CandP takes AlignFrame, not applet
[jalview.git] / src / jalview / appletgui / APopupMenu.java
index 858770a..b85c7d2 100755 (executable)
@@ -28,7 +28,7 @@ import jalview.datamodel.*;
 import jalview.schemes.*;\r
 \r
 public class APopupMenu\r
-    extends java.awt.PopupMenu\r
+    extends java.awt.PopupMenu implements ActionListener, ItemListener\r
 {\r
   Menu groupMenu = new Menu();\r
   protected MenuItem clustalColour = new MenuItem();\r
@@ -46,7 +46,7 @@ public class APopupMenu
   MenuItem noColourmenuItem = new MenuItem();\r
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
 \r
-  AlignmentPanel ap;\r
+  final AlignmentPanel ap;\r
   MenuItem unGroupMenuItem = new MenuItem();\r
   MenuItem nucleotideMenuItem = new MenuItem();\r
   Menu colourMenu = new Menu();\r
@@ -54,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();\r
   CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
 \r
-  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)\r
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
   {\r
     ///////////////////////////////////////////////////////////\r
     // If this is activated from the sequence panel, the user may want to\r
@@ -63,7 +63,7 @@ public class APopupMenu
     // If from the IDPanel, we must display the sequence menu\r
     //////////////////////////////////////////////////////////\r
 \r
-    this.ap = ap;\r
+    this.ap = apanel;\r
 \r
     try\r
     {\r
@@ -97,23 +97,98 @@ public class APopupMenu
         link = links.elementAt(i).toString();\r
         final String target = link.substring(0, link.indexOf("|"));\r
         item = new MenuItem(target);\r
+        String id = seq.getName();\r
+        if(id.indexOf("|")>-1)\r
+             id = id.substring(id.lastIndexOf("|")+1);\r
+\r
         final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
-               + seq.getName() +\r
+               + id +\r
                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 \r
            item.addActionListener(new java.awt.event.ActionListener()\r
            {\r
                public void actionPerformed(ActionEvent e)\r
                {\r
-                  jalview.bin.JalviewLite.showURL(url, target);\r
+                  ap.alignFrame.showURL(url, target);\r
                }\r
            });\r
           linkMenu.add(item);\r
       }\r
       add(linkMenu);\r
+\r
+      item = new MenuItem("Show PDB Structure");\r
+      item.addActionListener(new java.awt.event.ActionListener()\r
+           {\r
+               public void actionPerformed(ActionEvent e)\r
+               {\r
+                  addPDB(seq);\r
+               }\r
+           });\r
+\r
+      add(item);\r
+\r
+\r
     }\r
   }\r
 \r
+  public void itemStateChanged(ItemEvent evt)\r
+  {\r
+    if(evt.getSource()==abovePIDColour)\r
+      abovePIDColour_itemStateChanged();\r
+    else if(evt.getSource()==showColourText)\r
+      showColourText_itemStateChanged();\r
+    else if(evt.getSource()==showText)\r
+      showText_itemStateChanged();\r
+    else if(evt.getSource()==showBoxes)\r
+       showBoxes_itemStateChanged()   ;\r
+  }\r
+\r
+  public void actionPerformed(ActionEvent evt)\r
+  {\r
+    if(evt.getSource()==clustalColour)\r
+      clustalColour_actionPerformed();\r
+    else if(evt.getSource()==zappoColour)\r
+      zappoColour_actionPerformed();\r
+    else if(evt.getSource()==taylorColour)\r
+      taylorColour_actionPerformed();\r
+    else if(evt.getSource()==hydrophobicityColour)\r
+      hydrophobicityColour_actionPerformed();\r
+    else if(evt.getSource()==helixColour)\r
+      helixColour_actionPerformed();\r
+    else if(evt.getSource()==strandColour)\r
+      strandColour_actionPerformed();\r
+    else if(evt.getSource()==clustalColour)\r
+      turnColour_actionPerformed();\r
+    else if(evt.getSource()==buriedColour)\r
+      buriedColour_actionPerformed();\r
+    else if(evt.getSource()==nucleotideMenuItem)\r
+      nucleotideMenuItem_actionPerformed();\r
+\r
+    else if(evt.getSource()==userDefinedColour)\r
