2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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25 import java.awt.event.*;
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26 import javax.swing.*;
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27 import javax.swing.event.*;
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29 import jalview.datamodel.*;
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30 import jalview.io.*;
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31 import jalview.jbgui.*;
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32 import jalview.schemes.*;
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38 * @version $Revision$
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40 public class UserDefinedColours
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41 extends GUserDefinedColours implements ChangeListener
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44 SequenceGroup seqGroup;
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45 Vector selectedButtons;
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46 ColourSchemeI oldColourScheme;
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47 JInternalFrame frame;
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49 Vector upperCaseButtons;
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50 Vector lowerCaseButtons;
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53 * Creates a new UserDefinedColours object.
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55 * @param ap DOCUMENT ME!
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56 * @param sg DOCUMENT ME!
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58 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
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62 lcaseColour.setEnabled(false);
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67 if (seqGroup != null)
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69 oldColourScheme = seqGroup.cs;
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73 oldColourScheme = ap.av.getGlobalColourScheme();
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76 if (oldColourScheme instanceof UserColourScheme)
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78 schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
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79 if ( ( (UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
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81 caseSensitive.setSelected(true);
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82 lcaseColour.setEnabled(true);
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83 resetButtonPanel(true);
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87 resetButtonPanel(false);
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92 resetButtonPanel(false);
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98 public UserDefinedColours(AppJMol jmol, ColourSchemeI oldcs)
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103 colorChooser.getSelectionModel().addChangeListener(this);
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105 oldColourScheme = oldcs;
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107 if (oldColourScheme instanceof UserColourScheme)
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109 schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
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112 resetButtonPanel(false);
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120 colorChooser.getSelectionModel().addChangeListener(this);
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121 frame = new JInternalFrame();
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122 frame.setContentPane(this);
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123 Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
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125 if (seqGroup != null)
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127 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
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130 if (System.getProperty("os.name").startsWith("Mac"))
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132 frame.setSize(760, 370);
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136 void resetButtonPanel(boolean caseSensitive)
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138 buttonPanel.removeAll();
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140 if (upperCaseButtons == null)
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142 upperCaseButtons = new Vector();
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147 for (int i = 0; i < 20; i++)
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151 label = ResidueProperties.aa[i];
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155 label = ResidueProperties.aa2Triplet.get
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156 (ResidueProperties.aa[i]).toString();
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159 button = makeButton(label,
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160 ResidueProperties.aa[i],
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161 upperCaseButtons, i);
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163 buttonPanel.add(button);
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166 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
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167 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
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168 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
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169 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
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171 if (!caseSensitive)
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173 gridLayout.setRows(6);
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174 gridLayout.setColumns(4);
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178 gridLayout.setRows(7);
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180 gridLayout.setColumns(cols + 1);
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182 if (lowerCaseButtons == null)
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184 lowerCaseButtons = new Vector();
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187 for (int i = 0; i < 20; i++)
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189 int row = i / cols + 1;
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190 int index = (row * cols) + i;
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191 button = makeButton(
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192 ResidueProperties.aa[i].toLowerCase(),
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193 ResidueProperties.aa[i].toLowerCase(),
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197 buttonPanel.add(button, index);
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203 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
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204 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
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205 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
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208 buttonPanel.validate();
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215 * @param evt DOCUMENT ME!
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217 public void stateChanged(ChangeEvent evt)
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219 if (selectedButtons != null)
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221 JButton button = null;
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222 for (int i = 0; i < selectedButtons.size(); i++)
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224 button = (JButton) selectedButtons.elementAt(i);
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225 button.setBackground(colorChooser.getColor());
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226 button.setForeground(button.getBackground().brighter().brighter().
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229 if (button == lcaseColour)
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231 for (int i = 0; i < lowerCaseButtons.size(); i++)
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233 button = (JButton) lowerCaseButtons.elementAt(i);
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234 button.setBackground(colorChooser.getColor());
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235 button.setForeground(button.getBackground().brighter().brighter().
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245 * @param e DOCUMENT ME!
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247 public void colourButtonPressed(MouseEvent e)
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249 if (selectedButtons == null)
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251 selectedButtons = new Vector();
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254 JButton pressed = (JButton) e.getSource();
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256 if (e.isShiftDown())
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258 JButton start, end = (JButton) e.getSource();
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259 if (selectedButtons.size() > 0)
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261 start = (JButton) selectedButtons.elementAt(selectedButtons.size() - 1);
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265 start = (JButton) e.getSource();
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268 int startIndex = 0, endIndex = 0;
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269 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
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271 if (buttonPanel.getComponent(b) == start)
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275 if (buttonPanel.getComponent(b) == end)
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281 if (startIndex > endIndex)
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283 int temp = startIndex;
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284 startIndex = endIndex;
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288 for (int b = startIndex; b <= endIndex; b++)
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290 JButton button = (JButton) buttonPanel.getComponent(b);
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291 if (!selectedButtons.contains(button))
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293 button.setForeground(button.getBackground().brighter().brighter());
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294 selectedButtons.add(button);
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298 else if (!e.isControlDown())
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300 for (int b = 0; b < selectedButtons.size(); b++)
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302 JButton button = (JButton) selectedButtons.elementAt(b);
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303 button.setForeground(button.getBackground().darker().darker());
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305 selectedButtons.clear();
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306 pressed.setForeground(pressed.getBackground().brighter().brighter());
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307 selectedButtons.addElement(pressed);
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310 else if (e.isControlDown())
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312 if (selectedButtons.contains(pressed))
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314 pressed.setForeground(pressed.getBackground().darker().darker());
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315 selectedButtons.remove(pressed);
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319 pressed.setForeground(pressed.getBackground().brighter().brighter());
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320 selectedButtons.addElement(pressed);
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324 if (selectedButtons.size() > 0)
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326 colorChooser.setColor( ( (JButton) selectedButtons.elementAt(0)).
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334 * @param label DOCUMENT ME!
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335 * @param aa DOCUMENT ME!
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337 JButton makeButton(String label,
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339 Vector caseSensitiveButtons,
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342 final JButton button;
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345 if (buttonIndex < caseSensitiveButtons.size())
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347 button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
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348 col = button.getBackground();
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352 button = new JButton();
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353 button.addMouseListener(new java.awt.event.MouseAdapter()
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355 public void mouseClicked(MouseEvent e)
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357 colourButtonPressed(e);
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361 caseSensitiveButtons.addElement(button);
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367 col = oldColourScheme.findColour(aa.charAt(0), -1);
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369 catch (Exception ex)
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373 if (caseSensitive.isSelected())
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375 button.setMargin(new java.awt.Insets(2, 2, 2, 2));
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379 button.setMargin(new java.awt.Insets(2, 14, 2, 14));
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382 button.setBackground(col);
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383 button.setText(label);
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384 button.setForeground(col.darker().darker().darker());
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385 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
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393 * @param e DOCUMENT ME!
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395 protected void okButton_actionPerformed(ActionEvent e)
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397 applyButton_actionPerformed(null);
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401 frame.setClosed(true);
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403 catch (Exception ex)
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411 * @param e DOCUMENT ME!
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413 protected void applyButton_actionPerformed(ActionEvent e)
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415 UserColourScheme ucs = getSchemeFromButtons();
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416 ucs.setName(schemeName.getText());
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418 if (seqGroup != null)
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421 ap.paintAlignment(true);
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423 else if (ap != null)
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425 ap.alignFrame.changeColour(ucs);
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427 else if (jmol != null)
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429 jmol.setJalviewColourScheme(ucs);
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433 UserColourScheme getSchemeFromButtons()
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436 Color[] newColours = new Color[24];
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438 for (int i = 0; i < 24; i++)
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440 JButton button = (JButton) upperCaseButtons.elementAt(i);
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441 newColours[i] = button.getBackground();
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444 UserColourScheme ucs = new UserColourScheme(newColours);
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446 if (caseSensitive.isSelected())
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448 newColours = new Color[23];
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449 for (int i = 0; i < 23; i++)
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451 JButton button = (JButton) lowerCaseButtons.elementAt(i);
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452 newColours[i] = button.getBackground();
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454 ucs.setLowerCaseColours(newColours);
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459 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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468 * @param e DOCUMENT ME!
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470 protected void loadbutton_actionPerformed(ActionEvent e)
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472 upperCaseButtons = new Vector();
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473 lowerCaseButtons = new Vector();
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475 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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477 "LAST_DIRECTORY"), new String[]
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480 {"Jalview User Colours"}, "Jalview User Colours");
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481 chooser.setFileView(new jalview.io.JalviewFileView());
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482 chooser.setDialogTitle("Load colour scheme");
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483 chooser.setToolTipText("Load");
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485 int value = chooser.showOpenDialog(this);
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487 if (value == JalviewFileChooser.APPROVE_OPTION)
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489 File choice = chooser.getSelectedFile();
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490 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
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491 String defaultColours = jalview.bin.Cache.getDefault(
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492 "USER_DEFINED_COLOURS",
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494 if (defaultColours.indexOf(choice.getPath()) == -1)
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496 defaultColours = defaultColours.concat("|").concat(choice.getPath());
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499 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
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501 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
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502 Color[] colors = ucs.getColours();
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503 schemeName.setText(ucs.getName());
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505 if (ucs.getLowerCaseColours() != null)
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507 caseSensitive.setSelected(true);
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508 lcaseColour.setEnabled(true);
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509 resetButtonPanel(true);
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510 for (int i = 0; i < lowerCaseButtons.size(); i++)
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512 JButton button = (JButton) lowerCaseButtons.elementAt(i);
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513 button.setBackground(ucs.getLowerCaseColours()[i]);
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519 caseSensitive.setSelected(false);
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520 lcaseColour.setEnabled(false);
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521 resetButtonPanel(false);
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524 for (int i = 0; i < upperCaseButtons.size(); i++)
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526 JButton button = (JButton) upperCaseButtons.elementAt(i);
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527 button.setBackground(colors[i]);
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536 * @return DOCUMENT ME!
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538 public static UserColourScheme loadDefaultColours()
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540 UserColourScheme ret = null;
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542 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
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543 if (colours != null)
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545 if (colours.indexOf("|") > -1)
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547 colours = colours.substring(0, colours.indexOf("|"));
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550 ret = loadColours(colours);
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555 Color[] newColours = new Color[24];
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556 for (int i = 0; i < 24; i++)
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558 newColours[i] = Color.white;
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560 ret = new UserColourScheme(newColours);
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569 * @param file DOCUMENT ME!
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571 * @return DOCUMENT ME!
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573 static UserColourScheme loadColours(String file)
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575 UserColourScheme ucs = null;
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576 Color[] newColours = null;
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579 InputStreamReader in = new InputStreamReader(new FileInputStream(
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582 jalview.schemabinding.version2.JalviewUserColours jucs
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583 = new jalview.schemabinding.version2.JalviewUserColours();
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585 org.exolab.castor.xml.Unmarshaller unmar
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586 = new org.exolab.castor.xml.Unmarshaller(jucs);
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587 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.
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590 newColours = new Color[24];
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592 Color[] lowerCase = null;
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593 boolean caseSensitive = false;
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597 for (int i = 0; i < jucs.getColourCount(); i++)
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599 name = jucs.getColour(i).getName();
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600 if (ResidueProperties.aa3Hash.containsKey(name))
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602 index = ( (Integer) ResidueProperties.aa3Hash.get(name)).intValue();
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606 index = ResidueProperties.aaIndex[name.charAt(0)];
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613 if (name.toLowerCase().equals(name))
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615 if (lowerCase == null)
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617 lowerCase = new Color[23];
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619 caseSensitive = true;
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620 lowerCase[index] = new Color(Integer.parseInt(
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621 jucs.getColour(i).getRGB(), 16));
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625 newColours[index] = new Color(Integer.parseInt(
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626 jucs.getColour(i).getRGB(), 16));
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630 if (newColours != null)
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632 ucs = new UserColourScheme(newColours);
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633 ucs.setName(jucs.getSchemeName());
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636 ucs.setLowerCaseColours(lowerCase);
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641 catch (Exception ex)
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643 //Could be Archive Jalview format
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646 InputStreamReader in = new InputStreamReader(new FileInputStream(
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649 jalview.binding.JalviewUserColours jucs
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650 = new jalview.binding.JalviewUserColours();
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652 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
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654 newColours = new Color[jucs.getColourCount()];
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656 for (int i = 0; i < 24; i++)
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658 newColours[i] = new Color(Integer.parseInt(
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659 jucs.getColour(i).getRGB(), 16));
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661 if (newColours != null)
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663 ucs = new UserColourScheme(newColours);
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664 ucs.setName(jucs.getSchemeName());
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667 catch (Exception ex2)
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669 ex2.printStackTrace();
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672 if (newColours == null)
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674 System.out.println("Error loading User ColourFile\n" + ex);
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684 * @param e DOCUMENT ME!
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686 protected void savebutton_actionPerformed(ActionEvent e)
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688 if (schemeName.getText().trim().length() < 1)
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690 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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691 "User colour scheme must have a name!",
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692 "No name for colour scheme",
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693 JOptionPane.WARNING_MESSAGE);
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697 if (userColourSchemes != null &&
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698 userColourSchemes.containsKey(schemeName.getText()))
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700 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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701 "Colour scheme " + schemeName.getText() + " exists."
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702 + "\nContinue saving colour scheme as " + schemeName.getText() + "?",
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703 "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
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704 if (reply != JOptionPane.YES_OPTION)
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709 userColourSchemes.remove(schemeName.getText());
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711 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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713 "LAST_DIRECTORY"), new String[]
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716 {"Jalview User Colours"}, "Jalview User Colours");
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718 chooser.setFileView(new jalview.io.JalviewFileView());
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719 chooser.setDialogTitle("Save colour scheme");
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720 chooser.setToolTipText("Save");
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722 int value = chooser.showSaveDialog(this);
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724 if (value == JalviewFileChooser.APPROVE_OPTION)
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726 String choice = chooser.getSelectedFile().getPath();
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727 String defaultColours = jalview.bin.Cache.getDefault(
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728 "USER_DEFINED_COLOURS", choice);
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729 if (defaultColours.indexOf(choice) == -1)
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731 if (defaultColours.length() > 0)
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733 defaultColours = defaultColours.concat("|");
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735 defaultColours = defaultColours.concat(choice);
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738 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
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740 ap.alignFrame.updateUserColourMenu();
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742 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
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744 jalview.schemabinding.version2.JalviewUserColours ucs
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745 = new jalview.schemabinding.version2.JalviewUserColours();
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747 ucs.setSchemeName(schemeName.getText());
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750 PrintWriter out = new PrintWriter(new OutputStreamWriter(
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751 new FileOutputStream(choice), "UTF-8"));
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753 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
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755 JButton button = (JButton) buttonPanel.getComponent(i);
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756 jalview.schemabinding.version2.Colour col
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757 = new jalview.schemabinding.version2.Colour();
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758 col.setName(button.getText());
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759 col.setRGB(jalview.util.Format.getHexString(
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760 button.getBackground()));
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761 ucs.addColour(col);
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767 catch (Exception ex)
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769 ex.printStackTrace();
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777 * @param e DOCUMENT ME!
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779 protected void cancelButton_actionPerformed(ActionEvent e)
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783 if (seqGroup != null)
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785 seqGroup.cs = oldColourScheme;
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787 else if (ap != null)
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789 ap.av.setGlobalColourScheme(oldColourScheme);
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791 ap.paintAlignment(true);
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796 jmol.setJalviewColourScheme(oldColourScheme);
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801 frame.setClosed(true);
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803 catch (Exception ex)
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808 static Hashtable userColourSchemes;
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810 public static Hashtable getUserColourSchemes()
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812 return userColourSchemes;
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815 public static void initUserColourSchemes(String files)
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817 userColourSchemes = new Hashtable();
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819 if (files == null || files.length() == 0)
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824 // In case colours can't be loaded, we'll remove them
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825 // from the default list here.
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826 StringBuffer coloursFound = new StringBuffer();
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827 StringTokenizer st = new StringTokenizer(files, "|");
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828 while (st.hasMoreElements())
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830 String file = st.nextToken();
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833 UserColourScheme ucs = loadColours(file);
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836 if (coloursFound.length() > 0)
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838 coloursFound.append("|");
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840 coloursFound.append(file);
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841 userColourSchemes.put(ucs.getName(), ucs);
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844 catch (Exception ex)
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846 System.out.println("Error loading User ColourFile\n" + ex);
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849 if (!files.equals(coloursFound.toString()))
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851 if (coloursFound.toString().length() > 1)
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853 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
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854 coloursFound.toString());
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858 jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
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863 public static void removeColourFromDefaults(String target)
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865 // The only way to find colours by name is to load them in
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866 // In case colours can't be loaded, we'll remove them
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867 // from the default list here.
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869 userColourSchemes = new Hashtable();
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871 StringBuffer coloursFound = new StringBuffer();
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872 StringTokenizer st = new StringTokenizer(
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873 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
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875 while (st.hasMoreElements())
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877 String file = st.nextToken();
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880 UserColourScheme ucs = loadColours(file);
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881 if (ucs != null && !ucs.getName().equals(target))
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883 if (coloursFound.length() > 0)
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885 coloursFound.append("|");
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887 coloursFound.append(file);
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888 userColourSchemes.put(ucs.getName(), ucs);
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891 catch (Exception ex)
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893 System.out.println("Error loading User ColourFile\n" + ex);
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897 if (coloursFound.toString().length() > 1)
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899 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
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900 coloursFound.toString());
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904 jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
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909 public void caseSensitive_actionPerformed(ActionEvent e)
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911 resetButtonPanel(caseSensitive.isSelected());
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912 lcaseColour.setEnabled(caseSensitive.isSelected());
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915 public void lcaseColour_actionPerformed(ActionEvent e)
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917 if (selectedButtons == null)
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919 selectedButtons = new Vector();
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923 selectedButtons.clear();
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925 selectedButtons.add(lcaseColour);
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