-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.SequenceGroup;\r
-import jalview.io.JalviewFileChooser;\r
-import jalview.jbgui.GUserDefinedColours;\r
-import jalview.schemes.ColourSchemeI;\r
-import jalview.schemes.ResidueProperties;\r
-import jalview.schemes.UserColourScheme;\r
-import jalview.util.MessageManager;\r
-\r
-import java.awt.Color;\r
-import java.awt.Font;\r
-import java.awt.event.ActionEvent;\r
-import java.awt.event.MouseEvent;\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileOutputStream;\r
-import java.io.InputStreamReader;\r
-import java.io.OutputStreamWriter;\r
-import java.io.PrintWriter;\r
-import java.util.Hashtable;\r
-import java.util.StringTokenizer;\r
-import java.util.Vector;\r
-\r
-import javax.swing.JButton;\r
-import javax.swing.JInternalFrame;\r
-import javax.swing.JOptionPane;\r
-import javax.swing.event.ChangeEvent;\r
-import javax.swing.event.ChangeListener;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- * \r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class UserDefinedColours extends GUserDefinedColours implements\r
- ChangeListener\r
-{\r
- AlignmentPanel ap;\r
-\r
- SequenceGroup seqGroup;\r
-\r
- Vector selectedButtons;\r
-\r
- ColourSchemeI oldColourScheme;\r
-\r
- JInternalFrame frame;\r
-\r
- AppJmol jmol;\r
-\r
- Vector upperCaseButtons;\r
-\r
- Vector lowerCaseButtons;\r
-\r
- /**\r
- * Creates a new UserDefinedColours object.\r
- * \r
- * @param ap\r
- * DOCUMENT ME!\r
- * @param sg\r
- * DOCUMENT ME!\r
- */\r
- public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)\r
- {\r
- super();\r
-\r
- lcaseColour.setEnabled(false);\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
- if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)\r
- {\r
- caseSensitive.setSelected(true);\r
- lcaseColour.setEnabled(true);\r
- resetButtonPanel(true);\r
- }\r
- else\r
- {\r
- resetButtonPanel(false);\r
- }\r
- }\r
- else\r
- {\r
- resetButtonPanel(false);\r
- }\r
-\r
- showFrame();\r
- }\r
-\r
- public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs)\r
- {\r
- super();\r
- this.jmol = jmol;\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
-\r
- resetButtonPanel(false);\r
-\r
- showFrame();\r
-\r
- }\r
-\r
- void showFrame()\r
- {\r
- colorChooser.getSelectionModel().addChangeListener(this);\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, MessageManager.getString("label.user_defined_colours"), 720, 370, true);\r
-\r
- if (seqGroup != null)\r
- {\r
- frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");\r
- }\r
-\r
- if (new jalview.util.Platform().isAMac())\r
- {\r
- frame.setSize(760, 370);\r
- }\r
- }\r
-\r
- void resetButtonPanel(boolean caseSensitive)\r
- {\r
- buttonPanel.removeAll();\r
-\r
- if (upperCaseButtons == null)\r
- {\r
- upperCaseButtons = new Vector();\r
- }\r
-\r
- JButton button;\r
- String label;\r
- for (int i = 0; i < 20; i++)\r
- {\r
- if (caseSensitive)\r
- {\r
- label = ResidueProperties.aa[i];\r
- }\r
- else\r
- {\r
- label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])\r
- .toString();\r
- }\r
-\r
- button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,\r
- i);\r
-\r
- buttonPanel.add(button);\r
- }\r
-\r
- buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));\r
- buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));\r
- buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));\r
- buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));\r
-\r
- if (!caseSensitive)\r
- {\r
- gridLayout.setRows(6);\r
- gridLayout.setColumns(4);\r
- }\r
- else\r
- {\r
- gridLayout.setRows(7);\r
- int cols = 7;\r
- gridLayout.setColumns(cols + 1);\r
-\r
- if (lowerCaseButtons == null)\r
- {\r
- lowerCaseButtons = new Vector();\r
- }\r
-\r
- for (int i = 0; i < 20; i++)\r
- {\r
- int row = i / cols + 1;\r
- int index = (row * cols) + i;\r
- button = makeButton(ResidueProperties.aa[i].toLowerCase(),\r
- ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);\r
-\r
- buttonPanel.add(button, index);\r
- }\r
- }\r
-\r
- if (caseSensitive)\r
- {\r
- buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));\r
- buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));\r
- buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));\r
- }\r
-\r
- buttonPanel.validate();\r
- validate();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param evt\r
- * DOCUMENT ME!\r
- */\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- if (selectedButtons != null)\r
- {\r
- JButton button = null;\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()\r
- .brighter());\r
- }\r
- if (button == lcaseColour)\r
- {\r
- for (int i = 0; i < lowerCaseButtons.size(); i++)\r
- {\r
- button = (JButton) lowerCaseButtons.elementAt(i);\r
- button.setBackground(colorChooser.getColor());\r
- button.setForeground(button.getBackground().brighter().brighter()\r
- .brighter());\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void colourButtonPressed(MouseEvent e)\r
- {\r
- if (selectedButtons == null)\r
- {\r
- selectedButtons = new Vector();\r
- }\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
- {\r
- start = (JButton) selectedButtons\r
- .elementAt(selectedButtons.size() - 1);\r
- }\r
- else\r
- {\r
- start = (JButton) e.getSource();\r
- }\r
-\r
- int startIndex = 0, endIndex = 0;\r
- for (int b = 0; b < buttonPanel.getComponentCount(); b++)\r
- {\r
- if (buttonPanel.getComponent(b) == start)\r
- {\r
- startIndex = b;\r
- }\r
- if (buttonPanel.getComponent(b) == end)\r
- {\r
- endIndex = b;\r
- }\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
- {\r
- colorChooser.setColor(((JButton) selectedButtons.elementAt(0))\r
- .getBackground());\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param label\r
- * DOCUMENT ME!\r
- * @param aa\r
- * DOCUMENT ME!\r
- */\r
- JButton makeButton(String label, String aa, Vector caseSensitiveButtons,\r
- int buttonIndex)\r
- {\r
- final JButton button;\r
- Color col;\r
-\r
- if (buttonIndex < caseSensitiveButtons.size())\r
- {\r
- button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);\r
- col = button.getBackground();\r
- }\r
- else\r
- {\r
- button = new JButton();\r
- button.addMouseListener(new java.awt.event.MouseAdapter()\r
- {\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- colourButtonPressed(e);\r
- }\r
- });\r
-\r
- caseSensitiveButtons.addElement(button);\r
-\r
- col = Color.white;\r
- if (oldColourScheme != null)\r
- {\r
- try\r
- {\r
- col = oldColourScheme.findColour(aa.charAt(0), -1, null);\r
- } catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
-\r
- if (caseSensitive.isSelected())\r
- {\r
- button.setMargin(new java.awt.Insets(2, 2, 2, 2));\r
- }\r
- else\r
- {\r
- button.setMargin(new java.awt.Insets(2, 14, 2, 14));\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", Font.BOLD, 10));\r
-\r
- return button;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void okButton_actionPerformed(ActionEvent e)\r
- {\r
- applyButton_actionPerformed(null);\r
-\r
- try\r
- {\r
- frame.setClosed(true);\r
- } catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void applyButton_actionPerformed(ActionEvent e)\r
- {\r
- UserColourScheme ucs = getSchemeFromButtons();\r
- ucs.setName(schemeName.getText());\r
-\r
- if (seqGroup != null)\r
- {\r
- seqGroup.cs = ucs;\r
- ap.paintAlignment(true);\r
- }\r
- else if (ap != null)\r
- {\r
- ap.alignFrame.changeColour(ucs);\r
- }\r
- else if (jmol != null)\r
- {\r
- jmol.setJalviewColourScheme(ucs);\r
- }\r
- }\r
-\r
- UserColourScheme getSchemeFromButtons()\r
- {\r
-\r
- Color[] newColours = new Color[24];\r
-\r
- for (int i = 0; i < 24; i++)\r
- {\r
- JButton button = (JButton) upperCaseButtons.elementAt(i);\r
- newColours[i] = button.getBackground();\r
- }\r
-\r
- UserColourScheme ucs = new UserColourScheme(newColours);\r
-\r
- if (caseSensitive.isSelected())\r
- {\r
- newColours = new Color[23];\r
- for (int i = 0; i < 23; i++)\r
- {\r
- JButton button = (JButton) lowerCaseButtons.elementAt(i);\r
- newColours[i] = button.getBackground();\r
- }\r
- ucs.setLowerCaseColours(newColours);\r
- }\r
-\r
- if (ap != null)\r
- {\r
- ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
- }\r
-\r
- return ucs;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void loadbutton_actionPerformed(ActionEvent e)\r
- {\r
- upperCaseButtons = new Vector();\r
- lowerCaseButtons = new Vector();\r
-\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]\r
- { "jc" }, new String[]\r
- { "Jalview User Colours" }, "Jalview User Colours");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle(MessageManager.getString("label.load_colour_scheme"));\r
- chooser.setToolTipText(MessageManager.getString("action.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(\r
- "USER_DEFINED_COLOURS", choice.getPath());\r
- if (defaultColours.indexOf(choice.getPath()) == -1)\r
- {\r
- defaultColours = defaultColours.concat("|")\r
- .concat(choice.getPath());\r
- }\r
-\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
-\r
- UserColourScheme ucs = loadColours(choice.getAbsolutePath());\r
- Color[] colors = ucs.getColours();\r
- schemeName.setText(ucs.getName());\r
-\r
- if (ucs.getLowerCaseColours() != null)\r
- {\r
- caseSensitive.setSelected(true);\r
- lcaseColour.setEnabled(true);\r
- resetButtonPanel(true);\r
- for (int i = 0; i < lowerCaseButtons.size(); i++)\r
- {\r
- JButton button = (JButton) lowerCaseButtons.elementAt(i);\r
- button.setBackground(ucs.getLowerCaseColours()[i]);\r
- }\r
-\r
- }\r
- else\r
- {\r
- caseSensitive.setSelected(false);\r
- lcaseColour.setEnabled(false);\r
- resetButtonPanel(false);\r
- }\r
-\r
- for (int i = 0; i < upperCaseButtons.size(); i++)\r
- {\r
- JButton button = (JButton) upperCaseButtons.elementAt(i);\r
- button.setBackground(colors[i]);\r
- }\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
- {\r
- colours = colours.substring(0, colours.indexOf("|"));\r
- }\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\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- static UserColourScheme loadColours(String file)\r
- {\r
- UserColourScheme ucs = null;\r
- Color[] newColours = null;\r
- try\r
- {\r
- InputStreamReader in = new InputStreamReader(\r
- new FileInputStream(file), "UTF-8");\r
-\r
- jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();\r
-\r
- org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(\r
- jucs);\r
- jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar\r
- .unmarshal(in);\r
-\r
- newColours = new Color[24];\r
-\r
- Color[] lowerCase = null;\r
- boolean caseSensitive = false;\r
-\r
- String name;\r
- int index;\r
- for (int i = 0; i < jucs.getColourCount(); i++)\r
- {\r
- name = jucs.getColour(i).getName();\r
- if (ResidueProperties.aa3Hash.containsKey(name))\r
- {\r
- index = ((Integer) ResidueProperties.aa3Hash.get(name))\r
- .intValue();\r
- }\r
- else\r
- {\r
- index = ResidueProperties.aaIndex[name.charAt(0)];\r
- }\r
- if (index == -1)\r
- {\r
- continue;\r
- }\r
-\r
- if (name.toLowerCase().equals(name))\r
- {\r
- if (lowerCase == null)\r
- {\r
- lowerCase = new Color[23];\r
- }\r
- caseSensitive = true;\r
- lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)\r
- .getRGB(), 16));\r
- }\r
- else\r
- {\r
- newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)\r
- .getRGB(), 16));\r
- }\r
- }\r
-\r
- if (newColours != null)\r
- {\r
- ucs = new UserColourScheme(newColours);\r
- ucs.setName(jucs.getSchemeName());\r
- if (caseSensitive)\r
- {\r
- ucs.setLowerCaseColours(lowerCase);\r
- }\r
- }\r
-\r
- } catch (Exception ex)\r
- {\r
- // Could be Archive Jalview format\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
-\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(jucs.getColour(i)\r
- .getRGB(), 16));\r
- }\r
- if (newColours != null)\r
- {\r
- ucs = new UserColourScheme(newColours);\r
- ucs.setName(jucs.getSchemeName());\r
- }\r
- } catch (Exception ex2)\r
- {\r
- ex2.printStackTrace();\r
- }\r
-\r
- if (newColours == null)\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\r
- * 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
- MessageManager.getString("label.user_colour_scheme_must_have_name"),\r
- MessageManager.getString("label.no_name_colour_scheme"), JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- if (userColourSchemes != null\r
- && userColourSchemes.containsKey(schemeName.getText()))\r
- {\r
- int reply = JOptionPane.showInternalConfirmDialog(\r
- Desktop.desktop,\r
- MessageManager.formatMessage("label.colour_scheme_exists_overwrite", new String[]{schemeName.getText(),schemeName.getText()}),\r
- MessageManager.getString("label.duplicate_scheme_name"), JOptionPane.YES_NO_OPTION);\r
- if (reply != JOptionPane.YES_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- userColourSchemes.remove(schemeName.getText());\r
- }\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]\r
- { "jc" }, new String[]\r
- { "Jalview User Colours" }, "Jalview User Colours");\r
-\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Save colour scheme");\r
- chooser.setToolTipText(MessageManager.getString("action.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(\r
- "USER_DEFINED_COLOURS", choice);\r
- if (defaultColours.indexOf(choice) == -1)\r
- {\r
- if (defaultColours.length() > 0)\r
- {\r
- defaultColours = defaultColours.concat("|");\r
- }\r
- defaultColours = defaultColours.concat(choice);\r
- }\r
-\r
- userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());\r
-\r
- ap.alignFrame.updateUserColourMenu();\r
-\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
-\r
- jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();\r
-\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 < buttonPanel.getComponentCount(); i++)\r
- {\r
- JButton button = (JButton) buttonPanel.getComponent(i);\r
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
- col.setName(button.getText());\r
- col.setRGB(jalview.util.Format.getHexString(button\r
- .getBackground()));\r
- ucs.addColour(col);\r
- }\r
-\r
- ucs.marshal(out);\r
- out.close();\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * 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.paintAlignment(true);\r
- }\r
-\r
- if (jmol != null)\r
- {\r
- jmol.setJalviewColourScheme(oldColourScheme);\r
- }\r
-\r
- try\r
- {\r
- frame.setClosed(true);\r
- } catch (Exception ex)\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
- {\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
- {\r
- coloursFound.append("|");\r
- }\r
- coloursFound.append(file);\r
- userColourSchemes.put(ucs.getName(), ucs);\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
- {\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",\r
- coloursFound.toString());\r
- }\r
- else\r
- {\r
- jalview.bin.Cache.applicationProperties\r
- .remove("USER_DEFINED_COLOURS");\r
- }\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
- {\r
- coloursFound.append("|");\r
- }\r
- coloursFound.append(file);\r
- userColourSchemes.put(ucs.getName(), ucs);\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
- {\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",\r
- coloursFound.toString());\r
- }\r
- else\r
- {\r
- jalview.bin.Cache.applicationProperties\r
- .remove("USER_DEFINED_COLOURS");\r
- }\r
-\r
- }\r
-\r
- public void caseSensitive_actionPerformed(ActionEvent e)\r
- {\r
- resetButtonPanel(caseSensitive.isSelected());\r
- lcaseColour.setEnabled(caseSensitive.isSelected());\r
- }\r
-\r
- public void lcaseColour_actionPerformed(ActionEvent e)\r
- {\r
- if (selectedButtons == null)\r
- {\r
- selectedButtons = new Vector();\r
- }\r
- else\r
- {\r
- selectedButtons.clear();\r
- }\r
- selectedButtons.add(lcaseColour);\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.bin.Cache;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GUserDefinedColours;
+import jalview.schemabinding.version2.Colour;
+import jalview.schemabinding.version2.JalviewUserColours;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Insets;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JInternalFrame;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+/**
+ * This panel allows the user to assign colours to Amino Acid residue codes, and
+ * save the colour scheme.
+ *
+ * @author Andrew Waterhouse
+ * @author Mungo Carstairs
+ */
+public class UserDefinedColours extends GUserDefinedColours
+ implements ChangeListener
+{
+ private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD,
+ 10);
+
+ public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+
+ private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
+
+ private static final int MY_FRAME_HEIGHT = 440;
+
+ private static final int MY_FRAME_WIDTH = 810;
+
+ private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
+
+ AlignmentPanel ap;
+
+ /*
+ * the colour scheme when the dialog was opened, or
+ * the scheme last saved to file
+ */
+ ColourSchemeI oldColourScheme;
+
+ /*
+ * flag is true if the colour scheme has been changed since the
+ * dialog was opened, or the changes last saved to file
+ */
+ boolean changed;
+
+ JInternalFrame frame;
+
+ List<JButton> upperCaseButtons;
+
+ List<JButton> lowerCaseButtons;
+
+ /**
+ * Creates and displays a new UserDefinedColours panel
+ *
+ * @param alignPanel
+ */
+ public UserDefinedColours(AlignmentPanel alignPanel)
+ {
+ this();
+
+ lcaseColour.setEnabled(false);
+
+ this.ap = alignPanel;
+
+ oldColourScheme = alignPanel.av.getGlobalColourScheme();
+
+ if (oldColourScheme instanceof UserColourScheme)
+ {
+ schemeName.setText(oldColourScheme.getSchemeName());
+ if (((UserColourScheme) oldColourScheme)
+ .getLowerCaseColours() != null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ }
+ else
+ {
+ resetButtonPanel(false);
+ }
+ }
+ else
+ {
+ resetButtonPanel(false);
+ }
+
+ showFrame();
+ }
+
+ UserDefinedColours()
+ {
+ super();
+ selectedButtons = new ArrayList<>();
+ }
+
+ void showFrame()
+ {
+ colorChooser.getSelectionModel().addChangeListener(this);
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.user_defined_colours"),
+ MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
+ }
+
+ /**
+ * Rebuilds the panel with coloured buttons for residues. If not case
+ * sensitive colours, show 3-letter amino acid code as button text. If case
+ * sensitive, just show the single letter code, in order to make space for the
+ * additional buttons.
