2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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21 import jalview.datamodel.*;
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23 import jalview.io.*;
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25 import jalview.jbgui.*;
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27 import jalview.schemes.*;
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30 import java.awt.event.*;
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36 import javax.swing.*;
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37 import javax.swing.event.*;
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45 * @version $Revision$
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47 public class UserDefinedColours extends GUserDefinedColours
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48 implements ChangeListener
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51 SequenceGroup seqGroup;
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52 Vector selectedButtons;
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53 ColourSchemeI oldColourScheme;
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54 JInternalFrame frame;
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55 MCview.PDBCanvas pdbcanvas;
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56 Vector upperCaseButtons;
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57 Vector lowerCaseButtons;
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61 * Creates a new UserDefinedColours object.
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63 * @param ap DOCUMENT ME!
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64 * @param sg DOCUMENT ME!
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66 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
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69 lcaseColour.setEnabled(false);
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74 if (seqGroup != null)
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75 oldColourScheme = seqGroup.cs;
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77 oldColourScheme = ap.av.getGlobalColourScheme();
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79 if (oldColourScheme instanceof UserColourScheme)
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81 schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
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82 if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)
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84 caseSensitive.setSelected(true);
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85 lcaseColour.setEnabled(true);
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86 resetButtonPanel(true);
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89 resetButtonPanel(false);
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92 resetButtonPanel(false);
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97 public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
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102 colorChooser.getSelectionModel().addChangeListener(this);
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104 oldColourScheme = oldcs;
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106 if (oldColourScheme instanceof UserColourScheme)
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108 schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
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111 resetButtonPanel(false);
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119 colorChooser.getSelectionModel().addChangeListener(this);
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120 frame = new JInternalFrame();
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121 frame.setContentPane(this);
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122 Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
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124 if (seqGroup != null)
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125 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
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127 if (System.getProperty("os.name").startsWith("Mac"))
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129 frame.setSize(760, 370);
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133 void resetButtonPanel(boolean caseSensitive)
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135 buttonPanel.removeAll();
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138 if(upperCaseButtons==null)
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139 upperCaseButtons = new Vector();
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143 for (int i = 0; i < 20; i++)
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146 label = ResidueProperties.aa[i];
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148 label = ResidueProperties.aa2Triplet.get
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149 (ResidueProperties.aa[i]).toString();
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151 button = makeButton(label,
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152 ResidueProperties.aa[i],
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153 upperCaseButtons, i);
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155 buttonPanel.add(button);
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158 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
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159 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
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160 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
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161 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
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165 gridLayout.setRows(6);
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166 gridLayout.setColumns(4);
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170 gridLayout.setRows(7);
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172 gridLayout.setColumns(cols+1);
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174 if(lowerCaseButtons==null)
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175 lowerCaseButtons = new Vector();
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178 for (int i = 0; i < 20; i++)
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180 int row = i / cols + 1;
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181 int index = (row * cols) + i;
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182 button = makeButton(
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183 ResidueProperties.aa[i].toLowerCase(),
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184 ResidueProperties.aa[i].toLowerCase(),
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188 buttonPanel.add(button, index);
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195 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
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196 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
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197 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
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200 buttonPanel.validate();
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208 * @param evt DOCUMENT ME!
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210 public void stateChanged(ChangeEvent evt)
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212 if (selectedButtons != null)
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214 JButton button=null;
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215 for(int i=0; i<selectedButtons.size(); i++)
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217 button = (JButton)selectedButtons.elementAt(i);
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218 button.setBackground(colorChooser.getColor());
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219 button.setForeground( button.getBackground().brighter().brighter().brighter());
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221 if(button==lcaseColour)
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223 for(int i=0; i<lowerCaseButtons.size(); i++)
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225 button = (JButton)lowerCaseButtons.elementAt(i);
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226 button.setBackground(colorChooser.getColor());
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227 button.setForeground( button.getBackground().brighter().brighter().brighter());
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236 * @param e DOCUMENT ME!
