X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=ede020c6101fd71d3c79968e9024763c3adb4123;hb=e02486484d33e20dedb020a34f31f6024d5720a2;hp=651f40c60b5335f9624162745f96e0c34e589c67;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 651f40c..ede020c 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -37,6 +37,7 @@ import javax.swing.*;
 import javax.swing.event.*;
 
 
+
 /**
  * DOCUMENT ME!
  *
@@ -49,9 +50,9 @@ public class UserDefinedColours extends GUserDefinedColours
     AlignmentPanel ap;
     SequenceGroup seqGroup;
     Vector selectedButtons;
-    Vector oldColours = new Vector();
     ColourSchemeI oldColourScheme;
     JInternalFrame frame;
+    MCview.PDBCanvas pdbcanvas;
 
     /**
      * Creates a new UserDefinedColours object.
@@ -64,11 +65,11 @@ public class UserDefinedColours extends GUserDefinedColours
         super();
         frame = new JInternalFrame();
         frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "User Defined Colours", 450, 530, false);
+        Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
 
         if (System.getProperty("os.name").startsWith("Mac"))
         {
-            frame.setSize(450, 560);
+            frame.setSize(760, 370);
         }
 
         if (sg != null)
@@ -90,6 +91,10 @@ public class UserDefinedColours extends GUserDefinedColours
             oldColourScheme = ap.av.getGlobalColourScheme();
         }
 
+        if (oldColourScheme instanceof UserColourScheme)
+        {
+              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+        }
         for (int i = 0; i < 20; i++)
         {
             makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
@@ -99,14 +104,43 @@ public class UserDefinedColours extends GUserDefinedColours
         makeButton("B", "B");
         makeButton("Z", "Z");
         makeButton("X", "X");
-        makeButton("Gap", "'.','-',' '");
+        makeButton("Gap", "-");
+    }
+
+    public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
+    {
+        super();
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
+        pdbcanvas = pdb;
 
-        if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)
+        if (System.getProperty("os.name").startsWith("Mac"))
+        {
+            frame.setSize(760, 370);
+        }
+
+        colorChooser.getSelectionModel().addChangeListener(this);
+
+        oldColourScheme = oldcs;
+
+        if (oldColourScheme instanceof UserColourScheme)
+        {
+              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+        }
+        for (int i = 0; i < 20; i++)
         {
-            loadColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
+            makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
+                "", ResidueProperties.aa[i]);
         }
+
+        makeButton("B", "B");
+        makeButton("Z", "Z");
+        makeButton("X", "X");
+        makeButton("Gap", "-");
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -140,8 +174,12 @@ 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++)
         {
@@ -215,10 +253,10 @@ public class UserDefinedColours extends GUserDefinedColours
         }
         catch (Exception ex)
         {
+        //  ex.printStackTrace();
         }
 
         button.setBackground(col);
-        oldColours.addElement(col);
         button.setText(label);
         button.setForeground(col.darker().darker().darker());
         button.setFont(new java.awt.Font("Verdana", 1, 10));
@@ -258,28 +296,45 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     protected void applyButton_actionPerformed(ActionEvent e)
     {
-        Color[] newColours = new Color[24];
-
-        for (int i = 0; i < 24; i++)
-        {
-            JButton button = (JButton) buttonPanel.getComponent(i);
-            newColours[i] = button.getBackground();
-        }
-
-        UserColourScheme ucs = new UserColourScheme(newColours);
-        ucs.setThreshold(0);
+        UserColourScheme ucs = getSchemeFromGUI();
+        ucs.setName(schemeName.getText());
 
         if (seqGroup != null)
         {
             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()
+    {
+      Color[] newColours = new Color[24];
+
+      for (int i = 0; i < 24; i++)
+      {
+        JButton button = (JButton) buttonPanel.getComponent(i);
+        newColours[i] = button.getBackground();
+      }
+
+      UserColourScheme ucs = new UserColourScheme(newColours);
+      if(ap!=null)
+        ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+
+
+      return ucs;
+    }
+
+
+
     /**
      * DOCUMENT ME!
      *
@@ -300,10 +355,17 @@ public class UserDefinedColours extends GUserDefinedColours
         {
             File choice = chooser.getSelectedFile();
             jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-            jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR",
+            String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",
                 choice.getPath());
+            if (defaultColours.indexOf(choice.getPath()) == -1)
+              defaultColours = defaultColours.concat("|").concat(choice.getPath());
+
+            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
-            Color[] colors = loadColours(choice.getAbsolutePath());
+
+            UserColourScheme ucs = loadColours(choice.getAbsolutePath());
+            Color[] colors = ucs.getColours();
+            schemeName.setText(ucs.getName());
 
             for (int i = 0; i < colors.length; i++)
             {
@@ -320,15 +382,28 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     public static UserColourScheme loadDefaultColours()
     {
-        if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)
+        UserColourScheme ret = null;
+
+        String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
+        if ( colours != null )
         {
-            return loadDefaultColours(jalview.bin.Cache.getProperty(
-                    "USER_DEFINED_COLOUR"));
+          if(colours.indexOf("|")>-1)
+            colours = colours.substring(0, colours.indexOf("|"));
+
+          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;
     }
 