+ *
+ * @param isCaseSensitive
+ */
+ void resetButtonPanel(boolean isCaseSensitive)
+ {
+ buttonPanel.removeAll();
+
+ if (upperCaseButtons == null)
+ {
+ upperCaseButtons = new ArrayList<>();
+ }
+
+ for (int i = 0; i < 20; i++)
+ {
+ String label = isCaseSensitive ? ResidueProperties.aa[i]
+ : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
+ .toString();
+ JButton 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 (!isCaseSensitive)
+ {
+ gridLayout.setRows(6);
+ gridLayout.setColumns(4);
+ }
+ else
+ {
+ gridLayout.setRows(7);
+ int cols = 7;
+ gridLayout.setColumns(cols + 1);
+
+ if (lowerCaseButtons == null)
+ {
+ lowerCaseButtons = new ArrayList<>();
+ }
+
+ for (int i = 0; i < 20; i++)
+ {
+ int row = i / cols + 1;
+ int index = (row * cols) + i;
+ JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(),
+ ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
+
+ buttonPanel.add(button, index);
+ }
+ }
+
+ if (isCaseSensitive)
+ {
+ buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
+ buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
+ buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
+ }
+
+ // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
+ // codes
+ if (this.frame != null)
+ {
+ int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+ : MY_FRAME_WIDTH;
+ this.frame.setSize(newWidth, this.frame.getHeight());
+ }
+
+ buttonPanel.validate();
+ validate();
+ }
+
+ /**
+ * ChangeListener handler for when a colour is picked in the colour chooser.
+ * The action is to apply the colour to all selected buttons as their
+ * background colour. Foreground colour (text) is set to a lighter shade in
+ * order to highlight which buttons are selected. If 'Lower Case Colour' is
+ * active, then the colour is applied to all lower case buttons (as well as
+ * the Lower Case Colour button itself).
+ *
+ * @param evt
+ */
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ JButton button = null;
+ final Color newColour = colorChooser.getColor();
+ if (lcaseColour.isSelected())
+ {
+ selectedButtons.clear();
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
+ {
+ button = lowerCaseButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(
+ ColorUtils.brighterThan(button.getBackground()));
+ }
+ }
+ for (int i = 0; i < selectedButtons.size(); i++)
+ {
+ button = selectedButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(newColour));
+ }
+
+ changed = true;
+ }
+
+ /**
+ * Performs actions when a residue button is clicked. This manages the button
+ * selection set (highlighted by brighter foreground text).
+ * <p>
+ * On select button(s) with Ctrl/click or Shift/click: set button foreground
+ * text to brighter than background.
+ * <p>
+ * On unselect button(s) with Ctrl/click on selected, or click to release
+ * current selection: reset foreground text to darker than background.
+ * <p>
+ * Simple click: clear selection (resetting foreground to darker); set clicked
+ * button foreground to brighter
+ * <p>
+ * Finally, synchronize the colour chooser to the colour of the first button
+ * in the selected set.
+ *
+ * @param e
+ */
+ public void colourButtonPressed(MouseEvent e)
+ {
+ JButton pressed = (JButton) e.getSource();
+
+ if (e.isShiftDown())
+ {
+ JButton start, end = (JButton) e.getSource();
+ if (selectedButtons.size() > 0)
+ {
+ start = selectedButtons.get(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(
+ ColorUtils.brighterThan(button.getBackground()));
+ selectedButtons.add(button);
+ }
+ }
+ }
+ else if (!e.isControlDown())
+ {
+ for (int b = 0; b < selectedButtons.size(); b++)
+ {
+ JButton button = selectedButtons.get(b);
+ button.setForeground(ColorUtils.darkerThan(button.getBackground()));
+ }
+ selectedButtons.clear();
+ pressed.setForeground(
+ ColorUtils.brighterThan(pressed.getBackground()));
+ selectedButtons.add(pressed);
+
+ }
+ else if (e.isControlDown())
+ {
+ if (selectedButtons.contains(pressed))
+ {
+ pressed.setForeground(
+ ColorUtils.darkerThan(pressed.getBackground()));
+ selectedButtons.remove(pressed);
+ }
+ else
+ {
+ pressed.setForeground(
+ ColorUtils.brighterThan(pressed.getBackground()));
+ selectedButtons.add(pressed);
+ }
+ }
+
+ if (selectedButtons.size() > 0)
+ {
+ colorChooser.setColor((selectedButtons.get(0)).getBackground());
+ }
+ }
+
+ /**
+ * A helper method to update or make a colour button, whose background colour
+ * is the associated colour, and text colour a darker shade of the same. If
+ * the button is already in the list, then its text and margins are updated,
+ * if not then it is created and added. This method supports toggling between
+ * case-sensitive and case-insensitive button panels. The case-sensitive
+ * version has abbreviated button text in order to fit in more buttons.
+ *
+ * @param label
+ * @param residue
+ * @param the
+ * list of buttons
+ * @param buttonIndex
+ * the button's position in the list
+ */
+ JButton makeButton(String label, String residue, List<JButton> buttons,
+ int buttonIndex)
+ {
+ final JButton button;
+ Color col;
+
+ if (buttonIndex < buttons.size())
+ {
+ button = buttons.get(buttonIndex);
+ col = button.getBackground();
+ }
+ else
+ {
+ button = new JButton();
+ button.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ colourButtonPressed(e);
+ }
+ });
+
+ buttons.add(button);
+
+ /*
+ * make initial button colour that of the current colour scheme,
+ * if it is a simple per-residue colouring, else white
+ */
+ col = Color.white;
+ if (oldColourScheme != null && oldColourScheme.isSimple())
+ {
+ col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
+ 0f);
+ }
+ }
+
+ if (caseSensitive.isSelected())
+ {
+ button.setMargin(new Insets(2, 2, 2, 2));
+ }
+ else
+ {
+ button.setMargin(new Insets(2, 14, 2, 14));
+ }
+
+ button.setOpaque(true); // required for the next line to have effect
+ button.setBackground(col);
+ button.setText(label);
+ button.setForeground(ColorUtils.darkerThan(col));
+ button.setFont(VERDANA_BOLD_10);
+
+ return button;
+ }
+
+ /**
+ * On 'OK', check that at least one colour has been assigned to a residue (and
+ * if not issue a warning), and apply the chosen colour scheme and close the
+ * panel.
+ */
+ @Override
+ protected void okButton_actionPerformed()
+ {
+ if (isNoSelectionMade())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ /*
+ * OK is treated as 'apply colours and close'
+ */
+ applyButton_actionPerformed();
+
+ /*
+ * If editing a named colour scheme, warn if changes
+ * have not been saved
+ */
+ warnIfUnsavedChanges();
+
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+
+ /**
+ * If we have made changes to an existing user defined colour scheme but not
+ * saved them, show a dialog with the option to save. If the user chooses to
+ * save, do so, else clear the colour scheme name to indicate a new colour
+ * scheme.
+ */
+ protected void warnIfUnsavedChanges()
+ {
+ if (!changed)
+ {
+ return;
+ }
+
+ String name = schemeName.getText().trim();
+ if (oldColourScheme != null && !"".equals(name)
+ && name.equals(oldColourScheme.getSchemeName()))
+ {
+ String message = MessageManager.formatMessage("label.scheme_changed",
+ name);
+ String title = MessageManager.getString("label.save_changes");
+ String[] options = new String[] { title,
+ MessageManager.getString("label.dont_save_changes"), };
+ final String question = JvSwingUtils.wrapTooltip(true, message);
+ int response = JvOptionPane.showOptionDialog(Desktop.desktop,
+ question, title, JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.PLAIN_MESSAGE, null, options, options[0]);
+
+ boolean saved = false;
+ if (response == 0)
+ {
+ /*
+ * prompt to save changes to file
+ */
+ saved = savebutton_actionPerformed();
+ }
+
+ /*
+ * if user chooses not to save (either in this dialog or in the
+ * save as dialogs), treat this as a new user defined colour scheme
+ */
+ if (!saved)
+ {
+ /*
+ * clear scheme name and re-apply as an anonymous scheme
+ */
+ schemeName.setText("");
+ applyButton_actionPerformed();
+ }
+ }
+ }
+
+ /**
+ * Returns true if the user has not made any colour selection (including if
+ * 'case-sensitive' selected and no lower-case colour chosen).