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238 public void colourButtonPressed(MouseEvent e)
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240 if(selectedButtons == null)
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241 selectedButtons = new Vector();
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243 JButton pressed = (JButton) e.getSource();
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245 if(e.isShiftDown())
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247 JButton start, end = (JButton) e.getSource();
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248 if(selectedButtons.size()>0)
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249 start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
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251 start = (JButton) e.getSource();
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253 int startIndex=0, endIndex=0;
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254 for(int b=0; b<buttonPanel.getComponentCount(); b++)
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256 if(buttonPanel.getComponent(b)==start)
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258 if(buttonPanel.getComponent(b)==end)
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262 if(startIndex > endIndex)
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264 int temp = startIndex;
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265 startIndex = endIndex;
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269 for(int b=startIndex; b<=endIndex; b++)
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271 JButton button = (JButton)buttonPanel.getComponent(b);
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272 if(!selectedButtons.contains(button))
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274 button.setForeground(button.getBackground().brighter().brighter());
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275 selectedButtons.add(button);
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279 else if(!e.isControlDown())
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281 for(int b=0; b<selectedButtons.size(); b++)
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283 JButton button = (JButton)selectedButtons.elementAt(b);
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284 button.setForeground(button.getBackground().darker().darker());
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286 selectedButtons.clear();
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287 pressed.setForeground( pressed.getBackground().brighter().brighter());
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288 selectedButtons.addElement(pressed);
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291 else if(e.isControlDown())
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293 if(selectedButtons.contains(pressed))
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295 pressed.setForeground(pressed.getBackground().darker().darker());
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296 selectedButtons.remove(pressed);
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300 pressed.setForeground( pressed.getBackground().brighter().brighter());
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301 selectedButtons.addElement(pressed);
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305 if(selectedButtons.size()>0)
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306 colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());
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312 * @param label DOCUMENT ME!
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313 * @param aa DOCUMENT ME!
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315 JButton makeButton(String label,
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317 Vector caseSensitiveButtons,
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320 final JButton button;
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323 if(buttonIndex<caseSensitiveButtons.size())
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325 button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
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326 col = button.getBackground();
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330 button = new JButton();
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331 button.addMouseListener(new java.awt.event.MouseAdapter()
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333 public void mouseClicked(MouseEvent e)
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335 colourButtonPressed(e);
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339 caseSensitiveButtons.addElement(button);
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345 col = oldColourScheme.findColour(aa, -1);
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347 catch (Exception ex)
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351 if(caseSensitive.isSelected())
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352 button.setMargin(new java.awt.Insets(2,2,2,2));
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354 button.setMargin(new java.awt.Insets(2,14,2,14));
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356 button.setBackground(col);
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357 button.setText(label);
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358 button.setForeground(col.darker().darker().darker());
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359 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
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367 * @param e DOCUMENT ME!
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369 protected void okButton_actionPerformed(ActionEvent e)
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371 applyButton_actionPerformed(null);
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375 frame.setClosed(true);
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377 catch (Exception ex)
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385 * @param e DOCUMENT ME!
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387 protected void applyButton_actionPerformed(ActionEvent e)
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389 UserColourScheme ucs = getSchemeFromButtons();
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390 ucs.setName(schemeName.getText());
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392 if (seqGroup != null)
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399 ap.alignFrame.changeColour(ucs);
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401 else if(pdbcanvas!=null)
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403 pdbcanvas.pdb.setColours(ucs);
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404 pdbcanvas.updateSeqColours();
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408 UserColourScheme getSchemeFromButtons()
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411 Color[] newColours = new Color[24];
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413 for (int i = 0; i < 24; i++)
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415 JButton button = (JButton) upperCaseButtons.elementAt(i);
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416 newColours[i] = button.getBackground();
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419 UserColourScheme ucs = new UserColourScheme(newColours);
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422 if(caseSensitive.isSelected())
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424 newColours = new Color[23];
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425 for (int i = 0; i < 23; i++)
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427 JButton button = (JButton) lowerCaseButtons.elementAt(i);
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428 newColours[i] = button.getBackground();
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430 ucs.setLowerCaseColours(newColours);
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434 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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445 * @param e DOCUMENT ME!
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447 protected void loadbutton_actionPerformed(ActionEvent e)
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449 upperCaseButtons = new Vector();
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450 lowerCaseButtons = new Vector();
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452 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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453 "LAST_DIRECTORY"), new String[] { "jc" },
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454 new String[] { "Jalview User Colours" }, "Jalview User Colours");
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455 chooser.setFileView(new jalview.io.JalviewFileView());
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456 chooser.setDialogTitle("Load colour scheme");
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457 chooser.setToolTipText("Load");
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459 int value = chooser.showOpenDialog(this);
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461 if (value == JalviewFileChooser.APPROVE_OPTION)
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463 File choice = chooser.getSelectedFile();
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464 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
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465 String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",
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467 if (defaultColours.indexOf(choice.getPath()) == -1)
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468 defaultColours = defaultColours.concat("|").concat(choice.getPath());
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470 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
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473 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
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474 Color[] colors = ucs.getColours();
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475 schemeName.setText(ucs.getName());
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477 if(ucs.getLowerCaseColours()!=null)
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479 caseSensitive.setSelected(true);
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480 lcaseColour.setEnabled(true);
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481 resetButtonPanel(true);
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482 for (int i = 0; i < lowerCaseButtons.size(); i++)
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484 JButton button = (JButton) lowerCaseButtons.elementAt(i);
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485 button.setBackground(ucs.getLowerCaseColours()[i]);
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491 caseSensitive.setSelected(false);
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492 lcaseColour.setEnabled(false);
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493 resetButtonPanel(false);
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496 for (int i = 0; i < upperCaseButtons.size(); i++)
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498 JButton button = (JButton) upperCaseButtons.elementAt(i);
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499 button.setBackground(colors[i]);
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508 * @return DOCUMENT ME!
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510 public static UserColourScheme loadDefaultColours()
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512 UserColourScheme ret = null;
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514 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
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515 if ( colours != null )
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517 if(colours.indexOf("|")>-1)
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518 colours = colours.substring(0, colours.indexOf("|"));
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520 ret = loadColours(colours);
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525 Color[] newColours = new Color[24];
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526 for (int i = 0; i < 24; i++)
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528 newColours[i] = Color.white;
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530 ret = new UserColourScheme(newColours);
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539 * @param file DOCUMENT ME!
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541 * @return DOCUMENT ME!
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543 static UserColourScheme loadColours(String file)
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545 UserColourScheme ucs = null;
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546 Color[] newColours = null;
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549 InputStreamReader in = new InputStreamReader(new FileInputStream(
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552 jalview.schemabinding.version2.JalviewUserColours jucs
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553 = new jalview.schemabinding.version2.JalviewUserColours();
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555 org.exolab.castor.xml.Unmarshaller unmar
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556 = new org.exolab.castor.xml.Unmarshaller(jucs);
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557 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );
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559 newColours = new Color[24];
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561 Color [] lowerCase = null;
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562 boolean caseSensitive = false;
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567 for (int i = 0; i < jucs.getColourCount(); i++)
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569 name = jucs.getColour(i).getName();
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570 if(ResidueProperties.aa3Hash.containsKey(name))
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572 index = ((Integer)ResidueProperties.aa3Hash.get(name)).intValue();
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576 index = ((Integer)ResidueProperties.aaHash.get(name)).intValue();
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581 if(name.toLowerCase().equals(name))
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583 if(lowerCase==null)
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584 lowerCase = new Color[23];
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585 caseSensitive = true;
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586 lowerCase[index] = new Color(Integer.parseInt(
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587 jucs.getColour(i).getRGB(), 16));
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591 newColours[index] = new Color(Integer.parseInt(
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592 jucs.getColour(i).getRGB(), 16));
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596 if (newColours != null)
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598 ucs = new UserColourScheme(newColours);
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599 ucs.setName( jucs.getSchemeName() );
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602 ucs.setLowerCaseColours(lowerCase);
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607 catch (Exception ex)
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609 //Could be Archive Jalview format
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611 InputStreamReader in = new InputStreamReader(new FileInputStream(
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614 jalview.binding.JalviewUserColours jucs
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615 = new jalview.binding.JalviewUserColours();
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617 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
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619 newColours = new Color[jucs.getColourCount()];
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621 for (int i = 0; i < 24; i++)
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623 newColours[i] = new Color(Integer.parseInt(
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624 jucs.getColour(i).getRGB(), 16));
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626 if (newColours != null)
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628 ucs = new UserColourScheme(newColours);
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629 ucs.setName(jucs.getSchemeName());
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631 }catch(Exception ex2)
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632 { ex2.printStackTrace(); }
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634 if(newColours==null)
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635 System.out.println("Error loading User ColourFile\n"+ex);
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644 * @param e DOCUMENT ME!
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646 protected void savebutton_actionPerformed(ActionEvent e)
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648 if(schemeName.getText().trim().length()<1)
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650 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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651 "User colour scheme must have a name!",
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652 "No name for colour scheme",
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653 JOptionPane.WARNING_MESSAGE);
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657 if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )
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659 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."
