User colours have scheme name

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 4ad129b..0477391 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -37,6 +37,7 @@ import javax.swing.*;
 import javax.swing.event.*;\r
 \r
 \r
+\r
 /**\r
  * DOCUMENT ME!\r
  *\r
@@ -49,7 +50,6 @@ public class UserDefinedColours extends GUserDefinedColours
     AlignmentPanel ap;\r
     SequenceGroup seqGroup;\r
     Vector selectedButtons;\r
-    Vector oldColours = new Vector();\r
     ColourSchemeI oldColourScheme;\r
     JInternalFrame frame;\r
 \r
@@ -64,7 +64,7 @@ public class UserDefinedColours extends GUserDefinedColours
         super();\r
         frame = new JInternalFrame();\r
         frame.setContentPane(this);\r
-        Desktop.addInternalFrame(frame, "User Defined Colours", 450, 530, false);\r
+        Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
 \r
         if (System.getProperty("os.name").startsWith("Mac"))\r
         {\r
@@ -90,6 +90,10 @@ public class UserDefinedColours extends GUserDefinedColours
             oldColourScheme = ap.av.getGlobalColourScheme();\r
         }\r
 \r
+        if (oldColourScheme instanceof UserColourScheme)\r
+        {\r
+              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
+        }\r
         for (int i = 0; i < 20; i++)\r
         {\r
             makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
@@ -99,12 +103,7 @@ public class UserDefinedColours extends GUserDefinedColours
         makeButton("B", "B");\r
         makeButton("Z", "Z");\r
         makeButton("X", "X");\r
-        makeButton("Gap", "'.','-',' '");\r
-\r
-        if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)\r
-        {\r
-            loadColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));\r
-        }\r
+        makeButton("Gap", "-");\r
     }\r
 \r
     /**\r
@@ -215,10 +214,10 @@ public class UserDefinedColours extends GUserDefinedColours
         }\r
         catch (Exception ex)\r
         {\r
+        //  ex.printStackTrace();\r
         }\r
 \r
         button.setBackground(col);\r
-        oldColours.addElement(col);\r
         button.setText(label);\r
         button.setForeground(col.darker().darker().darker());\r
         button.setFont(new java.awt.Font("Verdana", 1, 10));\r
@@ -258,16 +257,8 @@ public class UserDefinedColours extends GUserDefinedColours
      */\r
     protected void applyButton_actionPerformed(ActionEvent e)\r
     {\r
-        Color[] newColours = new Color[24];\r
-\r
-        for (int i = 0; i < 24; i++)\r
-        {\r
-            JButton button = (JButton) buttonPanel.getComponent(i);\r
-            newColours[i] = button.getBackground();\r
-        }\r
-\r
-        UserColourScheme ucs = new UserColourScheme(newColours);\r
-        ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
+        UserColourScheme ucs = getSchemeFromGUI();\r
+        ucs.setName(schemeName.getText());\r
 \r
         if (seqGroup != null)\r
         {\r
@@ -280,6 +271,24 @@ public class UserDefinedColours extends GUserDefinedColours
         }\r
     }\r
 \r
+    UserColourScheme getSchemeFromGUI()\r
+    {\r
+      Color[] newColours = new Color[24];\r
+\r
+      for (int i = 0; i < 24; i++)\r
+      {\r
+        JButton button = (JButton) buttonPanel.getComponent(i);\r
+        newColours[i] = button.getBackground();\r
+      }\r
+\r
+      UserColourScheme ucs = new UserColourScheme(newColours);\r
+      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
+\r
+      return ucs;\r
+    }\r
+\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -300,10 +309,17 @@ public class UserDefinedColours extends GUserDefinedColours
         {\r
             File choice = chooser.getSelectedFile();\r
             jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
-            jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR",\r
+            String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",\r
                 choice.getPath());\r
+            if (defaultColours.indexOf(choice.getPath()) == -1)\r
+              defaultColours = defaultColours.concat("|").concat(choice.getPath());\r
+\r
+            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
+\r
 \r
-            Color[] colors = loadColours(choice.getAbsolutePath());\r
+            UserColourScheme ucs = loadColours(choice.getAbsolutePath());\r
+            Color[] colors = ucs.getColours();\r
+            schemeName.setText(ucs.getName());\r
 \r
             for (int i = 0; i < colors.length; i++)\r
             {\r
@@ -320,10 +336,13 @@ public class UserDefinedColours extends GUserDefinedColours
      */\r
     public static UserColourScheme loadDefaultColours()\r
     {\r
-        if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)\r
+      String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");\r
+        if ( colours != null)\r
         {\r
-            return loadDefaultColours(jalview.bin.Cache.getProperty(\r
-                    "USER_DEFINED_COLOUR"));\r
+          if(colours.indexOf("|")>-1)\r
+            colours = colours.substring(0, colours.indexOf("|"));\r
+\r
+            return loadColours(colours);\r
         }\r
         else\r
         {\r
@@ -338,45 +357,40 @@ public class UserDefinedColours extends GUserDefinedColours
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public static UserColourScheme loadDefaultColours(String file)\r
+    public static UserColourScheme loadColours(String file)\r
     {\r
-        UserColourScheme ucs = null;\r
-        Color[] cols = loadColours(file);\r
-\r
-        if (cols != null)\r
-        {\r
-            ucs = new UserColourScheme(cols);\r
-        }\r
-\r
-        return ucs;\r
-    }\r
-\r
-    static Color[] loadColours(String file)\r
-    {\r
-        Color[] newColours = null;\r
+         UserColourScheme ucs = null;\r
+         Color[]  newColours = null;\r
 \r
         try\r
         {\r
             InputStreamReader in = new InputStreamReader(new FileInputStream(\r
                         file), "UTF-8");\r
 \r
-            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
-            ucs = (jalview.binding.JalviewUserColours) ucs.unmarshal(in);\r
+            jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();\r
+            jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
 \r
-            newColours = new Color[ucs.getColourCount()];\r
+            newColours = new Color[jucs.getColourCount()];\r
 \r
             for (int i = 0; i < 24; i++)\r
             {\r
-                newColours[i] = new Color(Integer.parseInt(\r
-                            ucs.getColour(i).getRGB(), 16));\r
+              newColours[i] = new Color(Integer.parseInt(\r
+                  jucs.getColour(i).getRGB(), 16));\r
             }\r
+            if (newColours != null)\r
+            {\r
+              ucs = new UserColourScheme(newColours);\r
+              ucs.setName( jucs.getSchemeName() );\r
+            }\r
+\r
         }\r
         catch (Exception ex)\r
         {\r
-            System.out.println("Error loading UserColourFile " + file);\r
+            System.out.println("Error loading User ColourFile\n"+ex);\r
         }\r
 \r
-        return newColours;\r
+\r
+       return ucs;\r
     }\r
 \r
     /**\r
@@ -386,6 +400,25 @@ public class UserDefinedColours extends GUserDefinedColours
      */\r
     protected void savebutton_actionPerformed(ActionEvent e)\r
     {\r
+      if(schemeName.getText().trim().length()<1)\r
+      {\r
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                                              "User colour scheme must have a name!",\r
+                                              "No name for colour scheme",\r
+                                              JOptionPane.WARNING_MESSAGE);\r
+        return;\r
+      }\r
+\r
+      if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )\r
+      {\r
+        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."\r
+            +"\nContinue saving colour scheme as "+schemeName.getText()+"?",\r
+           "Duplicate scheme name", JOptionPane.YES_NO_OPTION);\r
+        if(reply != JOptionPane.YES_OPTION)\r
+          return;\r
+\r
+         userColourSchemes.remove(schemeName.getText());\r
+      }\r
         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
                     "LAST_DIRECTORY"), new String[] { "jc" },\r
                 new String[] { "Jalview User Colours" }, "Jalview User Colours");\r
@@ -399,10 +432,22 @@ public class UserDefinedColours extends GUserDefinedColours
         if (value == JalviewFileChooser.APPROVE_OPTION)\r
         {\r
             String choice = chooser.getSelectedFile().getPath();\r
-            jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);\r
+            String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);\r
+            if(defaultColours.indexOf(choice)==-1)\r
+            {\r
+              if(defaultColours.length()<1)\r
+                defaultColours = defaultColours.concat("|");\r
+              defaultColours = defaultColours.concat(choice);\r
+            }\r
 \r
-            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
+            userColourSchemes.put(schemeName.getText(), getSchemeFromGUI());\r
+\r
+            ap.alignFrame.updateUserColourMenu();\r
+\r
+            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
 \r
+            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
+            ucs.setSchemeName(schemeName.getText());\r
             try\r
             {\r
                 PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
@@ -435,23 +480,13 @@ public class UserDefinedColours extends GUserDefinedColours
      */\r
     protected void cancelButton_actionPerformed(ActionEvent e)\r
     {\r
-        Color[] newColours = new Color[24];\r
-\r
-        for (int i = 0; i < 24; i++)\r
-        {\r
-            newColours[i] = (Color) oldColours.elementAt(i);\r
-            buttonPanel.getComponent(i).setBackground(newColours[i]);\r
-        }\r
-\r
-        UserColourScheme ucs = new UserColourScheme(newColours);\r
-\r
         if (seqGroup != null)\r
         {\r
-            seqGroup.cs = ucs;\r
+            seqGroup.cs = oldColourScheme;\r
         }\r
         else\r
         {\r
-            ap.av.setGlobalColourScheme(ucs);\r
+            ap.av.setGlobalColourScheme(oldColourScheme);\r
         }\r
 \r
         ap.repaint();\r
@@ -464,4 +499,48 @@ public class UserDefinedColours extends GUserDefinedColours
         {\r
         }\r
     }\r
+\r
+\r
+    static Hashtable userColourSchemes;\r
+\r
+    public static Hashtable getUserColourSchemes()\r
+    {\r
+      return userColourSchemes;\r
+    }\r
+\r
+    public static void initUserColourSchemes(String files)\r
+    {\r
+      userColourSchemes = new Hashtable();\r
+\r
+      if(files==null)\r
+        return;\r
+\r
+      // In case colours can't be loaded, we'll remove them\r
+      // from the default list here.\r
+      StringBuffer coloursFound = new StringBuffer();\r
+      StringTokenizer st = new StringTokenizer(files, "|");\r
+      while (st.hasMoreElements())\r
+      {\r
+        String file = st.nextToken();\r
+        try\r
+        {\r
+          UserColourScheme ucs = loadColours(file);\r
+          if (ucs != null)\r
+          {\r
+            if (coloursFound.length() > 0)\r
+              coloursFound.append("|");\r
+            coloursFound.append(file);\r
+            userColourSchemes.put(ucs.getName(), ucs);\r
+          }\r
+        }\r
+        catch (Exception ex)\r
+        {\r
+          System.out.println("Error loading User ColourFile\n" + ex);\r
+        }\r
+      }\r
+      if (!files.equals(coloursFound.toString()))\r
+      {\r
+        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());\r
+      }\r
+    }\r
 }\r

diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 49174a0..131f202 100755 (executable)
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -41,9 +41,23 @@ public class GUserDefinedColours extends JPanel
     protected JButton loadbutton = new JButton();\r
     protected JButton savebutton = new JButton();\r
     protected JButton cancelButton = new JButton();\r
-    FlowLayout flowLayout1 = new FlowLayout();\r
-\r
-    /**\r
+  JPanel namePanel = new JPanel();\r
+  JLabel jLabel1 = new JLabel();\r
+  protected JTextField schemeName = new JTextField();\r
+  BorderLayout borderLayout1 = new BorderLayout();\r
+  JPanel panel1 = new JPanel();\r
+  JPanel jPanel1 = new JPanel();\r
+  JPanel jPanel3 = new JPanel();\r
+  BorderLayout borderLayout3 = new BorderLayout();\r
+  GridBagLayout gridBagLayout1 = new GridBagLayout();\r
+  BorderLayout borderLayout2 = new BorderLayout();\r
+  FlowLayout flowLayout1 = new FlowLayout();\r
+  BorderLayout borderLayout4 = new BorderLayout();\r
+  JPanel jPanel4 = new JPanel();\r
+  BorderLayout borderLayout5 = new BorderLayout();\r
+  JPanel jPanel6 = new JPanel();\r
+  JTextArea jTextArea1 = new JTextArea();\r
+  /**\r
      * Creates a new GUserDefinedColours object.\r
      */\r
     public GUserDefinedColours()\r
@@ -65,10 +79,10 @@ public class GUserDefinedColours extends JPanel
      */\r
     private void jbInit() throws Exception\r
     {\r
-        this.setLayout(flowLayout1);\r
+        this.setLayout(borderLayout4);\r
         buttonPanel.setLayout(gridLayout);\r
-        gridLayout.setColumns(6);\r
-        gridLayout.setRows(4);\r
+        gridLayout.setColumns(4);\r
+        gridLayout.setRows(6);\r
         okButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
         okButton.setText("OK");\r
         okButton.addActionListener(new java.awt.event.ActionListener()\r
@@ -116,16 +130,58 @@ public class GUserDefinedColours extends JPanel
             });\r
         this.setBackground(new Color(212, 208, 223));\r
         jPanel2.setOpaque(false);\r
-        colorChooser.setOpaque(false);\r
-        this.add(colorChooser, null);\r
-        this.add(buttonPanel, null);\r
-        this.add(jPanel2, null);\r
-        jPanel2.add(okButton, null);\r
-        jPanel2.add(applyButton, null);\r
-        jPanel2.add(loadbutton, null);\r
-        jPanel2.add(savebutton, null);\r
-        jPanel2.add(cancelButton, null);\r
-    }\r
+    jPanel2.setLayout(borderLayout3);\r
+    colorChooser.setOpaque(false);\r
+    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    jLabel1.setText("Name");\r
+    namePanel.setMinimumSize(new Dimension(300, 31));\r
+    namePanel.setOpaque(false);\r
+    namePanel.setPreferredSize(new Dimension(240, 25));\r
+    namePanel.setToolTipText("");\r
+    namePanel.setLayout(borderLayout1);\r
+    schemeName.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    schemeName.setPreferredSize(new Dimension(105, 21));\r
+    schemeName.setText("");\r
+    schemeName.setHorizontalAlignment(SwingConstants.CENTER);\r
+    panel1.setLayout(flowLayout1);\r
+    panel1.setOpaque(false);\r
+    jPanel1.setOpaque(false);\r
+    jPanel3.setOpaque(false);\r
+    jPanel4.setLayout(borderLayout5);\r
+    jPanel6.setBackground(Color.pink);\r
+    jPanel6.setMinimumSize(new Dimension(10, 70));\r
+    jPanel6.setOpaque(false);\r
+    jPanel6.setPreferredSize(new Dimension(10, 45));\r
+    jPanel6.setLayout(null);\r
+    jTextArea1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));\r
+    jTextArea1.setOpaque(false);\r
+    jTextArea1.setPreferredSize(new Dimension(260, 34));\r
+    jTextArea1.setText(\r
+        "Save your colour scheme with a unique name and it will be added " +\r
+        "to the Colour menu.");\r
+    jTextArea1.setLineWrap(true);\r
+    jTextArea1.setRows(2);\r
+    jTextArea1.setWrapStyleWord(true);\r
+    jPanel3.add(savebutton);\r
+    jPanel3.add(loadbutton);\r
+    jPanel1.add(applyButton);\r
+    jPanel1.add(okButton);\r
+    jPanel1.add(cancelButton);\r
+    jPanel2.add(jPanel3, java.awt.BorderLayout.NORTH);\r
+    jPanel2.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+\r
+    namePanel.add(schemeName, java.awt.BorderLayout.CENTER);\r
+    namePanel.add(jLabel1, java.awt.BorderLayout.WEST);\r
+    panel1.add(namePanel, null);\r
+    panel1.add(buttonPanel, null);\r
+    panel1.add(jPanel2, null);\r
+    panel1.add(jTextArea1);\r
+\r
+    jPanel4.add(panel1, java.awt.BorderLayout.CENTER);\r
+    jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);\r
+    this.add(jPanel4, java.awt.BorderLayout.CENTER);\r
+    this.add(colorChooser, java.awt.BorderLayout.EAST);\r
+  }\r
 \r
     /**\r
      * DOCUMENT ME!\r