+ *
+ * @return
+ */
+ protected boolean isNoSelectionMade()
+ {
+ final boolean noUpperCaseSelected = upperCaseButtons == null
+ || upperCaseButtons.isEmpty();
+ final boolean noLowerCaseSelected = caseSensitive.isSelected()
+ && (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
+ final boolean noSelectionMade = noUpperCaseSelected
+ || noLowerCaseSelected;
+ return noSelectionMade;
+ }
+
+ /**
+ * Applies the current colour scheme to the alignment or sequence group
+ */
+ @Override
+ protected void applyButton_actionPerformed()
+ {
+ if (isNoSelectionMade())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+ UserColourScheme ucs = getSchemeFromButtons();
+
+ ap.alignFrame.changeColour(ucs);
+ }
+
+ /**
+ * Constructs an instance of UserColourScheme with the residue colours
+ * currently set on the buttons on the panel
+ *
+ * @return
+ */
+ UserColourScheme getSchemeFromButtons()
+ {
+
+ Color[] newColours = new Color[24];
+
+ int length = upperCaseButtons.size();
+ if (length < 24)
+ {
+ int i = 0;
+ for (JButton btn : upperCaseButtons)
+ {
+ newColours[i] = btn.getBackground();
+ i++;
+ }
+ }
+ else
+ {
+ for (int i = 0; i < 24; i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ newColours[i] = button.getBackground();
+ }
+ }
+
+ UserColourScheme ucs = new UserColourScheme(newColours);
+ ucs.setName(schemeName.getText());
+
+ if (caseSensitive.isSelected())
+ {
+ newColours = new Color[23];
+ length = lowerCaseButtons.size();
+ if (length < 23)
+ {
+ int i = 0;
+ for (JButton btn : lowerCaseButtons)
+ {
+ newColours[i] = btn.getBackground();
+ i++;
+ }
+ }
+ else
+ {
+ for (int i = 0; i < 23; i++)
+ {
+ JButton button = lowerCaseButtons.get(i);
+ newColours[i] = button.getBackground();
+ }
+ }
+ ucs.setLowerCaseColours(newColours);
+ }
+
+ return ucs;
+ }
+
+ /**
+ * Action on clicking Load scheme button.
+ * <ul>
+ * <li>Open a file chooser to browse for files with extension .jc</li>
+ * <li>Load in the colour scheme and transfer it to this panel's buttons</li>
+ * <li>Register the loaded colour scheme</li>
+ * </ul>
+ */
+ @Override
+ protected void loadbutton_actionPerformed()
+ {
+ upperCaseButtons = new ArrayList<>();
+ lowerCaseButtons = new ArrayList<>();
+ // TODO: JAL-3048 requires Castor dependency for Jalview-JS
+ JalviewFileChooser chooser = new JalviewFileChooser("jc",
+ "Jalview User Colours");
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(
+ MessageManager.getString("label.load_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.load"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value != JalviewFileChooser.APPROVE_OPTION)
+ {
+ return;
+ }
+ File choice = chooser.getSelectedFile();
+ Cache.setProperty(LAST_DIRECTORY, choice.getParent());
+
+ UserColourScheme ucs = ColourSchemeLoader
+ .loadColourScheme(choice.getAbsolutePath());
+ Color[] colors = ucs.getColours();
+ schemeName.setText(ucs.getSchemeName());
+
+ if (ucs.getLowerCaseColours() != null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
+ {
+ JButton button = lowerCaseButtons.get(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 = upperCaseButtons.get(i);
+ button.setBackground(colors[i]);
+ }
+
+ addNewColourScheme(choice.getPath());
+ }
+
+ /**
+ * Loads the user-defined colour scheme from the first file listed in property
+ * "USER_DEFINED_COLOURS". If this fails, returns an all-white colour scheme.
+ *
+ * @return
+ */
+ public static UserColourScheme loadDefaultColours()
+ {
+ UserColourScheme ret = null;
+
+ String colours = Cache.getProperty(USER_DEFINED_COLOURS);
+ if (colours != null)
+ {
+ if (colours.indexOf("|") > -1)
+ {
+ colours = colours.substring(0, colours.indexOf("|"));
+ }
+ ret = ColourSchemeLoader.loadColourScheme(colours);
+ }
+
+ if (ret == null)
+ {
+ ret = new UserColourScheme("white");
+ }
+
+ return ret;
+ }
+
+ /**
+ * Action on pressing the Save button.
