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.getNumPlaceHolder()));
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());
571 suffixPanel.setPreferredSize(
572 new Dimension(width, suffixPanel.getHeight()));
573 keepfilesPanel.setPreferredSize(
574 new Dimension(width, keepfilesPanel.getHeight()));
575 exampleFilesPanel.setPreferredSize(
576 new Dimension(width, exampleFilesPanel.getHeight()));
582 * Save user selections on the Preferences tabs to the Cache and write out to
588 public void ok_actionPerformed(ActionEvent e)
590 if (!validateSettings())
596 * Save Visual settings
598 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
599 Boolean.toString(seqLimit.isSelected()));
600 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
601 Boolean.toString(rightAlign.isSelected()));
602 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
603 Boolean.toString(fullScreen.isSelected()));
604 Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
605 Boolean.toString(openoverv.isSelected()));
606 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
607 Boolean.toString(annotations.isSelected()));
608 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
609 Boolean.toString(conservation.isSelected()));
610 Cache.applicationProperties.setProperty("SHOW_QUALITY",
611 Boolean.toString(quality.isSelected()));
612 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
613 Boolean.toString(identity.isSelected()));
615 Cache.applicationProperties.setProperty("GAP_SYMBOL",
616 gapSymbolCB.getSelectedItem().toString());
618 Cache.applicationProperties.setProperty("FONT_NAME",
619 fontNameCB.getSelectedItem().toString());
620 Cache.applicationProperties.setProperty("FONT_STYLE",
621 fontStyleCB.getSelectedItem().toString());
622 Cache.applicationProperties.setProperty("FONT_SIZE",
623 fontSizeCB.getSelectedItem().toString());
625 Cache.applicationProperties.setProperty("ID_ITALICS",
626 Boolean.toString(idItalics.isSelected()));
627 Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
628 Boolean.toString(showUnconserved.isSelected()));
629 Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
630 Boolean.toString(showOccupancy.isSelected()));
631 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
632 Boolean.toString(showGroupConsensus.isSelected()));
633 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
634 Boolean.toString(showGroupConservation.isSelected()));
635 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
636 Boolean.toString(showConsensHistogram.isSelected()));
637 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
638 Boolean.toString(showConsensLogo.isSelected()));
639 Cache.applicationProperties.setProperty("ANTI_ALIAS",
640 Boolean.toString(smoothFont.isSelected()));
641 Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
642 Boolean.toString(scaleProteinToCdna.isSelected()));
643 Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
644 Boolean.toString(showNpTooltip.isSelected()));
645 Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
646 Boolean.toString(showDbRefTooltip.isSelected()));
648 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
649 Boolean.toString(wrap.isSelected()));
651 Cache.applicationProperties.setProperty("STARTUP_FILE",
652 startupFileTextfield.getText());
653 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
654 Boolean.toString(startupCheckbox.isSelected()));
656 Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
657 sortby.getSelectedItem().toString());
659 // convert description of sort order to enum name for save
660 SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
661 .forDescription(sortAnnBy.getSelectedItem().toString());
662 if (annSortOrder != null)
664 Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
665 annSortOrder.name());
668 final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
669 Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
670 Boolean.valueOf(showAutocalcFirst).toString());
673 * Save Colours settings
675 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
676 protColour.getSelectedItem().toString());
677 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
678 nucColour.getSelectedItem().toString());
679 Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
680 minColour.getBackground());
681 Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
682 maxColour.getBackground());
685 * Save Overview settings
687 Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
688 Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
689 Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
690 Boolean.toString(useLegacyGap.isSelected()));
691 Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
692 Boolean.toString(showHiddenAtStart.isSelected()));
695 * Save Structure settings
697 Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
698 Boolean.toString(addTempFactor.isSelected()));
699 Cache.applicationProperties.setProperty(ADD_SS_ANN,
700 Boolean.toString(addSecondaryStructure.isSelected()));
701 Cache.applicationProperties.setProperty(USE_RNAVIEW,
702 Boolean.toString(useRnaView.isSelected()));
703 Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
704 Boolean.toString(structFromPdb.isSelected()));
705 Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
706 structViewer.getSelectedItem().toString());
707 Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
708 Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
709 Boolean.toString(siftsMapping.isSelected()));
710 SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
713 * Save Output settings
715 Cache.applicationProperties.setProperty("EPS_RENDERING",
716 ((OptionsParam) epsRendering.getSelectedItem()).getCode());
719 * Save Connections settings
721 Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
723 jalview.util.BrowserLauncher.resetBrowser();
725 // save user-defined and selected links
726 String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
727 if (menuLinks.isEmpty())
729 Cache.applicationProperties.remove("SEQUENCE_LINKS");
733 Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
734 menuLinks.toString());
737 String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
738 if (nonMenuLinks.isEmpty())
740 Cache.applicationProperties.remove("STORED_LINKS");
744 Cache.applicationProperties.setProperty("STORED_LINKS",
745 nonMenuLinks.toString());
748 Cache.applicationProperties.setProperty("DEFAULT_URL",
749 sequenceUrlLinks.getPrimaryUrlId());
751 Cache.applicationProperties.setProperty("USE_PROXY",
752 Boolean.toString(useProxy.isSelected()));
754 Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
756 Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
758 if (useProxy.isSelected())
760 System.setProperty("http.proxyHost", proxyServerTB.getText());
761 System.setProperty("http.proxyPort", proxyPortTB.getText());
765 System.setProperty("http.proxyHost", "");
766 System.setProperty("http.proxyPort", "");
768 Cache.setProperty("VERSION_CHECK",
769 Boolean.toString(versioncheck.isSelected()));
770 if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
772 // default is false - we only set this if the user has actively agreed
773 Cache.setProperty("USAGESTATS",
774 Boolean.toString(usagestats.isSelected()));
776 if (!questionnaire.isSelected())
778 Cache.setProperty("NOQUESTIONNAIRES", "true");
782 // special - made easy to edit a property file to disable questionnaires
783 // by just adding the given line
784 Cache.removeProperty("NOQUESTIONNAIRES");
788 * Save Output settings
790 Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
791 Boolean.toString(blcjv.isSelected()));
792 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
793 Boolean.toString(clustaljv.isSelected()));
794 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
795 Boolean.toString(fastajv.isSelected()));
796 Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
797 Boolean.toString(msfjv.isSelected()));
798 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
799 Boolean.toString(pfamjv.isSelected()));
800 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
801 Boolean.toString(pileupjv.isSelected()));
802 Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
803 Boolean.toString(pirjv.isSelected()));
804 Cache.applicationProperties.setProperty("PIR_MODELLER",
805 Boolean.toString(modellerOutput.isSelected()));
806 Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
807 Boolean.toString(embbedBioJSON.isSelected()));
808 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
810 Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
811 Boolean.toString(autoIdWidth.isSelected()));
812 userIdWidth_actionPerformed();
813 Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
814 userIdWidth.getText());
817 * Save Editing settings
819 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
820 Boolean.toString(autoCalculateConsCheck.isSelected()));
821 Cache.applicationProperties.setProperty("SORT_BY_TREE",
822 Boolean.toString(sortByTree.isSelected()));
823 Cache.applicationProperties.setProperty("PAD_GAPS",
824 Boolean.toString(padGaps.isSelected()));
826 wsPrefs.updateAndRefreshWsMenuConfig(false);
829 * Save Backups settings
831 Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
832 Boolean.toString(backupfilesConfirmDelete.isSelected()));
833 Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
834 Boolean.toString(enableBackupFiles.isSelected()));
835 Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
836 Boolean.toString(backupfilesKeepAll.isSelected()));
837 Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
838 Boolean.toString(suffixReverse.isSelected()));
839 Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
840 suffixTemplate.getText());
841 Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
842 Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
843 Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
844 Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
846 Cache.saveProperties();
847 Desktop.instance.doConfigureStructurePrefs();
850 frame.setClosed(true);
851 } catch (Exception ex)
857 * Do any necessary validation before saving settings. Return focus to the
858 * first tab which fails validation.
862 private boolean validateSettings()
864 if (!validateStructure())
866 structureTab.requestFocusInWindow();
873 protected boolean validateStructure()
875 return validateChimeraPath();
883 public void startupFileTextfield_mouseClicked()
885 String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
886 JalviewFileChooser chooser = JalviewFileChooser
887 .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
888 chooser.setFileView(new JalviewFileView());
889 chooser.setDialogTitle(
890 MessageManager.getString("label.select_startup_file"));
892 int value = chooser.showOpenDialog(this);
894 if (value == JalviewFileChooser.APPROVE_OPTION)
896 FileFormatI format = chooser.getSelectedFormat();
899 Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
903 .setText(chooser.getSelectedFile().getAbsolutePath());
914 public void cancel_actionPerformed(ActionEvent e)
918 wsPrefs.updateWsMenuConfig(true);
919 wsPrefs.refreshWs_actionPerformed(e);
920 frame.setClosed(true);
921 } catch (Exception ex)
933 public void annotations_actionPerformed(ActionEvent e)
935 conservation.setEnabled(annotations.isSelected());
936 quality.setEnabled(annotations.isSelected());
937 identity.setEnabled(annotations.isSelected());
938 showOccupancy.setEnabled(annotations.isSelected());
939 showGroupConsensus.setEnabled(annotations.isSelected());
940 showGroupConservation.setEnabled(annotations.isSelected());
941 showConsensHistogram.setEnabled(annotations.isSelected()
942 && (identity.isSelected() || showGroupConsensus.isSelected()));
943 showConsensLogo.setEnabled(annotations.isSelected()
944 && (identity.isSelected() || showGroupConsensus.isSelected()));
948 public void newLink_actionPerformed(ActionEvent e)
950 GSequenceLink link = new GSequenceLink();
951 boolean valid = false;
954 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
955 MessageManager.getString("label.new_sequence_url_link"),
956 JvOptionPane.OK_CANCEL_OPTION, -1,
957 null) == JvOptionPane.OK_OPTION)
959 if (link.checkValid())
961 if (((UrlLinkTableModel) linkUrlTable.getModel())
962 .isUniqueName(link.getName()))
964 ((UrlLinkTableModel) linkUrlTable.getModel())
965 .insertRow(link.getName(), link.getURL());
970 link.notifyDuplicate();
983 public void editLink_actionPerformed(ActionEvent e)
985 GSequenceLink link = new GSequenceLink();
987 int index = linkUrlTable.getSelectedRow();
990 // button no longer enabled if row is not selected
991 Cache.log.debug("Edit with no row selected in linkUrlTable");
995 int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
997 int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
999 String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1000 link.setName(oldName);
1001 link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1003 boolean valid = false;
1006 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1007 MessageManager.getString("label.edit_sequence_url_link"),
1008 JvOptionPane.OK_CANCEL_OPTION, -1,
1009 null) == JvOptionPane.OK_OPTION)
1011 if (link.checkValid())
1013 if ((oldName.equals(link.getName()))
1014 || (((UrlLinkTableModel) linkUrlTable.getModel())
1015 .isUniqueName(link.getName())))
1017 linkUrlTable.setValueAt(link.getName(), index, nameCol);
1018 linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1023 link.notifyDuplicate();
1036 public void deleteLink_actionPerformed(ActionEvent e)
1038 int index = linkUrlTable.getSelectedRow();
1039 int modelIndex = -1;
1042 // button no longer enabled if row is not selected
1043 Cache.log.debug("Delete with no row selected in linkUrlTable");
1048 modelIndex = linkUrlTable.convertRowIndexToModel(index);
1051 // make sure we use the model index to delete, and not the table index
1052 ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1056 public void defaultBrowser_mouseClicked(MouseEvent e)
1058 JFileChooser chooser = new JFileChooser(".");
1059 chooser.setDialogTitle(
1060 MessageManager.getString("label.select_default_browser"));
1062 int value = chooser.showOpenDialog(this);
1064 if (value == JFileChooser.APPROVE_OPTION)
1066 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1075 * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1079 protected void showunconserved_actionPerformed(ActionEvent e)
1081 // TODO Auto-generated method stub
1082 super.showunconserved_actionPerformed(e);
1085 public static List<String> getGroupURLLinks()
1087 return groupURLLinks;
1091 public void minColour_actionPerformed(JPanel panel)
1093 Color col = JColorChooser.showDialog(this,
1094 MessageManager.getString("label.select_colour_minimum_value"),
1095 minColour.getBackground());
1098 panel.setBackground(col);
1104 public void maxColour_actionPerformed(JPanel panel)
1106 Color col = JColorChooser.showDialog(this,
1107 MessageManager.getString("label.select_colour_maximum_value"),
1108 maxColour.getBackground());
1111 panel.setBackground(col);
1117 public void gapColour_actionPerformed(JPanel gap)
1119 if (!useLegacyGap.isSelected())
1121 Color col = JColorChooser.showDialog(this,
1122 MessageManager.getString("label.select_gap_colour"),
1123 gapColour.getBackground());
1126 gap.setBackground(col);
1133 public void hiddenColour_actionPerformed(JPanel hidden)
1135 Color col = JColorChooser.showDialog(this,
1136 MessageManager.getString("label.select_hidden_colour"),
1137 hiddenColour.getBackground());
1140 hidden.setBackground(col);
1146 protected void useLegacyGaps_actionPerformed(ActionEvent e)
1148 boolean enabled = useLegacyGap.isSelected();
1151 gapColour.setBackground(
1152 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1156 gapColour.setBackground(
1157 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1159 gapColour.setEnabled(!enabled);
1160 gapLabel.setEnabled(!enabled);
1164 protected void resetOvDefaults_actionPerformed(ActionEvent e)
1166 useLegacyGap.setSelected(false);
1167 useLegacyGaps_actionPerformed(null);
1168 showHiddenAtStart.setSelected(true);
1169 hiddenColour.setBackground(
1170 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1174 protected void userIdWidth_actionPerformed()
1178 String val = userIdWidth.getText().trim();
1179 if (val.length() > 0)
1181 Integer iw = Integer.parseInt(val);
1182 if (iw.intValue() < 12)
1184 throw new NumberFormatException();
1186 userIdWidth.setText(iw.toString());
1188 } catch (NumberFormatException x)
1190 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1192 .getString("warn.user_defined_width_requirements"),
1193 MessageManager.getString("label.invalid_id_column_width"),
1194 JvOptionPane.WARNING_MESSAGE);
1195 userIdWidth.setText("");
1200 protected void autoIdWidth_actionPerformed()
1202 userIdWidth.setEnabled(!autoIdWidth.isSelected());
1203 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1207 * Returns true if chimera path is to a valid executable, else show an error
1210 private boolean validateChimeraPath()
1212 if (chimeraPath.getText().trim().length() > 0)
1214 File f = new File(chimeraPath.getText());
1215 if (!f.canExecute())
1217 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1218 MessageManager.getString("label.invalid_chimera_path"),
1219 MessageManager.getString("label.invalid_name"),
1220 JvOptionPane.ERROR_MESSAGE);
1228 * If Chimera is selected, check it can be found on default or user-specified
1229 * path, if not show a warning/help dialog.
1232 protected void structureViewer_actionPerformed(String selectedItem)
1234 if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1238 boolean found = false;
1241 * Try user-specified and standard paths for Chimera executable.
1243 List<String> paths = StructureManager.getChimeraPaths();
1244 paths.add(0, chimeraPath.getText());
1245 for (String path : paths)
1247 if (new File(path.trim()).canExecute())
1255 String[] options = { "OK", "Help" };
1256 int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1257 JvSwingUtils.wrapTooltip(true,
1258 MessageManager.getString("label.chimera_missing")),
1259 "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1260 null, options, options[0]);
1261 if (showHelp == JvOptionPane.NO_OPTION)
1265 Help.showHelpWindow(HelpId.StructureViewer);
1266 } catch (HelpSetException e)
1268 e.printStackTrace();
1274 public class OptionsParam
1276 private String name;
1278 private String code;
1280 public OptionsParam(String name, String code)
1286 public String getName()
1291 public void setName(String name)
1296 public String getCode()
1301 public void setCode(String code)
1307 public String toString()
1313 public boolean equals(Object that)
1315 if (!(that instanceof OptionsParam))
1319 return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1323 public int hashCode()
1325 return name.hashCode() + code.hashCode();
1329 private class UrlListSelectionHandler implements ListSelectionListener
1333 public void valueChanged(ListSelectionEvent e)
1335 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1337 int index = lsm.getMinSelectionIndex();
1340 // no selection, so disable delete/edit buttons
1341 editLink.setEnabled(false);
1342 deleteLink.setEnabled(false);
1345 int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1347 // enable/disable edit and delete link buttons
1348 if (((UrlLinkTableModel) linkUrlTable.getModel())
1349 .isRowDeletable(modelIndex))
1351 deleteLink.setEnabled(true);
1355 deleteLink.setEnabled(false);
1358 if (((UrlLinkTableModel) linkUrlTable.getModel())
1359 .isRowEditable(modelIndex))
1361 editLink.setEnabled(true);
1365 editLink.setEnabled(false);