X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=d2741a972d122e7487c1e4fdc5e73894672834c3;hb=b5d69834ef8b11df514d5b4c08c82945f15f8a2e;hp=0477391df7a4ba04311a2daabe7b7fb838f254de;hpb=4fe5e959d104419f1f313f493e00d683b6b5cd0a;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 0477391..d2741a9 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -52,6 +52,10 @@ public class UserDefinedColours extends GUserDefinedColours
     Vector selectedButtons;
     ColourSchemeI oldColourScheme;
     JInternalFrame frame;
+    MCview.PDBCanvas pdbcanvas;
+    Vector upperCaseButtons;
+    Vector lowerCaseButtons;
+
 
     /**
      * Creates a new UserDefinedColours object.
@@ -62,50 +66,150 @@ public class UserDefinedColours extends GUserDefinedColours
     public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
     {
         super();
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
 
-        if (System.getProperty("os.name").startsWith("Mac"))
-        {
-            frame.setSize(450, 560);
-        }
+        //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
+        casePanel.setVisible(false);
 
-        if (sg != null)
-        {
-            frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");
-        }
 
-        colorChooser.getSelectionModel().addChangeListener(this);
+        lcaseColour.setEnabled(false);
 
         this.ap = ap;
         seqGroup = sg;
 
         if (seqGroup != null)
-        {
             oldColourScheme = seqGroup.cs;
-        }
         else
-        {
             oldColourScheme = ap.av.getGlobalColourScheme();
-        }
 
         if (oldColourScheme instanceof UserColourScheme)
         {
-              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+          schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+          if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)
+          {
+            caseSensitive.setSelected(true);
+            lcaseColour.setEnabled(true);
+            resetButtonPanel(true);
+          }
+          else
+            resetButtonPanel(false);
         }
-        for (int i = 0; i < 20; i++)
+        else
+           resetButtonPanel(false);
+
+        showFrame();
+    }
+
+    public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
+    {
+        super();
+        pdbcanvas = pdb;
+
+        colorChooser.getSelectionModel().addChangeListener(this);
+
+        oldColourScheme = oldcs;
+
+        if (oldColourScheme instanceof UserColourScheme)
         {
-            makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
-                "", ResidueProperties.aa[i]);
+              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
         }
 
-        makeButton("B", "B");
-        makeButton("Z", "Z");
-        makeButton("X", "X");
-        makeButton("Gap", "-");
+        resetButtonPanel(false);
+
+        showFrame();
+
     }
 
+    void showFrame()
+    {
+      colorChooser.getSelectionModel().addChangeListener(this);
+      frame = new JInternalFrame();
+      frame.setContentPane(this);
+      Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
+
+      if (seqGroup != null)
+            frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
+
+      if (System.getProperty("os.name").startsWith("Mac"))
+      {
+        frame.setSize(760, 370);
+      }
+    }
+
+    void resetButtonPanel(boolean caseSensitive)
+    {
+      //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
+      caseSensitive = false;
+
+      buttonPanel.removeAll();
+
+
+      if(upperCaseButtons==null)
+        upperCaseButtons = new Vector();
+
+      JButton button;
+      String label;
+      for (int i = 0; i < 20; i++)
+      {
+        if(caseSensitive)
+          label = ResidueProperties.aa[i];
+        else
+          label = ResidueProperties.aa2Triplet.get
+              (ResidueProperties.aa[i]).toString();
+
+        button = makeButton(label,
+                              ResidueProperties.aa[i],
+                              upperCaseButtons, i);
+
+        buttonPanel.add(button);
+      }
+
+        buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
+        buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
+        buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
+        buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
+
+      if(!caseSensitive)
+      {
+        gridLayout.setRows(6);
+        gridLayout.setColumns(4);
+      }
+      else
+      {
+        gridLayout.setRows(7);
+        int cols = 7;
+        gridLayout.setColumns(cols+1);
+
+        if(lowerCaseButtons==null)
+          lowerCaseButtons = new Vector();
+
+
+          for (int i = 0; i < 20; i++)
+          {
+            int row = i / cols + 1;
+            int index = (row * cols) + i;
+            button = makeButton(
+                ResidueProperties.aa[i].toLowerCase(),
+                ResidueProperties.aa[i].toLowerCase(),
+                lowerCaseButtons,
+                i);
+
+            buttonPanel.add(button, index);
+          }
+      }
+
+
+      if(caseSensitive)
+      {
+        buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
+        buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
+        buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
+      }
+
+      buttonPanel.validate();
+      validate();
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -115,13 +219,22 @@ public class UserDefinedColours extends GUserDefinedColours
     {
         if (selectedButtons != null)
         {
-          JButton button;
+          JButton button=null;
           for(int i=0; i<selectedButtons.size(); i++)
           {
             button = (JButton)selectedButtons.elementAt(i);
             button.setBackground(colorChooser.getColor());
             button.setForeground( button.getBackground().brighter().brighter().brighter());
           }
+          if(button==lcaseColour)
+          {
+            for(int i=0; i<lowerCaseButtons.size(); i++)
+            {
+              button = (JButton)lowerCaseButtons.elementAt(i);
+              button.setBackground(colorChooser.getColor());
+              button.setForeground( button.getBackground().brighter().brighter().brighter());
+            }
+          }
         }
     }
 
