2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.bin.Cache;
25 import jalview.gui.Help.HelpId;
26 import jalview.gui.StructureViewer.ViewerType;
27 import jalview.io.JalviewFileChooser;
28 import jalview.io.JalviewFileView;
29 import jalview.jbgui.GPreferences;
30 import jalview.jbgui.GSequenceLink;
31 import jalview.schemes.ColourSchemeProperty;
32 import jalview.util.MessageManager;
33 import jalview.ws.sifts.SiftsSettings;
35 import java.awt.BorderLayout;
36 import java.awt.Color;
37 import java.awt.Dimension;
39 import java.awt.event.ActionEvent;
40 import java.awt.event.ActionListener;
41 import java.awt.event.MouseEvent;
43 import java.util.Collection;
44 import java.util.List;
45 import java.util.StringTokenizer;
46 import java.util.Vector;
48 import javax.help.HelpSetException;
49 import javax.swing.JColorChooser;
50 import javax.swing.JFileChooser;
51 import javax.swing.JInternalFrame;
52 import javax.swing.JOptionPane;
53 import javax.swing.JPanel;
55 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
63 public class Preferences extends GPreferences
65 public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
67 public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
69 public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
71 public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
73 public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
75 public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
77 public static final String ADD_SS_ANN = "ADD_SS_ANN";
79 public static final String USE_RNAVIEW = "USE_RNAVIEW";
81 public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
83 public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
85 public static final String CHIMERA_PATH = "CHIMERA_PATH";
87 public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
89 public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
91 public static final String HIDE_INTRONS = "HIDE_INTRONS";
93 private static final int MIN_FONT_SIZE = 1;
95 private static final int MAX_FONT_SIZE = 30;
98 * Holds name and link separated with | character. Sequence ID must be
99 * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
101 public static Vector sequenceURLLinks;
104 * Holds name and link separated with | character. Sequence IDS and Sequences
105 * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
106 * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
107 * for first and second token specified after a pipe character at end |,|.
108 * (TODO: proper escape for using | to separate ids or sequences
111 public static Vector groupURLLinks;
114 String string = Cache
117 "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
118 sequenceURLLinks = new Vector();
122 StringTokenizer st = new StringTokenizer(string, "|");
123 while (st.hasMoreElements())
125 String name = st.nextToken();
126 String url = st.nextToken();
127 // check for '|' within a regex
128 int rxstart = url.indexOf("$SEQUENCE_ID$");
129 while (rxstart == -1 && url.indexOf("/=$") == -1)
131 url = url + "|" + st.nextToken();
133 sequenceURLLinks.addElement(name + "|" + url);
135 } catch (Exception ex)
137 System.out.println(ex + "\nError parsing sequence links");
140 // upgrade old SRS link
141 int srsPos = sequenceURLLinks
142 .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
147 "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
153 * TODO: reformulate groupURL encoding so two or more can be stored in the
154 * .properties file as '|' separated strings
157 groupURLLinks = new Vector();
160 Vector nameLinks, urlLinks;
162 JInternalFrame frame;
164 DasSourceBrowser dasSource;
166 private WsPreferences wsPrefs;
169 * Creates a new Preferences object.
174 frame = new JInternalFrame();
175 frame.setContentPane(this);
176 dasSource = new DasSourceBrowser();
177 dasTab.add(dasSource, BorderLayout.CENTER);
178 wsPrefs = new WsPreferences();
179 wsTab.add(wsPrefs, BorderLayout.CENTER);
180 int width = 500, height = 470;
181 if (new jalview.util.Platform().isAMac())
187 Desktop.addInternalFrame(frame,
188 MessageManager.getString("label.preferences"), width, height);
189 frame.setMinimumSize(new Dimension(width, height));
192 * Set Visual tab defaults
194 seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
195 rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
196 fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
197 annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
199 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
200 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
201 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
202 openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
204 .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
205 showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
207 showGroupConservation.setSelected(Cache.getDefault(
208 "SHOW_GROUP_CONSERVATION", false));
209 showConsensHistogram.setSelected(Cache.getDefault(
210 "SHOW_CONSENSUS_HISTOGRAM", true));
211 showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
213 showNpTooltip.setSelected(Cache
214 .getDefault("SHOW_NPFEATS_TOOLTIP", true));
215 showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
218 String[] fonts = java.awt.GraphicsEnvironment
219 .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
220 for (int i = 0; i < fonts.length; i++)
222 fontNameCB.addItem(fonts[i]);
225 for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
227 fontSizeCB.addItem(i + "");
230 fontStyleCB.addItem("plain");
231 fontStyleCB.addItem("bold");
232 fontStyleCB.addItem("italic");
234 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
235 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
236 fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
239 smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
240 scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
243 idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
245 wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
246 hideIntrons.setSelected(Cache.getDefault(HIDE_INTRONS, true));
248 gapSymbolCB.addItem("-");
249 gapSymbolCB.addItem(".");
251 gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
253 sortby.addItem("No sort");
254 sortby.addItem("Id");
255 sortby.addItem("Pairwise Identity");
256 sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
258 sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
260 .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
262 .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
263 SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
264 .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
265 SequenceAnnotationOrder.NONE.name()));
266 sortAnnBy.setSelectedItem(savedSort.toString());
268 sortAutocalc.addItem("Autocalculated first");
269 sortAutocalc.addItem("Autocalculated last");
270 final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
271 sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
272 : sortAutocalc.getItemAt(1));
274 .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
275 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
276 Cache.getDefault("www.jalview.org", "http://www.jalview.org")
277 + "/examples/exampleFile_2_3.jar"));
280 * Set Colours tab defaults
282 for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
284 protColour.addItem(ColourSchemeProperty.getColourName(i));
285 nucColour.addItem(ColourSchemeProperty.getColourName(i));
287 String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
288 String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
289 protColour.setSelectedItem(newProp != null ? newProp : oldProp);
290 newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
291 nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
292 minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
294 maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
298 * Set Structure tab defaults.
300 final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
301 structFromPdb.setSelected(structSelected);
302 useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
303 useRnaView.setEnabled(structSelected);
304 addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
305 addSecondaryStructure.setEnabled(structSelected);
306 addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
307 addTempFactor.setEnabled(structSelected);
308 structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
309 ViewerType.JMOL.name()));
310 chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
311 chimeraPath.addActionListener(new ActionListener()
314 public void actionPerformed(ActionEvent e)
316 validateChimeraPath();
320 if (Cache.getDefault("MAP_WITH_SIFTS", false))
322 siftsMapping.setSelected(true);
326 nwMapping.setSelected(true);
330 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
333 * Set Connections tab defaults
335 nameLinks = new Vector();
336 urlLinks = new Vector();
337 for (int i = 0; i < sequenceURLLinks.size(); i++)
339 String link = sequenceURLLinks.elementAt(i).toString();
340 nameLinks.addElement(link.substring(0, link.indexOf("|")));
341 urlLinks.addElement(link.substring(link.indexOf("|") + 1));
346 useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
347 proxyServerTB.setEnabled(useProxy.isSelected());
348 proxyPortTB.setEnabled(useProxy.isSelected());
349 proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
350 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
352 defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
354 usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
355 // note antisense here: default is true
357 .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
358 versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
361 * Set Output tab defaults
364 .addItem(MessageManager.getString("label.prompt_each_time"));
365 epsRendering.addItem(MessageManager.getString("label.lineart"));
366 epsRendering.addItem(MessageManager.getString("action.text"));
367 epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
368 "Prompt each time"));
369 autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
370 userIdWidth.setEnabled(!autoIdWidth.isSelected());
371 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
372 Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
373 userIdWidth.setText(wi == null ? "" : wi.toString());
374 blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
375 clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
376 fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
377 msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
378 pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
379 pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
380 pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
381 modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
382 embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
386 * Set Editing tab defaults
388 autoCalculateConsCheck.setSelected(Cache.getDefault(
389 "AUTO_CALC_CONSENSUS", true));
390 padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
391 sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
393 annotations_actionPerformed(null); // update the display of the annotation
398 * Save user selections on the Preferences tabs to the Cache and write out to
404 public void ok_actionPerformed(ActionEvent e)
406 if (!validateSettings())
412 * Save Visual settings
414 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
415 Boolean.toString(seqLimit.isSelected()));
416 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
417 Boolean.toString(rightAlign.isSelected()));
418 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
419 Boolean.toString(fullScreen.isSelected()));
420 Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
421 Boolean.toString(openoverv.isSelected()));
422 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
423 Boolean.toString(annotations.isSelected()));
424 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
425 Boolean.toString(conservation.isSelected()));
426 Cache.applicationProperties.setProperty("SHOW_QUALITY",
427 Boolean.toString(quality.isSelected()));
428 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
429 Boolean.toString(identity.isSelected()));
431 Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
432 .getSelectedItem().toString());
434 Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
435 .getSelectedItem().toString());
436 Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
437 .getSelectedItem().toString());
438 Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
439 .getSelectedItem().toString());
441 Cache.applicationProperties.setProperty("ID_ITALICS",
442 Boolean.toString(idItalics.isSelected()));
443 Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
444 Boolean.toString(showUnconserved.isSelected()));
445 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
446 Boolean.toString(showGroupConsensus.isSelected()));
447 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
448 Boolean.toString(showGroupConservation.isSelected()));
449 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
450 Boolean.toString(showConsensHistogram.isSelected()));
451 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
452 Boolean.toString(showConsensLogo.isSelected()));
453 Cache.applicationProperties.setProperty("ANTI_ALIAS",
454 Boolean.toString(smoothFont.isSelected()));
455 Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
456 Boolean.toString(scaleProteinToCdna.isSelected()));
457 Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
458 Boolean.toString(showNpTooltip.isSelected()));
459 Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
460 Boolean.toString(showDbRefTooltip.isSelected()));
462 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
463 Boolean.toString(wrap.isSelected()));
464 Cache.applicationProperties.setProperty(HIDE_INTRONS,
465 Boolean.toString(hideIntrons.isSelected()));
467 Cache.applicationProperties.setProperty("STARTUP_FILE",
468 startupFileTextfield.getText());
469 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
470 Boolean.toString(startupCheckbox.isSelected()));
472 Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
473 .getSelectedItem().toString());
475 // convert description of sort order to enum name for save
476 SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
477 .forDescription(sortAnnBy.getSelectedItem().toString());
478 if (annSortOrder != null)
480 Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
481 annSortOrder.name());
484 final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
485 Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
486 .valueOf(showAutocalcFirst).toString());
489 * Save Colours settings
491 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
492 .getSelectedItem().toString());
493 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
494 .getSelectedItem().toString());
495 Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
496 minColour.getBackground());
497 Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
