-package jalview.gui;\r
-\r
-import jalview.jbgui.GUserDefinedColours;\r
-import javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.event.*;\r
-import jalview.schemes.*;\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-\r
-public class UserDefinedColours extends GUserDefinedColours implements ChangeListener\r
-{\r
-\r
- AlignViewport av;\r
- ColourSchemeI colourScheme;\r
- JButton selectedButton;\r
- Vector oldColours = new Vector();\r
- JInternalFrame frame;\r
-\r
- public UserDefinedColours(JInternalFrame f, AlignViewport av)\r
- {\r
- super();\r
- colorChooser.getSelectionModel().addChangeListener(this);\r
- this.av = av;\r
- frame = f;\r
- colourScheme = av.getGlobalColourScheme();\r
-\r
- for(int i=0; i<20; i++)\r
- makeButton(ResidueProperties.aa2Triplet.get( ResidueProperties.aa[i] )+"", ResidueProperties.aa[i]);\r
-\r
- makeButton("B","B");\r
- makeButton("Z","Z");\r
- makeButton("X","X");\r
- makeButton("'.','-',' '", "-");\r
-\r
- }\r
-\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- if(selectedButton!=null)\r
- selectedButton.setBackground( colorChooser.getColor() );\r
- }\r
-\r
- public void colourButtonPressed(MouseEvent e)\r
- {\r
- selectedButton = (JButton)e.getSource();\r
- colorChooser.setColor(selectedButton.getBackground());\r
- }\r
-\r
- void makeButton(String label, String aa)\r
- {\r
- final JButton button = new JButton();\r
- button.setBackground( colourScheme.findColour(null,aa,-1,null) );\r
- oldColours.addElement( colourScheme.findColour(null,aa,-1,null) );\r
- button.setText( label );\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);\r
- }\r
-\r
-\r
- protected void okButton_actionPerformed(ActionEvent e)\r
- {\r
- applyButton_actionPerformed(null);\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\r
- }\r
-\r
- protected void applyButton_actionPerformed(ActionEvent e)\r
- {\r
- UserColourScheme ucs = new UserColourScheme();\r
- Color [] newColours = new Color[24];\r
- for(int i=0; i<24; i++)\r
- {\r
- JButton button = (JButton)buttonPanel.getComponent(i);\r
- newColours[i] = button.getBackground();\r
- }\r
-\r
- ucs.setThreshold(0);\r
- ucs.setColourScheme( newColours );\r
- av.setGlobalColourScheme( ucs );\r
- }\r
-\r
- protected void loadbutton_actionPerformed(ActionEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
- chooser.setDialogTitle("Load colour scheme");\r
- chooser.setToolTipText("Load");\r
- int value = chooser.showOpenDialog(this);\r
- if (value == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.LAST_DIRECTORY = choice;\r
-\r
- try{\r
- BufferedReader in = new BufferedReader(new FileReader(choice));\r
- for(int i=0; i<24; i++)\r
- {\r
- JButton button = (JButton)buttonPanel.getComponent(i);\r
- Color c = new Color(Integer.parseInt(in.readLine()));\r
- button.setBackground(c);\r
- }\r
-\r
- }\r
- catch(Exception ex)\r
- {}\r
- }\r
-\r
- }\r
-\r
- protected void savebutton_actionPerformed(ActionEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
- chooser.setDialogTitle("Save colour scheme");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(this);\r
- if (value == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.LAST_DIRECTORY = choice;\r
-\r
- try{\r
- PrintWriter out = new PrintWriter(new FileWriter(choice));\r
- for(int i=0; i<24; i++)\r
- {\r
- JButton button = (JButton)buttonPanel.getComponent(i);\r
- out.println(button.getBackground().getRGB() + "");\r
- }\r
-\r
- out.close();\r
- }\r
- catch(Exception ex)\r
- {ex.printStackTrace();}\r
- }\r
-\r
- }\r
-\r
- protected void cancelButton_actionPerformed(ActionEvent e)\r
- {\r
- UserColourScheme ucs = new UserColourScheme();\r
- Color [] newColours = new Color[24];\r
- for(int i=0; i<24; i++)\r
- {\r
- newColours[i] = (Color)oldColours.elementAt(i);\r
- buttonPanel.getComponent(i).setBackground(newColours[i]);\r
- }\r
-\r
- ucs.setColourScheme( newColours );\r
- av.setGlobalColourScheme( ucs );\r
-\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.api.structures.JalviewStructureDisplayI;
+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.ColorUtils;
+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.ArrayList;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+
+import javax.swing.JButton;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+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 int MY_FRAME_HEIGHT = 420;
+
+ private static final int MY_FRAME_WIDTH = 810;
+
+ private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
+
+ AlignmentPanel ap;
+
+ SequenceGroup seqGroup;
+
+ ArrayList<JButton> selectedButtons;
+
+ ColourSchemeI oldColourScheme;
+
+ JInternalFrame frame;
+
+ JalviewStructureDisplayI jmol;
+
+ ArrayList<JButton> upperCaseButtons;
+
+ ArrayList<JButton> 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(JalviewStructureDisplayI 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,
+ MessageManager.getString("label.user_defined_colours"),
+ MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
+
+ if (seqGroup != null)
+ {
+ frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
+ }
+ }
+
+ void resetButtonPanel(boolean caseSensitive)
+ {
+ buttonPanel.removeAll();
+
+ if (upperCaseButtons == null)
+ {
+ upperCaseButtons = new ArrayList<JButton>();
+ }
+
+ 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 ArrayList<JButton>();
+ }
+
+ 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));
+ }
+
+ // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
+ // codes
+ if (this.frame != null)
+ {
+ int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+ : MY_FRAME_WIDTH;
+ this.frame.setSize(newWidth, this.frame.getHeight());
+ }
+
+ buttonPanel.validate();
+ validate();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ if (selectedButtons != null)
+ {
+ JButton button = null;
+ final Color newColour = colorChooser.getColor();
+ for (int i = 0; i < selectedButtons.size(); i++)
+ {
+ button = selectedButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(newColour));
+ }
+ if (button == lcaseColour)
+ {
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
+ {
+ button = lowerCaseButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(button
+ .getBackground()));
+ }
+ }
+ }
+ }
+
+ /**
+ * 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)
+ {
+ if (selectedButtons == null)
+ {
+ selectedButtons = new ArrayList<JButton>();
+ }
+
+ 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());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param label
+ * DOCUMENT ME!
+ * @param aa
+ * DOCUMENT ME!
+ */
+ JButton makeButton(String label, String aa,
+ ArrayList<JButton> caseSensitiveButtons, int buttonIndex)
+ {
+ final JButton button;
+ Color col;
+
+ if (buttonIndex < caseSensitiveButtons.size())
+ {
+ button = caseSensitiveButtons.get(buttonIndex);
+ col = button.getBackground();
+ }
+ else
+ {
+ button = new JButton();
+ button.addMouseListener(new java.awt.event.MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ colourButtonPressed(e);
+ }
+ });
+
+ caseSensitiveButtons.add(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.setOpaque(true); // required for the next line to have effect
+ button.setBackground(col);
+ button.setText(label);
+ button.setForeground(ColorUtils.darkerThan(col));
+ button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
+
+ return button;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void okButton_actionPerformed(ActionEvent e)
+ {
+ if (isNoSelectionMade())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ applyButton_actionPerformed(null);
+
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void applyButton_actionPerformed(ActionEvent e)
+ {
+ if (isNoSelectionMade())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JOptionPane.WARNING_MESSAGE);
+
+ }
+ 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];
+
+ 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);
+
+ 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);
+ }
+
+ if (ap != null)
+ {
+ ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ }
+
+ return ucs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void loadbutton_actionPerformed(ActionEvent e)
+ {
+ upperCaseButtons = new ArrayList<JButton>();
+ lowerCaseButtons = new ArrayList<JButton>();
+
+ 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(MessageManager
+ .getString("label.load_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.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 = 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]);
+ }
+
+ }
+ }
+
+ /**
+ * 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 = 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 = 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!
+ */
+ @Override
+ 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 Object[] {
+ 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(MessageManager
+ .getString("label.save_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.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!
+ */
+ @Override
+ 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");
+ }
+
+ }
+
+ @Override
+ public void caseSensitive_actionPerformed(ActionEvent e)
+ {
+ resetButtonPanel(caseSensitive.isSelected());
+ lcaseColour.setEnabled(caseSensitive.isSelected());
+ }
+
+ @Override
+ public void lcaseColour_actionPerformed(ActionEvent e)
+ {
+ if (selectedButtons == null)
+ {
+ selectedButtons = new ArrayList<JButton>();
+ }
+ else
+ {
+ selectedButtons.clear();
+ }
+ selectedButtons.add(lcaseColour);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff