boxes, colour text, show text added to groups

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 66b29a0..447055a 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -37,6 +37,10 @@ public class PopupMenu extends JPopupMenu
   JMenuItem pdbMenuItem = new JMenuItem();\r
   JMenuItem outline = new JMenuItem();\r
   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
+  JMenu colourMenu = new JMenu();\r
+  JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
+  JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
+  JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
 \r
   public PopupMenu(AlignmentPanel ap, Sequence seq)\r
   {\r
@@ -101,6 +105,10 @@ public class PopupMenu extends JPopupMenu
 \r
       if (sg.cs instanceof ConservationColourScheme)\r
         conservationMenuItem.setSelected(true);\r
+\r
+      showText.setSelected(sg.getDisplayText());\r
+      showColourText.setSelected(sg.getColourText());\r
+      showBoxes.setSelected(sg.getDisplayBoxes());\r
     }\r
 \r
     if( !ap.av.alignment.getGroups().contains(sg))\r
@@ -164,36 +172,64 @@ public class PopupMenu extends JPopupMenu
         nucleotideMenuItem_actionPerformed(e);\r
       }\r
     });\r
+    colourMenu.setText("Group Colour");\r
+    showBoxes.setText("Boxes");\r
+    showBoxes.setState(true);\r
+    showBoxes.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showBoxes_actionPerformed(e);\r
+      }\r
+    });\r
+    showText.setText("Text");\r
+    showText.setState(true);\r
+    showText.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showText_actionPerformed(e);\r
+      }\r
+    });\r
+    showColourText.setText("Colour Text");\r
+    showColourText.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showColourText_actionPerformed(e);\r
+      }\r
+    });\r
     add(groupMenu);\r
     add(sequenceMenu);\r
     groupMenu.add(groupName);\r
     groupMenu.addSeparator();\r
     groupMenu.add(unGroupMenuItem);\r
     groupMenu.addSeparator();\r
-    groupMenu.add(outline);\r
+    groupMenu.add(colourMenu);\r
     groupMenu.addSeparator();\r
-    groupMenu.add(noColourmenuItem);\r
-    groupMenu.add(clustalColour);\r
-    groupMenu.add(BLOSUM62Colour);\r
-    groupMenu.add(PIDColour);\r
-\r
-    groupMenu.add(zappoColour);\r
-    groupMenu.add(taylorColour);\r
-    groupMenu.add(hydrophobicityColour);\r
-    groupMenu.add(helixColour);\r
-    groupMenu.add(strandColour);\r
-    groupMenu.add(turnColour);\r
-    groupMenu.add(buriedColour);\r
-    groupMenu.add(nucleotideMenuItem);\r
-\r
-    groupMenu.add(userDefinedColour);\r
-\r
+    groupMenu.add(showBoxes);\r
+    groupMenu.add(showText);\r
+    groupMenu.add(showColourText);\r
     groupMenu.addSeparator();\r
-    groupMenu.add(abovePIDColour);\r
-    groupMenu.add(conservationMenuItem);\r
-\r
+    groupMenu.add(outline);\r
     sequenceMenu.add(sequenceName);\r
     sequenceMenu.add(pdbMenuItem);\r
+    colourMenu.add(noColourmenuItem);\r
+    colourMenu.add(clustalColour);\r
+    colourMenu.add(BLOSUM62Colour);\r
+    colourMenu.add(PIDColour);\r
+    colourMenu.add(zappoColour);\r
+    colourMenu.add(taylorColour);\r
+    colourMenu.add(hydrophobicityColour);\r
+    colourMenu.add(helixColour);\r
+    colourMenu.add(strandColour);\r
+    colourMenu.add(turnColour);\r
+    colourMenu.add(buriedColour);\r
+    colourMenu.add(nucleotideMenuItem);\r
+    colourMenu.add(userDefinedColour);\r
+    colourMenu.addSeparator();\r
+    colourMenu.add(abovePIDColour);\r
+    colourMenu.add(conservationMenuItem);\r
     noColourmenuItem.setText("None");\r
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -411,12 +447,16 @@ public class PopupMenu extends JPopupMenu
 \r
   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
   {\r
-    UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());\r
+    new UserDefinedColours( ap, getGroup());\r
   }\r
 \r
   protected void PIDColour_actionPerformed(ActionEvent e)\r
   {\r
-\r
+    SequenceGroup sg = getGroup();\r
+    sg.cs = new PIDColourScheme();\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+                                               ap.av.alignment.getWidth()));\r
+    refresh();\r
   }\r
 \r
   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
@@ -469,10 +509,6 @@ public class PopupMenu extends JPopupMenu
      refresh();\r
   }\r
 \r
-  protected void groupAnnotation_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
   protected void groupName_actionPerformed(ActionEvent e)\r
   {\r
@@ -556,7 +592,6 @@ public class PopupMenu extends JPopupMenu
       EBIFetchClient ebi = new EBIFetchClient();\r
       String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
 \r
-      System.out.println("Got "+ sequence.getPDBId() );\r
       PDBfile pdb = new PDBfile(result);\r
 \r
       rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
@@ -579,4 +614,22 @@ public class PopupMenu extends JPopupMenu
     ap.repaint();\r
   }\r
 \r
+  public void showBoxes_actionPerformed(ActionEvent e)\r
+  {\r
+    getGroup().setDisplayBoxes(showBoxes.isSelected());\r
+    refresh();\r
+  }\r
+\r
+  public void showText_actionPerformed(ActionEvent e)\r
+  {\r
+    getGroup().setDisplayText(showText.isSelected());\r
+    refresh();\r
+  }\r
+\r
+  public void showColourText_actionPerformed(ActionEvent e)\r
+  {\r
+    getGroup().setColourText(showColourText.isSelected());\r
+    refresh();\r
+  }\r
+\r
 }\r