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;
34 import java.awt.BorderLayout;
35 import java.awt.Color;
36 import java.awt.Dimension;
38 import java.awt.event.ActionEvent;
39 import java.awt.event.ActionListener;
40 import java.awt.event.MouseEvent;
42 import java.util.Collection;
43 import java.util.List;
44 import java.util.StringTokenizer;
45 import java.util.Vector;
47 import javax.help.HelpSetException;
48 import javax.swing.JColorChooser;
49 import javax.swing.JFileChooser;
50 import javax.swing.JInternalFrame;
51 import javax.swing.JOptionPane;
52 import javax.swing.JPanel;
54 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
62 public class Preferences extends GPreferences
64 public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
66 public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
68 public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
70 public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
72 public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
74 public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
76 public static final String ADD_SS_ANN = "ADD_SS_ANN";
78 public static final String USE_RNAVIEW = "USE_RNAVIEW";
80 public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
82 public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
84 public static final String CHIMERA_PATH = "CHIMERA_PATH";
86 public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
88 public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
90 private static final int MIN_FONT_SIZE = 1;
92 private static final int MAX_FONT_SIZE = 30;
95 * Holds name and link separated with | character. Sequence ID must be
96 * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
98 public static Vector sequenceURLLinks;
101 * Holds name and link separated with | character. Sequence IDS and Sequences
102 * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
103 * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
104 * for first and second token specified after a pipe character at end |,|.
105 * (TODO: proper escape for using | to separate ids or sequences
108 public static Vector groupURLLinks;
111 String string = Cache
114 "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
115 sequenceURLLinks = new Vector();
119 StringTokenizer st = new StringTokenizer(string, "|");
120 while (st.hasMoreElements())
122 String name = st.nextToken();
123 String url = st.nextToken();
124 // check for '|' within a regex
125 int rxstart = url.indexOf("$SEQUENCE_ID$");
126 while (rxstart == -1 && url.indexOf("/=$") == -1)
128 url = url + "|" + st.nextToken();
130 sequenceURLLinks.addElement(name + "|" + url);
132 } catch (Exception ex)
134 System.out.println(ex + "\nError parsing sequence links");
137 // upgrade old SRS link
138 int srsPos = sequenceURLLinks
139 .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
144 "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
150 * TODO: reformulate groupURL encoding so two or more can be stored in the
151 * .properties file as '|' separated strings
154 groupURLLinks = new Vector();
157 Vector nameLinks, urlLinks;
159 JInternalFrame frame;
161 DasSourceBrowser dasSource;
163 private WsPreferences wsPrefs;
166 * Creates a new Preferences object.
171 frame = new JInternalFrame();
172 frame.setContentPane(this);
173 dasSource = new DasSourceBrowser();
174 dasTab.add(dasSource, BorderLayout.CENTER);
175 wsPrefs = new WsPreferences();
176 wsTab.add(wsPrefs, BorderLayout.CENTER);
177 int width = 500, height = 450;
178 if (new jalview.util.Platform().isAMac())
184 Desktop.addInternalFrame(frame,
185 MessageManager.getString("label.preferences"), width, height);
186 frame.setMinimumSize(new Dimension(width, height));
189 * Set Visual tab defaults
191 seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
192 rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
193 fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
194 annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
196 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
197 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
198 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
199 openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
201 .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
202 showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
204 showGroupConservation.setSelected(Cache.getDefault(
205 "SHOW_GROUP_CONSERVATION", false));
206 showConsensHistogram.setSelected(Cache.getDefault(
207 "SHOW_CONSENSUS_HISTOGRAM", true));
208 showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
210 showNpTooltip.setSelected(Cache
211 .getDefault("SHOW_NPFEATS_TOOLTIP", true));
212 showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
215 String[] fonts = java.awt.GraphicsEnvironment
216 .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
217 for (int i = 0; i < fonts.length; i++)
219 fontNameCB.addItem(fonts[i]);
222 for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
224 fontSizeCB.addItem(i + "");
227 fontStyleCB.addItem("plain");
228 fontStyleCB.addItem("bold");
229 fontStyleCB.addItem("italic");
231 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
232 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
233 fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
236 smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
237 scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
240 idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
242 wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
244 gapSymbolCB.addItem("-");
245 gapSymbolCB.addItem(".");
247 gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
249 sortby.addItem("No sort");
250 sortby.addItem("Id");
251 sortby.addItem("Pairwise Identity");
252 sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
254 sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
256 .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
258 .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
259 SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
260 .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
261 SequenceAnnotationOrder.NONE.name()));
262 sortAnnBy.setSelectedItem(savedSort.toString());
264 sortAutocalc.addItem("Autocalculated first");
265 sortAutocalc.addItem("Autocalculated last");
266 final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
267 sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
268 : sortAutocalc.getItemAt(1));
270 .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
271 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
272 Cache.getDefault("www.jalview.org", "http://www.jalview.org")
273 + "/examples/exampleFile_2_3.jar"));
276 * Set Colours tab defaults
278 for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
280 protColour.addItem(ColourSchemeProperty.getColourName(i));
281 nucColour.addItem(ColourSchemeProperty.getColourName(i));
283 String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
284 String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
285 protColour.setSelectedItem(newProp != null ? newProp : oldProp);
286 newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
287 nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
288 minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
290 maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
294 * Set Structure tab defaults.
296 final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
297 structFromPdb.setSelected(structSelected);
298 useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
299 useRnaView.setEnabled(structSelected);
300 addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
301 addSecondaryStructure.setEnabled(structSelected);
302 addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
303 addTempFactor.setEnabled(structSelected);
304 structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
305 ViewerType.JMOL.name()));
306 chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
307 chimeraPath.addActionListener(new ActionListener()
310 public void actionPerformed(ActionEvent e)
312 validateChimeraPath();
316 if (Cache.getDefault("MAP_WITH_SIFTS", false))
318 siftsMapping.setSelected(true);
322 nwMapping.setSelected(true);
326 * Set Connections tab defaults
328 nameLinks = new Vector();
329 urlLinks = new Vector();
330 for (int i = 0; i < sequenceURLLinks.size(); i++)
332 String link = sequenceURLLinks.elementAt(i).toString();
333 nameLinks.addElement(link.substring(0, link.indexOf("|")));
334 urlLinks.addElement(link.substring(link.indexOf("|") + 1));
339 useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
340 proxyServerTB.setEnabled(useProxy.isSelected());
341 proxyPortTB.setEnabled(useProxy.isSelected());
342 proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
343 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
345 defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
347 usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
348 // note antisense here: default is true
350 .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
351 versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
354 * Set Output tab defaults
357 .addItem(MessageManager.getString("label.prompt_each_time"));
358 epsRendering.addItem(MessageManager.getString("label.lineart"));
359 epsRendering.addItem(MessageManager.getString("action.text"));
360 epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
361 "Prompt each time"));
362 autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
363 userIdWidth.setEnabled(!autoIdWidth.isSelected());
364 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
365 Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
366 userIdWidth.setText(wi == null ? "" : wi.toString());
367 blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
368 clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
369 fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
370 msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
371 pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
372 pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
373 pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
374 modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
375 embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
379 * Set Editing tab defaults
381 autoCalculateConsCheck.setSelected(Cache.getDefault(
382 "AUTO_CALC_CONSENSUS", true));
383 padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
384 sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
386 annotations_actionPerformed(null); // update the display of the annotation
391 * Save user selections on the Preferences tabs to the Cache and write out to
397 public void ok_actionPerformed(ActionEvent e)
399 if (!validateSettings())
405 * Save Visual settings
407 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
408 Boolean.toString(seqLimit.isSelected()));
409 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
410 Boolean.toString(rightAlign.isSelected()));
411 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
412 Boolean.toString(fullScreen.isSelected()));
413 Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
414 Boolean.toString(openoverv.isSelected()));
415 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
416 Boolean.toString(annotations.isSelected()));
417 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
418 Boolean.toString(conservation.isSelected()));
419 Cache.applicationProperties.setProperty("SHOW_QUALITY",
420 Boolean.toString(quality.isSelected()));
421 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
422 Boolean.toString(identity.isSelected()));
424 Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
425 .getSelectedItem().toString());
427 Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
428 .getSelectedItem().toString());
429 Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
430 .getSelectedItem().toString());
431 Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
432 .getSelectedItem().toString());
434 Cache.applicationProperties.setProperty("ID_ITALICS",
435 Boolean.toString(idItalics.isSelected()));
436 Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
437 Boolean.toString(showUnconserved.isSelected()));
438 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
439 Boolean.toString(showGroupConsensus.isSelected()));
440 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
441 Boolean.toString(showGroupConservation.isSelected()));
442 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
443 Boolean.toString(showConsensHistogram.isSelected()));
444 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
445 Boolean.toString(showConsensLogo.isSelected()));
446 Cache.applicationProperties.setProperty("ANTI_ALIAS",
447 Boolean.toString(smoothFont.isSelected()));
448 Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
449 Boolean.toString(scaleProteinToCdna.isSelected()));
450 Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
451 Boolean.toString(showNpTooltip.isSelected()));
452 Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
453 Boolean.toString(showDbRefTooltip.isSelected()));
455 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
456 Boolean.toString(wrap.isSelected()));
458 Cache.applicationProperties.setProperty("STARTUP_FILE",
459 startupFileTextfield.getText());
460 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
461 Boolean.toString(startupCheckbox.isSelected()));
463 Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
464 .getSelectedItem().toString());
466 // convert description of sort order to enum name for save
467 SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
468 .forDescription(sortAnnBy.getSelectedItem().toString());
469 if (annSortOrder != null)
471 Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
472 annSortOrder.name());
475 final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
476 Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
477 .valueOf(showAutocalcFirst).toString());
480 * Save Colours settings
482 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
483 .getSelectedItem().toString());
484 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
485 .getSelectedItem().toString());
486 Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
487 minColour.getBackground());
488 Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
489 maxColour.getBackground());
492 * Save Structure settings
494 Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
495 Boolean.toString(addTempFactor.isSelected()));
496 Cache.applicationProperties.setProperty(ADD_SS_ANN,
497 Boolean.toString(addSecondaryStructure.isSelected()));
498 Cache.applicationProperties.setProperty(USE_RNAVIEW,
499 Boolean.toString(useRnaView.isSelected()));
500 Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
501 Boolean.toString(structFromPdb.isSelected()));
502 Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
503 .getSelectedItem().toString());
504 Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
505 Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
506 Boolean.toString(siftsMapping.isSelected()));
509 * Save Output settings
511 if (epsRendering.getSelectedItem().equals("Prompt each time"))
513 Cache.applicationProperties.remove("EPS_RENDERING");
517 Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
518 .getSelectedItem().toString());
522 * Save Connections settings
524 Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
526 jalview.util.BrowserLauncher.resetBrowser();
528 if (nameLinks.size() > 0)
530 StringBuffer links = new StringBuffer();
531 sequenceURLLinks = new Vector();
532 for (int i = 0; i < nameLinks.size(); i++)
534 sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
535 + urlLinks.elementAt(i));
536 links.append(sequenceURLLinks.elementAt(i).toString());
540 links.setLength(links.length() - 1);
541 Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
546 Cache.applicationProperties.remove("SEQUENCE_LINKS");
549 Cache.applicationProperties.setProperty("USE_PROXY",
550 Boolean.toString(useProxy.isSelected()));
552 Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
554 Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
556 if (useProxy.isSelected())
558 System.setProperty("http.proxyHost", proxyServerTB.getText());
559 System.setProperty("http.proxyPort", proxyPortTB.getText());
563 System.setProperty("http.proxyHost", "");
564 System.setProperty("http.proxyPort", "");
566 Cache.setProperty("VERSION_CHECK",
567 Boolean.toString(versioncheck.isSelected()));
568 if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
570 // default is false - we only set this if the user has actively agreed
571 Cache.setProperty("USAGESTATS",
572 Boolean.toString(usagestats.isSelected()));
574 if (!questionnaire.isSelected())
576 Cache.setProperty("NOQUESTIONNAIRES", "true");
580 // special - made easy to edit a property file to disable questionnaires
581 // by just adding the given line
582 Cache.removeProperty("NOQUESTIONNAIRES");
586 * Save Output settings
588 Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
589 Boolean.toString(blcjv.isSelected()));
590 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
591 Boolean.toString(clustaljv.isSelected()));
592 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
593 Boolean.toString(fastajv.isSelected()));
594 Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
595 Boolean.toString(msfjv.isSelected()));
596 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
597 Boolean.toString(pfamjv.isSelected()));
598 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
599 Boolean.toString(pileupjv.isSelected()));
600 Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
601 Boolean.toString(pirjv.isSelected()));
602 Cache.applicationProperties.setProperty("PIR_MODELLER",
603 Boolean.toString(modellerOutput.isSelected()));
604 Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
605 Boolean.toString(embbedBioJSON.isSelected()));
606 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
608 Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
609 Boolean.toString(autoIdWidth.isSelected()));
610 userIdWidth_actionPerformed();
611 Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
612 userIdWidth.getText());
615 * Save Editing settings
617 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
618 Boolean.toString(autoCalculateConsCheck.isSelected()));
619 Cache.applicationProperties.setProperty("SORT_BY_TREE",
620 Boolean.toString(sortByTree.isSelected()));
621 Cache.applicationProperties.setProperty("PAD_GAPS",
622 Boolean.toString(padGaps.isSelected()));
624 dasSource.saveProperties(Cache.applicationProperties);
625 wsPrefs.updateAndRefreshWsMenuConfig(false);
626 Cache.saveProperties();
627 Desktop.instance.doConfigureStructurePrefs();
630 frame.setClosed(true);
631 } catch (Exception ex)
637 * Do any necessary validation before saving settings. Return focus to the
638 * first tab which fails validation.
642 private boolean validateSettings()
644 if (!validateStructure())
646 structureTab.requestFocusInWindow();
653 protected boolean validateStructure()
655 return validateChimeraPath();
663 public void startupFileTextfield_mouseClicked()
665 JalviewFileChooser chooser = new JalviewFileChooser(
666 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
667 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
668 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
669 "PIR", "BLC", "Jalview" },
670 jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
671 chooser.setFileView(new JalviewFileView());
672 chooser.setDialogTitle(MessageManager
673 .getString("label.select_startup_file"));
675 int value = chooser.showOpenDialog(this);
677 if (value == JalviewFileChooser.APPROVE_OPTION)
679 jalview.bin.Cache.applicationProperties.setProperty(
680 "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
681 startupFileTextfield.setText(chooser.getSelectedFile()
693 public void cancel_actionPerformed(ActionEvent e)
697 wsPrefs.updateWsMenuConfig(true);
698 wsPrefs.refreshWs_actionPerformed(e);
699 frame.setClosed(true);
700 } catch (Exception ex)
712 public void annotations_actionPerformed(ActionEvent e)
714 conservation.setEnabled(annotations.isSelected());
715 quality.setEnabled(annotations.isSelected());
716 identity.setEnabled(annotations.isSelected());
717 showGroupConsensus.setEnabled(annotations.isSelected());
718 showGroupConservation.setEnabled(annotations.isSelected());
719 showConsensHistogram.setEnabled(annotations.isSelected()
720 && (identity.isSelected() || showGroupConsensus.isSelected()));
721 showConsensLogo.setEnabled(annotations.isSelected()
722 && (identity.isSelected() || showGroupConsensus.isSelected()));
726 public void newLink_actionPerformed(ActionEvent e)
729 GSequenceLink link = new GSequenceLink();
730 boolean valid = false;
733 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
734 MessageManager.getString("label.new_sequence_url_link"),
735 JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
737 if (link.checkValid())
739 nameLinks.addElement(link.getName());
740 urlLinks.addElement(link.getURL());
753 public void editLink_actionPerformed(ActionEvent e)
755 GSequenceLink link = new GSequenceLink();
757 int index = linkNameList.getSelectedIndex();
760 JOptionPane.showInternalMessageDialog(Desktop.desktop,
761 MessageManager.getString("label.no_link_selected"),
762 MessageManager.getString("label.no_link_selected"),
763 JOptionPane.WARNING_MESSAGE);
767 link.setName(nameLinks.elementAt(index).toString());
768 link.setURL(urlLinks.elementAt(index).toString());
770 boolean valid = false;
774 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
775 MessageManager.getString("label.new_sequence_url_link"),
776 JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
778 if (link.checkValid())
780 nameLinks.setElementAt(link.getName(), index);
781 urlLinks.setElementAt(link.getURL(), index);
795 public void deleteLink_actionPerformed(ActionEvent e)
797 int index = linkNameList.getSelectedIndex();
800 JOptionPane.showInternalMessageDialog(Desktop.desktop,
801 MessageManager.getString("label.no_link_selected"),
802 MessageManager.getString("label.no_link_selected"),
803 JOptionPane.WARNING_MESSAGE);
806 nameLinks.removeElementAt(index);
807 urlLinks.removeElementAt(index);
811 void updateLinkData()
813 linkNameList.setListData(nameLinks);
814 linkURLList.setListData(urlLinks);
818 public void defaultBrowser_mouseClicked(MouseEvent e)
820 JFileChooser chooser = new JFileChooser(".");
821 chooser.setDialogTitle(MessageManager
822 .getString("label.select_default_browser"));
824 int value = chooser.showOpenDialog(this);
826 if (value == JFileChooser.APPROVE_OPTION)
828 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
837 * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
841 protected void showunconserved_actionPerformed(ActionEvent e)
843 // TODO Auto-generated method stub
844 super.showunconserved_actionPerformed(e);
847 public static Collection getGroupURLLinks()
849 return groupURLLinks;
853 public void minColour_actionPerformed(JPanel panel)
855 Color col = JColorChooser.showDialog(this,
856 MessageManager.getString("label.select_colour_minimum_value"),
857 minColour.getBackground());
860 panel.setBackground(col);
866 public void maxColour_actionPerformed(JPanel panel)
868 Color col = JColorChooser.showDialog(this,
869 MessageManager.getString("label.select_colour_maximum_value"),
870 maxColour.getBackground());
873 panel.setBackground(col);
879 protected void userIdWidth_actionPerformed()
883 String val = userIdWidth.getText().trim();
884 if (val.length() > 0)
886 Integer iw = Integer.parseInt(val);
887 if (iw.intValue() < 12)
889 throw new NumberFormatException();
891 userIdWidth.setText(iw.toString());
893 } catch (NumberFormatException x)
895 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
896 .getString("warn.user_defined_width_requirements"),
897 MessageManager.getString("label.invalid_id_column_width"),
898 JOptionPane.WARNING_MESSAGE);
899 userIdWidth.setText("");
904 protected void autoIdWidth_actionPerformed()
906 userIdWidth.setEnabled(!autoIdWidth.isSelected());
907 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
911 * Returns true if chimera path is to a valid executable, else show an error
914 private boolean validateChimeraPath()
916 if (chimeraPath.getText().trim().length() > 0)
918 File f = new File(chimeraPath.getText());
921 JOptionPane.showInternalMessageDialog(Desktop.desktop,
922 MessageManager.getString("label.invalid_chimera_path"),
923 MessageManager.getString("label.invalid_name"),
924 JOptionPane.ERROR_MESSAGE);
932 * If Chimera is selected, check it can be found on default or user-specified
933 * path, if not show a warning/help dialog.
936 protected void structureViewer_actionPerformed(String selectedItem)
938 if (!selectedItem.equals(ViewerType.CHIMERA.name()))
942 boolean found = false;
945 * Try user-specified and standard paths for Chimera executable.
947 List<String> paths = StructureManager.getChimeraPaths();
948 paths.add(0, chimeraPath.getText());
949 for (String path : paths)
951 if (new File(path.trim()).canExecute())
959 String[] options = { "OK", "Help" };
960 int showHelp = JOptionPane.showInternalOptionDialog(
962 JvSwingUtils.wrapTooltip(true,
963 MessageManager.getString("label.chimera_missing")),
964 "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
965 null, options, options[0]);
966 if (showHelp == JOptionPane.NO_OPTION)
970 Help.showHelpWindow(HelpId.StructureViewer);
971 } catch (HelpSetException e)