X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=001b2323d34be58ef353804711951da2efa357ab;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=a8afd43ba49fd21069d9347c66a951a7f3d34519;hpb=7f7fc2e5533f7b00c86465f964e37c55bcf12fd7;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index a8afd43..001b232 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -18,25 +18,18 @@ */ package jalview.gui; -import jalview.datamodel.*; - -import jalview.io.*; - -import jalview.jbgui.*; - -import jalview.schemes.*; - -import java.awt.*; -import java.awt.event.*; - import java.io.*; - import java.util.*; +import java.awt.*; +import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; - +import jalview.datamodel.*; +import jalview.io.*; +import jalview.jbgui.*; +import jalview.schemes.*; /** * DOCUMENT ME! @@ -44,819 +37,893 @@ import javax.swing.event.*; * @author $author$ * @version $Revision$ */ -public class UserDefinedColours extends GUserDefinedColours - implements ChangeListener +public class UserDefinedColours + extends GUserDefinedColours implements ChangeListener { - AlignmentPanel ap; - SequenceGroup seqGroup; - Vector selectedButtons; - ColourSchemeI oldColourScheme; - JInternalFrame frame; - MCview.PDBCanvas pdbcanvas; - Vector upperCaseButtons; - Vector lowerCaseButtons; - - - /** - * Creates a new UserDefinedColours object. - * - * @param ap DOCUMENT ME! - * @param sg DOCUMENT ME! - */ - public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg) - { - super(); + AlignmentPanel ap; + SequenceGroup seqGroup; + Vector selectedButtons; + ColourSchemeI oldColourScheme; + JInternalFrame frame; + MCview.PDBCanvas pdbcanvas; + Vector upperCaseButtons; + Vector lowerCaseButtons; + + /** + * Creates a new UserDefinedColours object. + * + * @param ap DOCUMENT ME! + * @param sg DOCUMENT ME! + */ + public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg) + { + super(); + + lcaseColour.setEnabled(false); + + this.ap = ap; + seqGroup = sg; + + if (seqGroup != null) + { + oldColourScheme = seqGroup.cs; + } + else + { + oldColourScheme = ap.av.getGlobalColourScheme(); + } - lcaseColour.setEnabled(false); + 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); + } - this.ap = ap; - seqGroup = sg; + showFrame(); + } - if (seqGroup != null) - oldColourScheme = seqGroup.cs; - else - oldColourScheme = ap.av.getGlobalColourScheme(); + public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs) + { + super(); + pdbcanvas = pdb; - 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); + colorChooser.getSelectionModel().addChangeListener(this); - showFrame(); - } + oldColourScheme = oldcs; - public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs) + if (oldColourScheme instanceof UserColourScheme) { - super(); - pdbcanvas = pdb; - - colorChooser.getSelectionModel().addChangeListener(this); + schemeName.setText( ( (UserColourScheme) oldColourScheme).getName()); + } - oldColourScheme = oldcs; + resetButtonPanel(false); - if (oldColourScheme instanceof UserColourScheme) - { - schemeName.setText( ( (UserColourScheme) oldColourScheme).getName()); - } + showFrame(); - 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() + ")"); } - void showFrame() + if (System.getProperty("os.name").startsWith("Mac")) { - colorChooser.getSelectionModel().addChangeListener(this); - frame = new JInternalFrame(); - frame.setContentPane(this); - Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true); + frame.setSize(760, 370); + } + } - if (seqGroup != null) - frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")"); + void resetButtonPanel(boolean caseSensitive) + { + buttonPanel.removeAll(); - if (System.getProperty("os.name").startsWith("Mac")) - { - frame.setSize(760, 370); - } + if (upperCaseButtons == null) + { + upperCaseButtons = new Vector(); } - void resetButtonPanel(boolean caseSensitive) + JButton button; + String label; + for (int i = 0; i < 20; i++) { - buttonPanel.removeAll(); - - - if(upperCaseButtons==null) - upperCaseButtons = new Vector(); - - JButton button; - String label; - for (int i = 0; i < 20; i++) + if (caseSensitive) { - 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); + label = ResidueProperties.aa[i]; } else { - gridLayout.setRows(7); - int cols = 7; - gridLayout.setColumns(cols+1); + label = ResidueProperties.aa2Triplet.get + (ResidueProperties.aa[i]).toString(); + } - if(lowerCaseButtons==null) - lowerCaseButtons = new Vector(); + button = makeButton(label, + ResidueProperties.aa[i], + upperCaseButtons, i); + buttonPanel.add(button); + } - 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); - } - } + 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(caseSensitive) + if (lowerCaseButtons == null) { - buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20)); - buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21)); - buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22)); + lowerCaseButtons = new Vector(); } - buttonPanel.validate(); - validate(); + 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)); + } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void stateChanged(ChangeEvent