2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.appletgui;
22 import java.awt.event.*;
24 import jalview.datamodel.*;
26 import jalview.schemes.TCoffeeColourScheme;
27 import jalview.util.MessageManager;
29 public class CutAndPasteTransfer extends Panel implements ActionListener,
32 boolean pdbImport = false;
34 boolean treeImport = false;
36 boolean annotationImport = false;
40 AlignFrame alignFrame;
42 public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
52 this.alignFrame = alignFrame;
56 buttonPanel.setVisible(false);
60 public String getText()
62 return textarea.getText();
65 public void setText(String text)
67 textarea.setText(text);
70 public void setPDBImport(Sequence seq)
73 accept.setLabel(MessageManager.getString("action.accept"));
74 addSequences.setVisible(false);
78 public void setTreeImport()
81 accept.setLabel(MessageManager.getString("action.accept"));
82 addSequences.setVisible(false);
85 public void setAnnotationImport()
87 annotationImport = true;
88 accept.setLabel(MessageManager.getString("action.accept"));
89 addSequences.setVisible(false);
92 public void actionPerformed(ActionEvent evt)
94 if (evt.getSource() == accept)
98 else if (evt.getSource() == addSequences)
102 else if (evt.getSource() == cancel)
108 protected void ok(boolean newWindow)
110 String text = getText();
111 int length = text.length();
112 textarea.append("\n");
113 if (textarea.getText().length() == length)
115 String warning = "\n\n#################################################\n"
116 + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
117 + "\nCAN'T INPUT FULL ALIGNMENT"
118 + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
119 + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
120 + "\n#################################################\n";
121 textarea.setText(text.substring(0, text.length() - warning.length())
124 textarea.setCaretPosition(text.length());
129 PDBEntry pdb = new PDBEntry();
132 if (alignFrame.alignPanel.av.applet.jmolAvailable)
133 new jalview.appletgui.AppletJmol(pdb, new Sequence[]
134 { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
137 new MCview.AppletPDBViewer(pdb, new Sequence[]
138 { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
145 jalview.io.NewickFile fin = new jalview.io.NewickFile(
146 textarea.getText(), "Paste");
149 if (fin.getTree() != null)
151 alignFrame.loadTree(fin, "Pasted tree file");
154 } catch (Exception ex)
156 // TODO: JAL-1102 - should have a warning message in dialog, not simply
157 // overwrite the broken input data with the exception
158 textarea.setText(MessageManager.formatMessage("label.could_not_parse_newick_file", new String[]{ex.getMessage()}));
162 else if (annotationImport)
164 TCoffeeScoreFile tcf = null;
167 tcf = new TCoffeeScoreFile(textarea.getText(),
168 jalview.io.AppletFormatAdapter.PASTE);
171 if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
174 alignFrame.tcoffeeColour.setEnabled(true);
175 alignFrame.alignPanel.fontChanged();
176 alignFrame.changeColour(new TCoffeeColourScheme(
177 alignFrame.viewport.getAlignment()));
179 .setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
183 // file valid but didn't get added to alignment for some reason
184 alignFrame.statusBar.setText(MessageManager.formatMessage("label.failed_add_tcoffee_scores", new String[]{(tcf.getWarningMessage() != null ? tcf.getWarningMessage() : "")}));
191 } catch (Exception x)
197 if (new AnnotationFile().readAnnotationFile(
198 alignFrame.viewport.getAlignment(), textarea.getText(),
199 jalview.io.AppletFormatAdapter.PASTE))
201 alignFrame.alignPanel.fontChanged();
202 alignFrame.alignPanel.setScrollValues(0, 0);
204 .setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
209 if (!alignFrame.parseFeaturesFile(textarea.getText(),
210 jalview.io.AppletFormatAdapter.PASTE))
213 .setText(MessageManager.getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
218 else if (alignFrame != null)
222 String format = new IdentifyFile().Identify(text,
223 AppletFormatAdapter.PASTE);
226 al = new AppletFormatAdapter().readFile(text,
227 AppletFormatAdapter.PASTE, format);
228 } catch (java.io.IOException ex)
230 ex.printStackTrace();
237 AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
238 "Cut & Paste input - " + format, false);
239 af.statusBar.setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
243 alignFrame.addSequences(al.getSequencesArray());
245 .setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
249 // TODO: dialog should indicate if data was parsed correctly or not - see
251 if (this.getParent() instanceof Frame)
253 ((Frame) this.getParent()).setVisible(false);
257 ((Dialog) this.getParent()).setVisible(false);
261 protected void cancel()
263 textarea.setText("");
264 if (this.getParent() instanceof Frame)
266 ((Frame) this.getParent()).setVisible(false);
270 ((Dialog) this.getParent()).setVisible(false);
274 protected TextArea textarea = new TextArea();
276 Button accept = new Button("New Window");
278 Button addSequences = new Button("Add to Current Alignment");
280 Button cancel = new Button("Close");
282 protected Panel buttonPanel = new Panel();
284 BorderLayout borderLayout1 = new BorderLayout();
286 private void jbInit() throws Exception
288 textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
289 textarea.setText(MessageManager.getString("label.paste_your_alignment_file"));
290 textarea.addMouseListener(this);
291 this.setLayout(borderLayout1);
292 accept.addActionListener(this);
293 addSequences.addActionListener(this);
294 cancel.addActionListener(this);
295 this.add(buttonPanel, BorderLayout.SOUTH);
296 buttonPanel.add(accept, null);
297 buttonPanel.add(addSequences);
298 buttonPanel.add(cancel, null);
299 this.add(textarea, java.awt.BorderLayout.CENTER);
302 public void mousePressed(MouseEvent evt)
304 if (textarea.getText().startsWith(MessageManager.getString("label.paste_your")))
306 textarea.setText("");
310 public void mouseReleased(MouseEvent evt)
314 public void mouseClicked(MouseEvent evt)
318 public void mouseEntered(MouseEvent evt)
322 public void mouseExited(MouseEvent evt)