applet has multiple views

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index dad22cb..f786bde 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -68,7 +68,6 @@ public class APopupMenu
 \r
   Sequence seq;\r
   MenuItem revealAll = new MenuItem();\r
-  MenuItem menuItem1 = new MenuItem();\r
   Menu menu1 = new Menu();\r
 \r
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
@@ -382,7 +381,6 @@ public class APopupMenu
     hideSeqs.setLabel("Hide Sequences");\r
     repGroup.setLabel("Represent Group with");\r
     revealAll.setLabel("Reveal All");\r
-    menuItem1.setLabel("Create Sequence Feature");\r
     menu1.setLabel("Group");\r
     add(groupMenu);\r
     this.add(seqMenu);\r
@@ -390,7 +388,6 @@ public class APopupMenu
     this.add(revealAll);\r
     groupMenu.add(editMenu);\r
     groupMenu.add(outputmenu);\r
-    groupMenu.add(menuItem1);\r
     groupMenu.add(menu1);\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 604da7b..04d2045 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -425,9 +425,16 @@ public class AlignFrame extends Frame implements ActionListener,
         break;\r
 \r
       case KeyEvent.VK_U:\r
+        if (evt.isControlDown())\r
+        {\r
+          this.deleteGroups_actionPerformed();\r
+        }\r
+      break;\r
+\r
+    case KeyEvent.VK_T:\r
       if (evt.isControlDown())\r
       {\r
-       this.deleteGroups_actionPerformed();\r
+       newView();\r
       }\r
       break;\r
 \r
@@ -447,21 +454,24 @@ public void itemStateChanged(ItemEvent evt)
     else if(evt.getSource()==wrapMenuItem)\r
             wrapMenuItem_actionPerformed();\r
     else if(evt.getSource()==scaleAbove)\r
-            scaleAbove_actionPerformed();\r
+            viewport.setScaleAboveWrapped(scaleAbove.getState());\r
     else if(evt.getSource()==scaleLeft)\r
-            scaleLeft_actionPerformed();\r
+            viewport.setScaleLeftWrapped(scaleLeft.getState());\r
     else if(evt.getSource()==scaleRight)\r
-            scaleRight_actionPerformed();\r
+            viewport.setScaleRightWrapped(scaleRight.getState());\r
      else if(evt.getSource()==seqLimits)\r
       seqLimits_itemStateChanged();\r
     else if(evt.getSource()==viewBoxesMenuItem)\r
-            viewBoxesMenuItem_actionPerformed();\r
+            viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
     else if(evt.getSource()==viewTextMenuItem)\r
-            viewTextMenuItem_actionPerformed();\r
+            viewport.setShowText(viewTextMenuItem.getState());\r
     else if(evt.getSource()==renderGapsMenuItem)\r
-            renderGapsMenuItem_actionPerformed();\r
+            viewport.setRenderGaps(renderGapsMenuItem.getState());\r
     else if(evt.getSource()==annotationPanelMenuItem)\r
-            annotationPanelMenuItem_actionPerformed();\r
+    {\r
+      viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+    }\r
       else if(evt.getSource()==sequenceFeatures)\r
       {\r
            viewport.showSequenceFeatures(sequenceFeatures.getState());\r
@@ -471,10 +481,12 @@ public void itemStateChanged(ItemEvent evt)
             conservationMenuItem_actionPerformed();\r
       else if(evt.getSource()==abovePIDThreshold)\r
             abovePIDThreshold_actionPerformed();\r
-          else if(evt.getSource()==applyToAllGroups)\r
-            applyToAllGroups_actionPerformed();\r
+      else if(evt.getSource()==applyToAllGroups)\r
+            viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
       else if(evt.getSource()==autoCalculate)\r
           viewport.autocalculateConsensus = autoCalculate.getState();\r
+\r
+      alignPanel.repaint();\r
   }\r
  public void actionPerformed(ActionEvent evt)\r
  {\r
@@ -533,7 +545,9 @@ public void itemStateChanged(ItemEvent evt)
     else if(source==findMenuItem)\r
             findMenuItem_actionPerformed();\r
     else if(source==font)\r
-            font_actionPerformed();\r
+            new FontChooser(alignPanel);\r
+    else if (source == newView)\r
+      newView();\r
     else if(source==showColumns)\r
     {\r
       viewport.showAllHiddenColumns(); alignPanel.repaint();\r
@@ -551,39 +565,43 @@ public void itemStateChanged(ItemEvent evt)
       viewport.hideAllSelectedSeqs();\r
     }\r
     else if(source==featureSettings)\r
-            featureSettings_actionPerformed();\r
+            new FeatureSettings(alignPanel);\r
     else if(source==overviewMenuItem)\r
             overviewMenuItem_actionPerformed();\r
     else if(source==noColourmenuItem)\r
-            noColourmenuItem_actionPerformed();\r
+            changeColour(null);\r
     else if(source==clustalColour)\r
-            clustalColour_actionPerformed();\r
+    {\r
+      abovePIDThreshold.setState(false);\r
+      changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