     /**
@@ -338,46 +413,69 @@ public class UserDefinedColours extends GUserDefinedColours
      *
      * @return DOCUMENT ME!
      */
-    public static UserColourScheme loadDefaultColours(String file)
+    static UserColourScheme loadColours(String file)
     {
-        UserColourScheme ucs = null;
-        Color[] cols = loadColours(file);
-
-        if (cols != null)
-        {
-            ucs = new UserColourScheme(cols);
-            ucs.setThreshold(0);
-        }
-
-        return ucs;
-    }
-
-    static Color[] loadColours(String file)
-    {
-        Color[] newColours = null;
+         UserColourScheme ucs = null;
+         Color[]  newColours = null;
 
         try
         {
             InputStreamReader in = new InputStreamReader(new FileInputStream(
                         file), "UTF-8");
 
-            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
-            ucs = (jalview.binding.JalviewUserColours) ucs.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[ucs.getColourCount()];
+              newColours = new Color[jucs.getColourCount()];
 
             for (int i = 0; i < 24; i++)
             {
-                newColours[i] = new Color(Integer.parseInt(
-                            ucs.getColour(i).getRGB(), 16));
+              newColours[i] = new Color(Integer.parseInt(
+                  jucs.getColour(i).getRGB(), 16));
+            }
+            if (newColours != null)
+            {
+              ucs = new UserColourScheme(newColours);
+              ucs.setName( jucs.getSchemeName() );
             }
+
         }
         catch (Exception ex)
         {
-            System.out.println("Error loading UserColourFile " + file);
+            //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 newColours;
+       return ucs;
     }
 
     /**
@@ -387,6 +485,25 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     protected void savebutton_actionPerformed(ActionEvent e)
     {
+      if(schemeName.getText().trim().length()<1)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              "User colour scheme must have a name!",
+                                              "No name for colour scheme",
+                                              JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
+      if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )
+      {
+        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."
+            +"\nContinue saving colour scheme as "+schemeName.getText()+"?",
+           "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
+        if(reply != JOptionPane.YES_OPTION)
+          return;
+
+         userColourSchemes.remove(schemeName.getText());
+      }
         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
                     "LAST_DIRECTORY"), new String[] { "jc" },
                 new String[] { "Jalview User Colours" }, "Jalview User Colours");
@@ -400,10 +517,22 @@ public class UserDefinedColours extends GUserDefinedColours
         if (value == JalviewFileChooser.APPROVE_OPTION)
         {
             String choice = chooser.getSelectedFile().getPath();
-            jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);
+            String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);
+            if(defaultColours.indexOf(choice)==-1)
+            {
+              if(defaultColours.length()>0)
+                defaultColours = defaultColours.concat("|");
+              defaultColours = defaultColours.concat(choice);
+            }
 
-            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
+            userColourSchemes.put(schemeName.getText(), getSchemeFromGUI());
+
+            ap.alignFrame.updateUserColourMenu();
+
+            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
+            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
+            ucs.setSchemeName(schemeName.getText());
             try
             {
                 PrintWriter out = new PrintWriter(new OutputStreamWriter(
@@ -436,33 +565,118 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     protected void cancelButton_actionPerformed(ActionEvent e)
     {
-        Color[] newColours = new Color[24];
+      if (ap != null)
+      {
+        if (seqGroup != null)
+        {
+          seqGroup.cs = oldColourScheme;
+        }
+        else if (ap != null)
+        {
+          ap.av.setGlobalColourScheme(oldColourScheme);
+        }
+        ap.repaint();
+      }
 
-        for (int i = 0; i < 24; i++)
+      if(pdbcanvas!=null)
+      {
+        pdbcanvas.pdb.setColours(oldColourScheme);
+      }
+
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
         {
-            newColours[i] = (Color) oldColours.elementAt(i);
-            buttonPanel.getComponent(i).setBackground(newColours[i]);
         }
+    }
 
-        UserColourScheme ucs = new UserColourScheme(newColours);
 
-        if (seqGroup != null)
+    static Hashtable userColourSchemes;
+
+    public static Hashtable getUserColourSchemes()
+    {
+      return userColourSchemes;
+    }
+
+    public static void initUserColourSchemes(String files)
+    {
+      userColourSchemes = new Hashtable();
+
+      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();
+      StringTokenizer st = new StringTokenizer(files, "|");
+      while (st.hasMoreElements())
+      {
+        String file = st.nextToken();
+        try
         {
-            seqGroup.cs = ucs;
+          UserColourScheme ucs = loadColours(file);
+          if (ucs != null)
+          {
+            if (coloursFound.length() > 0)
+              coloursFound.append("|");
+            coloursFound.append(file);
+            userColourSchemes.put(ucs.getName(), ucs);
+          }
         }
-        else
+        catch (Exception ex)
         {
-            ap.av.setGlobalColourScheme(ucs);
+          System.out.println("Error loading User ColourFile\n" + ex);
         }
+      }
+      if (!files.equals(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");
+      }
+    }
 
-        ap.repaint();
+    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
         {
-            frame.setClosed(true);
+          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");
+
     }
 }