evt) + buttonPanel.validate(); + validate(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void stateChanged(ChangeEvent evt) + { + if (selectedButtons != null) { - 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++) { - JButton button=null; - for(int i=0; i 0) { - JButton start, end = (JButton) e.getSource(); - if(selectedButtons.size()>0) - start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1); - else - start = (JButton) e.getSource(); + start = (JButton) selectedButtons.elementAt(selectedButtons.size() - 1); + } + else + { + start = (JButton) e.getSource(); + } - int startIndex=0, endIndex=0; - for(int b=0; b endIndex) + if (buttonPanel.getComponent(b) == end) { - int temp = startIndex; - startIndex = endIndex; - endIndex = temp; + endIndex = b; } + } - 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); - } - } + if (startIndex > endIndex) + { + int temp = startIndex; + startIndex = endIndex; + endIndex = temp; } - else if(!e.isControlDown()) + + for (int b = startIndex; b <= endIndex; b++) { - for(int b=0; b0) - 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) + else if (e.isControlDown()) { - final JButton button; - Color col; + if (selectedButtons.contains(pressed)) + { + pressed.setForeground(pressed.getBackground().darker().darker()); + selectedButtons.remove(pressed); + } + else + { + pressed.setForeground(pressed.getBackground().brighter().brighter()); + selectedButtons.addElement(pressed); + } + } - if(buttonIndex 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) { - button = (JButton) caseSensitiveButtons.elementAt(buttonIndex); - col = button.getBackground(); + colourButtonPressed(e); } - else - { - button = new JButton(); - button.addMouseListener(new java.awt.event.MouseAdapter() - { - public void mouseClicked(MouseEvent e) - { - colourButtonPressed(e); - } - }); + }); - caseSensitiveButtons.addElement(button); + caseSensitiveButtons.addElement(button); - col = Color.white; + col = Color.white; - try - { - col = oldColourScheme.findColour(aa, -1); - } - catch (Exception ex) - { } - } + try + { + col = oldColourScheme.findColour(aa.charAt(0), -1); + } + catch (Exception ex) + {} + } - if(caseSensitive.isSelected()) - button.setMargin(new java.awt.Insets(2,2,2,2)); - else - button.setMargin(new java.awt.Insets(2,14,2,14)); + 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)); + button.setBackground(col); + button.setText(label); + button.setForeground(col.darker().darker().darker()); + button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10)); - return button; - } + return button; + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void okButton_actionPerformed(ActionEvent e) - { - applyButton_actionPerformed(null); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void okButton_actionPerformed(ActionEvent e) + { + applyButton_actionPerformed(null); - try - { - frame.setClosed(true); - } - catch (Exception ex) - { - } + try + { + frame.setClosed(true); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void applyButton_actionPerformed(ActionEvent e) + catch (Exception ex) { - UserColourScheme ucs = getSchemeFromButtons(); - ucs.setName(schemeName.getText()); - - if (seqGroup != null) - { - seqGroup.cs = ucs; - ap.repaint(); - } - else if(ap!=null) - { - ap.alignFrame.changeColour(ucs); - } - else if(pdbcanvas!=null) - { - pdbcanvas.pdb.setColours(ucs); - pdbcanvas.updateSeqColours(); - } } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void applyButton_actionPerformed(ActionEvent e) + { + UserColourScheme ucs = getSchemeFromButtons(); + ucs.setName(schemeName.getText()); + + if (seqGroup != null) + { + seqGroup.cs = ucs; + ap.repaint(); + } + else if (ap != null) + { + ap.alignFrame.changeColour(ucs); + } + else if (pdbcanvas != null) + { + pdbcanvas.pdb.setColours(ucs); + pdbcanvas.updateSeqColours(); + } + } + + UserColourScheme getSchemeFromButtons() + { - UserColourScheme getSchemeFromButtons() + Color[] newColours = new Color[24]; + + for (int i = 0; i < 24; i++) { + JButton button = (JButton) upperCaseButtons.elementAt(i); + newColours[i] = button.getBackground(); + } - Color[] newColours = new Color[24]; + UserColourScheme ucs = new UserColourScheme(newColours); - for (int i = 0; i < 24; i++) + if (caseSensitive.isSelected()) + { + newColours = new Color[23]; + for (int i = 0; i < 23; i++) { - JButton button = (JButton) upperCaseButtons.elementAt(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()); + } - UserColourScheme ucs = new UserColourScheme(newColours); + jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours); + UserColourScheme ucs = loadColours(choice.getAbsolutePath()); + Color[] colors = ucs.getColours(); + schemeName.setText(ucs.getName()); - if(caseSensitive.isSelected()) + if (ucs.getLowerCaseColours() != null) { - newColours = new Color[23]; - for (int i = 0; i < 23; i++) + caseSensitive.setSelected(true); + lcaseColour.setEnabled(true); + resetButtonPanel(true); + for (int i = 0; i < lowerCaseButtons.size(); i++) { JButton button = (JButton) lowerCaseButtons.elementAt(i); - newColours[i] = button.getBackground(); + button.setBackground(ucs.getLowerCaseColours()[i]); } - ucs.setLowerCaseColours(newColours); - } - if(ap!