alignment.deleteAllGroups();\r
+    viewport.getAlignment().deleteAllGroups();\r
     viewport.sequenceColours = null;\r
     viewport.setSelectionGroup(null);\r
 \r
@@ -1792,7 +1934,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
     }\r
-    sg.setEndRes(viewport.alignment.getWidth() - 1);\r
+    sg.setEndRes(viewport.getAlignment().getWidth() - 1);\r
     viewport.setSelectionGroup(sg);\r
     alignPanel.paintAlignment(true);\r
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
@@ -1856,11 +1998,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       if (viewport.getSelectionGroup() != null)\r
       {\r
         seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
-                viewport.hiddenRepSequences);\r
+                viewport.getHiddenRepSequences());\r
       }\r
       else\r
       {\r
-        seqs = viewport.alignment.getSequencesArray();\r
+        seqs = viewport.getAlignment().getSequencesArray();\r
       }\r
 \r
       TrimRegionCommand trimRegion;\r
@@ -1868,32 +2010,28 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {\r
         trimRegion = new TrimRegionCommand("Remove Left",\r
                 TrimRegionCommand.TRIM_LEFT, seqs, column,\r
-                viewport.alignment, viewport.colSel,\r
-                viewport.selectionGroup);\r
+                viewport.getAlignment(), viewport.getColumnSelection(),\r
+                viewport.getSelectionGroup());\r
         viewport.setStartRes(0);\r
       }\r
       else\r
       {\r
         trimRegion = new TrimRegionCommand("Remove Right",\r
                 TrimRegionCommand.TRIM_RIGHT, seqs, column,\r
-                viewport.alignment, viewport.colSel,\r
-                viewport.selectionGroup);\r
+                viewport.getAlignment(), viewport.getColumnSelection(),\r
+                viewport.getSelectionGroup());\r
       }\r
 \r
       statusBar.setText("Removed " + trimRegion.getSize() + " columns.");\r
 \r
       addHistoryItem(trimRegion);\r
 \r
-      Vector groups = viewport.alignment.getGroups();\r
-\r
-      for (int i = 0; i < groups.size(); i++)\r
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())\r
       {\r
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
         if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
         {\r
-          viewport.alignment.deleteGroup(sg);\r
+          viewport.getAlignment().deleteGroup(sg);\r
         }\r
       }\r
 \r
@@ -1904,23 +2042,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
   public void removeGappedColumnMenuItem_actionPerformed()\r
   {\r
-    int start = 0, end = viewport.alignment.getWidth() - 1;\r
+    int start = 0, end = viewport.getAlignment().getWidth() - 1;\r
 \r
     SequenceI[] seqs;\r
     if (viewport.getSelectionGroup() != null)\r
     {\r
       seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
-              viewport.hiddenRepSequences);\r
+              viewport.getHiddenRepSequences());\r
       start = viewport.getSelectionGroup().getStartRes();\r
       end = viewport.getSelectionGroup().getEndRes();\r
     }\r
     else\r
     {\r
-      seqs = viewport.alignment.getSequencesArray();\r
+      seqs = viewport.getAlignment().getSequencesArray();\r
     }\r
 \r
     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(\r
-            "Remove Gapped Columns", seqs, start, end, viewport.alignment);\r
+            "Remove Gapped Columns", seqs, start, end,\r
+            viewport.getAlignment());\r
 \r
     addHistoryItem(removeGapCols);\r
 \r
@@ -1929,7 +2068,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
     // This is to maintain viewport position on first residue\r
     // of first sequence\r
-    SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+    SequenceI seq = viewport.getAlignment().getSequenceAt(0);\r
     int startRes = seq.findPosition(viewport.startRes);\r
     // ShiftList shifts;\r
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
@@ -1944,28 +2083,28 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
   public void removeAllGapsMenuItem_actionPerformed()\r
   {\r
-    int start = 0, end = viewport.alignment.getWidth() - 1;\r
+    int start = 0, end = viewport.getAlignment().getWidth() - 1;\r
 \r
     SequenceI[] seqs;\r
     if (viewport.getSelectionGroup() != null)\r
     {\r
       seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
-              viewport.hiddenRepSequences);\r
+              viewport.getHiddenRepSequences());\r
       start = viewport.getSelectionGroup().getStartRes();\r
       end = viewport.getSelectionGroup().getEndRes();\r
     }\r
     else\r
     {\r
-      seqs = viewport.alignment.getSequencesArray();\r
+      seqs = viewport.getAlignment().getSequencesArray();\r
     }\r
 \r
     // This is to maintain viewport position on first residue\r
     // of first sequence\r
-    SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+    SequenceI seq = viewport.getAlignment().getSequenceAt(0);\r
     int startRes = seq.findPosition(viewport.startRes);\r
 \r
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,\r
-            viewport.alignment));\r
+            viewport.getAlignment()));\r
 \r
     viewport.setStartRes(seq.findIndex(startRes) - 1);\r
 \r
@@ -1988,30 +2127,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public AlignFrame newView(String viewtitle)\r
   {\r
     AlignmentI newal;\r
-    if (viewport.hasHiddenRows)\r
+    if (viewport.hasHiddenRows())\r
     {\r
       newal = new Alignment(viewport.getAlignment().getHiddenSequences()\r
               .getFullAlignment().getSequencesArray());\r
     }\r
     else\r
     {\r
-      newal = new Alignment(viewport.alignment.getSequencesArray());\r
+      newal = new Alignment(viewport.getAlignment().getSequencesArray());\r
     }\r
 \r
-    if (viewport.alignment.getAlignmentAnnotation() != null)\r
+    if (viewport.getAlignment().getAlignmentAnnotation() != null)\r
     {\r
-      for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)\r
+      for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)\r
       {\r
-        if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+        if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)\r
         {\r
-          newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
+          newal.addAnnotation(viewport.getAlignment()\r
+                  .getAlignmentAnnotation()[i]);\r
         }\r
       }\r
     }\r
 \r
     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);\r
 \r
-    newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
+    newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());\r
     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
     PaintRefresher.Register(newaf.alignPanel,\r
             newaf.alignPanel.av.getSequenceSetId());\r
@@ -2156,11 +2296,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             overview.getPreferredSize().height + 50);\r
 \r
     frame.pack();\r
+    final AlignmentPanel ap = alignPanel;\r
     frame.addWindowListener(new WindowAdapter()\r
     {\r
+      @Override\r
       public void windowClosing(WindowEvent e)\r
       {\r
-        alignPanel.setOverviewPanel(null);\r
+        if (ap != null)\r
+        {\r
+          ap.setOverviewPanel(null);\r
+        }\r
       };\r
     });\r
 \r
@@ -2191,13 +2336,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       if (viewport.getConservationSelected())\r
       {\r
 \r
-        Alignment al = (Alignment) viewport.alignment;\r
+        Alignment al = (Alignment) viewport.getAlignment();\r
         Conservation c = new Conservation("All",\r
                 ResidueProperties.propHash, 3, al.getSequences(), 0,\r
                 al.getWidth() - 1);\r
 \r
         c.calculate();\r
-        c.verdict(false, viewport.ConsPercGaps);\r
+        c.verdict(false, viewport.getConsPercGaps());\r
 \r
         cs.setConservation(c);\r
 \r
@@ -2210,82 +2355,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         cs.setConservation(null);\r
       }\r
 \r
-      cs.setConsensus(viewport.hconsensus);\r
+      cs.setConsensus(viewport.getSequenceConsensusHash());\r
 \r
     }\r
     viewport.setGlobalColourScheme(cs);\r
 \r
-    if (viewport.getColourAppliesToAllGroups())\r
-    {\r
-      Vector groups = viewport.alignment.getGroups();\r
-      for (int i = 0; i < groups.size(); i++)\r
-      {\r
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
-        if (cs == null)\r
-        {\r
-          sg.cs = null;\r
-          continue;\r
-        }\r
-        if (cs instanceof ClustalxColourScheme)\r
-        {\r
-          sg.cs = new ClustalxColourScheme(\r
-                  sg.getSequences(viewport.hiddenRepSequences),\r
-                  sg.getWidth());\r
-        }\r
-        else\r
-        {\r
-          try\r
-          {\r
-            sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
-          } catch (Exception ex)\r
-          {\r
-            ex.printStackTrace();\r
-            sg.cs = cs;\r
-          }\r
-        }\r
-\r
-        if (viewport.getAbovePIDThreshold()\r
-                || cs instanceof PIDColourScheme\r
-                || cs instanceof Blosum62ColourScheme)\r
-        {\r
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-          sg.cs.setConsensus(AAFrequency.calculate(\r
-                  sg.getSequences(viewport.hiddenRepSequences), 0,\r
-                  sg.getWidth()));\r
-        }\r
-        else\r
-        {\r
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-        }\r
-\r
-        if (viewport.getConservationSelected())\r
-        {\r
-          Conservation c = new Conservation("Group",\r
-                  ResidueProperties.propHash, 3,\r
-                  sg.getSequences(viewport.hiddenRepSequences), 0,\r
-                  viewport.alignment.getWidth() - 1);\r
-          c.calculate();\r
-          c.verdict(false, viewport.ConsPercGaps);\r
-          sg.cs.setConservation(c);\r
-        }\r
-        else\r
-        {\r
-          sg.cs.setConservation(null);\r
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-        }\r
-\r
-      }\r
-    }\r
-\r
     if (alignPanel.getOverviewPanel() != null)\r
     {\r
       alignPanel.getOverviewPanel().updateOverviewImage();\r
     }\r
 \r
     jalview.structure.StructureSelectionManager\r
-            .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(\r
-                    alignPanel);\r
+            .getStructureSelectionManager(viewport.applet)\r
+            .sequenceColoursChanged(alignPanel);\r
 \r
     alignPanel.paintAlignment(true);\r
   }\r
@@ -2293,7 +2375,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   protected void modifyPID_actionPerformed()\r
   {\r
     if (viewport.getAbovePIDThreshold()\r
-            && viewport.globalColourScheme != null)\r
+            && viewport.getGlobalColourScheme() != null)\r
     {\r
       SliderPanel.setPIDSliderSource(alignPanel,\r
               viewport.getGlobalColourScheme(), "Background");\r
@@ -2304,10 +2386,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   protected void modifyConservation_actionPerformed()\r
   {\r
     if (viewport.getConservationSelected()\r
-            && viewport.globalColourScheme != null)\r
+            && viewport.getGlobalColourScheme() != null)\r
     {\r
       SliderPanel.setConservationSlider(alignPanel,\r
-              viewport.globalColourScheme, "Background");\r
+              viewport.getGlobalColourScheme(), "Background");\r
       SliderPanel.showConservationSlider();\r
     }\r
   }\r
@@ -2343,7 +2425,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getAlignment().getSequenceAt(0), null);\r
 \r
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,\r
-            viewport.alignment));\r
+            viewport.getAlignment()));\r
     alignPanel.paintAlignment(true);\r
   }\r
 \r
@@ -2351,7 +2433,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {\r
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
     AlignmentSorter.sortByID(viewport.getAlignment());\r
-    addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));\r
+    addHistoryItem(new OrderCommand("ID Sort", oldOrder,\r
+            viewport.getAlignment()));\r
     alignPanel.paintAlignment(true);\r
   }\r
 \r
