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.BackupFiles;
28 import jalview.io.FileFormatI;
29 import jalview.io.JalviewFileChooser;
30 import jalview.io.JalviewFileView;
31 import jalview.jbgui.GPreferences;
32 import jalview.jbgui.GSequenceLink;
33 import jalview.schemes.ColourSchemeI;
34 import jalview.schemes.ColourSchemes;
35 import jalview.schemes.ResidueColourScheme;
36 import jalview.urls.UrlLinkTableModel;
37 import jalview.urls.api.UrlProviderFactoryI;
38 import jalview.urls.api.UrlProviderI;
39 import jalview.urls.desktop.DesktopUrlProviderFactory;
40 import jalview.util.MessageManager;
41 import jalview.util.Platform;
42 import jalview.util.UrlConstants;
43 import jalview.ws.sifts.SiftsSettings;
45 import java.awt.BorderLayout;
46 import java.awt.Color;
47 import java.awt.Component;
48 import java.awt.Dimension;
50 import java.awt.event.ActionEvent;
51 import java.awt.event.ActionListener;
52 import java.awt.event.MouseEvent;
54 import java.util.ArrayList;
55 import java.util.List;
57 import javax.help.HelpSetException;
58 import javax.swing.JColorChooser;
59 import javax.swing.JFileChooser;
60 import javax.swing.JInternalFrame;
61 import javax.swing.JPanel;
62 import javax.swing.ListSelectionModel;
63 import javax.swing.RowFilter;
64 import javax.swing.RowSorter;
65 import javax.swing.SortOrder;
66 import javax.swing.event.DocumentEvent;
67 import javax.swing.event.DocumentListener;
68 import javax.swing.event.ListSelectionEvent;
69 import javax.swing.event.ListSelectionListener;
70 import javax.swing.table.TableCellRenderer;
71 import javax.swing.table.TableColumn;
72 import javax.swing.table.TableModel;
73 import javax.swing.table.TableRowSorter;
75 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
83 public class Preferences extends GPreferences
85 public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
87 public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
89 public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
91 public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
93 public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
95 public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
97 public static final String ADD_SS_ANN = "ADD_SS_ANN";
99 public static final String USE_RNAVIEW = "USE_RNAVIEW";
101 public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
103 public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
105 public static final String CHIMERA_PATH = "CHIMERA_PATH";
107 public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
109 public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
111 public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
113 public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
115 public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
117 public static final String GAP_COLOUR = "GAP_COLOUR";
119 public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
121 private static final int MIN_FONT_SIZE = 1;
123 private static final int MAX_FONT_SIZE = 30;
126 * Holds name and link separated with | character. Sequence ID must be
127 * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
129 public static UrlProviderI sequenceUrlLinks;
131 public static UrlLinkTableModel dataModel;
134 * Holds name and link separated with | character. Sequence IDS and Sequences
135 * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
136 * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
137 * for first and second token specified after a pipe character at end |,|.
138 * (TODO: proper escape for using | to separate ids or sequences
141 public static List<String> groupURLLinks;
144 // get links selected to be in the menu (SEQUENCE_LINKS)
145 // and links entered by the user but not selected (STORED_LINKS)
146 String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
147 String notInMenuString = Cache.getDefault("STORED_LINKS", "");
148 String defaultUrl = Cache.getDefault("DEFAULT_URL",
149 UrlConstants.DEFAULT_LABEL);
151 // if both links lists are empty, add the DEFAULT_URL link
152 // otherwise we assume the default link is in one of the lists
153 if (inMenuString.isEmpty() && notInMenuString.isEmpty())
155 inMenuString = UrlConstants.DEFAULT_STRING;
157 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
158 inMenuString, notInMenuString);
159 sequenceUrlLinks = factory.createUrlProvider();
160 dataModel = new UrlLinkTableModel(sequenceUrlLinks);
163 * TODO: reformulate groupURL encoding so two or more can be stored in the
164 * .properties file as '|' separated strings
167 groupURLLinks = new ArrayList<>();
170 JInternalFrame frame;
172 private WsPreferences wsPrefs;
174 private OptionsParam promptEachTimeOpt = new OptionsParam(
175 MessageManager.getString("label.prompt_each_time"),
178 private OptionsParam lineArtOpt = new OptionsParam(
179 MessageManager.getString("label.lineart"), "Lineart");
181 private OptionsParam textOpt = new OptionsParam(
182 MessageManager.getString("action.text"), "Text");
185 * Creates a new Preferences object.