@@ -139,8 +252,12 @@ public class UserDefinedColours extends GUserDefinedColours
 
       if(e.isShiftDown())
       {
-        JButton start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
-        JButton end = (JButton) e.getSource();
+        JButton start, end = (JButton) e.getSource();
+        if(selectedButtons.size()>0)
+          start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
+        else
+          start = (JButton) e.getSource();
+
         int startIndex=0, endIndex=0;
         for(int b=0; b<buttonPanel.getComponentCount(); b++)
         {
@@ -203,33 +320,55 @@ public class UserDefinedColours extends GUserDefinedColours
      * @param label DOCUMENT ME!
      * @param aa DOCUMENT ME!
      */
-    void makeButton(String label, String aa)
+    JButton makeButton(String label,
+                       String aa,
+                       Vector caseSensitiveButtons,
+                       int buttonIndex)
     {
-        final JButton button = new JButton();
-        Color col = Color.white;
+        final JButton button;
+        Color col;
 
-        try
+        if(buttonIndex<caseSensitiveButtons.size())
         {
-            col = oldColourScheme.findColour(aa, -1);
+          button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
+          col = button.getBackground();
         }
-        catch (Exception ex)
+        else
         {
-        //  ex.printStackTrace();
+          button = new JButton();
+          button.addMouseListener(new java.awt.event.MouseAdapter()
+          {
+            public void mouseClicked(MouseEvent e)
+            {
+              colourButtonPressed(e);
+            }
+          });
+
+          caseSensitiveButtons.addElement(button);
+
+          col = Color.white;
+
+          try
+          {
+            col = oldColourScheme.findColour(aa, -1);
+          }
+          catch (Exception ex)
+          {    }
         }
 
+      /* //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
+        if(caseSensitive.isSelected())
+          button.setMargin(new java.awt.Insets(2,2,2,2));
+        else
+         button.setMargin(new java.awt.Insets(2,14,2,14));
+      */
+
         button.setBackground(col);
         button.setText(label);
         button.setForeground(col.darker().darker().darker());
-        button.setFont(new java.awt.Font("Verdana", 1, 10));
-        button.addMouseListener(new java.awt.event.MouseAdapter()
-            {
-                public void mouseClicked(MouseEvent e)
-                {
-                    colourButtonPressed(e);
-                }
-            });
+        button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
 
-        buttonPanel.add(button, null);
+        return button;
     }
 
     /**
@@ -257,7 +396,7 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     protected void applyButton_actionPerformed(ActionEvent e)
     {
-        UserColourScheme ucs = getSchemeFromGUI();
+        UserColourScheme ucs = getSchemeFromButtons();
         ucs.setName(schemeName.getText());
 
         if (seqGroup != null)
@@ -265,24 +404,45 @@ public class UserDefinedColours extends GUserDefinedColours
             seqGroup.cs = ucs;
             ap.repaint();
         }
-        else
+        else if(ap!=null)
         {
             ap.alignFrame.changeColour(ucs);
         }
+        else if(pdbcanvas!=null)
+        {
+          pdbcanvas.pdb.setColours(ucs);
+          pdbcanvas.updateSeqColours();
+        }
     }
 
-    UserColourScheme getSchemeFromGUI()
+    UserColourScheme getSchemeFromButtons()
     {
+
       Color[] newColours = new Color[24];
 
       for (int i = 0; i < 24; i++)
       {
-        JButton button = (JButton) buttonPanel.getComponent(i);
+        JButton button = (JButton) upperCaseButtons.elementAt(i);
         newColours[i] = button.getBackground();
       }
 
       UserColourScheme ucs = new UserColourScheme(newColours);
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+
+
+      if(caseSensitive.isSelected())
+      {
+        newColours = new Color[23];
+        for (int i = 0; i < 23; i++)
+        {
+          JButton button = (JButton) lowerCaseButtons.elementAt(i);
+          newColours[i] = button.getBackground();
+        }
+        ucs.setLowerCaseColours(newColours);
+      }
+
+      if(ap!=null)
+        ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+
 
       return ucs;
     }
@@ -296,6 +456,9 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     protected void loadbutton_actionPerformed(ActionEvent e)
     {
+      upperCaseButtons = new Vector();
+      lowerCaseButtons = new Vector();
+
         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
                     "LAST_DIRECTORY"), new String[] { "jc" },
                 new String[] { "Jalview User Colours" }, "Jalview User Colours");
@@ -321,11 +484,31 @@ public class UserDefinedColours extends GUserDefinedColours
             Color[] colors = ucs.getColours();
             schemeName.setText(ucs.getName());
 
-            for (int i = 0; i < colors.length; i++)
+            if(ucs.getLowerCaseColours()!=null)
             {
-                JButton button = (JButton) buttonPanel.getComponent(i);
+              caseSensitive.setSelected(true);
+              lcaseColour.setEnabled(true);
+              resetButtonPanel(true);
+              for (int i = 0; i < lowerCaseButtons.size(); i++)
+              {
+                JButton button = (JButton) lowerCaseButtons.elementAt(i);
+                button.setBackground(ucs.getLowerCaseColours()[i]);
+              }
+
+            }
+            else
+            {
+              caseSensitive.setSelected(false);
+              lcaseColour.setEnabled(false);
+              resetButtonPanel(false);
+            }
+
+            for (int i = 0; i < upperCaseButtons.size(); i++)
+            {
+                JButton button = (JButton) upperCaseButtons.elementAt(i);
                 button.setBackground(colors[i]);
             }
+
         }
     }
 
@@ -336,18 +519,28 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     public static UserColourScheme loadDefaultColours()
     {
-      String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
-        if ( colours != null)
+        UserColourScheme ret = null;
+
+        String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
+        if ( colours != null )
         {
           if(colours.indexOf("|")>-1)
             colours = colours.substring(0, colours.indexOf("|"));
 
-            return loadColours(colours);
+          ret = loadColours(colours);
         }
-        else
+
+        if(ret == null)
         {
-            return null;
+          Color[] newColours = new Color[24];
+          for (int i = 0; i < 24; i++)
+          {
+            newColours[i] = Color.white;
+          }
+          ret =  new UserColourScheme(newColours);
         }
+
+        return ret;
     }
 
     /**
@@ -357,39 +550,101 @@ public class UserDefinedColours extends GUserDefinedColours
      *
      * @return DOCUMENT ME!
      */
-    public static UserColourScheme loadColours(String file)
+    static UserColourScheme loadColours(String file)
     {
          UserColourScheme ucs = null;
          Color[]  newColours = null;
-
         try
         {
             InputStreamReader in = new InputStreamReader(new FileInputStream(
                         file), "UTF-8");
 
-            jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-            jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+              jalview.schemabinding.version2.JalviewUserColours jucs
+                  = new jalview.schemabinding.version2.JalviewUserColours();
+
+              org.exolab.castor.xml.Unmarshaller unmar
+                  = new org.exolab.castor.xml.Unmarshaller(jucs);
+              jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );
+
+              newColours = new Color[24];
 
-            newColours = new Color[jucs.getColourCount()];
+              Color [] lowerCase = null;
+              boolean caseSensitive = false;
 
-            for (int i = 0; i < 24; i++)
+
+            String name;
+            int index;
+            for (int i = 0; i < jucs.getColourCount(); i++)
             {
-              newColours[i] = new Color(Integer.parseInt(
+              name =  jucs.getColour(i).getName();
+              if(ResidueProperties.aa3Hash.containsKey(name))
+              {
+                index = ((Integer)ResidueProperties.aa3Hash.get(name)).intValue();
+              }
+              else
+              {
+                index = ((Integer)ResidueProperties.aaHash.get(name)).intValue();
+              }
+              if(index == -1)
+                continue;
+
+              if(name.toLowerCase().equals(name))
+              {
+                if(lowerCase==null)
+                   lowerCase = new Color[23];
+                caseSensitive = true;
+                lowerCase[index] = new Color(Integer.parseInt(
                   jucs.getColour(i).getRGB(), 16));
+              }
+              else
+              {
+                newColours[index] = new Color(Integer.parseInt(
+                    jucs.getColour(i).getRGB(), 16));
+              }
             }
+
             if (newColours != null)
             {
               ucs = new UserColourScheme(newColours);
               ucs.setName( jucs.getSchemeName() );
+              if(caseSensitive)
+              {
+                ucs.setLowerCaseColours(lowerCase);
+              }
             }
 