@@ -2360,7 +2443,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
     AlignmentSorter.sortByLength(viewport.getAlignment());\r
     addHistoryItem(new OrderCommand("Length Sort", oldOrder,\r
-            viewport.alignment));\r
+            viewport.getAlignment()));\r
     alignPanel.paintAlignment(true);\r
   }\r
 \r
@@ -2369,7 +2452,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
     addHistoryItem(new OrderCommand("Group Sort", oldOrder,\r
-            viewport.alignment));\r
+            viewport.getAlignment()));\r
     alignPanel.paintAlignment(true);\r
 \r
   }\r
@@ -2394,7 +2477,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void PCAMenuItem_actionPerformed()\r
   {\r
     // are the sequences aligned?\r
-    if (!viewport.alignment.isAligned(false))\r
+    if (!viewport.getAlignment().isAligned(false))\r
     {\r
       SequenceI current;\r
       int Width = viewport.getAlignment().getWidth();\r
@@ -2451,7 +2534,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   void NewTreePanel(String type, String pwType, String title)\r
   {\r
     // are the sequences aligned?\r
-    if (!viewport.alignment.isAligned(false))\r
+    if (!viewport.getAlignment().isAligned(false))\r
     {\r
       SequenceI current;\r
       int Width = viewport.getAlignment().getWidth();\r
@@ -2471,8 +2554,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
     if ((viewport.getSelectionGroup() != null && viewport\r
             .getSelectionGroup().getSize() > 1)\r
-            || (viewport.getSelectionGroup() == null && viewport.alignment\r
-                    .getHeight() > 1))\r
+            || (viewport.getAlignment().getHeight() > 1))\r
     {\r
       final TreePanel tp = new TreePanel(alignPanel, type, pwType);\r
 \r
@@ -2515,7 +2597,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
     // HistoryItem.SORT));\r
     addHistoryItem(new OrderCommand("Order by " + title, oldOrder,\r
-            viewport.alignment));\r
+            viewport.getAlignment()));\r
     alignPanel.paintAlignment(true);\r
   }\r
 \r
@@ -2533,6 +2615,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     sortByTreeMenu.add(item);\r
     item.addActionListener(new java.awt.event.ActionListener()\r
     {\r
+      @Override\r
       public void actionPerformed(ActionEvent evt)\r
       {\r
         sortByTree(treePanel, title); // treePanel.getTitle());\r
@@ -2541,6 +2624,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
     treePanel.addWindowListener(new WindowAdapter()\r
     {\r
+      @Override\r
       public void windowOpened(WindowEvent e)\r
       {\r
         if (viewport.sortByTree)\r
@@ -2550,31 +2634,35 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         super.windowOpened(e);\r
       }\r
 \r
+      @Override\r
       public void windowClosing(WindowEvent e)\r
       {\r
         sortByTreeMenu.remove(item);\r
       };\r
     });\r
   }\r
+\r
   public boolean sortBy(AlignmentOrder alorder, String undoname)\r
   {\r
-    SequenceI[] oldOrder = viewport.getAlignment()\r
-    .getSequencesArray();\r
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
     if (viewport.applet.debug)\r
     {\r
-      System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");\r
+      System.err.println("Sorting " + alorder.getOrder().size()\r
+              + " in alignment '" + getTitle() + "'");\r
     }\r
     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
-    if (undoname!=null)\r
+    if (undoname != null)\r
     {\r
-      addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));\r
+      addHistoryItem(new OrderCommand(undoname, oldOrder,\r
+              viewport.getAlignment()));\r
     }\r
     alignPanel.paintAlignment(true);\r
     return true;\r
   }\r
+\r
   protected void documentation_actionPerformed()\r
   {\r
-    showURL("http://www.jalview.org/help.html", "HELP");\r
+    alignPanel.av.applet.openJalviewHelpUrl();\r
   }\r
 \r
   protected void about_actionPerformed()\r
@@ -2592,6 +2680,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         this.builddate = builddate;\r
       }\r
 \r
