2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
3 * Copyright (C) 2015 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();
317 * Set Connections tab defaults
319 nameLinks = new Vector();
320 urlLinks = new Vector();
321 for (int i = 0; i < sequenceURLLinks.size(); i++)
323 String link = sequenceURLLinks.elementAt(i).toString();
324 nameLinks.addElement(link.substring(0, link.indexOf("|")));
325 urlLinks.addElement(link.substring(link.indexOf("|") + 1));
330 useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
331 proxyServerTB.setEnabled(useProxy.isSelected());
332 proxyPortTB.setEnabled(useProxy.isSelected());
333 proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
334 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
336 defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
338 usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
339 // note antisense here: default is true
341 .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
342 versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
345 * Set Output tab defaults
348 .addItem(MessageManager.getString("label.prompt_each_time"));
349 epsRendering.addItem(MessageManager.getString("label.lineart"));
350 epsRendering.addItem(MessageManager.getString("action.text"));
351 epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
352 "Prompt each time"));
353 autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
354 userIdWidth.setEnabled(!autoIdWidth.isSelected());
355 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
356 Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
357 userIdWidth.setText(wi == null ? "" : wi.toString());
358 blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
359 clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
360 fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
361 msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
362 pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
363 pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
364 pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
365 modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
366 embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
370 * Set Editing tab defaults
372 autoCalculateConsCheck.setSelected(Cache.getDefault(
373 "AUTO_CALC_CONSENSUS", true));
374 padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
375 sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
377 annotations_actionPerformed(null); // update the display of the annotation
382 * Save user selections on the Preferences tabs to the Cache and write out to
387 public void ok_actionPerformed(ActionEvent e)
389 if (!validateSettings())
395 * Save Visual settings
397 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
398 Boolean.toString(seqLimit.isSelected()));
399 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
400 Boolean.toString(rightAlign.isSelected()));
401 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
402 Boolean.toString(fullScreen.isSelected()));
403 Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
404 Boolean.toString(openoverv.isSelected()));
405 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
406 Boolean.toString(annotations.isSelected()));
407 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
408 Boolean.toString(conservation.isSelected()));
409 Cache.applicationProperties.setProperty("SHOW_QUALITY",
410 Boolean.toString(quality.isSelected()));
411 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
412 Boolean.toString(identity.isSelected()));
414 Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
415 .getSelectedItem().toString());
417 Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
418 .getSelectedItem().toString());
419 Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
420 .getSelectedItem().toString());
421 Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
422 .getSelectedItem().toString());
424 Cache.applicationProperties.setProperty("ID_ITALICS",
425 Boolean.toString(idItalics.isSelected()));
426 Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
427 Boolean.toString(showUnconserved.isSelected()));
428 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
429 Boolean.toString(showGroupConsensus.isSelected()));
430 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
431 Boolean.toString(showGroupConservation.isSelected()));
432 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
433 Boolean.toString(showConsensHistogram.isSelected()));
434 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
435 Boolean.toString(showConsensLogo.isSelected()));
436 Cache.applicationProperties.setProperty("ANTI_ALIAS",
437 Boolean.toString(smoothFont.isSelected()));
438 Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
439 Boolean.toString(scaleProteinToCdna.isSelected()));
440 Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
441 Boolean.toString(showNpTooltip.isSelected()));
442 Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
443 Boolean.toString(showDbRefTooltip.isSelected()));
445 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
446 Boolean.toString(wrap.isSelected()));
448 Cache.applicationProperties.setProperty("STARTUP_FILE",
449 startupFileTextfield.getText());
450 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
451 Boolean.toString(startupCheckbox.isSelected()));
453 Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
454 .getSelectedItem().toString());
456 // convert description of sort order to enum name for save
457 SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
458 .forDescription(sortAnnBy.getSelectedItem().toString());
459 if (annSortOrder != null)
461 Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
462 annSortOrder.name());
465 final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
466 Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
467 .valueOf(showAutocalcFirst).toString());
470 * Save Colours settings
472 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
473 .getSelectedItem().toString());
474 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
475 .getSelectedItem().toString());
476 Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
477 minColour.getBackground());
478 Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
479 maxColour.getBackground());
482 * Save Structure settings
484 Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
485 Boolean.toString(addTempFactor.isSelected()));
486 Cache.applicationProperties.setProperty(ADD_SS_ANN,
487 Boolean.toString(addSecondaryStructure.isSelected()));
488 Cache.applicationProperties.setProperty(USE_RNAVIEW,
489 Boolean.toString(useRnaView.isSelected()));
490 Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
491 Boolean.toString(structFromPdb.isSelected()));
492 Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
493 .getSelectedItem().toString());
494 Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
497 * Save Output settings
499 if (epsRendering.getSelectedItem().equals("Prompt each time"))
501 Cache.applicationProperties.remove("EPS_RENDERING");
505 Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
506 .getSelectedItem().toString());
510 * Save Connections settings
512 Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
514 jalview.util.BrowserLauncher.resetBrowser();
516 if (nameLinks.size() > 0)
518 StringBuffer links = new StringBuffer();
519 sequenceURLLinks = new Vector();
520 for (int i = 0; i < nameLinks.size(); i++)
522 sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
523 + urlLinks.elementAt(i));
524 links.append(sequenceURLLinks.elementAt(i).toString());
528 links.setLength(links.length() - 1);
529 Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
534 Cache.applicationProperties.remove("SEQUENCE_LINKS");
537 Cache.applicationProperties.setProperty("USE_PROXY",
538 Boolean.toString(useProxy.isSelected()));
540 Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
542 Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
544 if (useProxy.isSelected())
546 System.setProperty("http.proxyHost", proxyServerTB.getText());
547 System.setProperty("http.proxyPort", proxyPortTB.getText());
551 System.setProperty("http.proxyHost", "");
552 System.setProperty("http.proxyPort", "");
554 Cache.setProperty("VERSION_CHECK",
555 Boolean.toString(versioncheck.isSelected()));
556 if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
558 // default is false - we only set this if the user has actively agreed
559 Cache.setProperty("USAGESTATS",
560 Boolean.toString(usagestats.isSelected()));
562 if (!questionnaire.isSelected())
564 Cache.setProperty("NOQUESTIONNAIRES", "true");
568 // special - made easy to edit a property file to disable questionnaires
569 // by just adding the given line
570 Cache.removeProperty("NOQUESTIONNAIRES");
574 * Save Output settings
576 Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
577 Boolean.toString(blcjv.isSelected()));
578 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
579 Boolean.toString(clustaljv.isSelected()));
580 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
581 Boolean.toString(fastajv.isSelected()));
582 Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
583 Boolean.toString(msfjv.isSelected()));
584 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
585 Boolean.toString(pfamjv.isSelected()));
586 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
587 Boolean.toString(pileupjv.isSelected()));
588 Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
589 Boolean.toString(pirjv.isSelected()));
590 Cache.applicationProperties.setProperty("PIR_MODELLER",
591 Boolean.toString(modellerOutput.isSelected()));
592 Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
593 Boolean.toString(embbedBioJSON.isSelected()));
594 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
596 Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
597 Boolean.toString(autoIdWidth.isSelected()));
598 userIdWidth_actionPerformed();
599 Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
600 userIdWidth.getText());
603 * Save Editing settings
605 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
606 Boolean.toString(autoCalculateConsCheck.isSelected()));
607 Cache.applicationProperties.setProperty("SORT_BY_TREE",
608 Boolean.toString(sortByTree.isSelected()));
609 Cache.applicationProperties.setProperty("PAD_GAPS",
610 Boolean.toString(padGaps.isSelected()));
612 dasSource.saveProperties(Cache.applicationProperties);
613 wsPrefs.updateAndRefreshWsMenuConfig(false);
614 Cache.saveProperties();
615 Desktop.instance.doConfigureStructurePrefs();
618 frame.setClosed(true);
619 } catch (Exception ex)
625 * Do any necessary validation before saving settings. Return focus to the
626 * first tab which fails validation.
630 private boolean validateSettings()
632 if (!validateStructure())
634 structureTab.requestFocusInWindow();
641 protected boolean validateStructure()
643 return validateChimeraPath();
650 public void startupFileTextfield_mouseClicked()
652 JalviewFileChooser chooser = new JalviewFileChooser(
653 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
654 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
655 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
656 "PIR", "BLC", "Jalview" },
657 jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
658 chooser.setFileView(new JalviewFileView());
659 chooser.setDialogTitle(MessageManager
660 .getString("label.select_startup_file"));
662 int value = chooser.showOpenDialog(this);
664 if (value == JalviewFileChooser.APPROVE_OPTION)
666 jalview.bin.Cache.applicationProperties.setProperty(
667 "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
668 startupFileTextfield.setText(chooser.getSelectedFile()
679 public void cancel_actionPerformed(ActionEvent e)
683 wsPrefs.updateWsMenuConfig(true);
684 wsPrefs.refreshWs_actionPerformed(e);
685 frame.setClosed(true);
686 } catch (Exception ex)
697 public void annotations_actionPerformed(ActionEvent e)
699 conservation.setEnabled(annotations.isSelected());
700 quality.setEnabled(annotations.isSelected());
701 identity.setEnabled(annotations.isSelected());
702 showGroupConsensus.setEnabled(annotations.isSelected());
703 showGroupConservation.setEnabled(annotations.isSelected());
704 showConsensHistogram.setEnabled(annotations.isSelected()
705 && (identity.isSelected() || showGroupConsensus.isSelected()));
706 showConsensLogo.setEnabled(annotations.isSelected()
707 && (identity.isSelected() || showGroupConsensus.isSelected()));
710 public void newLink_actionPerformed(ActionEvent e)
713 GSequenceLink link = new GSequenceLink();
714 boolean valid = false;
717 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
718 MessageManager.getString("label.new_sequence_url_link"),
719 JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
721 if (link.checkValid())
723 nameLinks.addElement(link.getName());
724 urlLinks.addElement(link.getURL());
736 public void editLink_actionPerformed(ActionEvent e)
738 GSequenceLink link = new GSequenceLink();
740 int index = linkNameList.getSelectedIndex();
743 JOptionPane.showInternalMessageDialog(Desktop.desktop,
744 MessageManager.getString("label.no_link_selected"),
745 MessageManager.getString("label.no_link_selected"),
746 JOptionPane.WARNING_MESSAGE);
750 link.setName(nameLinks.elementAt(index).toString());
751 link.setURL(urlLinks.elementAt(index).toString());
753 boolean valid = false;
757 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
758 MessageManager.getString("label.new_sequence_url_link"),
759 JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
761 if (link.checkValid())
763 nameLinks.setElementAt(link.getName(), index);
764 urlLinks.setElementAt(link.getURL(), index);
777 public void deleteLink_actionPerformed(ActionEvent e)
779 int index = linkNameList.getSelectedIndex();
782 JOptionPane.showInternalMessageDialog(Desktop.desktop,
783 MessageManager.getString("label.no_link_selected"),
784 MessageManager.getString("label.no_link_selected"),
785 JOptionPane.WARNING_MESSAGE);
788 nameLinks.removeElementAt(index);
789 urlLinks.removeElementAt(index);
793 void updateLinkData()
795 linkNameList.setListData(nameLinks);
796 linkURLList.setListData(urlLinks);
799 public void defaultBrowser_mouseClicked(MouseEvent e)
801 JFileChooser chooser = new JFileChooser(".");
802 chooser.setDialogTitle(MessageManager
803 .getString("label.select_default_browser"));
805 int value = chooser.showOpenDialog(this);
807 if (value == JFileChooser.APPROVE_OPTION)
809 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
818 * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
821 protected void showunconserved_actionPerformed(ActionEvent e)
823 // TODO Auto-generated method stub
824 super.showunconserved_actionPerformed(e);
827 public static Collection getGroupURLLinks()
829 return groupURLLinks;
833 public void minColour_actionPerformed(JPanel panel)
835 Color col = JColorChooser.showDialog(this,
836 MessageManager.getString("label.select_colour_minimum_value"),
837 minColour.getBackground());
840 panel.setBackground(col);
846 public void maxColour_actionPerformed(JPanel panel)
848 Color col = JColorChooser.showDialog(this,
849 MessageManager.getString("label.select_colour_maximum_value"),
850 maxColour.getBackground());
853 panel.setBackground(col);
859 protected void userIdWidth_actionPerformed()
863 String val = userIdWidth.getText().trim();
864 if (val.length() > 0)
866 Integer iw = Integer.parseInt(val);
867 if (iw.intValue() < 12)
869 throw new NumberFormatException();
871 userIdWidth.setText(iw.toString());
873 } catch (NumberFormatException x)
875 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
876 .getString("warn.user_defined_width_requirements"),
877 MessageManager.getString("label.invalid_id_column_width"),
878 JOptionPane.WARNING_MESSAGE);
879 userIdWidth.setText("");
884 protected void autoIdWidth_actionPerformed()
886 userIdWidth.setEnabled(!autoIdWidth.isSelected());
887 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
891 * Returns true if chimera path is to a valid executable, else show an error
894 private boolean validateChimeraPath()
896 if (chimeraPath.getText().trim().length() > 0)
898 File f = new File(chimeraPath.getText());
901 JOptionPane.showInternalMessageDialog(Desktop.desktop,
902 MessageManager.getString("label.invalid_chimera_path"),
903 MessageManager.getString("label.invalid_name"),
904 JOptionPane.ERROR_MESSAGE);
912 * If Chimera is selected, check it can be found on default or user-specified
913 * path, if not show a warning/help dialog.
916 protected void structureViewer_actionPerformed(String selectedItem)
918 if (!selectedItem.equals(ViewerType.CHIMERA.name()))
922 boolean found = false;
925 * Try user-specified and standard paths for Chimera executable.
927 List<String> paths = StructureManager.getChimeraPaths();
928 paths.add(0, chimeraPath.getText());
929 for (String path : paths)
931 if (new File(path.trim()).canExecute())
939 String[] options = { "OK", "Help" };
940 int showHelp = JOptionPane.showInternalOptionDialog(
942 JvSwingUtils.wrapTooltip(true,
943 MessageManager.getString("label.chimera_missing")),
944 "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
945 null, options, options[0]);
946 if (showHelp == JOptionPane.NO_OPTION)
950 Help.showHelpWindow(HelpId.StructureViewer);
951 } catch (HelpSetException e)