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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70 lcaseColour.setEnabled(false);
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75 if (seqGroup != null)
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76 oldColourScheme = seqGroup.cs;
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78 oldColourScheme = ap.av.getGlobalColourScheme();
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80 if (oldColourScheme instanceof UserColourScheme)
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82 schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
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83 if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)
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85 caseSensitive.setSelected(true);
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86 lcaseColour.setEnabled(true);
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87 resetButtonPanel(true);
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90 resetButtonPanel(false);
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93 resetButtonPanel(false);
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98 public UserDefinedColours(MCview.PDBCanvas pdb, 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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126 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
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128 if (System.getProperty("os.name").startsWith("Mac"))
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130 frame.setSize(760, 370);
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134 void resetButtonPanel(boolean caseSensitive)
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136 buttonPanel.removeAll();
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139 if(upperCaseButtons==null)
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140 upperCaseButtons = new Vector();
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144 for (int i = 0; i < 20; i++)
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147 label = ResidueProperties.aa[i];
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149 label = ResidueProperties.aa2Triplet.get
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150 (ResidueProperties.aa[i]).toString();
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152 button = makeButton(label,
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153 ResidueProperties.aa[i],
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154 upperCaseButtons, i);
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156 buttonPanel.add(button);
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159 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
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160 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
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161 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
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162 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
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166 gridLayout.setRows(6);
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167 gridLayout.setColumns(4);
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171 gridLayout.setRows(7);
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173 gridLayout.setColumns(cols+1);
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175 if(lowerCaseButtons==null)
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176 lowerCaseButtons = new Vector();
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179 for (int i = 0; i < 20; i++)
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181 int row = i / cols + 1;
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182 int index = (row * cols) + i;
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183 button = makeButton(
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184 ResidueProperties.aa[i].toLowerCase(),
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185 ResidueProperties.aa[i].toLowerCase(),
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189 buttonPanel.add(button, index);
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196 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
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197 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
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198 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
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201 buttonPanel.validate();
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209 * @param evt DOCUMENT ME!
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211 public void stateChanged(ChangeEvent evt)
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213 if (selectedButtons != null)
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215 JButton button=null;
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216 for(int i=0; i<selectedButtons.size(); i++)
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218 button = (JButton)selectedButtons.elementAt(i);
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219 button.setBackground(colorChooser.getColor());
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220 button.setForeground( button.getBackground().brighter().brighter().brighter());
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222 if(button==lcaseColour)
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224 for(int i=0; i<lowerCaseButtons.size(); i++)
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226 button = (JButton)lowerCaseButtons.elementAt(i);
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227 button.setBackground(colorChooser.getColor());
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228 button.setForeground( button.getBackground().brighter().brighter().brighter());
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237 * @param e DOCUMENT ME!
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239 public void colourButtonPressed(MouseEvent e)
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241 if(selectedButtons == null)
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242 selectedButtons = new Vector();
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244 JButton pressed = (JButton) e.getSource();
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246 if(e.isShiftDown())
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248 JButton start, end = (JButton) e.getSource();
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249 if(selectedButtons.size()>0)
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250 start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
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252 start = (JButton) e.getSource();
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254 int startIndex=0, endIndex=0;
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255 for(int b=0; b<buttonPanel.getComponentCount(); b++)
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257 if(buttonPanel.getComponent(b)==start)
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259 if(buttonPanel.getComponent(b)==end)
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263 if(startIndex > endIndex)
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265 int temp = startIndex;
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266 startIndex = endIndex;
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270 for(int b=startIndex; b<=endIndex; b++)
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272 JButton button = (JButton)buttonPanel.getComponent(b);
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273 if(!selectedButtons.contains(button))
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275 button.setForeground(button.getBackground().brighter().brighter());
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276 selectedButtons.add(button);
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280 else if(!e.isControlDown())
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282 for(int b=0; b<selectedButtons.size(); b++)
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284 JButton button = (JButton)selectedButtons.elementAt(b);
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285 button.setForeground(button.getBackground().darker().darker());
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287 selectedButtons.clear();
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288 pressed.setForeground( pressed.getBackground().brighter().brighter());
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289 selectedButtons.addElement(pressed);
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292 else if(e.isControlDown())
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294 if(selectedButtons.contains(pressed))
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296 pressed.setForeground(pressed.getBackground().darker().darker());
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297 selectedButtons.remove(pressed);
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301 pressed.setForeground( pressed.getBackground().brighter().brighter());
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302 selectedButtons.addElement(pressed);
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306 if(selectedButtons.size()>0)
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307 colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());
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313 * @param label DOCUMENT ME!
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314 * @param aa DOCUMENT ME!
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316 JButton makeButton(String label,
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318 Vector caseSensitiveButtons,
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321 final JButton button;
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324 if(buttonIndex<caseSensitiveButtons.size())
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326 button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
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327 col = button.getBackground();
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331 button = new JButton();
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332 button.addMouseListener(new java.awt.event.MouseAdapter()
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334 public void mouseClicked(MouseEvent e)
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336 colourButtonPressed(e);
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340 caseSensitiveButtons.addElement(button);
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346 col = oldColourScheme.findColour(aa.charAt(0), -1);
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348 catch (Exception ex)
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352 if(caseSensitive.isSelected())
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353 button.setMargin(new java.awt.Insets(2,2,2,2));
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355 button.setMargin(new java.awt.Insets(2,14,2,14));
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357 button.setBackground(col);
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358 button.setText(label);
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359 button.setForeground(col.darker().darker().darker());
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360 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
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368 * @param e DOCUMENT ME!
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370 protected void okButton_actionPerformed(ActionEvent e)
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372 applyButton_actionPerformed(null);
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376 frame.setClosed(true);
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378 catch (Exception ex)
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386 * @param e DOCUMENT ME!
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388 protected void applyButton_actionPerformed(ActionEvent e)
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390 UserColourScheme ucs = getSchemeFromButtons();
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391 ucs.setName(schemeName.getText());
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393 if (seqGroup != null)
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400 ap.alignFrame.changeColour(ucs);
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402 else if(pdbcanvas!=null)
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404 pdbcanvas.pdb.setColours(ucs);
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405 pdbcanvas.updateSeqColours();
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409 UserColourScheme getSchemeFromButtons()
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412 Color[] newColours = new Color[24];
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414 for (int i = 0; i < 24; i++)
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416 JButton button = (JButton) upperCaseButtons.elementAt(i);
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417 newColours[i] = button.getBackground();
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420 UserColourScheme ucs = new UserColourScheme(newColours);
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423 if(caseSensitive.isSelected())
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425 newColours = new Color[23];
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426 for (int i = 0; i < 23; i++)
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428 JButton button = (JButton) lowerCaseButtons.elementAt(i);
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429 newColours[i] = button.getBackground();
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431 ucs.setLowerCaseColours(newColours);
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435 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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446 * @param e DOCUMENT ME!
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448 protected void loadbutton_actionPerformed(ActionEvent e)
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450 upperCaseButtons = new Vector();
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451 lowerCaseButtons = new Vector();
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453 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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454 "LAST_DIRECTORY"), new String[] { "jc" },
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455 new String[] { "Jalview User Colours" }, "Jalview User Colours");
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456 chooser.setFileView(new jalview.io.JalviewFileView());
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457 chooser.setDialogTitle("Load colour scheme");
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458 chooser.setToolTipText("Load");
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460 int value = chooser.showOpenDialog(this);
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462 if (value == JalviewFileChooser.APPROVE_OPTION)
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464 File choice = chooser.getSelectedFile();
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465 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
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466 String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",
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468 if (defaultColours.indexOf(choice.getPath()) == -1)
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469 defaultColours = defaultColours.concat("|").concat(choice.getPath());
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471 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
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474 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
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475 Color[] colors = ucs.getColours();
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476 schemeName.setText(ucs.getName());
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478 if(ucs.getLowerCaseColours()!=null)
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480 caseSensitive.setSelected(true);
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481 lcaseColour.setEnabled(true);
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482 resetButtonPanel(true);
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483 for (int i = 0; i < lowerCaseButtons.size(); i++)
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485 JButton button = (JButton) lowerCaseButtons.elementAt(i);
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486 button.setBackground(ucs.getLowerCaseColours()[i]);
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492 caseSensitive.setSelected(false);
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493 lcaseColour.setEnabled(false);
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494 resetButtonPanel(false);
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497 for (int i = 0; i < upperCaseButtons.size(); i++)
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499 JButton button = (JButton) upperCaseButtons.elementAt(i);
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500 button.setBackground(colors[i]);
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509 * @return DOCUMENT ME!
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511 public static UserColourScheme loadDefaultColours()
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513 UserColourScheme ret = null;
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515 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
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516 if ( colours != null )
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518 if(colours.indexOf("|")>-1)
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519 colours = colours.substring(0, colours.indexOf("|"));
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521 ret = loadColours(colours);
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526 Color[] newColours = new Color[24];
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527 for (int i = 0; i < 24; i++)
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529 newColours[i] = Color.white;
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531 ret = new UserColourScheme(newColours);
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540 * @param file DOCUMENT ME!
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542 * @return DOCUMENT ME!
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544 static UserColourScheme loadColours(String file)
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546 UserColourScheme ucs = null;
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547 Color[] newColours = null;
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550 InputStreamReader in = new InputStreamReader(new FileInputStream(
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553 jalview.schemabinding.version2.JalviewUserColours jucs
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554 = new jalview.schemabinding.version2.JalviewUserColours();
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556 org.exolab.castor.xml.Unmarshaller unmar
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557 = new org.exolab.castor.xml.Unmarshaller(jucs);
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558 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );
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560 newColours = new Color[24];
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562 Color [] lowerCase = null;
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563 boolean caseSensitive = false;
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568 for (int i = 0; i < jucs.getColourCount(); i++)
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570 name = jucs.getColour(i).getName();
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571 if(ResidueProperties.aa3Hash.containsKey(name))
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573 index = ((Integer)ResidueProperties.aa3Hash.get(name)).intValue();
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577 index = ResidueProperties.aaIndex[name.charAt(0)];
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582 if(name.toLowerCase().equals(name))
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584 if(lowerCase==null)
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585 lowerCase = new Color[23];
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586 caseSensitive = true;
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587 lowerCase[index] = new Color(Integer.parseInt(
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588 jucs.getColour(i).getRGB(), 16));
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592 newColours[index] = new Color(Integer.parseInt(
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593 jucs.getColour(i).getRGB(), 16));
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597 if (newColours != null)
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599 ucs = new UserColourScheme(newColours);
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600 ucs.setName( jucs.getSchemeName() );
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603 ucs.setLowerCaseColours(lowerCase);
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608 catch (Exception ex)
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610 //Could be Archive Jalview format
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612 InputStreamReader in = new InputStreamReader(new FileInputStream(
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615 jalview.binding.JalviewUserColours jucs
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616 = new jalview.binding.JalviewUserColours();
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618 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
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620 newColours = new Color[jucs.getColourCount()];
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622 for (int i = 0; i < 24; i++)
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624 newColours[i] = new Color(Integer.parseInt(
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625 jucs.getColour(i).getRGB(), 16));
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627 if (newColours != null)
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629 ucs = new UserColourScheme(newColours);
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630 ucs.setName(jucs.getSchemeName());
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632 }catch(Exception ex2)
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633 { ex2.printStackTrace(); }
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635 if(newColours==null)
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636 System.out.println("Error loading User ColourFile\n"+ex);
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645 * @param e DOCUMENT ME!
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647 protected void savebutton_actionPerformed(ActionEvent e)
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649 if(schemeName.getText().trim().length()<1)
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651 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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652 "User colour scheme must have a name!",
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653 "No name for colour scheme",
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654 JOptionPane.WARNING_MESSAGE);
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658 if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )
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660 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."
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661 +"\nContinue saving colour scheme as "+schemeName.getText()+"?",
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662 "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
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663 if(reply != JOptionPane.YES_OPTION)
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666 userColourSchemes.remove(schemeName.getText());
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668 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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669 "LAST_DIRECTORY"), new String[] { "jc" },
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670 new String[] { "Jalview User Colours" }, "Jalview User Colours");
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672 chooser.setFileView(new jalview.io.JalviewFileView());
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673 chooser.setDialogTitle("Save colour scheme");
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674 chooser.setToolTipText("Save");
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676 int value = chooser.showSaveDialog(this);
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678 if (value == JalviewFileChooser.APPROVE_OPTION)
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680 String choice = chooser.getSelectedFile().getPath();
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681 String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);
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682 if(defaultColours.indexOf(choice)==-1)
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684 if(defaultColours.length()>0)
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685 defaultColours = defaultColours.concat("|");
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686 defaultColours = defaultColours.concat(choice);
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689 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
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691 ap.alignFrame.updateUserColourMenu();
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693 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
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695 jalview.schemabinding.version2.JalviewUserColours ucs
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696 = new jalview.schemabinding.version2.JalviewUserColours();
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698 ucs.setSchemeName(schemeName.getText());
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701 PrintWriter out = new PrintWriter(new OutputStreamWriter(
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702 new FileOutputStream(choice), "UTF-8"));
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704 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
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706 JButton button = (JButton) buttonPanel.getComponent(i);
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707 jalview.schemabinding.version2.Colour col
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708 = new jalview.schemabinding.version2.Colour();
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709 col.setName(button.getText());
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710 col.setRGB(jalview.util.Format.getHexString(
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711 button.getBackground()));
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712 ucs.addColour(col);
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718 catch (Exception ex)
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720 ex.printStackTrace();
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728 * @param e DOCUMENT ME!
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730 protected void cancelButton_actionPerformed(ActionEvent e)
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734 if (seqGroup != null)
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736 seqGroup.cs = oldColourScheme;
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738 else if (ap != null)
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740 ap.av.setGlobalColourScheme(oldColourScheme);
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745 if(pdbcanvas!=null)
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747 pdbcanvas.pdb.setColours(oldColourScheme);
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752 frame.setClosed(true);
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754 catch (Exception ex)
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760 static Hashtable userColourSchemes;
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762 public static Hashtable getUserColourSchemes()
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764 return userColourSchemes;
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767 public static void initUserColourSchemes(String files)
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769 userColourSchemes = new Hashtable();
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771 if(files==null || files.length()==0)
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775 // In case colours can't be loaded, we'll remove them
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776 // from the default list here.
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777 StringBuffer coloursFound = new StringBuffer();
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778 StringTokenizer st = new StringTokenizer(files, "|");
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779 while (st.hasMoreElements())
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781 String file = st.nextToken();
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784 UserColourScheme ucs = loadColours(file);
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787 if (coloursFound.length() > 0)
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788 coloursFound.append("|");
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789 coloursFound.append(file);
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790 userColourSchemes.put(ucs.getName(), ucs);
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793 catch (Exception ex)
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795 System.out.println("Error loading User ColourFile\n" + ex);
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798 if (!files.equals(coloursFound.toString()))
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800 if (coloursFound.toString().length() > 1)
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801 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
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802 coloursFound.toString());
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804 jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
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808 public static void removeColourFromDefaults(String target)
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810 // The only way to find colours by name is to load them in
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811 // In case colours can't be loaded, we'll remove them
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812 // from the default list here.
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814 userColourSchemes = new Hashtable();
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816 StringBuffer coloursFound = new StringBuffer();
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817 StringTokenizer st = new StringTokenizer(
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818 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
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820 while (st.hasMoreElements())
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822 String file = st.nextToken();
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825 UserColourScheme ucs = loadColours(file);
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826 if (ucs != null && !ucs.getName().equals(target))
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828 if (coloursFound.length() > 0)
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829 coloursFound.append("|");
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830 coloursFound.append(file);
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831 userColourSchemes.put(ucs.getName(), ucs);
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834 catch (Exception ex)
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836 System.out.println("Error loading User ColourFile\n" + ex);
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840 if (coloursFound.toString().length() > 1)
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841 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
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843 jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
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847 public void caseSensitive_actionPerformed(ActionEvent e)
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849 resetButtonPanel(caseSensitive.isSelected());
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850 lcaseColour.setEnabled(caseSensitive.isSelected());
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853 public void lcaseColour_actionPerformed(ActionEvent e)
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855 if(selectedButtons==null)
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856 selectedButtons = new Vector();
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858 selectedButtons.clear();
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859 selectedButtons.add(lcaseColour);
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