190 frame = new JInternalFrame();
191 frame.setContentPane(this);
192 wsPrefs = new WsPreferences();
193 wsTab.add(wsPrefs, BorderLayout.CENTER);
194 int width = 500, height = 450;
195 new jalview.util.Platform();
196 if (Platform.isAMac())
202 Desktop.addInternalFrame(frame,
203 MessageManager.getString("label.preferences"), width, height);
204 frame.setMinimumSize(new Dimension(width, height));
207 * Set Visual tab defaults
209 seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
210 rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
211 fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
212 annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
214 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
215 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
216 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
217 openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
219 .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
220 showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
222 .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
223 showGroupConservation.setSelected(
224 Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
225 showConsensHistogram.setSelected(
226 Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
228 .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
230 .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
232 .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
234 String[] fonts = java.awt.GraphicsEnvironment
235 .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
236 for (int i = 0; i < fonts.length; i++)
238 fontNameCB.addItem(fonts[i]);
241 for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
243 fontSizeCB.addItem(i + "");
246 fontStyleCB.addItem("plain");
247 fontStyleCB.addItem("bold");
248 fontStyleCB.addItem("italic");
250 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
251 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
252 fontStyleCB.setSelectedItem(
253 Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
255 smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
257 .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
259 idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
261 wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
263 gapSymbolCB.addItem("-");
264 gapSymbolCB.addItem(".");
266 gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
268 sortby.addItem("No sort");
269 sortby.addItem("Id");
270 sortby.addItem("Pairwise Identity");
271 sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
273 sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
275 .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
277 .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
278 SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
279 .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
280 SequenceAnnotationOrder.NONE.name()));
281 sortAnnBy.setSelectedItem(savedSort.toString());
283 sortAutocalc.addItem("Autocalculated first");
284 sortAutocalc.addItem("Autocalculated last");
285 final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
286 sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
287 : sortAutocalc.getItemAt(1));
289 .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
290 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
291 Cache.getDefault("www.jalview.org", "http://www.jalview.org")
292 + "/examples/exampleFile_2_3.jar"));
295 * Set Colours tab defaults
297 protColour.addItem(ResidueColourScheme.NONE);
298 nucColour.addItem(ResidueColourScheme.NONE);
299 for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
301 String name = cs.getSchemeName();
302 protColour.addItem(name);
303 nucColour.addItem(name);
305 String oldProp = Cache.getDefault(DEFAULT_COLOUR,
306 ResidueColourScheme.NONE);
307 String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
308 protColour.setSelectedItem(newProp != null ? newProp : oldProp);
309 newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
310 nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
311 minColour.setBackground(
312 Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
313 maxColour.setBackground(
314 Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
317 * Set overview panel defaults
319 gapColour.setBackground(
320 Cache.getDefaultColour(GAP_COLOUR,
321 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
322 hiddenColour.setBackground(
323 Cache.getDefaultColour(HIDDEN_COLOUR,
324 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
325 useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
326 gapLabel.setEnabled(!useLegacyGap.isSelected());
327 gapColour.setEnabled(!useLegacyGap.isSelected());
329 .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
332 * Set Structure tab defaults.
334 final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
335 structFromPdb.setSelected(structSelected);
336 useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
337 useRnaView.setEnabled(structSelected);
338 addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
339 addSecondaryStructure.setEnabled(structSelected);
340 addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
341 addTempFactor.setEnabled(structSelected);
342 structViewer.setSelectedItem(
343 Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
344 chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
345 chimeraPath.addActionListener(new ActionListener()
348 public void actionPerformed(ActionEvent e)
350 validateChimeraPath();
354 if (Cache.getDefault("MAP_WITH_SIFTS", false))
356 siftsMapping.setSelected(true);
360 nwMapping.setSelected(true);
364 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
367 * Set Connections tab defaults
371 linkUrlTable.setModel(dataModel);
372 final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
373 linkUrlTable.getModel());
374 linkUrlTable.setRowSorter(sorter);
375 List<RowSorter.SortKey> sortKeys = new ArrayList<>();
377 UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
378 sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
379 SortOrder.DESCENDING));
380 sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
381 SortOrder.DESCENDING));
383 new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
385 sorter.setSortKeys(sortKeys);
389 ActionListener onReset;
390 onReset = new ActionListener()
393 public void actionPerformed(ActionEvent e)
395 filterTB.setText("");
396 sorter.setRowFilter(RowFilter.regexFilter(""));
400 doReset.addActionListener(onReset);
402 // filter to display only custom urls
403 final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
406 public boolean include(
407 Entry<? extends TableModel, ? extends Object> entry)
409 return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
413 final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
414 linkUrlTable.getModel());
415 customSorter.setRowFilter(customUrlFilter);
417 ActionListener onCustomOnly;
418 onCustomOnly = new ActionListener()
421 public void actionPerformed(ActionEvent e)
423 filterTB.setText("");
424 sorter.setRowFilter(customUrlFilter);
427 userOnly.addActionListener(onCustomOnly);
429 filterTB.getDocument().addDocumentListener(new DocumentListener()
431 String caseInsensitiveFlag = "(?i)";
434 public void changedUpdate(DocumentEvent e)
436 sorter.setRowFilter(RowFilter
437 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
441 public void removeUpdate(DocumentEvent e)
443 sorter.setRowFilter(RowFilter
444 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
448 public void insertUpdate(DocumentEvent e)
450 sorter.setRowFilter(RowFilter
451 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
455 // set up list selection functionality
456 linkUrlTable.getSelectionModel()
457 .addListSelectionListener(new UrlListSelectionHandler());
459 // set up radio buttons
460 int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
462 String onClickName = linkUrlTable.getColumnName(onClickCol);
463 linkUrlTable.getColumn(onClickName)
464 .setCellRenderer(new RadioButtonRenderer());
465 linkUrlTable.getColumn(onClickName)
466 .setCellEditor(new RadioButtonEditor());
468 // get boolean columns and resize those to min possible
469 for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
471 if (linkUrlTable.getModel().getColumnClass(column)
472 .equals(Boolean.class))
474 TableColumn tableColumn = linkUrlTable.getColumnModel()
476 int preferredWidth = tableColumn.getMinWidth();
478 TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
480 Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
481 int cwidth = c.getPreferredSize().width
482 + linkUrlTable.getIntercellSpacing().width;
483 preferredWidth = Math.max(preferredWidth, cwidth);
485 tableColumn.setPreferredWidth(preferredWidth);
489 useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
490 useProxy_actionPerformed(); // make sure useProxy is correctly initialised
491 proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
492 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
494 defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
496 usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
497 // note antisense here: default is true
499 .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
500 versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
503 * Set Output tab defaults
505 epsRendering.addItem(promptEachTimeOpt);
506 epsRendering.addItem(lineArtOpt);
507 epsRendering.addItem(textOpt);
508 String defaultEPS = Cache.getDefault("EPS_RENDERING",
510 if (defaultEPS.equalsIgnoreCase("Text"))
512 epsRendering.setSelectedItem(textOpt);
514 else if (defaultEPS.equalsIgnoreCase("Lineart"))
516 epsRendering.setSelectedItem(lineArtOpt);
520 epsRendering.setSelectedItem(promptEachTimeOpt);
522 autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
523 userIdWidth.setEnabled(!autoIdWidth.isSelected());
524 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
525 Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
526 userIdWidth.setText(wi == null ? "" : wi.toString());
527 // TODO: refactor to use common enum via FormatAdapter and allow extension
528 // for new flat file formats
529 blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
530 clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
531 fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
532 msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
533 pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
