Applet Structure viewer has all colours available

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index f39a3fa..d91d43e 100755 (executable)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -418,7 +418,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       drawLabels(ig);\r
     }\r
 \r
-\r
+   void setColours(jalview.schemes.ColourSchemeI cs)\r
+   {\r
+     bysequence = false;\r
+     pdb.setColours(cs);\r
+     redrawneeded = true;\r
+     repaint();\r
+   }\r
     public void updateSeqColours()\r
     {\r
       if (pdbAction)\r

diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 901297b..2c0080e 100755 (executable)
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -23,6 +23,7 @@ import java.awt.*;
 import java.awt.event.*;\r
 import jalview.datamodel.*;\r
 import jalview.appletgui.*;\r
+import jalview.schemes.*;\r
 import java.awt.event.ActionListener;\r
 import java.awt.event.ActionEvent;\r
 \r
@@ -121,7 +122,7 @@ public class AppletPDBViewer extends Frame
         {\r
           public void actionPerformed(ActionEvent e)\r
           {\r
-            hydro_actionPerformed();\r
+            pdbcanvas.setColours(new HydrophobicColourScheme());\r
           }\r
         });\r
         chain.setLabel("By Chain");\r
@@ -147,19 +148,84 @@ public class AppletPDBViewer extends Frame
         allchains_itemStateChanged(itemEvent);\r
       }\r
     });\r
+    viewMenu.setLabel("View");\r
+    zappo.setLabel("Zappo");\r
+    zappo.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+        pdbcanvas.setColours(new ZappoColourScheme());\r
+      }\r
+    });\r
+    taylor.setLabel("Taylor");\r
+    taylor.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+        pdbcanvas.setColours(new TaylorColourScheme());\r
+      }\r
+    });\r
+    helix.setLabel("Helix Propensity");\r
+    helix.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+       pdbcanvas.setColours(new HelixColourScheme());\r
+      }\r
+    });\r
+    strand.setLabel("Strand Propensity");\r
+    strand.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+        pdbcanvas.setColours(new StrandColourScheme());\r
+      }\r
+    });\r
+    turn.setLabel("Turn Propensity");\r
+    turn.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+        pdbcanvas.setColours(new TurnColourScheme());\r
+      }\r
+    });\r
+    buried.setLabel("Buried Index");\r
+    buried.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+        pdbcanvas.setColours(new BuriedColourScheme());\r
+      }\r
+    });\r
+    user.setLabel("User Defined...");\r
+    user.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+        pdbcanvas.bysequence = false;\r
+        new jalview.appletgui.UserDefinedColours(pdbcanvas);\r
+      }\r
+    });\r
     jMenuBar1.add(fileMenu);\r
         jMenuBar1.add(coloursMenu);\r
-        fileMenu.add(mapping);;\r
+    jMenuBar1.add(viewMenu);\r
+    fileMenu.add(mapping);;\r
 \r
         coloursMenu.add(seqButton);\r
         coloursMenu.add(chain);\r
-    coloursMenu.add(hydro);\r
     coloursMenu.add(charge);\r
-    coloursMenu.addSeparator();\r
-        coloursMenu.add(wire);\r
-        coloursMenu.add(depth);\r
-        coloursMenu.add(zbuffer);\r
-    coloursMenu.add(allchains);\r
+    coloursMenu.add(zappo);\r
+    coloursMenu.add(taylor);\r
+    coloursMenu.add(hydro);\r
+    coloursMenu.add(helix);\r
+    coloursMenu.add(strand);\r
+    coloursMenu.add(turn);\r
+    coloursMenu.add(buried);\r
+    coloursMenu.add(user);\r
+    viewMenu.add(wire);\r
+    viewMenu.add(depth);\r
+    viewMenu.add(zbuffer);\r
+    viewMenu.add(allchains);\r
     allchains.setState(true);\r
   }\r
 \r
@@ -178,27 +244,27 @@ public class AppletPDBViewer extends Frame
       MenuItem seqButton = new MenuItem();\r
 \r
      CheckboxMenuItem allchains = new CheckboxMenuItem();\r
+  Menu viewMenu = new Menu();\r
+  MenuItem turn = new MenuItem();\r
+  MenuItem strand = new MenuItem();\r
+  MenuItem helix = new MenuItem();\r
+  MenuItem taylor = new MenuItem();\r
+  MenuItem zappo = new MenuItem();\r
+  MenuItem buried = new MenuItem();\r
+  MenuItem user = new MenuItem();\r
 \r
   public void charge_actionPerformed()\r
       {\r
-        clearButtonGroup();\r
+        pdbcanvas.bysequence = false;\r
         pdbcanvas.pdb.setChargeColours();\r
         pdbcanvas.redrawneeded=true;\r
         pdbcanvas.repaint();\r
       }\r
 \r
-      public void hydro_actionPerformed()\r
-      {\r
-        clearButtonGroup();\r
-       // pdbcanvas.pdb.setHydrophobicityColours();\r
-        pdbcanvas.redrawneeded=true;\r
-        pdbcanvas.repaint();\r
-      }\r
-\r
       public void chain_actionPerformed()\r
       {\r
-        clearButtonGroup();\r
-        pdbcanvas.pdb.setChainColours();\r
+         pdbcanvas.bysequence = false;\r
+         pdbcanvas.pdb.setChainColours();\r
         pdbcanvas.redrawneeded=true;\r
         pdbcanvas.repaint();\r
       }\r
@@ -226,17 +292,11 @@ public class AppletPDBViewer extends Frame
 \r
       public void seqButton_actionPerformed()\r
       {\r
-        clearButtonGroup();\r
         pdbcanvas.bysequence = true;\r
         pdbcanvas.updateSeqColours();\r
         pdbcanvas.repaint();\r
       }\r
 \r
-      void clearButtonGroup()\r
-      {\r
-       pdbcanvas.bysequence = false;\r
-       pdbcanvas.bymolecule = false;\r
-      }\r
 \r
       public void mapping_actionPerformed()\r
       {\r
@@ -252,4 +312,5 @@ public class AppletPDBViewer extends Frame
       {\r
         pdbcanvas.setAllchainsVisible(allchains.getState());\r
       }\r
+\r
 }\r

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 7cd0391..71bcaca 100755 (executable)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -37,6 +37,7 @@ public class UserDefinedColours
   Vector oldColours = new Vector();\r
   ColourSchemeI oldColourScheme;\r
   Frame frame;\r
+  MCview.AppletPDBCanvas pdbcanvas;\r
 \r
   int R = 0, G = 0, B = 0;\r
 \r
@@ -48,20 +49,6 @@ public class UserDefinedColours
 \r
   public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)\r
   {\r
-    try {\r
-        jbInit();\r
-    } catch (Exception e) {\r
-        e.printStackTrace();\r
-      }\r
-    frame = new Frame();\r
-    frame.add(this);\r
-    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);\r
-\r
-    if (sg != null)\r
-    {\r
-      frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");\r
-    }\r
-\r
     this.ap = ap;\r
     seqGroup = sg;\r
 \r
@@ -74,6 +61,34 @@ public class UserDefinedColours
       oldColourScheme = ap.av.getGlobalColourScheme();\r
     }\r
 \r
+    init();\r
+  }\r
+\r
+  public UserDefinedColours(MCview.AppletPDBCanvas pdb)\r
+  {\r
+    this.pdbcanvas = pdb;\r
+    init();\r
+  }\r
+\r
+  void init()\r
+  {\r
+    try\r
+    {\r
+      jbInit();\r
+    }\r
+    catch (Exception e)\r
+    {\r
+      e.printStackTrace();\r
+    }\r
+    frame = new Frame();\r
+    frame.add(this);\r
+    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);\r
+\r
+    if (seqGroup != null)\r
+    {\r
+      frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");\r
+    }\r
+\r
     for (int i = 0; i < 20; i++)\r
     {\r
       makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
@@ -86,9 +101,7 @@ public class UserDefinedColours
     makeButton("Gap", "'.','-',' '");\r
 \r
     validate();\r
-\r
   }\r
-\r
   protected void rText_actionPerformed(ActionEvent e)\r
   {\r
     try\r
@@ -214,7 +227,6 @@ public class UserDefinedColours
 \r
   protected void applyButton_actionPerformed(ActionEvent e)\r
   {\r
-\r
     Color[] newColours = new Color[24];\r
     for (int i = 0; i < 24; i++)\r
     {\r
@@ -223,19 +235,27 @@ public class UserDefinedColours
     }\r
 \r
     UserColourScheme ucs = new UserColourScheme(newColours);\r
-    ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
+    if(ap!=null)\r
+      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 \r
-    if (seqGroup != null)\r
+    if(ap!=null)\r
     {\r
-      seqGroup.cs = ucs;\r
+      if (seqGroup != null)\r
+      {\r
+        seqGroup.cs = ucs;\r
+      }\r
+      else\r
+      {\r
+        ap.av.setGlobalColourScheme(ucs);\r
+      }\r
+      ap.seqPanel.seqCanvas.img = null;\r
+      ap.repaint();\r
     }\r
-    else\r
+    else if(pdbcanvas!=null)\r
     {\r
-      ap.av.setGlobalColourScheme(ucs);\r
+      pdbcanvas.pdb.setColours(ucs);\r
+      pdbcanvas.updateSeqColours();\r
     }\r
-\r
-    ap.seqPanel.seqCanvas.img = null;\r
-    ap.repaint();\r
   }\r
 \r
 \r
@@ -251,17 +271,23 @@ public class UserDefinedColours
 \r
     UserColourScheme ucs = new UserColourScheme(newColours);\r
 \r
-    if (seqGroup != null)\r
+   if(ap!=null)\r
     {\r
-      seqGroup.cs = ucs;\r
+      if (seqGroup != null)\r
+      {\r
+        seqGroup.cs = ucs;\r
+      }\r
+      else\r
+      {\r
+        ap.av.setGlobalColourScheme(ucs);\r
+      }\r
+      ap.repaint();\r
     }\r
-    else\r
+    else if(pdbcanvas!=null)\r
     {\r
-      ap.av.setGlobalColourScheme(ucs);\r
+      pdbcanvas.pdb.setColours(ucs);\r
     }\r
 \r
-    ap.repaint();\r
-\r
     frame.setVisible(false);\r
   }\r
 \r