-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * 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/>.
- */
-package jalview.gui;
-
-import jalview.datamodel.SequenceGroup;
-import jalview.io.JalviewFileChooser;
-import jalview.jbgui.GUserDefinedColours;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.util.MessageManager;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.event.ActionEvent;
-import java.awt.event.MouseEvent;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class UserDefinedColours extends GUserDefinedColours implements
- ChangeListener
-{
- AlignmentPanel ap;
-
- SequenceGroup seqGroup;
-
- Vector selectedButtons;
-
- ColourSchemeI oldColourScheme;
-
- JInternalFrame frame;
-
- AppJmol jmol;
-
- 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(AppJmol jmol, ColourSchemeI oldcs)
- {
- super();
- this.jmol = jmol;
-
- 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 (new jalview.util.Platform().isAMac())
- {
- 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;
- if (oldColourScheme != null)
- {
- try
- {
- col = oldColourScheme.findColour(aa.charAt(0), -1, null);
- } 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.paintAlignment(true);
- }
- else if (ap != null)
- {
- ap.alignFrame.changeColour(ucs);
- }
- else if (jmol != null)
- {
- jmol.setJalviewColourScheme(ucs);
- }
- }
-
- 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 = ResidueProperties.aaIndex[name.charAt(0)];
- }
- 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,
- MessageManager.getString("label.user_colour_scheme_must_have_name"),
- MessageManager.getString("label.no_name_colour_scheme"), JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- if (userColourSchemes != null
- && userColourSchemes.containsKey(schemeName.getText()))
- {
- int reply = JOptionPane.showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager.formatMessage("label.colour_scheme_exists_overwrite", new String[]{schemeName.getText(),schemeName.getText()}),
- MessageManager.getString("label.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.paintAlignment(true);
- }
-
- if (jmol != null)
- {
- jmol.setJalviewColourScheme(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);
- }
-
-}
+/*\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
git://source.jalview.org / jalview.git / blobdiff