534 pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
535 pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
536 modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
538 .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
541 * Set Editing tab defaults
543 autoCalculateConsCheck
544 .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
545 padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
546 sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
548 annotations_actionPerformed(null); // update the display of the annotation
553 * Set Backups tab defaults
556 .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
557 suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX,
558 "-v" + BackupFiles.NUM_PLACEHOLDER));
560 .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3));
561 suffixReverse.setSelected(
562 Cache.getDefault(BackupFiles.REVERSE_ORDER, false));
564 .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false));
565 backupfilesRollMaxSpinner
566 .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 4));
567 backupfilesConfirmDelete.setSelected(
568 Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true));
569 backupsOptionsSetEnabled(enableBackupFiles.isSelected());
570 updateBackupFilesExampleLabel();
572 suffixPanel.setPreferredSize(
573 new Dimension(width, suffixPanel.getHeight()));
574 keepfilesPanel.setPreferredSize(
575 new Dimension(width, keepfilesPanel.getHeight()));
576 exampleFilesPanel.setPreferredSize(
577 new Dimension(width, exampleFilesPanel.getHeight()));
583 * Save user selections on the Preferences tabs to the Cache and write out to
589 public void ok_actionPerformed(ActionEvent e)
591 if (!validateSettings())
597 * Save Visual settings
599 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
600 Boolean.toString(seqLimit.isSelected()));
601 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
602 Boolean.toString(rightAlign.isSelected()));
603 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
604 Boolean.toString(fullScreen.isSelected()));
605 Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
606 Boolean.toString(openoverv.isSelected()));
607 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
608 Boolean.toString(annotations.isSelected()));
609 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
610 Boolean.toString(conservation.isSelected()));
611 Cache.applicationProperties.setProperty("SHOW_QUALITY",
612 Boolean.toString(quality.isSelected()));
613 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
614 Boolean.toString(identity.isSelected()));
616 Cache.applicationProperties.setProperty("GAP_SYMBOL",
617 gapSymbolCB.getSelectedItem().toString());
619 Cache.applicationProperties.setProperty("FONT_NAME",
620 fontNameCB.getSelectedItem().toString());
621 Cache.applicationProperties.setProperty("FONT_STYLE",
622 fontStyleCB.getSelectedItem().toString());
623 Cache.applicationProperties.setProperty("FONT_SIZE",
624 fontSizeCB.getSelectedItem().toString());
626 Cache.applicationProperties.setProperty("ID_ITALICS",
627 Boolean.toString(idItalics.isSelected()));
628 Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
629 Boolean.toString(showUnconserved.isSelected()));
630 Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
631 Boolean.toString(showOccupancy.isSelected()));
632 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
633 Boolean.toString(showGroupConsensus.isSelected()));
634 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
635 Boolean.toString(showGroupConservation.isSelected()));
636 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
637 Boolean.toString(showConsensHistogram.isSelected()));
638 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
639 Boolean.toString(showConsensLogo.isSelected()));
640 Cache.applicationProperties.setProperty("ANTI_ALIAS",
641 Boolean.toString(smoothFont.isSelected()));
642 Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
643 Boolean.toString(scaleProteinToCdna.isSelected()));
644 Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
645 Boolean.toString(showNpTooltip.isSelected()));
646 Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
647 Boolean.toString(showDbRefTooltip.isSelected()));
649 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
650 Boolean.toString(wrap.isSelected()));
652 Cache.applicationProperties.setProperty("STARTUP_FILE",
653 startupFileTextfield.getText());
654 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
655 Boolean.toString(startupCheckbox.isSelected()));
657 Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
658 sortby.getSelectedItem().toString());
660 // convert description of sort order to enum name for save
661 SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
662 .forDescription(sortAnnBy.getSelectedItem().toString());
663 if (annSortOrder != null)
665 Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
666 annSortOrder.name());
669 final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
670 Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
671 Boolean.valueOf(showAutocalcFirst).toString());
674 * Save Colours settings
676 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
677 protColour.getSelectedItem().toString());
678 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
679 nucColour.getSelectedItem().toString());
680 Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
681 minColour.getBackground());
682 Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
683 maxColour.getBackground());
686 * Save Overview settings
688 Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
689 Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
690 Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
691 Boolean.toString(useLegacyGap.isSelected()));
692 Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
693 Boolean.toString(showHiddenAtStart.isSelected()));
696 * Save Structure settings
698 Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
699 Boolean.toString(addTempFactor.isSelected()));
700 Cache.applicationProperties.setProperty(ADD_SS_ANN,
701 Boolean.toString(addSecondaryStructure.isSelected()));
702 Cache.applicationProperties.setProperty(USE_RNAVIEW,
703 Boolean.toString(useRnaView.isSelected()));
704 Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
705 Boolean.toString(structFromPdb.isSelected()));
706 Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
707 structViewer.getSelectedItem().toString());
708 Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
709 Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
710 Boolean.toString(siftsMapping.isSelected()));
711 SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
714 * Save Output settings
716 Cache.applicationProperties.setProperty("EPS_RENDERING",
717 ((OptionsParam) epsRendering.getSelectedItem()).getCode());
720 * Save Connections settings
722 Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
724 jalview.util.BrowserLauncher.resetBrowser();
726 // save user-defined and selected links
727 String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
728 if (menuLinks.isEmpty())
730 Cache.applicationProperties.remove("SEQUENCE_LINKS");
734 Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
735 menuLinks.toString());
738 String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
739 if (nonMenuLinks.isEmpty())
741 Cache.applicationProperties.remove("STORED_LINKS");
745 Cache.applicationProperties.setProperty("STORED_LINKS",
746 nonMenuLinks.toString());
749 Cache.applicationProperties.setProperty("DEFAULT_URL",
750 sequenceUrlLinks.getPrimaryUrlId());
752 Cache.applicationProperties.setProperty("USE_PROXY",
753 Boolean.toString(useProxy.isSelected()));
755 Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
757 Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
759 if (useProxy.isSelected())
761 System.setProperty("http.proxyHost", proxyServerTB.getText());
762 System.setProperty("http.proxyPort", proxyPortTB.getText());
766 System.setProperty("http.proxyHost", "");
767 System.setProperty("http.proxyPort", "");
769 Cache.setProperty("VERSION_CHECK",
770 Boolean.toString(versioncheck.isSelected()));
771 if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
773 // default is false - we only set this if the user has actively agreed
774 Cache.setProperty("USAGESTATS",
775 Boolean.toString(usagestats.isSelected()));
777 if (!questionnaire.isSelected())
779 Cache.setProperty("NOQUESTIONNAIRES", "true");
783 // special - made easy to edit a property file to disable questionnaires
784 // by just adding the given line
785 Cache.removeProperty("NOQUESTIONNAIRES");
789 * Save Output settings
791 Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
792 Boolean.toString(blcjv.isSelected()));
793 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
794 Boolean.toString(clustaljv.isSelected()));
795 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
796 Boolean.toString(fastajv.isSelected()));
797 Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
798 Boolean.toString(msfjv.isSelected()));
799 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
800 Boolean.toString(pfamjv.isSelected()));
801 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
802 Boolean.toString(pileupjv.isSelected()));
803 Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
804 Boolean.toString(pirjv.isSelected()));
805 Cache.applicationProperties.setProperty("PIR_MODELLER",
806 Boolean.toString(modellerOutput.isSelected()));
807 Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
808 Boolean.toString(embbedBioJSON.isSelected()));
809 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
811 Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
812 Boolean.toString(autoIdWidth.isSelected()));
813 userIdWidth_actionPerformed();
814 Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
815 userIdWidth.getText());
818 * Save Editing settings
820 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
821 Boolean.toString(autoCalculateConsCheck.isSelected()));
822 Cache.applicationProperties.setProperty("SORT_BY_TREE",
823 Boolean.toString(sortByTree.isSelected()));
824 Cache.applicationProperties.setProperty("PAD_GAPS",
825 Boolean.toString(padGaps.isSelected()));
827 wsPrefs.updateAndRefreshWsMenuConfig(false);
830 * Save Backups settings
832 Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
833 Boolean.toString(backupfilesConfirmDelete.isSelected()));
834 Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
835 Boolean.toString(enableBackupFiles.isSelected()));
836 Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
837 Boolean.toString(backupfilesKeepAll.isSelected()));
838 Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
839 Boolean.toString(suffixReverse.isSelected()));
840 Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
841 suffixTemplate.getText());
842 Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
843 Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
844 Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
845 Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
847 Cache.saveProperties();
848 Desktop.instance.doConfigureStructurePrefs();
851 frame.setClosed(true);
852 } catch (Exception ex)
858 * Do any necessary validation before saving settings. Return focus to the
859 * first tab which fails validation.
863 private boolean validateSettings()
865 if (!validateStructure())
867 structureTab.requestFocusInWindow();
874 protected boolean validateStructure()
876 return validateChimeraPath();
884 public void startupFileTextfield_mouseClicked()
886 String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
887 JalviewFileChooser chooser = JalviewFileChooser
888 .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
889 chooser.setFileView(new JalviewFileView());
890 chooser.setDialogTitle(
891 MessageManager.getString("label.select_startup_file"));
893 int value = chooser.showOpenDialog(this);
895 if (value == JalviewFileChooser.APPROVE_OPTION)
897 FileFormatI format = chooser.getSelectedFormat();
900 Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
904 .setText(chooser.getSelectedFile().getAbsolutePath());
915 public void cancel_actionPerformed(ActionEvent e)
919 wsPrefs.updateWsMenuConfig(true);
920 wsPrefs.refreshWs_actionPerformed(e);
921 frame.setClosed(true);
922 } catch (Exception ex)
934 public void annotations_actionPerformed(ActionEvent e)
936 conservation.setEnabled(annotations.isSelected());
937 quality.setEnabled(annotations.isSelected());
938 identity.setEnabled(annotations.isSelected());
939 showOccupancy.setEnabled(annotations.isSelected());
940 showGroupConsensus.setEnabled(annotations.isSelected());
941 showGroupConservation.setEnabled(annotations.isSelected());
942 showConsensHistogram.setEnabled(annotations.isSelected()
943 && (identity.isSelected() || showGroupConsensus.isSelected()));
944 showConsensLogo.setEnabled(annotations.isSelected()
945 && (identity.isSelected() || showGroupConsensus.isSelected()));
949 public void newLink_actionPerformed(ActionEvent e)
951 GSequenceLink link = new GSequenceLink();
952 boolean valid = false;
955 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
956 MessageManager.getString("label.new_sequence_url_link"),
957 JvOptionPane.OK_CANCEL_OPTION, -1,
958 null) == JvOptionPane.OK_OPTION)
960 if (link.checkValid())
962 if (((UrlLinkTableModel) linkUrlTable.getModel())
963 .isUniqueName(link.getName()))
965 ((UrlLinkTableModel) linkUrlTable.getModel())
966 .insertRow(link.getName(), link.getURL());
971 link.notifyDuplicate();
984 public void editLink_actionPerformed(ActionEvent e)
986 GSequenceLink link = new GSequenceLink();
988 int index = linkUrlTable.getSelectedRow();
991 // button no longer enabled if row is not selected
992 Cache.log.debug("Edit with no row selected in linkUrlTable");
996 int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
998 int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1000 String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1001 link.setName(oldName);
1002 link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1004 boolean valid = false;
1007 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1008 MessageManager.getString("label.edit_sequence_url_link"),
1009 JvOptionPane.OK_CANCEL_OPTION, -1,
1010 null) == JvOptionPane.OK_OPTION)
1012 if (link.checkValid())
1014 if ((oldName.equals(link.getName()))
1015 || (((UrlLinkTableModel) linkUrlTable.getModel())
1016 .isUniqueName(link.getName())))
1018 linkUrlTable.setValueAt(link.getName(), index, nameCol);
1019 linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1024 link.notifyDuplicate();
1037 public void deleteLink_actionPerformed(ActionEvent e)
1039 int index = linkUrlTable.getSelectedRow();
1040 int modelIndex = -1;
1043 // button no longer enabled if row is not selected
1044 Cache.log.debug("Delete with no row selected in linkUrlTable");
1049 modelIndex = linkUrlTable.convertRowIndexToModel(index);
1052 // make sure we use the model index to delete, and not the table index
1053 ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1057 public void defaultBrowser_mouseClicked(MouseEvent e)
1059 JFileChooser chooser = new JFileChooser(".");
1060 chooser.setDialogTitle(
1061 MessageManager.getString("label.select_default_browser"));
1063 int value = chooser.showOpenDialog(this);
1065 if (value == JFileChooser.APPROVE_OPTION)
1067 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1076 * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1080 protected void showunconserved_actionPerformed(ActionEvent e)
1082 // TODO Auto-generated method stub
1083 super.showunconserved_actionPerformed(e);
1086 public static List<String> getGroupURLLinks()
1088 return groupURLLinks;
1092 public void minColour_actionPerformed(JPanel panel)
1094 Color col = JColorChooser.showDialog(this,
1095 MessageManager.getString("label.select_colour_minimum_value"),
1096 minColour.getBackground());
1099 panel.setBackground(col);
1105 public void maxColour_actionPerformed(JPanel panel)
1107 Color col = JColorChooser.showDialog(this,