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660 +"\nContinue saving colour scheme as "+schemeName.getText()+"?",
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661 "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
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662 if(reply != JOptionPane.YES_OPTION)
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665 userColourSchemes.remove(schemeName.getText());
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667 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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668 "LAST_DIRECTORY"), new String[] { "jc" },
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669 new String[] { "Jalview User Colours" }, "Jalview User Colours");
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671 chooser.setFileView(new jalview.io.JalviewFileView());
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672 chooser.setDialogTitle("Save colour scheme");
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673 chooser.setToolTipText("Save");
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675 int value = chooser.showSaveDialog(this);
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677 if (value == JalviewFileChooser.APPROVE_OPTION)
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679 String choice = chooser.getSelectedFile().getPath();
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680 String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);
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681 if(defaultColours.indexOf(choice)==-1)
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683 if(defaultColours.length()>0)
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684 defaultColours = defaultColours.concat("|");
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685 defaultColours = defaultColours.concat(choice);
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688 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
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690 ap.alignFrame.updateUserColourMenu();
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692 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
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694 jalview.schemabinding.version2.JalviewUserColours ucs
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695 = new jalview.schemabinding.version2.JalviewUserColours();
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697 ucs.setSchemeName(schemeName.getText());
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700 PrintWriter out = new PrintWriter(new OutputStreamWriter(
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701 new FileOutputStream(choice), "UTF-8"));
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703 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
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705 JButton button = (JButton) buttonPanel.getComponent(i);
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706 jalview.schemabinding.version2.Colour col
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707 = new jalview.schemabinding.version2.Colour();
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708 col.setName(button.getText());
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709 col.setRGB(jalview.util.Format.getHexString(
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710 button.getBackground()));
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711 ucs.addColour(col);
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717 catch (Exception ex)
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719 ex.printStackTrace();
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727 * @param e DOCUMENT ME!
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729 protected void cancelButton_actionPerformed(ActionEvent e)
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733 if (seqGroup != null)
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735 seqGroup.cs = oldColourScheme;
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737 else if (ap != null)
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739 ap.av.setGlobalColourScheme(oldColourScheme);
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744 if(pdbcanvas!=null)
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746 pdbcanvas.pdb.setColours(oldColourScheme);
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751 frame.setClosed(true);
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753 catch (Exception ex)
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759 static Hashtable userColourSchemes;
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761 public static Hashtable getUserColourSchemes()
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763 return userColourSchemes;
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766 public static void initUserColourSchemes(String files)
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768 userColourSchemes = new Hashtable();
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770 if(files==null || files.length()==0)
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774 // In case colours can't be loaded, we'll remove them
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775 // from the default list here.
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776 StringBuffer coloursFound = new StringBuffer();
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777 StringTokenizer st = new StringTokenizer(files, "|");
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778 while (st.hasMoreElements())
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780 String file = st.nextToken();
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783 UserColourScheme ucs = loadColours(file);
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786 if (coloursFound.length() > 0)
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787 coloursFound.append("|");
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788 coloursFound.append(file);
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789 userColourSchemes.put(ucs.getName(), ucs);
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792 catch (Exception ex)
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794 System.out.println("Error loading User ColourFile\n" + ex);
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797 if (!files.equals(coloursFound.toString()))
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799 if (coloursFound.toString().length() > 1)
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800 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
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801 coloursFound.toString());
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803 jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
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807 public static void removeColourFromDefaults(String target)
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809 // The only way to find colours by name is to load them in
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810 // In case colours can't be loaded, we'll remove them
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811 // from the default list here.
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813 userColourSchemes = new Hashtable();
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815 StringBuffer coloursFound = new StringBuffer();
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816 StringTokenizer st = new StringTokenizer(
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817 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
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819 while (st.hasMoreElements())
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821 String file = st.nextToken();
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824 UserColourScheme ucs = loadColours(file);
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825 if (ucs != null && !ucs.getName().equals(target))
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827 if (coloursFound.length() > 0)
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828 coloursFound.append("|");
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829 coloursFound.append(file);
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830 userColourSchemes.put(ucs.getName(), ucs);
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833 catch (Exception ex)
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835 System.out.println("Error loading User ColourFile\n" + ex);
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839 if (coloursFound.toString().length() > 1)
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840 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
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842 jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
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846 public void caseSensitive_actionPerformed(ActionEvent e)
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848 resetButtonPanel(caseSensitive.isSelected());
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849 lcaseColour.setEnabled(caseSensitive.isSelected());
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852 public void lcaseColour_actionPerformed(ActionEvent e)
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854 if(selectedButtons==null)
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855 selectedButtons = new Vector();
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857 selectedButtons.clear();
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858 selectedButtons.add(lcaseColour);
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