+ * <ul>
+ * <li>Check a name has been entered</li>
+ * <li>Warn if the name already exists, remove any existing scheme of the same
+ * name if overwriting</li>
+ * <li>Do the standard file chooser thing to write with extension .jc</li>
+ * <li>If saving changes (possibly not yet applied) to the currently selected
+ * colour scheme, then apply the changes, as it is too late to back out
+ * now</li>
+ * <li>Don't apply the changes if the currently selected scheme is different,
+ * to allow a new scheme to be configured and saved but not applied</li>
+ * </ul>
+ * Returns true if the scheme is saved to file, false if it is not
+ *
+ * @return
+ */
+ @Override
+ protected boolean savebutton_actionPerformed()
+ {
+ String name = schemeName.getText().trim();
+ if (name.length() < 1)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.user_colour_scheme_must_have_name"),
+ MessageManager.getString("label.no_name_colour_scheme"),
+ JvOptionPane.WARNING_MESSAGE);
+ return false;
+ }
+
+ if (ColourSchemes.getInstance().nameExists(name))
+ {
+ int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.colour_scheme_exists_overwrite", new Object[]
+ { name, name }),
+ MessageManager.getString("label.duplicate_scheme_name"),
+ JvOptionPane.YES_NO_OPTION);
+ if (reply != JvOptionPane.YES_OPTION)
+ {
+ return false;
+ }
+ }
+ // TODO: JAL-3048 saveas, also requires Castor dependency for Jalview-JS
+
+ JalviewFileChooser chooser = new JalviewFileChooser("jc",
+ "Jalview User Colours");
+
+ JalviewFileView fileView = new JalviewFileView();
+ chooser.setFileView(fileView);
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value != JalviewFileChooser.APPROVE_OPTION)
+ {
+ return false;
+ }
+
+ File file = chooser.getSelectedFile();
+ UserColourScheme updatedScheme = addNewColourScheme(file.getPath());
+ saveToFile(file);
+ changed = false;
+
+ /*
+ * changes saved - apply to alignment if we are changing
+ * the currently selected colour scheme; also make the updated
+ * colours the 'backout' scheme on Cancel
+ */
+ if (oldColourScheme != null
+ && name.equals(oldColourScheme.getSchemeName()))
+ {
+ oldColourScheme = updatedScheme;
+ applyButton_actionPerformed();
+ }
+ return true;
+ }
+
+ /**
+ * Adds the current colour scheme to the Jalview properties file so it is
+ * loaded on next startup, and updates the Colour menu in the parent
+ * AlignFrame (if there is one). Note this action does not including applying
+ * the colour scheme.
+ *
+ * @param filePath
+ * @return
+ */
+ protected UserColourScheme addNewColourScheme(String filePath)
+ {
+ /*
+ * update the delimited list of user defined colour files in
+ * Jalview property USER_DEFINED_COLOURS
+ */
+ String defaultColours = Cache.getDefault(USER_DEFINED_COLOURS,
+ filePath);
+ if (defaultColours.indexOf(filePath) == -1)
+ {
+ if (defaultColours.length() > 0)
+ {
+ defaultColours = defaultColours.concat("|");
+ }
+ defaultColours = defaultColours.concat(filePath);
+ }
+ Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
+
+ /*
+ * construct and register the colour scheme
+ */
+ UserColourScheme ucs = getSchemeFromButtons();
+ ColourSchemes.getInstance().registerColourScheme(ucs);
+
+ /*
+ * update the Colour menu items
+ */
+ if (ap != null)
+ {
+ ap.alignFrame.buildColourMenu();
+ }
+
+ return ucs;
+ }
+
+ /**
+ * Saves the colour scheme to file in XML format
+ *
+ * @param path
+ */
+ protected void saveToFile(File toFile)
+ {
+ /*
+ * build a Java model of colour scheme as XML, and
+ * marshal to file
+ */
+ JalviewUserColours ucs = new JalviewUserColours();
+ String name = schemeName.getText();
+ ucs.setSchemeName(name);
+ try
+ {
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(toFile), "UTF-8"));
+
+ for (int i = 0; i < buttonPanel.getComponentCount(); i++)
+ {
+ JButton button = (JButton) buttonPanel.getComponent(i);
+ Colour col = new Colour();
+ col.setName(button.getText());
+ col.setRGB(Format.getHexString(button.getBackground()));
+ ucs.addColour(col);
+ }
+ ucs.marshal(out);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * On cancel, restores the colour scheme that was selected before the dialogue
+ * was opened
+ */
+ @Override
+ protected void cancelButton_actionPerformed()
+ {
+ ap.alignFrame.changeColour(oldColourScheme);
+ ap.paintAlignment(true, true);
+
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * Action on selecting or deselecting the Case Sensitive option. When
+ * selected, separate buttons are shown for lower case residues, and the panel
+ * is resized to accommodate them. Also, the checkbox for 'apply colour to all
+ * lower case' is enabled.
+ */
+ @Override
+ public void caseSensitive_actionPerformed()
+ {
+ boolean selected = caseSensitive.isSelected();
+ resetButtonPanel(selected);
+ lcaseColour.setEnabled(selected);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff