2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3
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10 * of the License, or (at your option) any later version.
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12 * Jalview is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty
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14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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15 * PURPOSE. See the GNU General Public License for more details.
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17 * You should have received a copy of the GNU General Public License
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18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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19 * The Jalview Authors are detailed in the 'AUTHORS' file.
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21 package jalview.appletgui;
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23 import jalview.analysis.AlignmentUtils;
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24 import jalview.api.ComplexAlignFile;
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25 import jalview.bin.JalviewLite;
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26 import jalview.datamodel.AlignmentI;
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27 import jalview.datamodel.ColumnSelection;
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28 import jalview.datamodel.PDBEntry;
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29 import jalview.datamodel.SequenceI;
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30 import jalview.io.AlignFile;
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31 import jalview.io.AnnotationFile;
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32 import jalview.io.AppletFormatAdapter;
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33 import jalview.io.FileParse;
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34 import jalview.io.IdentifyFile;
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35 import jalview.io.NewickFile;
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36 import jalview.jsdev.GenericFileAdapter;
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37 import jalview.schemes.ColourSchemeI;
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38 import jalview.schemes.TCoffeeColourScheme;
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39 import jalview.util.MessageManager;
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41 import java.awt.BorderLayout;
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42 import java.awt.Font;
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43 import java.awt.event.ActionEvent;
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44 import java.awt.event.ActionListener;
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45 import java.awt.event.MouseEvent;
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46 import java.awt.event.MouseListener;
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48 import javax.swing.JButton;
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49 import javax.swing.JDialog;
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50 import javax.swing.JFrame;
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51 import javax.swing.JLabel;
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52 import javax.swing.JPanel;
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53 import javax.swing.JTextArea;
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55 public class CutAndPasteTransfer extends JPanel implements ActionListener,
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58 boolean pdbImport = false;
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60 boolean treeImport = false;
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62 boolean annotationImport = false;
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66 AlignFrame alignFrame;
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68 FileParse source = null;
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70 public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
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75 } catch (Exception e)
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77 e.printStackTrace();
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80 this.alignFrame = alignFrame;
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84 buttonPanel.setVisible(false);
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88 public String getText()
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90 return textarea.getText();
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93 public void setText(String text)
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95 textarea.setText(text);
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98 public void setPDBImport(SequenceI seq)
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101 accept.setLabel(MessageManager.getString("action.accept"));
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102 addSequences.setVisible(false);
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106 public void setTreeImport()
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109 accept.setLabel(MessageManager.getString("action.accept"));
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110 addSequences.setVisible(false);
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113 public void setAnnotationImport()
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115 annotationImport = true;
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116 accept.setLabel(MessageManager.getString("action.accept"));
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117 addSequences.setVisible(false);
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120 public void actionPerformed(ActionEvent evt)
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122 if (evt.getSource() == accept)
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126 else if (evt.getSource() == addSequences)
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130 else if (evt.getSource() == cancel)
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136 protected void ok(boolean newWindow)
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138 String text = getText();
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139 int length = text.length();
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140 textarea.append("\n");
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141 if (textarea.getText().length() == length)
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143 String warning = "\n\n#################################################\n"
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144 + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
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145 + "\nCAN'T INPUT FULL ALIGNMENT"
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146 + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
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147 + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
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148 + "\n#################################################\n";
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149 textarea.setText(text.substring(0, text.length() - warning.length())
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152 textarea.setCaretPosition(text.length());
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157 openPdbViewer(text);
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160 else if (treeImport)
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167 else if (annotationImport)
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171 else if (alignFrame != null)
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173 loadAlignment(text, newWindow, alignFrame.getAlignViewport());
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176 // TODO: dialog should indicate if data was parsed correctly or not - see
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178 if (this.getParent() instanceof JFrame)
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180 ((JFrame) this.getParent()).setVisible(false);
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184 ((JDialog) this.getParent()).setVisible(false);
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189 * Parses text as Newick Tree format, and loads on to the alignment. Returns
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190 * true if successful, else false.
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192 protected boolean loadTree()
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196 NewickFile fin = new NewickFile(textarea.getText(), "Paste");
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199 if (fin.getTree() != null)
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201 alignFrame.loadTree(fin, "Pasted tree file");
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204 } catch (Exception ex)
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206 // TODO: JAL-1102 - should have a warning message in dialog, not simply
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207 // overwrite the broken input data with the exception
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208 textarea.setText(MessageManager.formatMessage(
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209 "label.could_not_parse_newick_file", new Object[]
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210 { ex.getMessage() }));
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217 * Parse text as an alignment file and add to the current or a new window.
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222 protected void loadAlignment(String text, boolean newWindow,
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223 AlignViewport viewport)
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225 AlignmentI al = null;
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227 String format = new IdentifyFile().Identify(text,
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228 AppletFormatAdapter.PASTE);
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229 AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
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232 al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
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233 source = afa.getAlignFile();
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234 } catch (java.io.IOException ex)
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236 ex.printStackTrace();
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241 al.setDataset(null); // set dataset on alignment/sequences
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244 * SplitFrame option dependent on applet parameter for now.
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246 boolean allowSplitFrame = alignFrame.viewport.applet
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247 .getDefaultParameter("enableSplitFrame", false);
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248 if (allowSplitFrame && openSplitFrame(al, format))
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256 if (source instanceof ComplexAlignFile)
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258 ColumnSelection colSel = ((ComplexAlignFile) source)
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259 .getColumnSelection();
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260 SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
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261 .getHiddenSequences();
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262 boolean showSeqFeatures = ((ComplexAlignFile) source)
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263 .isShowSeqFeatures();
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264 ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
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265 af = new AlignFrame(al, hiddenSeqs, colSel,
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266 alignFrame.viewport.applet, "Cut & Paste input - "
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268 af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
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269 af.changeColour(cs);
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273 af = new AlignFrame(al, alignFrame.viewport.applet,
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274 "Cut & Paste input - " + format, false);
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278 .setText(MessageManager
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279 .getString("label.successfully_pasted_annotation_to_alignment"));
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283 alignFrame.addSequences(al.getSequencesArray());
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284 alignFrame.statusBar.setText(MessageManager
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285 .getString("label.successfully_pasted_alignment_file"));
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291 * Check whether the new alignment could be mapped to the current one as
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292 * cDNA/protein, if so offer the option to open as split frame view. Returns
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293 * true if a split frame view is opened, false if not.
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298 protected boolean openSplitFrame(AlignmentI al, String format)
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300 final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
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301 if (thisAlignment.isNucleotide() == al.isNucleotide())
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303 // both nucleotide or both protein
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306 AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
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307 AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
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308 boolean mapped = AlignmentUtils.mapProteinToCdna(protein, dna);
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315 * A mapping is possible; ask user if they want a split frame.
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317 String title = MessageManager.getString("label.open_split_window");
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318 final JVDialog dialog = new JVDialog((JFrame) this.getParent(), title,
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320 dialog.ok.setLabel(MessageManager.getString("action.yes"));
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321 dialog.cancel.setLabel(MessageManager.getString("action.no"));
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322 JPanel question = new JPanel(new BorderLayout());
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323 final String text = MessageManager
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324 .getString("label.open_split_window?");
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325 question.add(new JLabel(text, JLabel.CENTER), BorderLayout.CENTER);
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326 dialog.setMainPanel(question);
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327 dialog.setVisible(true);
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330 if (!dialog.accept)
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336 * Open SplitFrame with DNA above and protein below, including the alignment
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337 * from textbox and a copy of the original.
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339 final JalviewLite applet = this.alignFrame.viewport.applet;
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340 AlignFrame copyFrame = new AlignFrame(
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341 this.alignFrame.viewport.getAlignment(), applet,
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342 alignFrame.getTitle(), false, false);
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343 AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
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344 "Cut & Paste input - " + format, false, false);
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345 AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
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346 AlignFrame proteinFrame = al.isNucleotide() ? copyFrame
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348 SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
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349 sf.addToDisplay(false, applet);
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354 * Parse the text as a TCoffee score file, if successful add scores as
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355 * alignment annotations.
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357 protected void loadAnnotations()
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359 AlignFile tcf = null;
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362 tcf = GenericFileAdapter.newTCoffeeScoreFile(textarea.getText(),
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363 AppletFormatAdapter.PASTE);
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366 if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
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369 alignFrame.tcoffeeColour.setEnabled(true);
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370 alignFrame.alignPanel.fontChanged();
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371 alignFrame.changeColour(new TCoffeeColourScheme(
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372 alignFrame.viewport.getAlignment()));
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373 alignFrame.statusBar
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374 .setText(MessageManager
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375 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
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379 // file valid but didn't get added to alignment for some reason
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380 alignFrame.statusBar.setText(MessageManager.formatMessage(
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381 "label.failed_add_tcoffee_scores",
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383 { (tcf.getWarningMessage() != null ? tcf
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384 .getWarningMessage() : "") }));
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391 } catch (Exception x)
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397 if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
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398 textarea.getText(), AppletFormatAdapter.PASTE))
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400 alignFrame.alignPanel.fontChanged();
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401 alignFrame.alignPanel.setScrollValues(0, 0);
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402 alignFrame.statusBar
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403 .setText(MessageManager
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404 .getString("label.successfully_pasted_annotation_to_alignment"));
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409 if (!alignFrame.parseFeaturesFile(textarea.getText(),
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410 AppletFormatAdapter.PASTE))
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412 alignFrame.statusBar
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413 .setText(MessageManager
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414 .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
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421 * Open a Jmol viewer (if available), failing that the built-in PDB viewer,
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422 * passing the input text as the PDB file data.
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426 protected void openPdbViewer(String text)
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428 PDBEntry pdb = new PDBEntry();
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431 // if (alignFrame.alignPanel.av.applet.jmolAvailable)
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433 new AppletJmol(pdb, new SequenceI[]
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434 { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
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438 // new MCview.AppletPDBViewer(pdb, new SequenceI[]
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439 // { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
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443 protected void cancel()
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445 textarea.setText("");
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446 if (this.getParent() instanceof JFrame)
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448 ((JFrame) this.getParent()).setVisible(false);
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452 ((JDialog) this.getParent()).setVisible(false);
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456 protected JTextArea textarea = new JTextArea();
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458 JButton accept = new JButton("New Window");
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460 JButton addSequences = new JButton("Add to Current Alignment");
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462 JButton cancel = new JButton("Close");
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464 protected JPanel buttonPanel = new JPanel();
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466 BorderLayout borderLayout1 = new BorderLayout();
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468 private void jbInit() throws Exception
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470 textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
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471 textarea.setText(MessageManager
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472 .getString("label.paste_your_alignment_file"));
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473 textarea.addMouseListener(this);
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474 this.setLayout(borderLayout1);
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475 accept.addActionListener(this);
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476 addSequences.addActionListener(this);
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477 cancel.addActionListener(this);
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478 this.add(buttonPanel, BorderLayout.SOUTH);
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479 buttonPanel.add(accept, null);
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480 buttonPanel.add(addSequences);
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481 buttonPanel.add(cancel, null);
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482 this.add(textarea, java.awt.BorderLayout.CENTER);
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485 public void mousePressed(MouseEvent evt)
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487 if (textarea.getText().startsWith(
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488 MessageManager.getString("label.paste_your")))
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490 textarea.setText("");
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494 public void mouseReleased(MouseEvent evt)
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498 public void mouseClicked(MouseEvent evt)
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502 public void mouseEntered(MouseEvent evt)
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506 public void mouseExited(MouseEvent evt)
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