=null) - ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + } + 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]); + } - return ucs; } + } + + /** + * 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); + } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void loadbutton_actionPerformed(ActionEvent e) + if (ret == null) { - upperCaseButtons = new Vector(); - lowerCaseButtons = new Vector(); + Color[] newColours = new Color[24]; + for (int i = 0; i < 24; i++) + { + newColours[i] = Color.white; + } + ret = new UserColourScheme(newColours); + } - 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"); + 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"); - int value = chooser.showOpenDialog(this); + jalview.schemabinding.version2.JalviewUserColours jucs + = new jalview.schemabinding.version2.JalviewUserColours(); - 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]); - } + 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]; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static UserColourScheme loadDefaultColours() - { - UserColourScheme ret = null; + Color[] lowerCase = null; + boolean caseSensitive = false; - String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"); - if ( colours != null ) + String name; + int index; + for (int i = 0; i < jucs.getColourCount(); i++) + { + name = jucs.getColour(i).getName(); + if (ResidueProperties.aa3Hash.containsKey(name)) { - if(colours.indexOf("|")>-1) - colours = colours.substring(0, colours.indexOf("|")); - - ret = loadColours(colours); + index = ( (Integer) ResidueProperties.aa3Hash.get(name)).intValue(); + } + else + { + index = ResidueProperties.aaIndex[name.charAt(0)]; + } + if (index == -1) + { + continue; } - if(ret == null) + if (name.toLowerCase().equals(name)) { - Color[] newColours = new Color[24]; - for (int i = 0; i < 24; i++) + if (lowerCase == null) { - newColours[i] = Color.white; + lowerCase = new Color[23]; } - ret = new UserColourScheme(newColours); + 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)); + } + } - return ret; - } + if (newColours != null) + { + ucs = new UserColourScheme(newColours); + ucs.setName(jucs.getSchemeName()); + if (caseSensitive) + { + ucs.setLowerCaseColours(lowerCase); + } + } - /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - static UserColourScheme loadColours(String file) + } + catch (Exception ex) { - 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); - } - } + //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)); } - catch (Exception ex) + if (newColours != null) { - //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); + ucs = new UserColourScheme(newColours); + ucs.setName(jucs.getSchemeName()); } + } + catch (Exception ex2) + { + ex2.printStackTrace(); + } - return ucs; + if (newColours == null) + { + System.out.println("Error loading User ColourFile\n" + ex); + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void savebutton_actionPerformed(ActionEvent e) + return ucs; + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void savebutton_actionPerformed(ActionEvent e) + { + if (schemeName.getText().trim().length() < 1) { - if(schemeName.getText().trim().length()<1) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "User colour scheme must have a name!", - "No name for colour scheme", - JOptionPane.WARNING_MESSAGE); - return; - } + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "User colour scheme must have a name!", + "No name for colour scheme", + JOptionPane.WARNING_MESSAGE); + return; + } - if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) ) + if (userColourSchemes != null && + userColourSchemes.containsKey(schemeName.getText())) + { + int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + "Colour scheme " + schemeName.getText() + " exists." + + "\nContinue saving colour scheme as " + schemeName.getText() + "?", + "Duplicate scheme name", JOptionPane.YES_NO_OPTION); + if (reply != JOptionPane.YES_OPTION) { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists." - +"\nContinue saving colour scheme as "+schemeName.getText()+"?", - "Duplicate scheme name", JOptionPane.YES_NO_OPTION); - if(reply != JOptionPane.YES_OPTION) - return; - - userColourSchemes.remove(schemeName.getText()); + return; } - 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"); + 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"); - int value = chooser.showSaveDialog(this); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Save colour scheme"); + chooser.setToolTipText("Save"); - 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(); - } - } - } + int value = chooser.showSaveDialog(this); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void cancelButton_actionPerformed(ActionEvent e) + if (value == JalviewFileChooser.APPROVE_OPTION) { - if (ap != null) + String choice = chooser.getSelectedFile().getPath(); + String defaultColours = jalview.bin.Cache.getDefault( + "USER_DEFINED_COLOURS", choice); + if (defaultColours.indexOf(choice) == -1) { - if (seqGroup != null) + if (defaultColours.length() > 0) { - seqGroup.cs = oldColourScheme; + defaultColours = defaultColours.concat("|"); } - else if (ap != null) - { - ap.av.setGlobalColourScheme(oldColourScheme); - } - ap.repaint(); + defaultColours = defaultColours.concat(choice); } - if(pdbcanvas!=null) + 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 { - pdbcanvas.pdb.setColours(oldColourScheme); - } + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(choice), "UTF-8")); - try + for (int i = 0; i < buttonPanel.getComponentCount(); i++) { - frame.setClosed(true); + 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); } - catch (Exception ex) - { - } - } + ucs.marshal(out); + out.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void cancelButton_actionPerformed(ActionEvent e) + { + if (ap != null) + { + if (seqGroup != null) + { + seqGroup.cs = oldColourScheme; + } + else if (ap != null) + { + ap.av.setGlobalColourScheme(oldColourScheme); + } + ap.repaint(); + } - static Hashtable userColourSchemes; - - public static Hashtable getUserColourSchemes() + if (pdbcanvas != null) { - return userColourSchemes; + pdbcanvas.pdb.setColours(oldColourScheme); } - public static void initUserColourSchemes(String files) + try + { + frame.setClosed(true); + } + catch (Exception ex) { - userColourSchemes = new Hashtable(); + } + } - if(files==null || files.length()==0) - return; + 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()) + // 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 { - String file = st.nextToken(); - try + UserColourScheme ucs = loadColours(file); + if (ucs != null) { - UserColourScheme ucs = loadColours(file); - if (ucs != null) + if (coloursFound.length() > 0) { - if (coloursFound.length() > 0) - coloursFound.append("|"); - coloursFound.append(file); - userColourSchemes.put(ucs.getName(), ucs); + coloursFound.append("|"); } - } - catch (Exception ex) - { - System.out.println("Error loading User ColourFile\n" + ex); + coloursFound.append(file); + userColourSchemes.put(ucs.getName(), ucs); } } - if (!files.equals(coloursFound.toString())) + catch (Exception ex) { - if (coloursFound.toString().length() > 1) - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", - coloursFound.toString()); - else - jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS"); + System.out.println("Error loading User ColourFile\n" + ex); } } - - public static void removeColourFromDefaults(String target) + if (!files.equals(coloursFound.toString())) { - // 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. + if (coloursFound.toString().length() > 1) + { + jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", + coloursFound.toString()); + } + else + { + jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS"); + } + } + } - userColourSchemes = new Hashtable(); + 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. - StringBuffer coloursFound = new StringBuffer(); - StringTokenizer st = new StringTokenizer( - jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|"); + userColourSchemes = new Hashtable(); - while (st.hasMoreElements()) + StringBuffer coloursFound = new StringBuffer(); + StringTokenizer st = new StringTokenizer( + jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|"); + + while (st.hasMoreElements()) + { + String file = st.nextToken(); + try { - String file = st.nextToken(); - try + UserColourScheme ucs = loadColours(file); + if (ucs != null && !ucs.getName().equals(target)) { - UserColourScheme ucs = loadColours(file); - if (ucs != null && !ucs.getName().equals(target)) + if (coloursFound.length() > 0) { - if (coloursFound.length() > 0) - coloursFound.append("|"); - coloursFound.append(file); - userColourSchemes.put(ucs.getName(), ucs); + coloursFound.append("|"); } - } - catch (Exception ex) - { - System.out.println("Error loading User ColourFile\n" + ex); + coloursFound.append(file); + userColourSchemes.put(ucs.getName(), ucs); } } - - if (coloursFound.toString().length() > 1) - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString()); - else - jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS"); - + catch (Exception ex) + { + System.out.println("Error loading User ColourFile\n" + ex); + } } - public void caseSensitive_actionPerformed(ActionEvent e) + if (coloursFound.toString().length() > 1) { - resetButtonPanel(caseSensitive.isSelected()); - lcaseColour.setEnabled(caseSensitive.isSelected()); + jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", + coloursFound.toString()); } + else + { + jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS"); + } + + } - public void lcaseColour_actionPerformed(ActionEvent e) + public void caseSensitive_actionPerformed(ActionEvent e) + { + resetButtonPanel(caseSensitive.isSelected()); + lcaseColour.setEnabled(caseSensitive.isSelected()); + } + + public void lcaseColour_actionPerformed(ActionEvent e) + { + if (selectedButtons == null) { - if(selectedButtons==null) - selectedButtons = new Vector(); - else - selectedButtons.clear(); - selectedButtons.add(lcaseColour); + selectedButtons = new Vector(); + } + else + { + selectedButtons.clear(); } + selectedButtons.add(lcaseColour); + } }