-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class UserDefinedColours extends GUserDefinedColours\r
- implements ChangeListener\r
-{\r
- AlignmentPanel ap;\r
- SequenceGroup seqGroup;\r
- Vector selectedButtons;\r
- ColourSchemeI oldColourScheme;\r
- JInternalFrame frame;\r
- MCview.PDBCanvas pdbcanvas;\r
-\r
- /**\r
- * Creates a new UserDefinedColours object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param sg DOCUMENT ME!\r
- */\r
- public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)\r
- {\r
- super();\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
-\r
- if (System.getProperty("os.name").startsWith("Mac"))\r
- {\r
- frame.setSize(760, 370);\r
- }\r
-\r
- if (sg != null)\r
- {\r
- frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");\r
- }\r
-\r
- colorChooser.getSelectionModel().addChangeListener(this);\r
-\r
- this.ap = ap;\r
- seqGroup = sg;\r
-\r
- if (seqGroup != null)\r
- {\r
- oldColourScheme = seqGroup.cs;\r
- }\r
- else\r
- {\r
- 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
- "", ResidueProperties.aa[i]);\r
- }\r
-\r
- makeButton("B", "B");\r
- makeButton("Z", "Z");\r
- makeButton("X", "X");\r
- makeButton("Gap", "-");\r
- }\r
-\r
- public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)\r
- {\r
- super();\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
- pdbcanvas = pdb;\r
-\r
- if (System.getProperty("os.name").startsWith("Mac"))\r
- {\r
- frame.setSize(760, 370);\r
- }\r
-\r
- colorChooser.getSelectionModel().addChangeListener(this);\r
-\r
- oldColourScheme = oldcs;\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
- "", ResidueProperties.aa[i]);\r
- }\r
-\r
- makeButton("B", "B");\r
- makeButton("Z", "Z");\r
- makeButton("X", "X");\r
- makeButton("Gap", "-");\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- if (selectedButtons != null)\r
- {\r
- JButton button;\r
- for(int i=0; i<selectedButtons.size(); i++)\r
- {\r
- button = (JButton)selectedButtons.elementAt(i);\r
- button.setBackground(colorChooser.getColor());\r
- button.setForeground( button.getBackground().brighter().brighter().brighter());\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void colourButtonPressed(MouseEvent e)\r
- {\r
- if(selectedButtons == null)\r
- selectedButtons = new Vector();\r
-\r
- JButton pressed = (JButton) e.getSource();\r
-\r
- if(e.isShiftDown())\r
- {\r
- JButton start, end = (JButton) e.getSource();\r
- if(selectedButtons.size()>0)\r
- start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);\r
- else\r
- start = (JButton) e.getSource();\r
-\r
- int startIndex=0, endIndex=0;\r
- for(int b=0; b<buttonPanel.getComponentCount(); b++)\r
- {\r
- if(buttonPanel.getComponent(b)==start)\r
- startIndex = b;\r
- if(buttonPanel.getComponent(b)==end)\r
- endIndex = b;\r
- }\r
-\r
- if(startIndex > endIndex)\r
- {\r
- int temp = startIndex;\r
- startIndex = endIndex;\r
- endIndex = temp;\r
- }\r
-\r
- for(int b=startIndex; b<=endIndex; b++)\r
- {\r
- JButton button = (JButton)buttonPanel.getComponent(b);\r
- if(!selectedButtons.contains(button))\r
- {\r
- button.setForeground(button.getBackground().brighter().brighter());\r
- selectedButtons.add(button);\r
- }\r
- }\r
- }\r
- else if(!e.isControlDown())\r
- {\r
- for(int b=0; b<selectedButtons.size(); b++)\r
- {\r
- JButton button = (JButton)selectedButtons.elementAt(b);\r
- button.setForeground(button.getBackground().darker().darker());\r
- }\r
- selectedButtons.clear();\r
- pressed.setForeground( pressed.getBackground().brighter().brighter());\r
- selectedButtons.addElement(pressed);\r
-\r
- }\r
- else if(e.isControlDown())\r
- {\r
- if(selectedButtons.contains(pressed))\r
- {\r
- pressed.setForeground(pressed.getBackground().darker().darker());\r
- selectedButtons.remove(pressed);\r
- }\r
- else\r
- {\r
- pressed.setForeground( pressed.getBackground().brighter().brighter());\r
- selectedButtons.addElement(pressed);\r
- }\r
- }\r
-\r
- if(selectedButtons.size()>0)\r
- colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param label DOCUMENT ME!\r
- * @param aa DOCUMENT ME!\r
- */\r
- void makeButton(String label, String aa)\r
- {\r
- final JButton button = new JButton();\r
- Color col = Color.white;\r
-\r
- try\r
- {\r