+          userDefinedColour_actionPerformed();\r
+        else if(evt.getSource()==PIDColour)\r
+       PIDColour_actionPerformed();\r
+     else if(evt.getSource()==BLOSUM62Colour)\r
+      BLOSUM62Colour_actionPerformed();\r
+    else if(evt.getSource()==noColourmenuItem)\r
+      noColourmenuItem_actionPerformed();\r
+    else if(evt.getSource()==conservationMenuItem)\r
+        conservationMenuItem_itemStateChanged();\r
+      else if(evt.getSource()==unGroupMenuItem)\r
+      unGroupMenuItem_actionPerformed();\r
+\r
+  }\r
+\r
+  void addPDB(Sequence seq)\r
+  {\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
+    cap.setText("Paste your PDB file here.");\r
+    cap.setPDBImport(seq);\r
+    Frame frame = new Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
+  }\r
+\r
   private void jbInit()\r
       throws Exception\r
   {\r
@@ -121,63 +196,21 @@ public class APopupMenu
     groupMenu.setLabel("Define");\r
 \r
     unGroupMenuItem.setLabel("Remove Group");\r
-    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        unGroupMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
+    unGroupMenuItem.addActionListener(this);\r
 \r
     nucleotideMenuItem.setLabel("Nucleotide");\r
-    nucleotideMenuItem.addActionListener(new ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        nucleotideMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    conservationMenuItem.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
-      {\r
-        conservationMenuItem_itemStateChanged(itemEvent);\r
-      }\r
-    });\r
-    abovePIDColour.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
-      {\r
-        abovePIDColour_itemStateChanged(itemEvent);\r
-      }\r
-    });\r
+    nucleotideMenuItem.addActionListener(this);\r
+    conservationMenuItem.addItemListener(this);\r
+    abovePIDColour.addItemListener(this);\r
     colourMenu.setLabel("Group Colour");\r
     showBoxes.setLabel("Boxes");\r
     showBoxes.setState(true);\r
-    showBoxes.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
-      {\r
-        showBoxes_itemStateChanged(itemEvent);\r
-      }\r
-    });\r
+    showBoxes.addItemListener(this);\r
 \r
     showText.setLabel("Text");\r
-    showText.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
-      {\r
-        showText_itemStateChanged(itemEvent);\r
-      }\r
-    });\r
+    showText.addItemListener(this);\r
     showColourText.setLabel("Colour Text");\r
-    showColourText.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
-      {\r
-        showColourText_itemStateChanged(itemEvent);\r
-      }\r
-    });\r
+    showColourText.addItemListener(this);\r
 \r
     add(groupMenu);\r
     groupMenu.add(unGroupMenuItem);\r
@@ -204,216 +237,131 @@ public class APopupMenu
     colourMenu.add(conservationMenuItem);\r
 \r
     noColourmenuItem.setLabel("None");\r
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        noColourmenuItem_actionPerformed(e);\r
-      }\r
-    });\r
+    noColourmenuItem.addActionListener(this);\r
 \r
     clustalColour.setLabel("Clustalx colours");\r
-    clustalColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        clustalColour_actionPerformed(e);\r
-      }\r
-    });\r
+    clustalColour.addActionListener(this);\r
     zappoColour.setLabel("Zappo");\r
-    zappoColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        zappoColour_actionPerformed(e);\r
-      }\r
-    });\r
+    zappoColour.addActionListener(this);\r
     taylorColour.setLabel("Taylor");\r
-    taylorColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        taylorColour_actionPerformed(e);\r
-      }\r
-    });\r
+    taylorColour.addActionListener(this);\r
     hydrophobicityColour.setLabel("Hydrophobicity");\r
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        hydrophobicityColour_actionPerformed(e);\r
-      }\r
-    });\r
+    hydrophobicityColour.addActionListener(this);\r
     helixColour.setLabel("Helix propensity");\r
-    helixColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        helixColour_actionPerformed(e);\r
-      }\r
-    });\r
+    helixColour.addActionListener(this);\r
     strandColour.setLabel("Strand propensity");\r
-    strandColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        strandColour_actionPerformed(e);\r
-      }\r
-    });\r
+    strandColour.addActionListener(this);\r
     turnColour.setLabel("Turn propensity");\r
-    turnColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        turnColour_actionPerformed(e);\r
-      }\r
-    });\r
+    turnColour.addActionListener(this);\r
     buriedColour.setLabel("Buried Index");\r
-    buriedColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        buriedColour_actionPerformed(e);\r
-      }\r
-    });\r
+    buriedColour.addActionListener(this);\r
     abovePIDColour.setLabel("Above % Identity");\r
 \r
     userDefinedColour.setLabel("User Defined");\r
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        userDefinedColour_actionPerformed(e);\r
-      }\r
-    });\r
+    userDefinedColour.addActionListener(this);\r
     PIDColour.setLabel("Percentage Identity");\r
-    PIDColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        PIDColour_actionPerformed(e);\r
-      }\r
-    });\r
+    PIDColour.addActionListener(this);\r
     BLOSUM62Colour.setLabel("BLOSUM62");\r
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        BLOSUM62Colour_actionPerformed(e);\r
-      }\r
-    });\r
+    BLOSUM62Colour.addActionListener(this);\r
     conservationMenuItem.setLabel("Conservation");\r
 \r
   }\r
 \r
   void refresh()\r
   {\r
-    SequenceGroup sg = getGroup();\r
-    if(sg!=null)\r
-    {\r
-      SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
-\r
-      if (superG != null)\r
-      {\r
-        superG.setSuperGroupProperties(sg);\r
-      }\r
-        }\r
     ap.seqPanel.seqCanvas.repaint();\r
+    if(ap.overviewPanel!=null)\r
+      ap.overviewPanel.updateOverviewImage();\r
   }\r
 \r
-  protected void clustalColour_actionPerformed(ActionEvent e)\r
+  protected void clustalColour_actionPerformed()\r
   {\r
     SequenceGroup sg = getGroup();\r
     sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
     refresh();\r
   }\r
 \r
-  protected void zappoColour_actionPerformed(ActionEvent e)\r
+  protected void zappoColour_actionPerformed()\r
   {\r
     getGroup().cs = new ZappoColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void taylorColour_actionPerformed(ActionEvent e)\r
+  protected void taylorColour_actionPerformed()\r
   {\r
     getGroup().cs = new TaylorColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+  protected void hydrophobicityColour_actionPerformed()\r
   {\r
     getGroup().cs = new HydrophobicColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void helixColour_actionPerformed(ActionEvent e)\r
+  protected void helixColour_actionPerformed()\r
   {\r
     getGroup().cs = new HelixColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void strandColour_actionPerformed(ActionEvent e)\r
+  protected void strandColour_actionPerformed()\r
   {\r
     getGroup().cs = new StrandColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void turnColour_actionPerformed(ActionEvent e)\r
+  protected void turnColour_actionPerformed()\r
   {\r
     getGroup().cs = new TurnColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void buriedColour_actionPerformed(ActionEvent e)\r
+  protected void buriedColour_actionPerformed()\r
   {\r
     getGroup().cs = new BuriedColourScheme();\r
     refresh();\r
   }\r
 \r
-  public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
+  public void nucleotideMenuItem_actionPerformed()\r
   {\r
     getGroup().cs = new NucleotideColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
+  protected void abovePIDColour_itemStateChanged()\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
+\r
     if (abovePIDColour.getState())\r
     {\r
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
                                                ap.av.alignment.getWidth()));\r
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
           getGroup().getName());\r
-      if (sg.cs instanceof ResidueColourScheme)\r
-      {\r
-        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
-      }\r
-      else if (sg.cs instanceof ScoreColourScheme)\r
-      {\r
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-      }\r
+\r
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 \r
       SliderPanel.showPIDSlider();\r
 \r
     }\r
     else // remove PIDColouring\r
     {\r
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
-      rcs.setThreshold(0);\r
-      sg.cs = rcs;\r
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
     }\r
 \r
     refresh();\r
 \r
   }\r
 \r
-  protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+  protected void userDefinedColour_actionPerformed()\r
   {\r
     new UserDefinedColours(ap, getGroup());\r
   }\r
 \r
-  protected void PIDColour_actionPerformed(ActionEvent e)\r
+  protected void PIDColour_actionPerformed()\r
   {\r
     SequenceGroup sg = getGroup();\r
     sg.cs = new PIDColourScheme();\r
@@ -422,7 +370,7 @@ public class APopupMenu
     refresh();\r
   }\r
 \r
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+  protected void BLOSUM62Colour_actionPerformed()\r
   {\r
     SequenceGroup sg = getGroup();\r
 \r
@@ -434,15 +382,17 @@ public class APopupMenu
     refresh();\r
   }\r
 \r
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+  protected void noColourmenuItem_actionPerformed()\r
   {\r
     getGroup().cs = null;\r
     refresh();\r
   }\r
 \r
-  protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
+  protected void conservationMenuItem_itemStateChanged()\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
 \r
     if (conservationMenuItem.getState())\r
     {\r
@@ -454,42 +404,20 @@ public class APopupMenu
 \r
       c.calculate();\r
       c.verdict(false, ap.av.ConsPercGaps);\r
-      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 \r
-      sg.cs = ccs;\r
+      sg.cs.setConservation(c);\r
 \r
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
       SliderPanel.showConservationSlider();\r
     }\r
     else // remove ConservationColouring\r
     {\r
-      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
-      sg.cs = ccs.cs;\r
+      sg.cs.setConservation(null);\r
     }\r
 \r
     refresh();\r
   }\r
 \r
-  protected void analyze_actionPerformed(ActionEvent e)\r
-  {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
-    Frame frame = new Frame();\r
-    frame.add(cap);\r
-    jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
-    SequenceGroup sg = getGroup();\r
-    StringBuffer sb = new StringBuffer();\r
-\r
-    for (int i = 0; i < sg.sequences.size(); i++)\r
-    {\r
-      Sequence tmp = (Sequence) sg.sequences.elementAt(i);\r
-      sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
-      sb.append("\n");\r
-    }\r
-\r
-    sb.append("Something amazing will happen soon");\r
-    cap.setText(sb.toString());\r
-\r
-  }\r
 \r
   SequenceGroup getGroup()\r
   {\r
@@ -502,7 +430,7 @@ public class APopupMenu
     return sg;\r
   }\r
 \r
-  void unGroupMenuItem_actionPerformed(ActionEvent e)\r
+  void unGroupMenuItem_actionPerformed()\r
   {\r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
     ap.av.alignment.deleteGroup(sg);\r
@@ -510,19 +438,19 @@ public class APopupMenu
     ap.repaint();\r
   }\r
 \r
-  public void showColourText_itemStateChanged(ItemEvent itemEvent)\r
+  public void showColourText_itemStateChanged()\r
   {\r
     getGroup().setColourText(showColourText.getState());\r
     refresh();\r
   }\r
 \r
-  public void showText_itemStateChanged(ItemEvent itemEvent)\r
+  public void showText_itemStateChanged()\r
   {\r
     getGroup().setDisplayText(showText.getState());\r
     refresh();\r
   }\r
 \r
-  public void showBoxes_itemStateChanged(ItemEvent itemEvent)\r
+  public void showBoxes_itemStateChanged()\r
   {\r
     getGroup().setDisplayBoxes(showBoxes.getState());\r
     refresh();\r