Jalview colour schemes added

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 9ff3078..82dab26 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -30,6 +30,7 @@ import jalview.io.*;
 import org.jmol.api.*;\r
 import org.jmol.adapter.smarter.SmarterJmolAdapter;\r
 import org.jmol.popup.*;\r
+import jalview.schemes.*;\r
 \r
 \r
 public class AppletJmol extends Frame\r
@@ -39,9 +40,25 @@ public class AppletJmol extends Frame
 {\r
   Menu fileMenu = new Menu("File");\r
   Menu viewMenu = new Menu("View");\r
+  Menu coloursMenu = new Menu("Colours");\r
   Menu chainMenu = new Menu("Show Chain");\r
+  Menu helpMenu = new Menu("Help");\r
   MenuItem mappingMenuItem = new MenuItem("View Mapping");\r
 \r
+  CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);\r
+  MenuItem chain = new MenuItem("By Chain");\r
+  MenuItem charge = new MenuItem("Charge & Cysteine");\r
+  MenuItem zappo = new MenuItem("Zappo");\r
+  MenuItem taylor = new MenuItem("Taylor");\r
+  MenuItem hydro = new MenuItem("Hydrophobicity");\r
+  MenuItem helix = new MenuItem("Helix Propensity");\r
+  MenuItem strand = new MenuItem("Strand Propensity");\r
+  MenuItem turn = new MenuItem("Turn Propensity");\r
+  MenuItem buried = new MenuItem("Buried Index");\r
+  MenuItem user = new MenuItem("User Defined Colours");\r
+\r
+  MenuItem jmolHelp = new MenuItem("Jmol Help");\r
+\r
   JmolViewer viewer;\r
   JmolPopup jmolpopup;\r
 \r
@@ -56,6 +73,7 @@ public class AppletJmol extends Frame
   boolean loadedInline;\r
   PDBEntry pdbentry;\r
   boolean colourBySequence = true;\r
+  Vector atomsPicked = new Vector();\r
 \r
   public AppletJmol(PDBEntry pdbentry,\r
                     SequenceI[] seq,\r
@@ -106,6 +124,37 @@ public class AppletJmol extends Frame
     menuBar.add(viewMenu);\r
     mappingMenuItem.addActionListener(this);\r
     viewMenu.add(chainMenu);\r
+    menuBar.add(coloursMenu);\r
+    menuBar.add(helpMenu);\r
+\r
+    charge.addActionListener(this);\r
+    hydro.addActionListener(this);\r
+    chain.addActionListener(this);\r
+    seqColour.addItemListener(this);\r
+    zappo.addActionListener(this);\r
+    taylor.addActionListener(this);\r
+    helix.addActionListener(this);\r
+    strand.addActionListener(this);\r
+    turn.addActionListener(this);\r
+    buried.addActionListener(this);\r
+    user.addActionListener(this);\r
+\r
+    jmolHelp.addActionListener(this);\r
+\r
+    coloursMenu.add(seqColour);\r
+    coloursMenu.add(chain);\r
+    coloursMenu.add(charge);\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
+\r
+    helpMenu.add(jmolHelp);\r
+\r
     this.setMenuBar(menuBar);\r
 \r
     if(pdbentry.getFile()!=null)\r
@@ -200,6 +249,60 @@ public class AppletJmol extends Frame
               pdbentry.getFile())\r
           );\r
     }\r
+    else if (evt.getSource() == charge)\r
+    {\r
+      colourBySequence = false;\r
+      seqColour.setState(false);\r
+      viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"\r
+                      +"select LYS,ARG;color blue;select CYS;color yellow");\r
+    }\r
+\r
+    else if (evt.getSource() == chain)\r
+    {\r
+      colourBySequence = false;\r
+      seqColour.setState(false);\r
+      viewer.evalStringQuiet("select *;color chain");\r
+    }\r
+    else if (evt.getSource() == zappo)\r
+    {\r
+      setJalviewColourScheme(new ZappoColourScheme());\r
+    }\r
+    else if (evt.getSource() == taylor)\r
+    {\r
+     setJalviewColourScheme(new TaylorColourScheme());\r
+    }\r
+    else if (evt.getSource() == hydro)\r
+    {\r
+      setJalviewColourScheme(new HydrophobicColourScheme());\r
+    }\r
+    else if (evt.getSource() == helix)\r
+    {\r
+      setJalviewColourScheme(new HelixColourScheme());\r
+    }\r
+    else if (evt.getSource() == strand)\r
+    {\r
+      setJalviewColourScheme(new StrandColourScheme());\r
+    }\r
+    else if (evt.getSource() == turn)\r
+    {\r
+      setJalviewColourScheme(new TurnColourScheme());\r
+    }\r
+    else if (evt.getSource() == buried)\r
+    {\r
+      setJalviewColourScheme(new BuriedColourScheme());\r
+    }\r
+    else if (evt.getSource() == user)\r
+    {\r
+      new UserDefinedColours(this);\r
+    }\r
+    else if(evt.getSource() == jmolHelp)\r
+    {\r
+      try{\r
+        ap.av.applet.getAppletContext().showDocument(\r
+            new java.net.URL("http://jmol.sourceforge.net/docs/JmolUserGuide/"),\r
+            "jmolHelp");\r
+      }catch(java.net.MalformedURLException ex){}\r
+    }\r
     else\r
     {\r
       allChainsSelected = true;\r
@@ -213,9 +316,46 @@ public class AppletJmol extends Frame
     }\r
   }\r
 \r
+  public void setJalviewColourScheme(ColourSchemeI cs)\r
+  {\r
+    colourBySequence = false;\r
+    seqColour.setState(false);\r
+\r
+    if(cs==null)\r
+      return;\r
+\r
+    String res;\r
+    int index;\r
+    Color col;\r
+\r
+    Enumeration en = ResidueProperties.aa3Hash.keys();\r
+    StringBuffer command = new StringBuffer("select *;color white;");\r
+    while(en.hasMoreElements())\r
+    {\r
+      res = en.nextElement().toString();\r
+      index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();\r
+      if(index>20)\r
+        continue;\r
+\r
+      col = cs.findColour(ResidueProperties.aa[index].charAt(0));\r
+\r
+      command.append("select "+res+";color["\r
+                        + col.getRed() + ","\r
+                        + col.getGreen() + ","\r
+                        + col.getBlue() + "];");\r
+    }\r
+\r
+    viewer.evalStringQuiet(command.toString());\r
+  }\r
+\r
   public void itemStateChanged(ItemEvent evt)\r
   {\r
-    if (!allChainsSelected)\r
+    if (evt.getSource() == seqColour)\r
+    {\r
+      colourBySequence = seqColour.getState();\r
+      colourBySequence(ap);\r
+    }\r
+    else if (!allChainsSelected)\r
       centerViewer();\r
   }\r
 \r
@@ -248,14 +388,21 @@ public class AppletJmol extends Frame
   String lastMessage;\r
   public void mouseOverStructure(int atomIndex, String strInfo)\r
   {\r
-      int pdbResNum = Integer.parseInt(\r
-          strInfo.substring(strInfo.indexOf("]")+ 1, strInfo.indexOf(":")));\r
+      int pdbResNum;\r
+\r
+      int chainSeparator = strInfo.indexOf(":");\r
 \r
-      String chainId = strInfo.substring\r
-          (strInfo.indexOf(":"), strInfo.indexOf("."));\r
+      if(chainSeparator==-1)\r
+        chainSeparator = strInfo.indexOf(".");\r
 \r
-      if (chainId != null)\r
-        chainId = chainId.substring(1, chainId.length());\r
+      pdbResNum = Integer.parseInt(\r
+          strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator));\r
+\r
+      String chainId;\r
+\r
+      if (strInfo.indexOf(":") > -1)\r
+        chainId = strInfo.substring\r
+            (strInfo.indexOf(":")+1, strInfo.indexOf("."));\r
       else\r
       {\r
         chainId = " ";\r
@@ -518,8 +665,10 @@ public class AppletJmol extends Frame
 \r
   public void sendConsoleEcho(String strEcho)\r
   {\r
-  //  if (scriptWindow != null)\r
-   //   scriptWindow.sendConsoleEcho(strEcho);\r
+    if (scriptWindow == null)\r
+      showConsole(true);\r
+\r
+    history.append("\n"+strEcho);\r
   }\r
 \r
   public void sendConsoleMessage(String strStatus)\r
@@ -532,10 +681,7 @@ public class AppletJmol extends Frame
   }\r
 \r
   public void notifyScriptTermination(String strStatus, int msWalltime)\r
-  {\r
-   // if (scriptWindow != null)\r
-   //   scriptWindow.notifyScriptTermination(strStatus, msWalltime);\r
-  }\r
+  {  }\r
 \r
   public void handlePopupMenu(int x, int y)\r
   {\r
@@ -552,10 +698,31 @@ public class AppletJmol extends Frame
 \r
   public void notifyAtomPicked(int atomIndex, String strInfo)\r
   {\r
-   // if (scriptWindow != null)\r
+\r
+    int chainSeparator = strInfo.indexOf(":");\r
+\r
+    if(chainSeparator==-1)\r
+      chainSeparator = strInfo.indexOf(".");\r
+\r
+    String picked =\r
+        strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator);\r
+\r
+\r
+    if (strInfo.indexOf(":") > -1)\r
+      picked+=strInfo.substring(strInfo.indexOf(":")+1,\r
+                               strInfo.indexOf("."));\r
+\r
+    picked+=".C";\r
+\r
+    if (!atomsPicked.contains(picked))\r
+    {\r
+      viewer.evalString("select "+picked+";label %n %r:%c");\r
+      atomsPicked.addElement(picked);\r
+    }\r
+    else\r
     {\r
-   //   scriptWindow.sendConsoleMessage(strInfo);\r
-   //   scriptWindow.sendConsoleMessage("\n");\r
+      viewer.evalString("select "+picked+";label off");\r
+      atomsPicked.removeElement(picked);\r
     }\r
   }\r
 \r
@@ -568,7 +735,13 @@ public class AppletJmol extends Frame
   {}\r
 \r
   public void showUrl(String url)\r
-  {}\r
+  {\r
+    try{\r
+      ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),\r
+          "jmolOutput");\r
+    }catch(java.net.MalformedURLException ex)\r
+    {}\r
+  }\r
 \r
   public void showConsole(boolean showConsole)\r
   {\r