From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 9 Dec 2005 14:10:59 +0000 (+0000)
Subject: Applet Structure viewer has all colours available
X-Git-Tag: Release_2_07~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dfb45c8f874124d3ff3caac2902ed0c4a0e87cf5;p=jalview.git

Applet Structure viewer has all colours available
---

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index f39a3fa..d91d43e 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -418,7 +418,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       drawLabels(ig);
     }
 
-
+   void setColours(jalview.schemes.ColourSchemeI cs)
+   {
+     bysequence = false;
+     pdb.setColours(cs);
+     redrawneeded = true;
+     repaint();
+   }
     public void updateSeqColours()
     {
       if (pdbAction)
diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 901297b..2c0080e 100755
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -23,6 +23,7 @@ import java.awt.*;
 import java.awt.event.*;
 import jalview.datamodel.*;
 import jalview.appletgui.*;
+import jalview.schemes.*;
 import java.awt.event.ActionListener;
 import java.awt.event.ActionEvent;
 
@@ -121,7 +122,7 @@ public class AppletPDBViewer extends Frame
         {
           public void actionPerformed(ActionEvent e)
           {
-            hydro_actionPerformed();
+            pdbcanvas.setColours(new HydrophobicColourScheme());
           }
         });
         chain.setLabel("By Chain");
@@ -147,19 +148,84 @@ public class AppletPDBViewer extends Frame
         allchains_itemStateChanged(itemEvent);
       }
     });
+    viewMenu.setLabel("View");
+    zappo.setLabel("Zappo");
+    zappo.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        pdbcanvas.setColours(new ZappoColourScheme());
+      }
+    });
+    taylor.setLabel("Taylor");
+    taylor.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        pdbcanvas.setColours(new TaylorColourScheme());
+      }
+    });
+    helix.setLabel("Helix Propensity");
+    helix.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+       pdbcanvas.setColours(new HelixColourScheme());
+      }
+    });
+    strand.setLabel("Strand Propensity");
+    strand.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        pdbcanvas.setColours(new StrandColourScheme());
+      }
+    });
+    turn.setLabel("Turn Propensity");
+    turn.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        pdbcanvas.setColours(new TurnColourScheme());
+      }
+    });
+    buried.setLabel("Buried Index");
+    buried.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        pdbcanvas.setColours(new BuriedColourScheme());
+      }
+    });
+    user.setLabel("User Defined...");
+    user.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        pdbcanvas.bysequence = false;
+        new jalview.appletgui.UserDefinedColours(pdbcanvas);
+      }
+    });
     jMenuBar1.add(fileMenu);
         jMenuBar1.add(coloursMenu);
-        fileMenu.add(mapping);;
+    jMenuBar1.add(viewMenu);
+    fileMenu.add(mapping);;
 
         coloursMenu.add(seqButton);
         coloursMenu.add(chain);
-    coloursMenu.add(hydro);
     coloursMenu.add(charge);
-    coloursMenu.addSeparator();
-        coloursMenu.add(wire);
-        coloursMenu.add(depth);
-        coloursMenu.add(zbuffer);
-    coloursMenu.add(allchains);
+    coloursMenu.add(zappo);
+    coloursMenu.add(taylor);
+    coloursMenu.add(hydro);
+    coloursMenu.add(helix);
+    coloursMenu.add(strand);
+    coloursMenu.add(turn);
+    coloursMenu.add(buried);
+    coloursMenu.add(user);
+    viewMenu.add(wire);
+    viewMenu.add(depth);
+    viewMenu.add(zbuffer);
+    viewMenu.add(allchains);
     allchains.setState(true);
   }
 
@@ -178,27 +244,27 @@ public class AppletPDBViewer extends Frame
       MenuItem seqButton = new MenuItem();
 
      CheckboxMenuItem allchains = new CheckboxMenuItem();
+  Menu viewMenu = new Menu();
+  MenuItem turn = new MenuItem();
+  MenuItem strand = new MenuItem();
+  MenuItem helix = new MenuItem();
+  MenuItem taylor = new MenuItem();
+  MenuItem zappo = new MenuItem();
+  MenuItem buried = new MenuItem();
+  MenuItem user = new MenuItem();
 
   public void charge_actionPerformed()
       {
-        clearButtonGroup();
+        pdbcanvas.bysequence = false;
         pdbcanvas.pdb.setChargeColours();
         pdbcanvas.redrawneeded=true;
         pdbcanvas.repaint();
       }
 
-      public void hydro_actionPerformed()
-      {
-        clearButtonGroup();
-       // pdbcanvas.pdb.setHydrophobicityColours();
-        pdbcanvas.redrawneeded=true;
-        pdbcanvas.repaint();
-      }
-
       public void chain_actionPerformed()
       {
-        clearButtonGroup();
-        pdbcanvas.pdb.setChainColours();
+         pdbcanvas.bysequence = false;
+         pdbcanvas.pdb.setChainColours();
         pdbcanvas.redrawneeded=true;
         pdbcanvas.repaint();
       }
@@ -226,17 +292,11 @@ public class AppletPDBViewer extends Frame
 
       public void seqButton_actionPerformed()
       {
-        clearButtonGroup();
         pdbcanvas.bysequence = true;
         pdbcanvas.updateSeqColours();
         pdbcanvas.repaint();
       }
 
-      void clearButtonGroup()
-      {
-       pdbcanvas.bysequence = false;
-       pdbcanvas.bymolecule = false;
-      }
 
       public void mapping_actionPerformed()
       {
@@ -252,4 +312,5 @@ public class AppletPDBViewer extends Frame
       {
         pdbcanvas.setAllchainsVisible(allchains.getState());
       }
+
 }
diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 7cd0391..71bcaca 100755
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -37,6 +37,7 @@ public class UserDefinedColours
   Vector oldColours = new Vector();
   ColourSchemeI oldColourScheme;
   Frame frame;
+  MCview.AppletPDBCanvas pdbcanvas;
 
   int R = 0, G = 0, B = 0;
 
@@ -48,20 +49,6 @@ public class UserDefinedColours
 
   public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
   {
-    try {
-        jbInit();
-    } catch (Exception e) {
-        e.printStackTrace();
-      }
-    frame = new Frame();
-    frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);
-
-    if (sg != null)
-    {
-      frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");
-    }
-
     this.ap = ap;
     seqGroup = sg;
 
@@ -74,6 +61,34 @@ public class UserDefinedColours
       oldColourScheme = ap.av.getGlobalColourScheme();
     }
 
+    init();
+  }
+
+  public UserDefinedColours(MCview.AppletPDBCanvas pdb)
+  {
+    this.pdbcanvas = pdb;
+    init();
+  }
+
+  void init()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    frame = new Frame();
+    frame.add(this);
+    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);
+
+    if (seqGroup != null)
+    {
+      frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
+    }
+
     for (int i = 0; i < 20; i++)
     {
       makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
@@ -86,9 +101,7 @@ public class UserDefinedColours
     makeButton("Gap", "'.','-',' '");
 
     validate();
-
   }
-
   protected void rText_actionPerformed(ActionEvent e)
   {
     try
@@ -214,7 +227,6 @@ public class UserDefinedColours
 
   protected void applyButton_actionPerformed(ActionEvent e)
   {
-
     Color[] newColours = new Color[24];
     for (int i = 0; i < 24; i++)
     {
@@ -223,19 +235,27 @@ public class UserDefinedColours
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
-    ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+    if(ap!=null)
+      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
 
-    if (seqGroup != null)
+    if(ap!=null)
     {
-      seqGroup.cs = ucs;
+      if (seqGroup != null)
+      {
+        seqGroup.cs = ucs;
+      }
+      else
+      {
+        ap.av.setGlobalColourScheme(ucs);
+      }
+      ap.seqPanel.seqCanvas.img = null;
+      ap.repaint();
     }
-    else
+    else if(pdbcanvas!=null)
     {
-      ap.av.setGlobalColourScheme(ucs);
+      pdbcanvas.pdb.setColours(ucs);
+      pdbcanvas.updateSeqColours();
     }
-
-    ap.seqPanel.seqCanvas.img = null;
-    ap.repaint();
   }
 
 
@@ -251,17 +271,23 @@ public class UserDefinedColours
 
     UserColourScheme ucs = new UserColourScheme(newColours);
 
-    if (seqGroup != null)
+   if(ap!=null)
     {
-      seqGroup.cs = ucs;
+      if (seqGroup != null)
+      {
+        seqGroup.cs = ucs;
+      }
+      else
+      {
+        ap.av.setGlobalColourScheme(ucs);
+      }
+      ap.repaint();
     }
-    else
+    else if(pdbcanvas!=null)
     {
-      ap.av.setGlobalColourScheme(ucs);
+      pdbcanvas.pdb.setColours(ucs);
     }
 
-    ap.repaint();
-
     frame.setVisible(false);
   }