- col = oldColourScheme.findColour(aa, -1);\r
- }\r
- catch (Exception ex)\r
- {\r
- // ex.printStackTrace();\r
- }\r
-\r
- button.setBackground(col);\r
- button.setText(label);\r
- button.setForeground(col.darker().darker().darker());\r
- button.setFont(new java.awt.Font("Verdana", 1, 10));\r
- button.addMouseListener(new java.awt.event.MouseAdapter()\r
- {\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- colourButtonPressed(e);\r
- }\r
- });\r
-\r
- buttonPanel.add(button, null);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void okButton_actionPerformed(ActionEvent e)\r
- {\r
- applyButton_actionPerformed(null);\r
-\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void applyButton_actionPerformed(ActionEvent e)\r
- {\r
- UserColourScheme ucs = getSchemeFromGUI();\r
- ucs.setName(schemeName.getText());\r
-\r
- if (seqGroup != null)\r
- {\r
- seqGroup.cs = ucs;\r
- ap.repaint();\r
- }\r
- else if(ap!=null)\r
- {\r
- ap.alignFrame.changeColour(ucs);\r
- }\r
- else if(pdbcanvas!=null)\r
- {\r
- pdbcanvas.pdb.setColours(ucs);\r
- pdbcanvas.updateSeqColours();\r
- }\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
- if(ap!=null)\r
- ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
-\r
-\r
- return ucs;\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void loadbutton_actionPerformed(ActionEvent e)\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
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Load colour scheme");\r
- chooser.setToolTipText("Load");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- File choice = chooser.getSelectedFile();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\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
- 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
- JButton button = (JButton) buttonPanel.getComponent(i);\r
- button.setBackground(colors[i]);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static UserColourScheme loadDefaultColours()\r
- {\r
- UserColourScheme ret = null;\r
-\r
- String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");\r
- if ( colours != null )\r
- {\r
- if(colours.indexOf("|")>-1)\r
- colours = colours.substring(0, colours.indexOf("|"));\r
-\r
- ret = loadColours(colours);\r
- }\r
-\r
- if(ret == null)\r
- {\r
- Color[] newColours = new Color[24];\r
- for (int i = 0; i < 24; i++)\r
- {\r
- newColours[i] = Color.white;\r
- }\r
- ret = new UserColourScheme(newColours);\r
- }\r
-\r
- return ret;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param file DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- static UserColourScheme loadColours(String file)\r
- {\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 jucs = new jalview.binding.JalviewUserColours();\r
- jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
-\r
- newColours = new Color[jucs.getColourCount()];\r
-\r
- for (int i = 0; i < 24; i++)\r
- {\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 User ColourFile\n"+ex);\r
- }\r
-\r
-\r
- return ucs;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\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
-\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Save colour scheme");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);\r
- if(defaultColours.indexOf(choice)==-1)\r
- {\r
- if(defaultColours.length()>0)\r
- defaultColours = defaultColours.concat("|");\r
- defaultColours = defaultColours.concat(choice);\r
- }\r
-\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
- new FileOutputStream(choice), "UTF-8"));\r
-\r
- for (int i = 0; i < 24; i++)\r
- {\r
- JButton button = (JButton) buttonPanel.getComponent(i);\r
- jalview.binding.Colour col = new jalview.binding.Colour();\r
- col.setName(button.getText());\r
- col.setRGB(jalview.util.Format.getHexString(\r
- button.getBackground()));\r
- ucs.addColour(col);\r
- }\r
-\r
- ucs.marshal(out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void cancelButton_actionPerformed(ActionEvent e)\r
- {\r
- if (ap != null)\r
- {\r
- if (seqGroup != null)\r
- {\r
- seqGroup.cs = oldColourScheme;\r
- }\r
- else if (ap != null)\r
- {\r
- ap.av.setGlobalColourScheme(oldColourScheme);\r
- }\r
- ap.repaint();\r
- }\r
-\r
- if(pdbcanvas!=null)\r
- {\r
- pdbcanvas.pdb.setColours(oldColourScheme);\r
- }\r
-\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\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 || files.length()==0)\r
- return;\r
-\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
- if (coloursFound.toString().length() > 1)\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",\r
- coloursFound.toString());\r
- else\r
- jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");\r
- }\r
- }\r
-\r
- public static void removeColourFromDefaults(String target)\r
- {\r
- // The only way to find colours by name is to load them in\r
- // In case colours can't be loaded, we'll remove them\r
- // from the default list here.\r
-\r
- userColourSchemes = new Hashtable();\r
-\r
- StringBuffer coloursFound = new StringBuffer();\r
- StringTokenizer st = new StringTokenizer(\r
- jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");\r
-\r
- while (st.hasMoreElements())\r
- {\r
- String file = st.nextToken();\r
- try\r
- {\r
- UserColourScheme ucs = loadColours(file);\r
- if (ucs != null && !ucs.getName().equals(target))\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
-\r
- if (coloursFound.toString().length() > 1)\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());\r
- else\r
- jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.io.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class UserDefinedColours extends GUserDefinedColours
+ implements ChangeListener
+{
+ AlignmentPanel ap;
+ SequenceGroup seqGroup;
+ Vector selectedButtons;
+ ColourSchemeI oldColourScheme;
+ JInternalFrame frame;
+ MCview.PDBCanvas pdbcanvas;
+ Vector upperCaseButtons;
+ Vector lowerCaseButtons;
+
+
+ /**
+ * Creates a new UserDefinedColours object.
+ *
+ * @param ap DOCUMENT ME!
+ * @param sg DOCUMENT ME!
+ */
+ public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
+ {
+ super();
+ 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());
+ if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ }
+ else
+ resetButtonPanel(false);
+ }
+ else
+ resetButtonPanel(false);
+
+ showFrame();
+ }
+
+ public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
+ {
+ super();
+ pdbcanvas = pdb;
+
+ colorChooser.getSelectionModel().addChangeListener(this);
+
+ oldColourScheme = oldcs;
+
+ if (oldColourScheme instanceof UserColourScheme)
+ {
+ schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+ }
+
+ 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)
+ {
+ 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!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void stateChanged(ChangeEvent evt)
+ {
+ if (selectedButtons != null)
+ {
+ 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());
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void colourButtonPressed(MouseEvent e)
+ {
+ if(selectedButtons == null)
+ selectedButtons = new Vector();
+
+ JButton pressed = (JButton) e.getSource();
+
+ if(e.isShiftDown())
+ {
+ 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++)
+ {
+ if(buttonPanel.getComponent(b)==start)
+ startIndex = b;
+ if(buttonPanel.getComponent(b)==end)
+ endIndex = b;
+ }
+
+ if(startIndex > endIndex)
+ {
+ int temp = startIndex;
+ startIndex = endIndex;
+ endIndex = temp;
+ }
+
+ for(int b=startIndex; b<=endIndex; b++)
+ {
+ JButton button = (JButton)buttonPanel.getComponent(b);
+ if(!selectedButtons.contains(button))
+ {
+ button.setForeground(button.getBackground().brighter().brighter());
+ selectedButtons.add(button);
+ }
+ }
+ }
+ else if(!e.isControlDown())
+ {
+ for(int b=0; b<selectedButtons.size(); b++)
+ {
+ JButton button = (JButton)selectedButtons.elementAt(b);
+ button.setForeground(button.getBackground().darker().darker());
+ }
+ selectedButtons.clear();
+ pressed.setForeground( pressed.getBackground().brighter().brighter());
+ selectedButtons.addElement(pressed);
+
+ }
+ else if(e.isControlDown())
+ {
+ if(selectedButtons.contains(pressed))
+ {
+ pressed.setForeground(pressed.getBackground().darker().darker());
+ selectedButtons.remove(pressed);
+ }
+ else
+ {
+ pressed.setForeground( pressed.getBackground().brighter().brighter());
+ selectedButtons.addElement(pressed);
+ }
+ }
+
+ if(selectedButtons.size()>0)
+ colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param label DOCUMENT ME!
+ * @param aa DOCUMENT ME!
+ */
+ JButton makeButton(String label,
+ String aa,
+ Vector caseSensitiveButtons,
+ int buttonIndex)
+ {
+ final JButton button;
+ Color col;
+
+ if(buttonIndex<caseSensitiveButtons.size())
+ {
+ button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
+ col = button.getBackground();
+ }
+ else
+ {
+ 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)
+ { }
+ }
+
+ 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", Font.BOLD, 10));
+
+ return button;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void okButton_actionPerformed(ActionEvent e)
+ {
+ applyButton_actionPerformed(null);
+
+ try
+ {
+ frame.setClosed(true);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void applyButton_actionPerformed(ActionEvent e)
+ {
+ UserColourScheme ucs = getSchemeFromButtons();
+ ucs.setName(schemeName.getText());
+
+ if (seqGroup != null)
+ {
+ seqGroup.cs = ucs;
+ ap.repaint();
+ }
+ else if(ap!=null)
+ {
+ ap.alignFrame.changeColour(ucs);
+ }
+ else if(pdbcanvas!=null)
+ {
+ pdbcanvas.pdb.setColours(ucs);
+ pdbcanvas.updateSeqColours();
+ }
+ }
+
+ UserColourScheme getSchemeFromButtons()
+ {
+
+ Color[] newColours = new Color[24];
+
+ for (int i = 0; i < 24; i++)
+ {
+ JButton button = (JButton) upperCaseButtons.elementAt(i);
+ newColours[i] = button.getBackground();
+ }
+
+ UserColourScheme ucs = new UserColourScheme(newColours);
+
+
+ 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;
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ 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");
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Load colour scheme");
+ chooser.setToolTipText("Load");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File choice = chooser.getSelectedFile();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ 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);
+
+
+ UserColourScheme ucs = loadColours(choice.getAbsolutePath());
+ Color[] colors = ucs.getColours();
+ schemeName.setText(ucs.getName());
+
+ if(ucs.getLowerCaseColours()!=null)
+ {
+ 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]);
+ }
+
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static UserColourScheme loadDefaultColours()
+ {
+ 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("|"));
+
+ ret = loadColours(colours);
+ }
+
+ if(ret == null)
+ {
+ Color[] newColours = new Color[24];
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = Color.white;
+ }
+ ret = new UserColourScheme(newColours);
+ }
+
+ return ret;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param file DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ static UserColourScheme loadColours(String file)
+ {
+ UserColourScheme ucs = null;
+ Color[] newColours = null;
+ try
+ {
+ InputStreamReader in = new InputStreamReader(new FileInputStream(
+ file), "UTF-8");
+
+ 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];
+
+ Color [] lowerCase = null;
+ boolean caseSensitive = false;
+
+
+ String name;
+ int index;
+ for (int i = 0; i < jucs.getColourCount(); i++)
+ {
+ 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)
+ {
+ //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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ 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");
+
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Save colour scheme");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ 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);
+ }
+
+ userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
+
+ ap.alignFrame.updateUserColourMenu();
+
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
+
+ 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 < buttonPanel.getComponentCount(); i++)
+ {
+ JButton button = (JButton) buttonPanel.getComponent(i);
+ jalview.schemabinding.version2.Colour col
+ = new jalview.schemabinding.version2.Colour();
+ col.setName(button.getText());
+ col.setRGB(jalview.util.Format.getHexString(
+ button.getBackground()));
+ ucs.addColour(col);
+ }
+
+ ucs.marshal(out);
+ out.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void cancelButton_actionPerformed(ActionEvent e)
+ {
+ if (ap != null)
+ {
+ if (seqGroup != null)
+ {
+ seqGroup.cs = oldColourScheme;
+ }
+ else if (ap != null)
+ {
+ ap.av.setGlobalColourScheme(oldColourScheme);
+ }
+ ap.repaint();
+ }
+
+ if(pdbcanvas!=null)
+ {
+ pdbcanvas.pdb.setColours(oldColourScheme);
+ }
+
+ try
+ {
+ frame.setClosed(true);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+
+
+ 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
+ {
+ UserColourScheme ucs = loadColours(file);
+ if (ucs != null)
+ {
+ 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 (!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");
+ }
+ }
+
+ 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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff