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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.gui

File Preferences.java

 

Coverage histogram

../../img/srcFileCovDistChart1.png
52% of files have more coverage

Code metrics

118
492
41
3
1,468
1,105
117
0.24
12
13.67
2.85

Classes

Class Line # Actions
Preferences 84 468 104
0.0196721312%
Preferences.OptionsParam 1373 11 9
0.00%
Preferences.UrlListSelectionHandler 1428 13 4
0.00%
 

Contributing tests

This file is covered by 1 test. .

Source view

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 java.awt.BorderLayout;
24    import java.awt.Color;
25    import java.awt.Component;
26    import java.awt.Dimension;
27    import java.awt.Font;
28    import java.awt.event.ActionEvent;
29    import java.awt.event.ActionListener;
30    import java.awt.event.MouseEvent;
31    import java.io.File;
32    import java.util.ArrayList;
33    import java.util.List;
34   
35    import javax.help.HelpSetException;
36    import javax.swing.JComboBox;
37    import javax.swing.JFileChooser;
38    import javax.swing.JInternalFrame;
39    import javax.swing.JPanel;
40    import javax.swing.ListSelectionModel;
41    import javax.swing.RowFilter;
42    import javax.swing.RowSorter;
43    import javax.swing.SortOrder;
44    import javax.swing.event.DocumentEvent;
45    import javax.swing.event.DocumentListener;
46    import javax.swing.event.ListSelectionEvent;
47    import javax.swing.event.ListSelectionListener;
48    import javax.swing.table.TableCellRenderer;
49    import javax.swing.table.TableColumn;
50    import javax.swing.table.TableModel;
51    import javax.swing.table.TableRowSorter;
52   
53    import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
54    import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
55    import jalview.bin.Cache;
56    import jalview.ext.pymol.PymolManager;
57    import jalview.gui.Help.HelpId;
58    import jalview.gui.StructureViewer.ViewerType;
59    import jalview.io.BackupFiles;
60    import jalview.io.BackupFilesPresetEntry;
61    import jalview.io.FileFormatI;
62    import jalview.io.JalviewFileChooser;
63    import jalview.io.JalviewFileView;
64    import jalview.jbgui.GPreferences;
65    import jalview.jbgui.GSequenceLink;
66    import jalview.schemes.ColourSchemeI;
67    import jalview.schemes.ColourSchemes;
68    import jalview.schemes.ResidueColourScheme;
69    import jalview.urls.UrlLinkTableModel;
70    import jalview.urls.api.UrlProviderFactoryI;
71    import jalview.urls.api.UrlProviderI;
72    import jalview.urls.desktop.DesktopUrlProviderFactory;
73    import jalview.util.MessageManager;
74    import jalview.util.Platform;
75    import jalview.util.UrlConstants;
76    import jalview.ws.sifts.SiftsSettings;
77   
78    /**
79    * DOCUMENT ME!
80    *
81    * @author $author$
82    * @version $Revision$
83    */
 
84    public class Preferences extends GPreferences
85    {
86    public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
87   
88    public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
89   
90    public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
91   
92    public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
93   
94    public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
95   
96    public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
97   
98    public static final String ADD_SS_ANN = "ADD_SS_ANN";
99   
100    public static final String USE_RNAVIEW = "USE_RNAVIEW";
101   
102    public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
103   
104    public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
105   
106    public static final String CHIMERA_PATH = "CHIMERA_PATH";
107   
108    public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
109   
110    public static final String PYMOL_PATH = "PYMOL_PATH";
111   
112    public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
113   
114    public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
115   
116    public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
117   
118    public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
119   
120    public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
121   
122    public static final String GAP_COLOUR = "GAP_COLOUR";
123   
124    public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
125   
126    private static final int MIN_FONT_SIZE = 1;
127   
128    private static final int MAX_FONT_SIZE = 30;
129   
130    /**
131    * Holds name and link separated with | character. Sequence ID must be
132    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
133    */
134    public static UrlProviderI sequenceUrlLinks;
135   
136    public static UrlLinkTableModel dataModel;
137   
138    /**
139    * Holds name and link separated with | character. Sequence IDS and Sequences
140    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
141    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
142    * for first and second token specified after a pipe character at end |,|.
143    * (TODO: proper escape for using | to separate ids or sequences
144    */
145   
146    public static List<String> groupURLLinks;
 
147  2 toggle static
148    {
149    // get links selected to be in the menu (SEQUENCE_LINKS)
150    // and links entered by the user but not selected (STORED_LINKS)
151  2 String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
152  2 String notInMenuString = Cache.getDefault("STORED_LINKS", "");
153  2 String defaultUrl = Cache.getDefault("DEFAULT_URL",
154    UrlConstants.DEFAULT_LABEL);
155   
156    // if both links lists are empty, add the DEFAULT_URL link
157    // otherwise we assume the default link is in one of the lists
158  2 if (inMenuString.isEmpty() && notInMenuString.isEmpty())
159    {
160  1 inMenuString = UrlConstants.DEFAULT_STRING;
161    }
162  2 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
163    inMenuString, notInMenuString);
164  2 sequenceUrlLinks = factory.createUrlProvider();
165  2 dataModel = new UrlLinkTableModel(sequenceUrlLinks);
166   
167    /**
168    * TODO: reformulate groupURL encoding so two or more can be stored in the
169    * .properties file as '|' separated strings
170    */
171   
172  2 groupURLLinks = new ArrayList<>();
173    }
174   
175    JInternalFrame frame;
176   
177    private WsPreferences wsPrefs;
178   
179    private OptionsParam promptEachTimeOpt = new OptionsParam(
180    MessageManager.getString("label.prompt_each_time"),
181    "Prompt each time");
182   
183    private OptionsParam lineArtOpt = new OptionsParam(
184    MessageManager.getString("label.lineart"), "Lineart");
185   
186    private OptionsParam textOpt = new OptionsParam(
187    MessageManager.getString("action.text"), "Text");
188   
189    /**
190    * Creates a new Preferences object.
191    */
 
192  0 toggle public Preferences()
193    {
194  0 super();
195  0 frame = new JInternalFrame();
196  0 frame.setContentPane(this);
197  0 if (!Platform.isJS())
198    /**
199    * Java only
200    *
201    * @j2sIgnore
202    */
203    {
204  0 wsPrefs = new WsPreferences();
205  0 wsTab.add(wsPrefs, BorderLayout.CENTER);
206    }
207  0 int width = 500, height = 450;
208  0 if (Platform.isAMacAndNotJS())
209    {
210  0 width = 570;
211  0 height = 480;
212    }
213   
214  0 Desktop.addInternalFrame(frame,
215    MessageManager.getString("label.preferences"), width, height);
216  0 frame.setMinimumSize(new Dimension(width, height));
217   
218    /*
219    * Set Visual tab defaults
220    */
221  0 seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
222  0 rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
223  0 fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
224  0 annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
225   
226  0 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
227  0 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
228  0 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
229  0 openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
230  0 showUnconserved
231    .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
232  0 showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
233  0 showGroupConsensus
234    .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
235  0 showGroupConservation.setSelected(
236    Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
237  0 showConsensHistogram.setSelected(
238    Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
239  0 showConsensLogo
240    .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
241  0 showNpTooltip
242    .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
243  0 showDbRefTooltip
244    .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
245   
246  0 String[] fonts = java.awt.GraphicsEnvironment
247    .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
248  0 for (int i = 0; i < fonts.length; i++)
249    {
250  0 fontNameCB.addItem(fonts[i]);
251    }
252   
253  0 for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
254    {
255  0 fontSizeCB.addItem(i + "");
256    }
257   
258  0 fontStyleCB.addItem("plain");
259  0 fontStyleCB.addItem("bold");
260  0 fontStyleCB.addItem("italic");
261   
262  0 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
263  0 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
264  0 fontStyleCB.setSelectedItem(
265    Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
266   
267  0 smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
268  0 scaleProteinToCdna
269    .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
270   
271  0 idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
272   
273  0 wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
274   
275  0 gapSymbolCB.addItem("-");
276  0 gapSymbolCB.addItem(".");
277   
278  0 gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
279   
280  0 sortby.addItem("No sort");
281  0 sortby.addItem("Id");
282  0 sortby.addItem("Pairwise Identity");
283  0 sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
284   
285  0 sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
286  0 sortAnnBy
287    .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
288  0 sortAnnBy
289    .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
290  0 SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
291    .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
292    SequenceAnnotationOrder.NONE.name()));
293  0 sortAnnBy.setSelectedItem(savedSort.toString());
294   
295  0 sortAutocalc.addItem("Autocalculated first");
296  0 sortAutocalc.addItem("Autocalculated last");
297  0 final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
298  0 sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
299    : sortAutocalc.getItemAt(1));
300  0 startupCheckbox
301    .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
302  0 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
303    Cache.getDefault("www.jalview.org", "http://www.jalview.org")
304    + "/examples/exampleFile_2_3.jar"));
305   
306    /*
307    * Set Colours tab defaults
308    */
309  0 protColour.addItem(ResidueColourScheme.NONE);
310  0 nucColour.addItem(ResidueColourScheme.NONE);
311  0 for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
312    {
313  0 String name = cs.getSchemeName();
314  0 protColour.addItem(name);
315  0 nucColour.addItem(name);
316    }
317  0 String oldProp = Cache.getDefault(DEFAULT_COLOUR,
318    ResidueColourScheme.NONE);
319  0 String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
320  0 protColour.setSelectedItem(newProp != null ? newProp : oldProp);
321  0 newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
322  0 nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
323  0 minColour.setBackground(
324    Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
325  0 maxColour.setBackground(
326    Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
327   
328    /*
329    * Set overview panel defaults
330    */
331  0 gapColour.setBackground(
332    Cache.getDefaultColour(GAP_COLOUR,
333    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
334  0 hiddenColour.setBackground(
335    Cache.getDefaultColour(HIDDEN_COLOUR,
336    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
337  0 useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
338  0 gapLabel.setEnabled(!useLegacyGap.isSelected());
339  0 gapColour.setEnabled(!useLegacyGap.isSelected());
340  0 showHiddenAtStart
341    .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
342   
343    /*
344    * Set Structure tab defaults
345    */
346  0 final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
347  0 structFromPdb.setSelected(structSelected);
348  0 useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
349  0 useRnaView.setEnabled(structSelected);
350  0 addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
351  0 addSecondaryStructure.setEnabled(structSelected);
352  0 addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
353  0 addTempFactor.setEnabled(structSelected);
354   
355    /*
356    * set choice of structure viewer, and path if saved as a preference;
357    * default to Jmol (first choice) if an unexpected value is found
358    */
359  0 String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
360  0 structViewer.setSelectedItem(viewerType);
361  0 String viewerPath = "";
362  0 ViewerType type = null;
363  0 try
364    {
365  0 type = ViewerType.valueOf(viewerType);
366  0 switch (type)
367    {
368  0 case JMOL:
369  0 break;
370  0 case CHIMERA:
371  0 viewerPath = Cache.getDefault(CHIMERA_PATH, "");
372  0 break;
373  0 case CHIMERAX:
374  0 viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
375  0 break;
376  0 case PYMOL:
377  0 viewerPath = Cache.getDefault(PYMOL_PATH, "");
378  0 break;
379    }
380    } catch (IllegalArgumentException e)
381    {
382  0 Cache.log.error("Unknown structure viewer type: " + viewerType
383    + ", defaulting to Jmol");
384  0 type = ViewerType.JMOL;
385    }
386  0 structureViewerPath.setText(viewerPath);
387   
388  0 structureViewerPath.addActionListener(new ActionListener()
389    {
 
390  0 toggle @Override
391    public void actionPerformed(ActionEvent e)
392    {
393  0 if (validateViewerPath())
394    {
395  0 Cache.setProperty(structViewer.getSelectedItem()
396    .equals(ViewerType.CHIMERAX.name())
397    ? CHIMERAX_PATH
398    : CHIMERA_PATH, structureViewerPath.getText());
399    }
400    }
401    });
402   
403  0 if (Cache.getDefault("MAP_WITH_SIFTS", false))
404    {
405  0 siftsMapping.setSelected(true);
406    }
407    else
408    {
409  0 nwMapping.setSelected(true);
410    }
411   
412  0 SiftsSettings
413    .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
414   
415    /*
416    * Set Connections tab defaults
417    */
418   
419    // set up sorting
420  0 linkUrlTable.setModel(dataModel);
421  0 final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
422    linkUrlTable.getModel());
423  0 linkUrlTable.setRowSorter(sorter);
424  0 List<RowSorter.SortKey> sortKeys = new ArrayList<>();
425   
426  0 UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
427  0 sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
428    SortOrder.DESCENDING));
429  0 sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
430    SortOrder.DESCENDING));
431  0 sortKeys.add(
432    new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
433   
434  0 sorter.setSortKeys(sortKeys);
435    // BH 2018 setSortKeys will do the sort
436    // sorter.sort();
437   
438    // set up filtering
439  0 ActionListener onReset;
440  0 onReset = new ActionListener()
441    {
 
442  0 toggle @Override
443    public void actionPerformed(ActionEvent e)
444    {
445  0 filterTB.setText("");
446  0 sorter.setRowFilter(RowFilter.regexFilter(""));
447    }
448   
449    };
450  0 doReset.addActionListener(onReset);
451   
452    // filter to display only custom urls
453  0 final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
454    {
 
455  0 toggle @Override
456    public boolean include(
457    Entry<? extends TableModel, ? extends Object> entry)
458    {
459  0 return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
460    }
461    };
462   
463  0 final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
464    linkUrlTable.getModel());
465  0 customSorter.setRowFilter(customUrlFilter);
466   
467  0 ActionListener onCustomOnly;
468  0 onCustomOnly = new ActionListener()
469    {
 
470  0 toggle @Override
471    public void actionPerformed(ActionEvent e)
472    {
473  0 filterTB.setText("");
474  0 sorter.setRowFilter(customUrlFilter);
475    }
476    };
477  0 userOnly.addActionListener(onCustomOnly);
478   
479  0 filterTB.getDocument().addDocumentListener(new DocumentListener()
480    {
481    String caseInsensitiveFlag = "(?i)";
482   
 
483  0 toggle @Override
484    public void changedUpdate(DocumentEvent e)
485    {
486  0 sorter.setRowFilter(RowFilter
487    .regexFilter(caseInsensitiveFlag + filterTB.getText()));
488    }
489   
 
490  0 toggle @Override
491    public void removeUpdate(DocumentEvent e)
492    {
493  0 sorter.setRowFilter(RowFilter
494    .regexFilter(caseInsensitiveFlag + filterTB.getText()));
495    }
496   
 
497  0 toggle @Override
498    public void insertUpdate(DocumentEvent e)
499    {
500  0 sorter.setRowFilter(RowFilter
501    .regexFilter(caseInsensitiveFlag + filterTB.getText()));
502    }
503    });
504   
505    // set up list selection functionality
506  0 linkUrlTable.getSelectionModel()
507    .addListSelectionListener(new UrlListSelectionHandler());
508   
509    // set up radio buttons
510  0 int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
511    .getPrimaryColumn();
512  0 String onClickName = linkUrlTable.getColumnName(onClickCol);
513  0 linkUrlTable.getColumn(onClickName)
514    .setCellRenderer(new RadioButtonRenderer());
515  0 linkUrlTable.getColumn(onClickName)
516    .setCellEditor(new RadioButtonEditor());
517   
518    // get boolean columns and resize those to min possible
519  0 for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
520    {
521  0 if (linkUrlTable.getModel().getColumnClass(column)
522    .equals(Boolean.class))
523    {
524  0 TableColumn tableColumn = linkUrlTable.getColumnModel()
525    .getColumn(column);
526  0 int preferredWidth = tableColumn.getMinWidth();
527   
528  0 TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
529    column);
530  0 Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
531  0 int cwidth = c.getPreferredSize().width
532    + linkUrlTable.getIntercellSpacing().width;
533  0 preferredWidth = Math.max(preferredWidth, cwidth);
534   
535  0 tableColumn.setPreferredWidth(preferredWidth);
536    }
537    }
538   
539  0 useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
540  0 useProxy_actionPerformed(); // make sure useProxy is correctly initialised
541  0 proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
542  0 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
543   
544  0 defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
545   
546  0 usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
547    // note antisense here: default is true
548  0 questionnaire
549    .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
550  0 versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
551   
552    /*
553    * Set Output tab defaults
554    */
555  0 setupOutputCombo(epsRendering, "EPS_RENDERING");
556  0 setupOutputCombo(htmlRendering, "HTML_RENDERING");
557  0 setupOutputCombo(svgRendering, "SVG_RENDERING");
558  0 autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
559  0 userIdWidth.setEnabled(!autoIdWidth.isSelected());
560  0 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
561  0 Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
562  0 userIdWidth.setText(wi == null ? "" : wi.toString());
563    // TODO: refactor to use common enum via FormatAdapter and allow extension
564    // for new flat file formats
565  0 blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
566  0 clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
567  0 fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
568  0 msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
569  0 pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
570  0 pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
571  0 pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
572  0 modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
573  0 embbedBioJSON
574    .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
575   
576    /*
577    * Set Editing tab defaults
578    */
579  0 autoCalculateConsCheck
580    .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
581  0 padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
582  0 sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
583   
584  0 annotations_actionPerformed(null); // update the display of the annotation
585    // settings
586   
587   
588    /*
589    * Set Backups tab defaults
590    */
591  0 loadLastSavedBackupsOptions();
592    }
593   
594    /**
595    * A helper method that sets the items and initial selection in a character
596    * rendering option list (Prompt each time/Lineart/Text)
597    *
598    * @param comboBox
599    * @param propertyKey
600    */
 
601  0 toggle protected void setupOutputCombo(JComboBox<Object> comboBox,
602    String propertyKey)
603    {
604  0 comboBox.addItem(promptEachTimeOpt);
605  0 comboBox.addItem(lineArtOpt);
606  0 comboBox.addItem(textOpt);
607   
608    /*
609    * JalviewJS doesn't support Lineart so force it to Text
610    */
611  0 String defaultOption = Platform.isJS() ? "Text"
612    : Cache.getDefault(propertyKey, "Prompt each time");
613  0 if (defaultOption.equalsIgnoreCase("Text"))
614    {
615  0 comboBox.setSelectedItem(textOpt);
616    }
617  0 else if (defaultOption.equalsIgnoreCase("Lineart"))
618    {
619  0 comboBox.setSelectedItem(lineArtOpt);
620    }
621    else
622    {
623  0 comboBox.setSelectedItem(promptEachTimeOpt);
624    }
625    }
626   
627    /**
628    * Save user selections on the Preferences tabs to the Cache and write out to
629    * file.
630    *
631    * @param e
632    */
 
633  0 toggle @Override
634    public void ok_actionPerformed(ActionEvent e)
635    {
636  0 if (!validateSettings())
637    {
638  0 return;
639    }
640   
641    /*
642    * Save Visual settings
643    */
644  0 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
645    Boolean.toString(seqLimit.isSelected()));
646  0 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
647    Boolean.toString(rightAlign.isSelected()));
648  0 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
649    Boolean.toString(fullScreen.isSelected()));
650  0 Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
651    Boolean.toString(openoverv.isSelected()));
652  0 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
653    Boolean.toString(annotations.isSelected()));
654  0 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
655    Boolean.toString(conservation.isSelected()));
656  0 Cache.applicationProperties.setProperty("SHOW_QUALITY",
657    Boolean.toString(quality.isSelected()));
658  0 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
659    Boolean.toString(identity.isSelected()));
660   
661  0 Cache.applicationProperties.setProperty("GAP_SYMBOL",
662    gapSymbolCB.getSelectedItem().toString());
663   
664  0 Cache.applicationProperties.setProperty("FONT_NAME",
665    fontNameCB.getSelectedItem().toString());
666  0 Cache.applicationProperties.setProperty("FONT_STYLE",
667    fontStyleCB.getSelectedItem().toString());
668  0 Cache.applicationProperties.setProperty("FONT_SIZE",
669    fontSizeCB.getSelectedItem().toString());
670   
671  0 Cache.applicationProperties.setProperty("ID_ITALICS",
672    Boolean.toString(idItalics.isSelected()));
673  0 Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
674    Boolean.toString(showUnconserved.isSelected()));
675  0 Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
676    Boolean.toString(showOccupancy.isSelected()));
677  0 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
678    Boolean.toString(showGroupConsensus.isSelected()));
679  0 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
680    Boolean.toString(showGroupConservation.isSelected()));
681  0 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
682    Boolean.toString(showConsensHistogram.isSelected()));
683  0 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
684    Boolean.toString(showConsensLogo.isSelected()));
685  0 Cache.applicationProperties.setProperty("ANTI_ALIAS",
686    Boolean.toString(smoothFont.isSelected()));
687  0 Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
688    Boolean.toString(scaleProteinToCdna.isSelected()));
689  0 Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
690    Boolean.toString(showNpTooltip.isSelected()));
691  0 Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
692    Boolean.toString(showDbRefTooltip.isSelected()));
693   
694  0 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
695    Boolean.toString(wrap.isSelected()));
696   
697  0 Cache.applicationProperties.setProperty("STARTUP_FILE",
698    startupFileTextfield.getText());
699  0 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
700    Boolean.toString(startupCheckbox.isSelected()));
701   
702  0 Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
703    sortby.getSelectedItem().toString());
704   
705    // convert description of sort order to enum name for save
706  0 SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
707    .forDescription(sortAnnBy.getSelectedItem().toString());
708  0 if (annSortOrder != null)
709    {
710  0 Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
711    annSortOrder.name());
712    }
713   
714  0 final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
715  0 Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
716    Boolean.valueOf(showAutocalcFirst).toString());
717   
718    /*
719    * Save Colours settings
720    */
721  0 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
722    protColour.getSelectedItem().toString());
723  0 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
724    nucColour.getSelectedItem().toString());
725  0 Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
726    minColour.getBackground());
727  0 Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
728    maxColour.getBackground());
729   
730    /*
731    * Save Overview settings
732    */
733  0 Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
734  0 Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
735  0 Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
736    Boolean.toString(useLegacyGap.isSelected()));
737  0 Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
738    Boolean.toString(showHiddenAtStart.isSelected()));
739   
740    /*
741    * Save Structure settings
742    */
743  0 Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
744    Boolean.toString(addTempFactor.isSelected()));
745  0 Cache.applicationProperties.setProperty(ADD_SS_ANN,
746    Boolean.toString(addSecondaryStructure.isSelected()));
747  0 Cache.applicationProperties.setProperty(USE_RNAVIEW,
748    Boolean.toString(useRnaView.isSelected()));
749  0 Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
750    Boolean.toString(structFromPdb.isSelected()));
751  0 String viewer = structViewer.getSelectedItem().toString();
752  0 String viewerPath = structureViewerPath.getText();
753  0 Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
754    viewer);
755  0 if (viewer.equals(ViewerType.CHIMERA.name()))
756    {
757  0 Cache.setOrRemove(CHIMERA_PATH, viewerPath);
758    }
759  0 else if (viewer.equals(ViewerType.CHIMERAX.name()))
760    {
761  0 Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
762    }
763  0 else if (viewer.equals(ViewerType.PYMOL.name()))
764    {
765  0 Cache.setOrRemove(PYMOL_PATH, viewerPath);
766    }
767  0 Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
768    Boolean.toString(siftsMapping.isSelected()));
769  0 SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
770   
771    /*
772    * Save Output settings
773    */
774  0 Cache.applicationProperties.setProperty("EPS_RENDERING",
775    ((OptionsParam) epsRendering.getSelectedItem()).getCode());
776  0 Cache.applicationProperties.setProperty("HTML_RENDERING",
777    ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
778  0 Cache.applicationProperties.setProperty("SVG_RENDERING",
779    ((OptionsParam) svgRendering.getSelectedItem()).getCode());
780   
781    /*
782    * Save Connections settings
783    */
784  0 Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
785   
786  0 jalview.util.BrowserLauncher.resetBrowser();
787   
788    // save user-defined and selected links
789  0 String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
790  0 if (menuLinks.isEmpty())
791    {
792  0 Cache.applicationProperties.remove("SEQUENCE_LINKS");
793    }
794    else
795    {
796  0 Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
797    menuLinks.toString());
798    }
799   
800  0 String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
801  0 if (nonMenuLinks.isEmpty())
802    {
803  0 Cache.applicationProperties.remove("STORED_LINKS");
804    }
805    else
806    {
807  0 Cache.applicationProperties.setProperty("STORED_LINKS",
808    nonMenuLinks.toString());
809    }
810   
811  0 Cache.applicationProperties.setProperty("DEFAULT_URL",
812    sequenceUrlLinks.getPrimaryUrlId());
813   
814  0 Cache.applicationProperties.setProperty("USE_PROXY",
815    Boolean.toString(useProxy.isSelected()));
816   
817  0 Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
818   
819  0 Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
820   
821  0 if (useProxy.isSelected())
822    {
823  0 System.setProperty("http.proxyHost", proxyServerTB.getText());
824  0 System.setProperty("http.proxyPort", proxyPortTB.getText());
825    }
826    else
827    {
828  0 System.setProperty("http.proxyHost", "");
829  0 System.setProperty("http.proxyPort", "");
830    }
831  0 Cache.setProperty("VERSION_CHECK",
832    Boolean.toString(versioncheck.isSelected()));
833  0 if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
834    {
835    // default is false - we only set this if the user has actively agreed
836  0 Cache.setProperty("USAGESTATS",
837    Boolean.toString(usagestats.isSelected()));
838    }
839  0 if (!questionnaire.isSelected())
840    {
841  0 Cache.setProperty("NOQUESTIONNAIRES", "true");
842    }
843    else
844    {
845    // special - made easy to edit a property file to disable questionnaires
846    // by just adding the given line
847  0 Cache.removeProperty("NOQUESTIONNAIRES");
848    }
849   
850    /*
851    * Save Output settings
852    */
853  0 Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
854    Boolean.toString(blcjv.isSelected()));
855  0 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
856    Boolean.toString(clustaljv.isSelected()));
857  0 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
858    Boolean.toString(fastajv.isSelected()));
859  0 Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
860    Boolean.toString(msfjv.isSelected()));
861  0 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
862    Boolean.toString(pfamjv.isSelected()));
863  0 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
864    Boolean.toString(pileupjv.isSelected()));
865  0 Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
866    Boolean.toString(pirjv.isSelected()));
867  0 Cache.applicationProperties.setProperty("PIR_MODELLER",
868    Boolean.toString(modellerOutput.isSelected()));
869  0 Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
870    Boolean.toString(embbedBioJSON.isSelected()));
871  0 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
872   
873  0 Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
874    Boolean.toString(autoIdWidth.isSelected()));
875  0 userIdWidth_actionPerformed();
876  0 Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
877    userIdWidth.getText());
878   
879    /*
880    * Save Editing settings
881    */
882  0 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
883    Boolean.toString(autoCalculateConsCheck.isSelected()));
884  0 Cache.applicationProperties.setProperty("SORT_BY_TREE",
885    Boolean.toString(sortByTree.isSelected()));
886  0 Cache.applicationProperties.setProperty("PAD_GAPS",
887    Boolean.toString(padGaps.isSelected()));
888   
889  0 if (!Platform.isJS())
890    {
891  0 wsPrefs.updateAndRefreshWsMenuConfig(false);
892    }
893   
894    /*
895    * Save Backups settings
896    */
897  0 Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
898    Boolean.toString(enableBackupFiles.isSelected()));
899  0 int preset = getComboIntStringKey(backupfilesPresetsCombo);
900  0 Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
901   
902  0 if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
903    {
904  0 BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
905  0 BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
906    BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
907  0 Cache.applicationProperties
908    .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
909    customBFPE.toString());
910    }
911   
912  0 BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
913    .get(preset);
914  0 Cache.applicationProperties.setProperty(
915    BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
916   
917  0 Cache.saveProperties();
918  0 Desktop.instance.doConfigureStructurePrefs();
919  0 try
920    {
921  0 frame.setClosed(true);
922    } catch (Exception ex)
923    {
924    }
925    }
926   
927    /**
928    * Do any necessary validation before saving settings. Return focus to the
929    * first tab which fails validation.
930    *
931    * @return
932    */
 
933  0 toggle private boolean validateSettings()
934    {
935  0 if (!validateStructure())
936    {
937  0 structureTab.requestFocusInWindow();
938  0 return false;
939    }
940  0 return true;
941    }
942   
 
943  0 toggle @Override
944    protected boolean validateStructure()
945    {
946  0 return validateViewerPath();
947   
948    }
949   
950    /**
951    * DOCUMENT ME!
952    */
 
953  0 toggle @Override
954    public void startupFileTextfield_mouseClicked()
955    {
956    // TODO: JAL-3048 not needed for Jalview-JS
957  0 String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
958  0 JalviewFileChooser chooser = JalviewFileChooser
959    .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
960  0 chooser.setFileView(new JalviewFileView());
961  0 chooser.setDialogTitle(
962    MessageManager.getString("label.select_startup_file"));
963   
964  0 int value = chooser.showOpenDialog(this);
965   
966  0 if (value == JalviewFileChooser.APPROVE_OPTION)
967    {
968  0 FileFormatI format = chooser.getSelectedFormat();
969  0 if (format != null)
970    {
971  0 Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
972    format.getName());
973    }
974  0 startupFileTextfield
975    .setText(chooser.getSelectedFile().getAbsolutePath());
976    }
977    }
978   
979    /**
980    * DOCUMENT ME!
981    *
982    * @param e
983    * DOCUMENT ME!
984    */
 
985  0 toggle @Override
986    public void cancel_actionPerformed(ActionEvent e)
987    {
988  0 try
989    {
990  0 if (!Platform.isJS())
991    {
992  0 wsPrefs.updateWsMenuConfig(true);
993  0 wsPrefs.refreshWs_actionPerformed(e);
994    }
995  0 frame.setClosed(true);
996    } catch (Exception ex)
997    {
998    }
999    }
1000   
1001    /**
1002    * DOCUMENT ME!
1003    *
1004    * @param e
1005    * DOCUMENT ME!
1006    */
 