+                                            viewport.alignment.getWidth()));\r
+  }\r
     else if(source==zappoColour)\r
-            zappoColour_actionPerformed();\r
+            changeColour(new ZappoColourScheme());\r
     else if(source==taylorColour)\r
-            taylorColour_actionPerformed();\r
+            changeColour(new TaylorColourScheme());\r
     else if(source==hydrophobicityColour)\r
-            hydrophobicityColour_actionPerformed();\r
+            changeColour(new HydrophobicColourScheme());\r
     else if(source==helixColour)\r
-            helixColour_actionPerformed();\r
+            changeColour(new HelixColourScheme());\r
     else if(source==strandColour)\r
-            strandColour_actionPerformed();\r
+            changeColour(new StrandColourScheme());\r
     else if(source==turnColour)\r
-            turnColour_actionPerformed();\r
+            changeColour(new TurnColourScheme());\r
     else if(source==buriedColour)\r
-            buriedColour_actionPerformed();\r
+            changeColour(new BuriedColourScheme());\r
     else if(source==nucleotideColour)\r
-            nucleotideColour_actionPerformed();\r
+            changeColour(new NucleotideColourScheme());\r
     else if(source==modifyPID)\r
             modifyPID_actionPerformed();\r
     else if(source==modifyConservation)\r
             modifyConservation_actionPerformed();\r
     else if(source==userDefinedColour)\r
-            userDefinedColour_actionPerformed();\r
+            new UserDefinedColours(alignPanel, null);\r
     else if(source==PIDColour)\r
-            PIDColour_actionPerformed();\r
+            changeColour(new PIDColourScheme());\r
     else if(source==BLOSUM62Colour)\r
-            BLOSUM62Colour_actionPerformed();\r
+            changeColour(new Blosum62ColourScheme());\r
     else if(source==annotationColour)\r
            new AnnotationColourChooser(viewport, alignPanel);\r
     else if(source==sortPairwiseMenuItem)\r
@@ -784,6 +802,9 @@ public void itemStateChanged(ItemEvent evt)
    */\r
   protected void redoMenuItem_actionPerformed()\r
   {\r
+    if(viewport.redoList.size()<1)\r
+      return;\r
+\r
     CommandI command = (CommandI) viewport.redoList.pop();\r
     viewport.historyList.push(command);\r
     command.doCommand();\r
@@ -1305,10 +1326,38 @@ public void itemStateChanged(ItemEvent evt)
     new Finder(alignPanel);\r
   }\r
 \r
-  public void font_actionPerformed()\r
+  public void newView()\r
   {\r
-    new FontChooser(alignPanel);\r
-  }\r
+    AlignmentI newal;\r
+    if (viewport.hasHiddenRows)\r
+      newal = new Alignment(viewport.getAlignment().\r
+                            getHiddenSequences()\r
+                            .getFullAlignment().\r
+                            getSequencesArray());\r
+    else\r
+      newal = new Alignment(viewport.alignment.getSequencesArray());\r
+\r
+\r
+\r
+    AlignFrame newaf = new AlignFrame(newal,\r
+                                      viewport.applet,\r
+                                      this.getTitle()+" (New View)",\r
+                                      false);\r
+\r
+    newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
+    PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
+    PaintRefresher.Register(newaf.alignPanel,\r
+                            newaf.alignPanel.av.getSequenceSetId());\r
+\r
+    PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
+                            newaf.alignPanel.av.getSequenceSetId());\r
+    PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
+                            newaf.alignPanel.av.getSequenceSetId());\r
+\r
+    newaf.viewport.historyList = viewport.historyList;\r
+    newaf.viewport.redoList = viewport.redoList;\r
+\r
+   }\r
 \r
 \r
   public void seqLimits_itemStateChanged()\r
@@ -1336,53 +1385,6 @@ public void itemStateChanged(ItemEvent evt)
   }\r
 \r
 \r
-  protected void scaleAbove_actionPerformed()\r
-  {\r
-    viewport.setScaleAboveWrapped(scaleAbove.getState());\r
-    alignPanel.repaint();\r
-  }\r
-\r
-  protected void scaleLeft_actionPerformed()\r
-  {\r
-    viewport.setScaleLeftWrapped(scaleLeft.getState());\r
-    alignPanel.repaint();\r
-  }\r
-\r
-  protected void scaleRight_actionPerformed()\r
-  {\r
-    viewport.setScaleRightWrapped(scaleRight.getState());\r
-    alignPanel.repaint();\r
-  }\r
-\r
-  public void viewBoxesMenuItem_actionPerformed()\r
-  {\r
-    viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
-    alignPanel.repaint();\r
-  }\r
-\r
-  public void viewTextMenuItem_actionPerformed()\r
-  {\r
-    viewport.setShowText(viewTextMenuItem.getState());\r
-    alignPanel.repaint();\r
-  }\r
-\r
-  protected void renderGapsMenuItem_actionPerformed()\r
-  {\r