+      @Override\r
       public void paint(Graphics g)\r
       {\r
         g.setColor(Color.white);\r
@@ -2645,45 +2734,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }\r
     else\r
     {\r
-      try\r
-      {\r
-        if (url.indexOf(":") == -1)\r
-        {\r
-          // TODO: verify (Bas Vroling bug) prepend codebase or server URL to\r
-          // form valid URL\r
-          // Should really use docbase, not codebase.\r
-          if (url.indexOf("/") == 0)\r
-          {\r
-            String codebase = viewport.applet.getCodeBase().toString();\r
-            url = codebase.substring(0, codebase.length()\r
-                    - viewport.applet.getCodeBase().getFile().length())\r
-                    + url;\r
-          }\r
-          else\r
-          {\r
-            url = viewport.applet.getCodeBase() + url;\r
-          }\r
-          System.out.println("Show url (prepended codebase): " + url);\r
-        }\r
-        else\r
-        {\r
-          System.out.println("Show url: " + url);\r
-        }\r
-        if (url.indexOf("javascript:") == 0)\r
-        {\r
-          // no target for the javascript context\r
-          viewport.applet.getAppletContext().showDocument(\r
-                  new java.net.URL(url));\r
-        }\r
-        else\r
-        {\r
-          viewport.applet.getAppletContext().showDocument(\r
-                  new java.net.URL(url), target);\r
-        }\r
-      } catch (Exception ex)\r
-      {\r
-        ex.printStackTrace();\r
-      }\r
+      viewport.applet.showURL(url, target);\r
     }\r
   }\r
 \r
@@ -2772,12 +2823,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
   MenuItem buriedColour = new MenuItem();\r
 \r
+  MenuItem purinePyrimidineColour = new MenuItem();\r
+\r
+  MenuItem RNAHelixColour = new MenuItem();\r
+\r
   MenuItem userDefinedColour = new MenuItem();\r
 \r
   MenuItem PIDColour = new MenuItem();\r
 \r
   MenuItem BLOSUM62Colour = new MenuItem();\r
 \r
+  MenuItem tcoffeeColour = new MenuItem();\r
+\r
   MenuItem njTreeBlosumMenuItem = new MenuItem();\r
 \r
   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
@@ -2843,6 +2900,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(\r
           "Autocalculate Consensus", true);\r
 \r
+  CheckboxMenuItem sortByTree = new CheckboxMenuItem(\r
+          "Sort Alignment With New Tree", true);\r
+\r
   Menu sortByTreeMenu = new Menu();\r
 \r
   Menu sort = new Menu();\r
@@ -2860,15 +2920,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
 \r
   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();\r
-  \r
+\r
   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();\r
-  Menu autoAnnMenu=new Menu();\r
-  CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();\r
+\r
+  Menu autoAnnMenu = new Menu();\r
+\r
+  CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();\r
+\r
   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();\r
+\r
   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
+\r
   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
+\r
   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
 \r
+  CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();\r
+\r
   private void jbInit() throws Exception\r
   {\r
 \r
@@ -2885,6 +2953,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
       item.addActionListener(new java.awt.event.ActionListener()\r
       {\r
+        @Override\r
         public void actionPerformed(ActionEvent e)\r
         {\r
           outputText_actionPerformed(e);\r
@@ -2957,12 +3026,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     turnColour.addActionListener(this);\r
     buriedColour.setLabel("Buried Index");\r
     buriedColour.addActionListener(this);\r
+    purinePyrimidineColour.setLabel("Purine/Pyrimidine");\r
+    purinePyrimidineColour.addActionListener(this);\r
+    RNAHelixColour.setLabel("by RNA Helices");\r
+    RNAHelixColour.addActionListener(this);\r
     userDefinedColour.setLabel("User Defined...");\r
     userDefinedColour.addActionListener(this);\r
     PIDColour.setLabel("Percentage Identity");\r
     PIDColour.addActionListener(this);\r
     BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
     BLOSUM62Colour.addActionListener(this);\r
+    tcoffeeColour.setLabel("T-Coffee Scores");\r
+    tcoffeeColour.setEnabled(false); // it will enabled only if a score file is\r
+                                     // provided\r
+    tcoffeeColour.addActionListener(this);\r
     avDistanceTreeBlosumMenuItem\r
             .setLabel("Average Distance Using BLOSUM62");\r
     avDistanceTreeBlosumMenuItem.addActionListener(this);\r
@@ -3038,6 +3115,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     sort.setLabel("Sort");\r
     calculate.setLabel("Calculate Tree");\r
     autoCalculate.addItemListener(this);\r
+    sortByTree.addItemListener(this);\r
     inputText.setLabel("Input from textbox");\r
     inputText.addActionListener(this);\r
     centreColumnLabelFlag.setLabel("Centre column labels");\r
@@ -3075,10 +3153,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     showGroupConservation.setLabel("Group Conservation");\r
     showConsensusHistogram.setLabel("Show Consensus Histogram");\r
     showSequenceLogo.setLabel("Show Consensus Logo");\r
+    normSequenceLogo.setLabel("Normalise Consensus Logo");\r
     applyAutoAnnotationSettings.setLabel("Apply to all groups");\r
     applyAutoAnnotationSettings.setState(true);\r
     autoAnnMenu.setLabel("Autocalculated Annotation");\r
-    \r
+\r
     invertColSel.addActionListener(this);\r
     showColumns.addActionListener(this);\r
     showSeqs.addActionListener(this);\r
@@ -3091,6 +3170,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     showGroupConservation.addItemListener(this);\r
     showConsensusHistogram.addItemListener(this);\r
     showSequenceLogo.addItemListener(this);\r
+    normSequenceLogo.addItemListener(this);\r
+\r
     applyAutoAnnotationSettings.addItemListener(this);\r
     formatMenu.setLabel("Format");\r
     selectMenu.setLabel("Select");\r
@@ -3144,6 +3225,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     autoAnnMenu.add(applyAutoAnnotationSettings);\r
     autoAnnMenu.add(showConsensusHistogram);\r
     autoAnnMenu.add(showSequenceLogo);\r
+    autoAnnMenu.add(normSequenceLogo);\r
     autoAnnMenu.addSeparator();\r
     autoAnnMenu.add(showGroupConservation);\r
     autoAnnMenu.add(showGroupConsensus);\r
@@ -3169,6 +3251,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(turnColour);\r
     colourMenu.add(buriedColour);\r
     colourMenu.add(nucleotideColour);\r
+    colourMenu.add(purinePyrimidineColour);\r
+    colourMenu.add(tcoffeeColour);\r
     colourMenu.add(userDefinedColour);\r
     colourMenu.addSeparator();\r
     colourMenu.add(conservationMenuItem);\r
@@ -3176,12 +3260,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(abovePIDThreshold);\r
     colourMenu.add(modifyPID);\r
     colourMenu.add(annotationColour);\r
+    colourMenu.add(RNAHelixColour);\r
     calculateMenu.add(sort);\r
     calculateMenu.add(calculate);\r
     calculateMenu.addSeparator();\r
     calculateMenu.add(pairwiseAlignmentMenuItem);\r
     calculateMenu.add(PCAMenuItem);\r
     calculateMenu.add(autoCalculate);\r
+    calculateMenu.add(sortByTree);\r
     this.add(statusBar, BorderLayout.SOUTH);\r
     pasteMenu.add(pasteNew);\r
     pasteMenu.add(pasteThis);\r
@@ -3290,14 +3376,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       final AlignFrame me = this;\r
       viewport.applet.addFocusListener(new FocusListener()\r
       {\r
-        \r
+\r
         @Override\r
         public void focusLost(FocusEvent e)\r
         {\r
-          if (me.viewport.applet.currentAlignFrame==me) {\r
-                  me.viewport.applet.currentAlignFrame = null;\r
-        }}\r
-        \r
+          if (me.viewport.applet.currentAlignFrame == me)\r
+          {\r
+            me.viewport.applet.currentAlignFrame = null;\r
+          }\r
+        }\r
+\r
         @Override\r
         public void focusGained(FocusEvent e)\r
         {\r
@@ -3390,11 +3478,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // TODO: search for a jmv that involves viewer\r