         }
         catch (Exception ex)
         {
-            System.out.println("Error loading User ColourFile\n"+ex);
+            //Could be Archive Jalview format
+            try{
+              InputStreamReader in = new InputStreamReader(new FileInputStream(
+                  file), "UTF-8");
+
+              jalview.binding.JalviewUserColours jucs
+                  = new jalview.binding.JalviewUserColours();
+
+              jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+
+              newColours = new Color[jucs.getColourCount()];
+
+              for (int i = 0; i < 24; i++)
+              {
+                newColours[i] = new Color(Integer.parseInt(
+                    jucs.getColour(i).getRGB(), 16));
+              }
+              if (newColours != null)
+              {
+                ucs = new UserColourScheme(newColours);
+                ucs.setName(jucs.getSchemeName());
+              }
+            }catch(Exception ex2)
+            { ex2.printStackTrace(); }
+
+            if(newColours==null)
+              System.out.println("Error loading User ColourFile\n"+ex);
         }
 
-
        return ucs;
     }
 
@@ -435,28 +690,31 @@ public class UserDefinedColours extends GUserDefinedColours
             String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);
             if(defaultColours.indexOf(choice)==-1)
             {
-              if(defaultColours.length()<1)
+              if(defaultColours.length()>0)
                 defaultColours = defaultColours.concat("|");
               defaultColours = defaultColours.concat(choice);
             }
 
-            userColourSchemes.put(schemeName.getText(), getSchemeFromGUI());
+            userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
 
             ap.alignFrame.updateUserColourMenu();
 
             jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
-            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
+            jalview.schemabinding.version2.JalviewUserColours ucs
+                = new jalview.schemabinding.version2.JalviewUserColours();
+
             ucs.setSchemeName(schemeName.getText());
             try
             {
                 PrintWriter out = new PrintWriter(new OutputStreamWriter(
                             new FileOutputStream(choice), "UTF-8"));
 
-                for (int i = 0; i < 24; i++)
+                for (int i = 0; i < buttonPanel.getComponentCount(); i++)
                 {
                     JButton button = (JButton) buttonPanel.getComponent(i);
-                    jalview.binding.Colour col = new jalview.binding.Colour();
+                    jalview.schemabinding.version2.Colour col
+                        = new jalview.schemabinding.version2.Colour();
                     col.setName(button.getText());
                     col.setRGB(jalview.util.Format.getHexString(
                             button.getBackground()));
@@ -480,16 +738,23 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     protected void cancelButton_actionPerformed(ActionEvent e)
     {
+      if (ap != null)
+      {
         if (seqGroup != null)
         {
-            seqGroup.cs = oldColourScheme;
+          seqGroup.cs = oldColourScheme;
         }
-        else
+        else if (ap != null)
         {
-            ap.av.setGlobalColourScheme(oldColourScheme);
+          ap.av.setGlobalColourScheme(oldColourScheme);
         }
-
         ap.repaint();
+      }
+
+      if(pdbcanvas!=null)
+      {
+        pdbcanvas.pdb.setColours(oldColourScheme);
+      }
 
         try
         {
@@ -512,9 +777,10 @@ public class UserDefinedColours extends GUserDefinedColours
     {
       userColourSchemes = new Hashtable();
 
-      if(files==null)
+      if(files==null || files.length()==0)
         return;
 
+
       // In case colours can't be loaded, we'll remove them
       // from the default list here.
       StringBuffer coloursFound = new StringBuffer();
@@ -540,7 +806,66 @@ public class UserDefinedColours extends GUserDefinedColours
       }
       if (!files.equals(coloursFound.toString()))
       {
-        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
+        if (coloursFound.toString().length() > 1)
+          jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
+                                        coloursFound.toString());
+        else
+          jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+      }
+    }
+
+    public static void removeColourFromDefaults(String target)
+    {
+      // The only way to find colours by name is to load them in
+      // In case colours can't be loaded, we'll remove them
+      // from the default list here.
+
+      userColourSchemes = new Hashtable();
+
+      StringBuffer coloursFound = new StringBuffer();
+      StringTokenizer st = new StringTokenizer(
+           jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
+
+      while (st.hasMoreElements())
+      {
+        String file = st.nextToken();
+        try
+        {
+          UserColourScheme ucs = loadColours(file);
+          if (ucs != null && !ucs.getName().equals(target))
+          {
+            if (coloursFound.length() > 0)
+              coloursFound.append("|");
+            coloursFound.append(file);
+            userColourSchemes.put(ucs.getName(), ucs);
+          }
+        }
+        catch (Exception ex)
+        {
+          System.out.println("Error loading User ColourFile\n" + ex);
+        }
       }
+
+      if (coloursFound.toString().length() > 1)
+        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
+      else
+        jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+
+    }
+
+    public void caseSensitive_actionPerformed(ActionEvent e)
+    {
+      resetButtonPanel(caseSensitive.isSelected());
+      lcaseColour.setEnabled(caseSensitive.isSelected());
+    }
+
+    public void lcaseColour_actionPerformed(ActionEvent e)
+    {
+      if(selectedButtons==null)
+        selectedButtons = new Vector();
+      else
+        selectedButtons.clear();
+      selectedButtons.add(lcaseColour);
     }
+
 }