JAL-1759 corrected syntax for 'atom picked' callback (toggles label
[jalview.git] / src / jalview / gui / Preferences.java
1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
4  * 
5  * This file is part of Jalview.
6  * 
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.
11  *  
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.
16  * 
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.
20  */
21 package jalview.gui;
22
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.bin.Cache;
25 import jalview.gui.Help.HelpId;
26 import jalview.gui.StructureViewer.ViewerType;
27 import jalview.io.JalviewFileChooser;
28 import jalview.io.JalviewFileView;
29 import jalview.jbgui.GPreferences;
30 import jalview.jbgui.GSequenceLink;
31 import jalview.schemes.ColourSchemeProperty;
32 import jalview.util.MessageManager;
33
34 import java.awt.BorderLayout;
35 import java.awt.Color;
36 import java.awt.Dimension;
37 import java.awt.Font;
38 import java.awt.event.ActionEvent;
39 import java.awt.event.ActionListener;
40 import java.awt.event.MouseEvent;
41 import java.io.File;
42 import java.util.Collection;
43 import java.util.List;
44 import java.util.StringTokenizer;
45 import java.util.Vector;
46
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;
53
54 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
55
56 /**
57  * DOCUMENT ME!
58  * 
59  * @author $author$
60  * @version $Revision$
61  */
62 public class Preferences extends GPreferences
63 {
64   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
65
66   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
67
68   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
69
70   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
71
72   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
73
74   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
75
76   public static final String ADD_SS_ANN = "ADD_SS_ANN";
77
78   public static final String USE_RNAVIEW = "USE_RNAVIEW";
79
80   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
81
82   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
83
84   public static final String CHIMERA_PATH = "CHIMERA_PATH";
85
86   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
87
88   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
89
90   private static final int MIN_FONT_SIZE = 1;
91
92   private static final int MAX_FONT_SIZE = 30;
93
94   /**
95    * Holds name and link separated with | character. Sequence ID must be
96    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
97    */
98   public static Vector sequenceURLLinks;
99
100   /**
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
106    */
107
108   public static Vector groupURLLinks;
109   static
110   {
111     String string = Cache
112             .getDefault(
113                     "SEQUENCE_LINKS",
114                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
115     sequenceURLLinks = new Vector();
116
117     try
118     {
119       StringTokenizer st = new StringTokenizer(string, "|");
120       while (st.hasMoreElements())
121       {
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("/=$") == -1)
127         {
128           url = url + "|" + st.nextToken();
129         }
130         sequenceURLLinks.addElement(name + "|" + url);
131       }
132     } catch (Exception ex)
133     {
134       System.out.println(ex + "\nError parsing sequence links");
135     }
136     {
137       // upgrade old SRS link
138       int srsPos = sequenceURLLinks
139               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
140       if (srsPos > -1)
141       {
142         sequenceURLLinks
143                 .setElementAt(
144                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
145                         srsPos);
146       }
147     }
148
149     /**
150      * TODO: reformulate groupURL encoding so two or more can be stored in the
151      * .properties file as '|' separated strings
152      */
153
154     groupURLLinks = new Vector();
155   }
156
157   Vector nameLinks, urlLinks;
158
159   JInternalFrame frame;
160
161   DasSourceBrowser dasSource;
162
163   private WsPreferences wsPrefs;
164
165   /**
166    * Creates a new Preferences object.
167    */
168   public Preferences()
169   {
170     super();
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())
179     {
180       width = 570;
181       height = 480;
182     }
183
184     Desktop.addInternalFrame(frame,
185             MessageManager.getString("label.preferences"), width, height);
186     frame.setMinimumSize(new Dimension(width, height));
187
188     /*
189      * Set Visual tab defaults
190      */
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));
195
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));
200     showUnconserved
201             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
202     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
203             false));
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",
209             false));
210     showNpTooltip.setSelected(Cache
211             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
212     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
213             true));
214
215     String[] fonts = java.awt.GraphicsEnvironment
216             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
217     for (int i = 0; i < fonts.length; i++)
218     {
219       fontNameCB.addItem(fonts[i]);
220     }
221
222     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
223     {
224       fontSizeCB.addItem(i + "");
225     }
226
227     fontStyleCB.addItem("plain");
228     fontStyleCB.addItem("bold");
229     fontStyleCB.addItem("italic");
230
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
234             + ""));
235
236     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
237     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
238             false));
239
240     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
241
242     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
243
244     gapSymbolCB.addItem("-");
245     gapSymbolCB.addItem(".");
246
247     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
248
249     sortby.addItem("No sort");
250     sortby.addItem("Id");
251     sortby.addItem("Pairwise Identity");
252     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
253
254     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
255     sortAnnBy
256             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
257     sortAnnBy
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());
263
264     sortAutocalc.addItem("Autocalculated first");
265     sortAutocalc.addItem("Autocalculated last");
266     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
267             true);
268     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
269             : sortAutocalc.getItemAt(1));
270     startupCheckbox
271             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
272     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
273             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
274                     + "/examples/exampleFile_2_3.jar"));
275
276     /*
277      * Set Colours tab defaults
278      */
279     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
280     {
281       protColour.addItem(ColourSchemeProperty.getColourName(i));
282       nucColour.addItem(ColourSchemeProperty.getColourName(i));
283     }
284     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
285     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
286     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
287     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
288     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
289     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
290             Color.orange));
291     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
292             Color.red));
293
294     /*
295      * Set Structure tab defaults.
296      */
297     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
298     structFromPdb.setSelected(structSelected);
299     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
300     useRnaView.setEnabled(structSelected);
301     addSecondaryStructure
302             .setSelected(Cache.getDefault(ADD_SS_ANN, false));
303     addSecondaryStructure.setEnabled(structSelected);
304     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
305     addTempFactor.setEnabled(structSelected);
306     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
307             ViewerType.JMOL.name()));
308     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
309     chimeraPath.addActionListener(new ActionListener()
310     {
311       @Override
312       public void actionPerformed(ActionEvent e)
313       {
314         validateChimeraPath();
315       }
316     });
317
318     /*
319      * Set Connections tab defaults
320      */
321     nameLinks = new Vector();
322     urlLinks = new Vector();
323     for (int i = 0; i < sequenceURLLinks.size(); i++)
324     {
325       String link = sequenceURLLinks.elementAt(i).toString();
326       nameLinks.addElement(link.substring(0, link.indexOf("|")));
327       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
328     }
329
330     updateLinkData();
331
332     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
333     proxyServerTB.setEnabled(useProxy.isSelected());
334     proxyPortTB.setEnabled(useProxy.isSelected());
335     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
336     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
337
338     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
339
340     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
341     // note antisense here: default is true
342     questionnaire
343             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
344     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
345
346     /*
347      * Set Output tab defaults
348      */
349     epsRendering
350             .addItem(MessageManager.getString("label.prompt_each_time"));
351     epsRendering.addItem(MessageManager.getString("label.lineart"));
352     epsRendering.addItem(MessageManager.getString("action.text"));
353     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
354             "Prompt each time"));
355     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
356     userIdWidth.setEnabled(autoIdWidth.isSelected());
357     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
358     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
359     userIdWidth.setText(wi == null ? "" : wi.toString());
360     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
361     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
362     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
363     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
364     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
365     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
366     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
367     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
368     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
369             true));
370
371     /*
372      * Set Editing tab defaults
373      */
374     autoCalculateConsCheck.setSelected(Cache.getDefault(
375             "AUTO_CALC_CONSENSUS", true));
376     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
377     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
378
379     annotations_actionPerformed(null); // update the display of the annotation
380                                        // settings
381   }
382
383   /**
384    * Save user selections on the Preferences tabs to the Cache and write out to
385    * file.
386    * 
387    * @param e
388    */
389   public void ok_actionPerformed(ActionEvent e)
390   {
391     if (!validateSettings())
392     {
393       return;
394     }
395
396     /*
397      * Save Visual settings
398      */
399     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
400             Boolean.toString(seqLimit.isSelected()));
401     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
402             Boolean.toString(rightAlign.isSelected()));
403     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
404             Boolean.toString(fullScreen.isSelected()));
405     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
406             Boolean.toString(openoverv.isSelected()));
407     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
408             Boolean.toString(annotations.isSelected()));
409     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
410             Boolean.toString(conservation.isSelected()));
411     Cache.applicationProperties.setProperty("SHOW_QUALITY",
412             Boolean.toString(quality.isSelected()));
413     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
414             Boolean.toString(identity.isSelected()));
415
416     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
417             .getSelectedItem().toString());
418
419     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
420             .getSelectedItem().toString());
421     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
422             .getSelectedItem().toString());
423     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
424             .getSelectedItem().toString());
425
426     Cache.applicationProperties.setProperty("ID_ITALICS",
427             Boolean.toString(idItalics.isSelected()));
428     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
429             Boolean.toString(showUnconserved.isSelected()));
430     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
431             Boolean.toString(showGroupConsensus.isSelected()));
432     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
433             Boolean.toString(showGroupConservation.isSelected()));
434     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
435             Boolean.toString(showConsensHistogram.isSelected()));
436     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
437             Boolean.toString(showConsensLogo.isSelected()));
438     Cache.applicationProperties.setProperty("ANTI_ALIAS",
439             Boolean.toString(smoothFont.isSelected()));
440     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
441             Boolean.toString(scaleProteinToCdna.isSelected()));
442     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
443             Boolean.toString(showNpTooltip.isSelected()));
444     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
445             Boolean.toString(showDbRefTooltip.isSelected()));
446
447     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
448             Boolean.toString(wrap.isSelected()));
449
450     Cache.applicationProperties.setProperty("STARTUP_FILE",
451             startupFileTextfield.getText());
452     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
453             Boolean.toString(startupCheckbox.isSelected()));
454
455     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
456             .getSelectedItem().toString());
457
458     // convert description of sort order to enum name for save
459     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
460             .forDescription(sortAnnBy.getSelectedItem().toString());
461     if (annSortOrder != null)
462     {
463       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
464               annSortOrder.name());
465     }
466
467     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
468     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
469             Boolean.valueOf(showAutocalcFirst).toString());
470
471     /*
472      * Save Colours settings
473      */
474     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
475             .getSelectedItem().toString());
476     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
477             .getSelectedItem().toString());
478     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
479             minColour.getBackground());
480     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
481             maxColour.getBackground());
482
483     /*
484      * Save Structure settings
485      */
486     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
487             Boolean.toString(addTempFactor.isSelected()));
488     Cache.applicationProperties.setProperty(ADD_SS_ANN,
489             Boolean.toString(addSecondaryStructure.isSelected()));
490     Cache.applicationProperties.setProperty(USE_RNAVIEW,
491             Boolean.toString(useRnaView.isSelected()));
492     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
493             Boolean.toString(structFromPdb.isSelected()));
494     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
495             .getSelectedItem().toString());
496     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
497
498     /*
499      * Save Output settings
500      */
501     if (epsRendering.getSelectedItem().equals("Prompt each time"))
502     {
503       Cache.applicationProperties.remove("EPS_RENDERING");
504     }
505     else
506     {
507       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
508               .getSelectedItem().toString());
509     }
510
511     /*
512      * Save Connections settings
513      */
514     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
515
516     jalview.util.BrowserLauncher.resetBrowser();
517
518     if (nameLinks.size() > 0)
519     {
520       StringBuffer links = new StringBuffer();
521       sequenceURLLinks = new Vector();
522       for (int i = 0; i < nameLinks.size(); i++)
523       {
524         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
525                 + urlLinks.elementAt(i));
526         links.append(sequenceURLLinks.elementAt(i).toString());
527         links.append("|");
528       }
529       // remove last "|"
530       links.setLength(links.length() - 1);
531       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
532               links.toString());
533     }
534     else
535     {
536       Cache.applicationProperties.remove("SEQUENCE_LINKS");
537     }
538
539     Cache.applicationProperties.setProperty("USE_PROXY",
540             Boolean.toString(useProxy.isSelected()));
541
542     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
543
544     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
545
546     if (useProxy.isSelected())
547     {
548       System.setProperty("http.proxyHost", proxyServerTB.getText());
549       System.setProperty("http.proxyPort", proxyPortTB.getText());
550     }
551     else
552     {
553       System.setProperty("http.proxyHost", "");
554       System.setProperty("http.proxyPort", "");
555     }
556     Cache.setProperty("VERSION_CHECK",
557             Boolean.toString(versioncheck.isSelected()));
558     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
559     {
560       // default is false - we only set this if the user has actively agreed
561       Cache.setProperty("USAGESTATS",
562               Boolean.toString(usagestats.isSelected()));
563     }
564     if (!questionnaire.isSelected())
565     {
566       Cache.setProperty("NOQUESTIONNAIRES", "true");
567     }
568     else
569     {
570       // special - made easy to edit a property file to disable questionnaires
571       // by just adding the given line
572       Cache.removeProperty("NOQUESTIONNAIRES");
573     }
574
575     /*
576      * Save Output settings
577      */
578     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
579             Boolean.toString(blcjv.isSelected()));
580     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
581             Boolean.toString(clustaljv.isSelected()));
582     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
583             Boolean.toString(fastajv.isSelected()));
584     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
585             Boolean.toString(msfjv.isSelected()));
586     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
587             Boolean.toString(pfamjv.isSelected()));
588     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
589             Boolean.toString(pileupjv.isSelected()));
590     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
591             Boolean.toString(pirjv.isSelected()));
592     Cache.applicationProperties.setProperty("PIR_MODELLER",
593             Boolean.toString(modellerOutput.isSelected()));
594     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
595             Boolean.toString(embbedBioJSON.isSelected()));
596     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
597
598     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
599             Boolean.toString(autoIdWidth.isSelected()));
600     userIdWidth_actionPerformed();
601     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
602             userIdWidth.getText());
603
604     /*
605      * Save Editing settings
606      */
607     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
608             Boolean.toString(autoCalculateConsCheck.isSelected()));
609     Cache.applicationProperties.setProperty("SORT_BY_TREE",
610             Boolean.toString(sortByTree.isSelected()));
611     Cache.applicationProperties.setProperty("PAD_GAPS",
612             Boolean.toString(padGaps.isSelected()));
613
614     dasSource.saveProperties(Cache.applicationProperties);
615     wsPrefs.updateAndRefreshWsMenuConfig(false);
616     Cache.saveProperties();
617     Desktop.instance.doConfigureStructurePrefs();
618     try
619     {
620       frame.setClosed(true);
621     } catch (Exception ex)
622     {
623     }
624   }
625
626   /**
627    * Do any necessary validation before saving settings. Return focus to the
628    * first tab which fails validation.
629    * 
630    * @return
631    */
632   private boolean validateSettings()
633   {
634     if (!validateStructure())
635     {
636       structureTab.requestFocusInWindow();
637       return false;
638     }
639     return true;
640   }
641
642   @Override
643   protected boolean validateStructure()
644   {
645     return validateChimeraPath();
646
647   }
648   /**
649    * DOCUMENT ME!
650    */
651   public void startupFileTextfield_mouseClicked()
652   {
653     JalviewFileChooser chooser = new JalviewFileChooser(
654             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
655             new String[]
656             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
657             new String[]
658             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
659             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
660     chooser.setFileView(new JalviewFileView());
661     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
662
663     int value = chooser.showOpenDialog(this);
664
665     if (value == JalviewFileChooser.APPROVE_OPTION)
666     {
667       jalview.bin.Cache.applicationProperties.setProperty(
668               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
669       startupFileTextfield.setText(chooser.getSelectedFile()
670               .getAbsolutePath());
671     }
672   }
673
674   /**
675    * DOCUMENT ME!
676    * 
677    * @param e
678    *          DOCUMENT ME!
679    */
680   public void cancel_actionPerformed(ActionEvent e)
681   {
682     try
683     {
684       wsPrefs.updateWsMenuConfig(true);
685       wsPrefs.refreshWs_actionPerformed(e);
686       frame.setClosed(true);
687     } catch (Exception ex)
688     {
689     }
690   }
691
692   /**
693    * DOCUMENT ME!
694    * 
695    * @param e
696    *          DOCUMENT ME!
697    */
698   public void annotations_actionPerformed(ActionEvent e)
699   {
700     conservation.setEnabled(annotations.isSelected());
701     quality.setEnabled(annotations.isSelected());
702     identity.setEnabled(annotations.isSelected());
703     showGroupConsensus.setEnabled(annotations.isSelected());
704     showGroupConservation.setEnabled(annotations.isSelected());
705     showConsensHistogram.setEnabled(annotations.isSelected()
706             && (identity.isSelected() || showGroupConsensus.isSelected()));
707     showConsensLogo.setEnabled(annotations.isSelected()
708             && (identity.isSelected() || showGroupConsensus.isSelected()));
709   }
710
711   public void newLink_actionPerformed(ActionEvent e)
712   {
713
714     GSequenceLink link = new GSequenceLink();
715     boolean valid = false;
716     while (!valid)
717     {
718       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
719               MessageManager.getString("label.new_sequence_url_link"),
720               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
721       {
722         if (link.checkValid())
723         {
724           nameLinks.addElement(link.getName());
725           urlLinks.addElement(link.getURL());
726           updateLinkData();
727           valid = true;
728         }
729       }
730       else
731       {
732         break;
733       }
734     }
735   }
736
737   public void editLink_actionPerformed(ActionEvent e)
738   {
739     GSequenceLink link = new GSequenceLink();
740
741     int index = linkNameList.getSelectedIndex();
742     if (index == -1)
743     {
744       JOptionPane.showInternalMessageDialog(Desktop.desktop,
745               MessageManager.getString("label.no_link_selected"),
746               MessageManager.getString("label.no_link_selected"),
747               JOptionPane.WARNING_MESSAGE);
748       return;
749     }
750
751     link.setName(nameLinks.elementAt(index).toString());
752     link.setURL(urlLinks.elementAt(index).toString());
753
754     boolean valid = false;
755     while (!valid)
756     {
757
758       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
759               MessageManager.getString("label.new_sequence_url_link"),
760               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
761       {
762         if (link.checkValid())
763         {
764           nameLinks.setElementAt(link.getName(), index);
765           urlLinks.setElementAt(link.getURL(), index);
766           updateLinkData();
767           valid = true;
768         }
769       }
770
771       else
772       {
773         break;
774       }
775     }
776   }
777
778   public void deleteLink_actionPerformed(ActionEvent e)
779   {
780     int index = linkNameList.getSelectedIndex();
781     if (index == -1)
782     {
783       JOptionPane.showInternalMessageDialog(Desktop.desktop,
784               MessageManager.getString("label.no_link_selected"),
785               MessageManager.getString("label.no_link_selected"),
786               JOptionPane.WARNING_MESSAGE);
787       return;
788     }
789     nameLinks.removeElementAt(index);
790     urlLinks.removeElementAt(index);
791     updateLinkData();
792   }
793
794   void updateLinkData()
795   {
796     linkNameList.setListData(nameLinks);
797     linkURLList.setListData(urlLinks);
798   }
799
800   public void defaultBrowser_mouseClicked(MouseEvent e)
801   {
802     JFileChooser chooser = new JFileChooser(".");
803     chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
804
805     int value = chooser.showOpenDialog(this);
806
807     if (value == JFileChooser.APPROVE_OPTION)
808     {
809       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
810     }
811
812   }
813
814   /*
815    * (non-Javadoc)
816    * 
817    * @see
818    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
819    * .ActionEvent)
820    */
821   protected void showunconserved_actionPerformed(ActionEvent e)
822   {
823     // TODO Auto-generated method stub
824     super.showunconserved_actionPerformed(e);
825   }
826
827   public static Collection getGroupURLLinks()
828   {
829     return groupURLLinks;
830   }
831
832   @Override
833   public void minColour_actionPerformed(JPanel panel)
834   {
835     Color col = JColorChooser.showDialog(this,
836             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
837     if (col != null)
838     {
839       panel.setBackground(col);
840     }
841     panel.repaint();
842   }
843
844   @Override
845   public void maxColour_actionPerformed(JPanel panel)
846   {
847     Color col = JColorChooser.showDialog(this,
848             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
849     if (col != null)
850     {
851       panel.setBackground(col);
852     }
853     panel.repaint();
854   }
855
856   @Override
857   protected void userIdWidth_actionPerformed()
858   {
859     try
860     {
861       String val = userIdWidth.getText().trim();
862       if (val.length() > 0)
863       {
864         Integer iw = Integer.parseInt(val);
865         if (iw.intValue() < 12)
866         {
867           throw new NumberFormatException();
868         }
869         userIdWidth.setText(iw.toString());
870       }
871     } catch (NumberFormatException x)
872     {
873       JOptionPane
874               .showInternalMessageDialog(
875                       Desktop.desktop,
876                       MessageManager.getString("warn.user_defined_width_requirements"),
877                       MessageManager.getString("label.invalid_id_column_width"),
878                       JOptionPane.WARNING_MESSAGE);
879       userIdWidth.setText("");
880     }
881   }
882
883   @Override
884   protected void autoIdWidth_actionPerformed()
885   {
886     userIdWidth.setEnabled(!autoIdWidth.isSelected());
887     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
888   }
889
890   /**
891    * Returns true if chimera path is to a valid executable, else show an error
892    * dialog.
893    */
894   private boolean validateChimeraPath()
895   {
896     if (chimeraPath.getText().trim().length() > 0)
897     {
898       File f = new File(chimeraPath.getText());
899       if (!f.canExecute())
900       {
901         JOptionPane.showInternalMessageDialog(Desktop.desktop,
902                 MessageManager.getString("label.invalid_chimera_path"),
903                 MessageManager.getString("label.invalid_name"),
904                 JOptionPane.ERROR_MESSAGE);
905         return false;
906       }
907     }
908     return true;
909   }
910
911   /**
912    * If Chimera is selected, check it can be found on default or user-specified
913    * path, if not show a warning/help dialog.
914    */
915   @Override
916   protected void structureViewer_actionPerformed(String selectedItem)
917   {
918     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
919     {
920       return;
921     }
922     boolean found = false;
923
924     /*
925      * Try user-specified and standard paths for Chimera executable.
926      */
927     List<String> paths = StructureManager.getChimeraPaths();
928     paths.add(0, chimeraPath.getText());
929     for (String path : paths)
930     {
931       if (new File(path.trim()).canExecute())
932       {
933         found = true;
934         break;
935       }
936     }
937     if (!found)
938     {
939       String[] options =
940       { "OK", "Help" };
941       int showHelp = JOptionPane.showInternalOptionDialog(
942               Desktop.desktop,
943               JvSwingUtils.wrapTooltip(true,
944                       MessageManager.getString("label.chimera_missing")),
945               "", JOptionPane.YES_NO_OPTION,
946               JOptionPane.WARNING_MESSAGE, null, options, options[0]);
947       if (showHelp == JOptionPane.NO_OPTION)
948       {
949         try
950         {
951           Help.showHelpWindow(HelpId.StructureViewer);
952         } catch (HelpSetException e)
953         {
954           e.printStackTrace();
955         }
956       }
957     }
958   }
959
960 }