-    viewport.setRenderGaps(renderGapsMenuItem.getState());\r
-    alignPanel.repaint();\r
-  }\r
-\r
-  public void annotationPanelMenuItem_actionPerformed()\r
-  {\r
-    viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
-    alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
-  }\r
-\r
-  public void featureSettings_actionPerformed()\r
-  {\r
-    new FeatureSettings(viewport, alignPanel);\r
-  }\r
-\r
   public void overviewMenuItem_actionPerformed()\r
   {\r
     if (alignPanel.overviewPanel != null)\r
@@ -1411,62 +1413,6 @@ public void itemStateChanged(ItemEvent evt)
 \r
   }\r
 \r
-  protected void noColourmenuItem_actionPerformed()\r
-  {\r
-    changeColour(null);\r
-  }\r
-\r
-  public void clustalColour_actionPerformed()\r
-  {\r
-    abovePIDThreshold.setState(false);\r
-    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
-                                          viewport.alignment.getWidth()));\r
-  }\r
-\r
-  public void zappoColour_actionPerformed()\r
-  {\r
-    changeColour(new ZappoColourScheme());\r
-  }\r
-\r
-  public void taylorColour_actionPerformed()\r
-  {\r
-    changeColour(new TaylorColourScheme());\r
-  }\r
-\r
-  public void hydrophobicityColour_actionPerformed()\r
-  {\r
-    changeColour(new HydrophobicColourScheme());\r
-  }\r
-\r
-  public void helixColour_actionPerformed()\r
-  {\r
-    changeColour(new HelixColourScheme());\r
-  }\r
-\r
-  public void strandColour_actionPerformed()\r
-  {\r
-    changeColour(new StrandColourScheme());\r
-  }\r
-\r
-  public void turnColour_actionPerformed()\r
-  {\r
-    changeColour(new TurnColourScheme());\r
-  }\r
-\r
-  public void buriedColour_actionPerformed()\r
-  {\r
-    changeColour(new BuriedColourScheme());\r
-  }\r
-\r
-  public void nucleotideColour_actionPerformed()\r
-  {\r
-    changeColour(new NucleotideColourScheme());\r
-  }\r
-\r
-  protected void applyToAllGroups_actionPerformed()\r
-  {\r
-    viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
-  }\r
 \r
   void changeColour(ColourSchemeI cs)\r
   {\r
@@ -1628,20 +1574,7 @@ public void itemStateChanged(ItemEvent evt)
     modifyPID_actionPerformed();\r
   }\r
 \r
-  public void userDefinedColour_actionPerformed()\r
-  {\r
-    new UserDefinedColours(alignPanel, null);\r
-  }\r
 \r
-  public void PIDColour_actionPerformed()\r
-  {\r
-    changeColour(new PIDColourScheme());\r
-  }\r
-\r
-  public void BLOSUM62Colour_actionPerformed()\r
-  {\r
-    changeColour(new Blosum62ColourScheme());\r
-  }\r
 \r
   public void sortPairwiseMenuItem_actionPerformed()\r
   {\r
@@ -2201,6 +2134,8 @@ public void itemStateChanged(ItemEvent evt)
     hideSequences.addActionListener(this);\r
     formatMenu.setLabel("Format");\r
     selectMenu.setLabel("Select");\r
+    newView.setLabel("New View");\r
+    newView.addActionListener(this);\r
     alignFrameMenuBar.add(fileMenu);\r
         alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(selectMenu);\r
@@ -2228,6 +2163,8 @@ public void itemStateChanged(ItemEvent evt)
         editMenu.add(removeGappedColumnMenuItem);\r
         editMenu.add(removeAllGapsMenuItem);\r
         editMenu.add(removeRedundancyMenuItem);\r
+    viewMenu.add(newView);\r
+    viewMenu.addSeparator();\r
     viewMenu.add(menu1);\r
     viewMenu.add(menu2);\r
     viewMenu.addSeparator();\r
@@ -2376,6 +2313,7 @@ public void itemStateChanged(ItemEvent evt)
   MenuItem hideSequences = new MenuItem();\r
   Menu formatMenu = new Menu();\r
   Menu selectMenu = new Menu();\r
+  MenuItem newView = new MenuItem();\r
 \r
   public void mousePressed(MouseEvent evt)\r
   {\r

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index a24525e..2e193aa 100755 (executable)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -412,10 +412,10 @@ public class FeatureRenderer
   {\r
     void setTransparency(Graphics g, float value)\r
     {\r
-     Graphics2D g2 = (Graphics2D) g;\r
-     g2.setComposite(\r
-        AlphaComposite.getInstance(\r
-             AlphaComposite.SRC_OVER, value));\r
+     //Graphics2D g2 = (Graphics2D) g;\r
+    // g2.setComposite(\r
+     //   AlphaComposite.getInstance(\r
+     //        AlphaComposite.SRC_OVER, value));\r
     }\r
   }\r
 \r

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index f829826..c855672 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -38,10 +38,10 @@ public class FeatureSettings extends Panel implements ItemListener,
   Image linkImage;\r
   Scrollbar transparency ;\r
 \r
-  public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
+  public FeatureSettings(final AlignmentPanel ap)\r
   {\r
     this.ap = ap;\r
-    this.av = av;\r
+    this.av = ap.av;\r
     fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
 \r
     transparency = new Scrollbar(Scrollbar.HORIZONTAL,\r