498 maxColour.getBackground());
501 * Save Structure settings
503 Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
504 Boolean.toString(addTempFactor.isSelected()));
505 Cache.applicationProperties.setProperty(ADD_SS_ANN,
506 Boolean.toString(addSecondaryStructure.isSelected()));
507 Cache.applicationProperties.setProperty(USE_RNAVIEW,
508 Boolean.toString(useRnaView.isSelected()));
509 Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
510 Boolean.toString(structFromPdb.isSelected()));
511 Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
512 .getSelectedItem().toString());
513 Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
514 Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
515 Boolean.toString(siftsMapping.isSelected()));
516 SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
519 * Save Output settings
521 if (epsRendering.getSelectedItem().equals("Prompt each time"))
523 Cache.applicationProperties.remove("EPS_RENDERING");
527 Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
528 .getSelectedItem().toString());
532 * Save Connections settings
534 Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
536 jalview.util.BrowserLauncher.resetBrowser();
538 if (nameLinks.size() > 0)
540 StringBuffer links = new StringBuffer();
541 sequenceURLLinks = new Vector();
542 for (int i = 0; i < nameLinks.size(); i++)
544 sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
545 + urlLinks.elementAt(i));
546 links.append(sequenceURLLinks.elementAt(i).toString());
550 links.setLength(links.length() - 1);
551 Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
556 Cache.applicationProperties.remove("SEQUENCE_LINKS");
559 Cache.applicationProperties.setProperty("USE_PROXY",
560 Boolean.toString(useProxy.isSelected()));
562 Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
564 Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
566 if (useProxy.isSelected())
568 System.setProperty("http.proxyHost", proxyServerTB.getText());
569 System.setProperty("http.proxyPort", proxyPortTB.getText());
573 System.setProperty("http.proxyHost", "");
574 System.setProperty("http.proxyPort", "");
576 Cache.setProperty("VERSION_CHECK",
577 Boolean.toString(versioncheck.isSelected()));
578 if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
580 // default is false - we only set this if the user has actively agreed
581 Cache.setProperty("USAGESTATS",
582 Boolean.toString(usagestats.isSelected()));
584 if (!questionnaire.isSelected())
586 Cache.setProperty("NOQUESTIONNAIRES", "true");
590 // special - made easy to edit a property file to disable questionnaires
591 // by just adding the given line
592 Cache.removeProperty("NOQUESTIONNAIRES");
596 * Save Output settings
598 Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
599 Boolean.toString(blcjv.isSelected()));
600 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
601 Boolean.toString(clustaljv.isSelected()));
602 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
603 Boolean.toString(fastajv.isSelected()));
604 Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
605 Boolean.toString(msfjv.isSelected()));
606 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
607 Boolean.toString(pfamjv.isSelected()));
608 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
609 Boolean.toString(pileupjv.isSelected()));
610 Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
611 Boolean.toString(pirjv.isSelected()));
612 Cache.applicationProperties.setProperty("PIR_MODELLER",
613 Boolean.toString(modellerOutput.isSelected()));
614 Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
615 Boolean.toString(embbedBioJSON.isSelected()));
616 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
618 Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
619 Boolean.toString(autoIdWidth.isSelected()));
620 userIdWidth_actionPerformed();
621 Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
622 userIdWidth.getText());
625 * Save Editing settings
627 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
628 Boolean.toString(autoCalculateConsCheck.isSelected()));
629 Cache.applicationProperties.setProperty("SORT_BY_TREE",
630 Boolean.toString(sortByTree.isSelected()));
631 Cache.applicationProperties.setProperty("PAD_GAPS",
632 Boolean.toString(padGaps.isSelected()));
634 dasSource.saveProperties(Cache.applicationProperties);
635 wsPrefs.updateAndRefreshWsMenuConfig(false);
636 Cache.saveProperties();
637 Desktop.instance.doConfigureStructurePrefs();
640 frame.setClosed(true);
641 } catch (Exception ex)
647 * Do any necessary validation before saving settings. Return focus to the
648 * first tab which fails validation.
652 private boolean validateSettings()
654 if (!validateStructure())
656 structureTab.requestFocusInWindow();
663 protected boolean validateStructure()
665 return validateChimeraPath();
673 public void startupFileTextfield_mouseClicked()
675 JalviewFileChooser chooser = new JalviewFileChooser(
676 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
677 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
678 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
679 "PIR", "BLC", "Jalview" },
680 jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
681 chooser.setFileView(new JalviewFileView());
682 chooser.setDialogTitle(MessageManager
683 .getString("label.select_startup_file"));
685 int value = chooser.showOpenDialog(this);
687 if (value == JalviewFileChooser.APPROVE_OPTION)
689 jalview.bin.Cache.applicationProperties.setProperty(
690 "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
691 startupFileTextfield.setText(chooser.getSelectedFile()
703 public void cancel_actionPerformed(ActionEvent e)
707 wsPrefs.updateWsMenuConfig(true);
708 wsPrefs.refreshWs_actionPerformed(e);
709 frame.setClosed(true);
710 } catch (Exception ex)
722 public void annotations_actionPerformed(ActionEvent e)
724 conservation.setEnabled(annotations.isSelected());
725 quality.setEnabled(annotations.isSelected());
726 identity.setEnabled(annotations.isSelected());
727 showGroupConsensus.setEnabled(annotations.isSelected());
728 showGroupConservation.setEnabled(annotations.isSelected());
729 showConsensHistogram.setEnabled(annotations.isSelected()
730 && (identity.isSelected() || showGroupConsensus.isSelected()));
731 showConsensLogo.setEnabled(annotations.isSelected()
732 && (identity.isSelected() || showGroupConsensus.isSelected()));
736 public void newLink_actionPerformed(ActionEvent e)
739 GSequenceLink link = new GSequenceLink();
740 boolean valid = false;
743 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
744 MessageManager.getString("label.new_sequence_url_link"),
745 JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
747 if (link.checkValid())
749 nameLinks.addElement(link.getName());
750 urlLinks.addElement(link.getURL());
763 public void editLink_actionPerformed(ActionEvent e)
765 GSequenceLink link = new GSequenceLink();
767 int index = linkNameList.getSelectedIndex();
770 JOptionPane.showInternalMessageDialog(Desktop.desktop,
771 MessageManager.getString("label.no_link_selected"),
772 MessageManager.getString("label.no_link_selected"),
773 JOptionPane.WARNING_MESSAGE);
777 link.setName(nameLinks.elementAt(index).toString());
778 link.setURL(urlLinks.elementAt(index).toString());
780 boolean valid = false;
784 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
785 MessageManager.getString("label.new_sequence_url_link"),
786 JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
788 if (link.checkValid())
790 nameLinks.setElementAt(link.getName(), index);
791 urlLinks.setElementAt(link.getURL(), index);
805 public void deleteLink_actionPerformed(ActionEvent e)
807 int index = linkNameList.getSelectedIndex();
810 JOptionPane.showInternalMessageDialog(Desktop.desktop,
811 MessageManager.getString("label.no_link_selected"),
812 MessageManager.getString("label.no_link_selected"),
813 JOptionPane.WARNING_MESSAGE);
816 nameLinks.removeElementAt(index);
817 urlLinks.removeElementAt(index);
821 void updateLinkData()
823 linkNameList.setListData(nameLinks);
824 linkURLList.setListData(urlLinks);
828 public void defaultBrowser_mouseClicked(MouseEvent e)
830 JFileChooser chooser = new JFileChooser(".");
831 chooser.setDialogTitle(MessageManager
832 .getString("label.select_default_browser"));
834 int value = chooser.showOpenDialog(this);
836 if (value == JFileChooser.APPROVE_OPTION)
838 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
847 * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
851 protected void showunconserved_actionPerformed(ActionEvent e)
853 // TODO Auto-generated method stub
854 super.showunconserved_actionPerformed(e);
857 public static Collection getGroupURLLinks()
859 return groupURLLinks;
863 public void minColour_actionPerformed(JPanel panel)
865 Color col = JColorChooser.showDialog(this,
866 MessageManager.getString("label.select_colour_minimum_value"),
867 minColour.getBackground());
870 panel.setBackground(col);
876 public void maxColour_actionPerformed(JPanel panel)
878 Color col = JColorChooser.showDialog(this,
879 MessageManager.getString("label.select_colour_maximum_value"),
880 maxColour.getBackground());
883 panel.setBackground(col);
889 protected void userIdWidth_actionPerformed()
893 String val = userIdWidth.getText().trim();
894 if (val.length() > 0)
896 Integer iw = Integer.parseInt(val);
897 if (iw.intValue() < 12)
899 throw new NumberFormatException();
901 userIdWidth.setText(iw.toString());
903 } catch (NumberFormatException x)
905 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
906 .getString("warn.user_defined_width_requirements"),
907 MessageManager.getString("label.invalid_id_column_width"),
908 JOptionPane.WARNING_MESSAGE);
909 userIdWidth.setText("");
914 protected void autoIdWidth_actionPerformed()
916 userIdWidth.setEnabled(!autoIdWidth.isSelected());
917 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
921 * Returns true if chimera path is to a valid executable, else show an error
924 private boolean validateChimeraPath()
926 if (chimeraPath.getText().trim().length() > 0)
928 File f = new File(chimeraPath.getText());
931 JOptionPane.showInternalMessageDialog(Desktop.desktop,
932 MessageManager.getString("label.invalid_chimera_path"),
933 MessageManager.getString("label.invalid_name"),
934 JOptionPane.ERROR_MESSAGE);
942 * If Chimera is selected, check it can be found on default or user-specified
943 * path, if not show a warning/help dialog.
946 protected void structureViewer_actionPerformed(String selectedItem)
948 if (!selectedItem.equals(ViewerType.CHIMERA.name()))
952 boolean found = false;
955 * Try user-specified and standard paths for Chimera executable.
957 List<String> paths = StructureManager.getChimeraPaths();
958 paths.add(0, chimeraPath.getText());
959 for (String path : paths)
961 if (new File(path.trim()).canExecute())
969 String[] options = { "OK", "Help" };
970 int showHelp = JOptionPane.showInternalOptionDialog(
972 JvSwingUtils.wrapTooltip(true,
973 MessageManager.getString("label.chimera_missing")),
974 "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
975 null, options, options[0]);
976 if (showHelp == JOptionPane.NO_OPTION)
980 Help.showHelpWindow(HelpId.StructureViewer);
981 } catch (HelpSetException e)