     if (jmv == null)\r
     { // create a new viewer/jalview binding.\r
-      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});\r
+      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]\r
+      { seqs });\r
     }\r
     return jmv;\r
 \r
   }\r
+\r
   /**\r
    * bind a pdb file to a sequence in the current view\r
    * \r
@@ -3515,8 +3605,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (applet.useXtrnalSviewer)\r
     {\r
       // register the association(s) and quit, don't create any windows.\r
-      if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {\r
-        System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");\r
+      if (StructureSelectionManager.getStructureSelectionManager(applet)\r
+              .setMapping(seqs, chains, pdb.getFile(), protocol) == null)\r
+      {\r
+        System.err.println("Failed to map " + pdb.getFile() + " ("\r
+                + protocol + ") to any sequences");\r
       }\r
       return;\r
     }\r
@@ -3568,9 +3661,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }\r
 \r
   /**\r
-   * modify the current selection, providing the user has not made a selection already.\r
-   * @param sel - sequences from this alignment \r
-   * @param csel - columns to be selected on the alignment\r
+   * modify the current selection, providing the user has not made a selection\r
+   * already.\r
+   * \r
+   * @param sel\r
+   *          - sequences from this alignment\r
+   * @param csel\r
+   *          - columns to be selected on the alignment\r
    */\r
   public void select(SequenceGroup sel, ColumnSelection csel)\r
   {\r
@@ -3579,6 +3676,81 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
   public void scrollTo(int row, int column)\r
   {\r
-    alignPanel.seqPanel.scrollTo(row, column);    \r
+    alignPanel.seqPanel.scrollTo(row, column);\r
   }\r
+\r
+  public void scrollToRow(int row)\r
+  {\r
+    alignPanel.seqPanel.scrollToRow(row);\r
+  }\r
+\r
+  public void scrollToColumn(int column)\r
+  {\r
+    alignPanel.seqPanel.scrollToColumn(column);\r
+  }\r
+\r
+  /**\r
+   * @return the alignments unique ID.\r
+   */\r
+  public String getSequenceSetId()\r
+  {\r
+    return viewport.getSequenceSetId();\r
+  }\r
+\r
+  /**\r
+   * Load the (T-Coffee) score file from the specified url\r
+   * \r
+   * @param source\r
+   *          File/URL/T-COFFEE score file contents\r
+   * @throws IOException\r
+   * @return true if alignment was annotated with data from source\r
+   */\r
+  public boolean loadScoreFile(String source) throws IOException\r
+  {\r
+\r
+    TCoffeeScoreFile file = new TCoffeeScoreFile(source,\r
+            AppletFormatAdapter.checkProtocol(source));\r
+    if (!file.isValid())\r
+    {\r
+      // TODO: raise dialog for gui\r
+      System.err.println("Problems parsing T-Coffee scores: "\r
+              + file.getWarningMessage());\r
+      System.err.println("Origin was:\n" + source);\r
+      return false;\r
+    }\r
+\r
+    /*\r
+     * check that the score matrix matches the alignment dimensions\r
+     */\r
+    AlignmentI aln;\r
+    if ((aln = viewport.getAlignment()) != null\r
+            && (aln.getHeight() != file.getHeight() || aln.getWidth() != file\r
+                    .getWidth()))\r
+    {\r
+      // TODO: raise a dialog box here rather than bomb out.\r
+      System.err\r
+              .println("The scores matrix does not match the alignment dimensions");\r
+\r
+    }\r
+\r
+    // TODO add parameter to indicate if matching should be done\r
+    if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
+    {\r
+      alignPanel.fontChanged();\r
+      tcoffeeColour.setEnabled(true);\r
+      // switch to this color\r
+      changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+      return true;\r
+    }\r
+    else\r
+    {\r
+      System.err.println("Problems resolving T-Coffee scores:");\r
+      if (file.getWarningMessage() != null)\r
+      {\r
+        System.err.println(file.getWarningMessage());\r
+      }\r
+    }\r
+    return false;\r
+  }\r
+\r
 }\r