1108 MessageManager.getString("label.select_colour_maximum_value"),
1109 maxColour.getBackground());
1112 panel.setBackground(col);
1118 public void gapColour_actionPerformed(JPanel gap)
1120 if (!useLegacyGap.isSelected())
1122 Color col = JColorChooser.showDialog(this,
1123 MessageManager.getString("label.select_gap_colour"),
1124 gapColour.getBackground());
1127 gap.setBackground(col);
1134 public void hiddenColour_actionPerformed(JPanel hidden)
1136 Color col = JColorChooser.showDialog(this,
1137 MessageManager.getString("label.select_hidden_colour"),
1138 hiddenColour.getBackground());
1141 hidden.setBackground(col);
1147 protected void useLegacyGaps_actionPerformed(ActionEvent e)
1149 boolean enabled = useLegacyGap.isSelected();
1152 gapColour.setBackground(
1153 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1157 gapColour.setBackground(
1158 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1160 gapColour.setEnabled(!enabled);
1161 gapLabel.setEnabled(!enabled);
1165 protected void resetOvDefaults_actionPerformed(ActionEvent e)
1167 useLegacyGap.setSelected(false);
1168 useLegacyGaps_actionPerformed(null);
1169 showHiddenAtStart.setSelected(true);
1170 hiddenColour.setBackground(
1171 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1175 protected void userIdWidth_actionPerformed()
1179 String val = userIdWidth.getText().trim();
1180 if (val.length() > 0)
1182 Integer iw = Integer.parseInt(val);
1183 if (iw.intValue() < 12)
1185 throw new NumberFormatException();
1187 userIdWidth.setText(iw.toString());
1189 } catch (NumberFormatException x)
1191 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1193 .getString("warn.user_defined_width_requirements"),
1194 MessageManager.getString("label.invalid_id_column_width"),
1195 JvOptionPane.WARNING_MESSAGE);
1196 userIdWidth.setText("");
1201 protected void autoIdWidth_actionPerformed()
1203 userIdWidth.setEnabled(!autoIdWidth.isSelected());
1204 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1208 * Returns true if chimera path is to a valid executable, else show an error
1211 private boolean validateChimeraPath()
1213 if (chimeraPath.getText().trim().length() > 0)
1215 File f = new File(chimeraPath.getText());
1216 if (!f.canExecute())
1218 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1219 MessageManager.getString("label.invalid_chimera_path"),
1220 MessageManager.getString("label.invalid_name"),
1221 JvOptionPane.ERROR_MESSAGE);
1229 * If Chimera is selected, check it can be found on default or user-specified
1230 * path, if not show a warning/help dialog.
1233 protected void structureViewer_actionPerformed(String selectedItem)
1235 if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1239 boolean found = false;
1242 * Try user-specified and standard paths for Chimera executable.
1244 List<String> paths = StructureManager.getChimeraPaths();
1245 paths.add(0, chimeraPath.getText());
1246 for (String path : paths)
1248 if (new File(path.trim()).canExecute())
1256 String[] options = { "OK", "Help" };
1257 int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1258 JvSwingUtils.wrapTooltip(true,
1259 MessageManager.getString("label.chimera_missing")),
1260 "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1261 null, options, options[0]);
1262 if (showHelp == JvOptionPane.NO_OPTION)
1266 Help.showHelpWindow(HelpId.StructureViewer);
1267 } catch (HelpSetException e)
1269 e.printStackTrace();
1275 public class OptionsParam
1277 private String name;
1279 private String code;
1281 public OptionsParam(String name, String code)
1287 public String getName()
1292 public void setName(String name)
1297 public String getCode()
1302 public void setCode(String code)
1308 public String toString()
1314 public boolean equals(Object that)
1316 if (!(that instanceof OptionsParam))
1320 return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1324 public int hashCode()
1326 return name.hashCode() + code.hashCode();
1330 private class UrlListSelectionHandler implements ListSelectionListener
1334 public void valueChanged(ListSelectionEvent e)
1336 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1338 int index = lsm.getMinSelectionIndex();
1341 // no selection, so disable delete/edit buttons
1342 editLink.setEnabled(false);
1343 deleteLink.setEnabled(false);
1346 int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1348 // enable/disable edit and delete link buttons
1349 if (((UrlLinkTableModel) linkUrlTable.getModel())
1350 .isRowDeletable(modelIndex))
1352 deleteLink.setEnabled(true);
1356 deleteLink.setEnabled(false);
1359 if (((UrlLinkTableModel) linkUrlTable.getModel())
1360 .isRowEditable(modelIndex))
1362 editLink.setEnabled(true);
1366 editLink.setEnabled(false);