1007  0 toggle @Override
1008    public void annotations_actionPerformed(ActionEvent e)
1009    {
1010  0 conservation.setEnabled(annotations.isSelected());
1011  0 quality.setEnabled(annotations.isSelected());
1012  0 identity.setEnabled(annotations.isSelected());
1013  0 showOccupancy.setEnabled(annotations.isSelected());
1014  0 showGroupConsensus.setEnabled(annotations.isSelected());
1015  0 showGroupConservation.setEnabled(annotations.isSelected());
1016  0 showConsensHistogram.setEnabled(annotations.isSelected()
1017    && (identity.isSelected() || showGroupConsensus.isSelected()));
1018  0 showConsensLogo.setEnabled(annotations.isSelected()
1019    && (identity.isSelected() || showGroupConsensus.isSelected()));
1020    }
1021   
 
1022  0 toggle @Override
1023    public void newLink_actionPerformed(ActionEvent e)
1024    {
1025  0 GSequenceLink link = new GSequenceLink();
1026  0 boolean valid = false;
1027  0 while (!valid)
1028    {
1029  0 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1030    MessageManager.getString("label.new_sequence_url_link"),
1031    JvOptionPane.OK_CANCEL_OPTION, -1,
1032    null) == JvOptionPane.OK_OPTION)
1033    {
1034  0 if (link.checkValid())
1035    {
1036  0 if (((UrlLinkTableModel) linkUrlTable.getModel())
1037    .isUniqueName(link.getName()))
1038    {
1039  0 ((UrlLinkTableModel) linkUrlTable.getModel())
1040    .insertRow(link.getName(), link.getURL());
1041  0 valid = true;
1042    }
1043    else
1044    {
1045  0 link.notifyDuplicate();
1046  0 continue;
1047    }
1048    }
1049    }
1050    else
1051    {
1052  0 break;
1053    }
1054    }
1055    }
1056   
 
1057  0 toggle @Override
1058    public void editLink_actionPerformed(ActionEvent e)
1059    {
1060  0 GSequenceLink link = new GSequenceLink();
1061   
1062  0 int index = linkUrlTable.getSelectedRow();
1063  0 if (index == -1)
1064    {
1065    // button no longer enabled if row is not selected
1066  0 Cache.log.debug("Edit with no row selected in linkUrlTable");
1067  0 return;
1068    }
1069   
1070  0 int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1071    .getNameColumn();
1072  0 int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1073    .getUrlColumn();
1074  0 String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1075  0 link.setName(oldName);
1076  0 link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1077   
1078  0 boolean valid = false;
1079  0 while (!valid)
1080    {
1081  0 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1082    MessageManager.getString("label.edit_sequence_url_link"),
1083    JvOptionPane.OK_CANCEL_OPTION, -1,
1084    null) == JvOptionPane.OK_OPTION)
1085    {
1086  0 if (link.checkValid())
1087    {
1088  0 if ((oldName.equals(link.getName()))
1089    || (((UrlLinkTableModel) linkUrlTable.getModel())
1090    .isUniqueName(link.getName())))
1091    {
1092  0 linkUrlTable.setValueAt(link.getName(), index, nameCol);
1093  0 linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1094  0 valid = true;
1095    }
1096    else
1097    {
1098  0 link.notifyDuplicate();
1099  0 continue;
1100    }
1101    }
1102    }
1103    else
1104    {
1105  0 break;
1106    }
1107    }
1108    }
1109   
 
1110  0 toggle @Override
1111    public void deleteLink_actionPerformed(ActionEvent e)
1112    {
1113  0 int index = linkUrlTable.getSelectedRow();
1114  0 int modelIndex = -1;
1115  0 if (index == -1)
1116    {
1117    // button no longer enabled if row is not selected
1118  0 Cache.log.debug("Delete with no row selected in linkUrlTable");
1119  0 return;
1120    }
1121    else
1122    {
1123  0 modelIndex = linkUrlTable.convertRowIndexToModel(index);
1124    }
1125   
1126    // make sure we use the model index to delete, and not the table index
1127  0 ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1128    }
1129   
 
1130  0 toggle @Override
1131    public void defaultBrowser_mouseClicked(MouseEvent e)
1132    {
1133    // TODO: JAL-3048 not needed for j2s
1134  0 if (!Platform.isJS()) // BH 2019
1135    /**
1136    * Java only
1137    *
1138    * @j2sIgnore
1139    */
1140    {
1141  0 JFileChooser chooser = new JFileChooser(".");
1142  0 chooser.setDialogTitle(
1143    MessageManager.getString("label.select_default_browser"));
1144   
1145  0 int value = chooser.showOpenDialog(this);
1146   
1147  0 if (value == JFileChooser.APPROVE_OPTION)
1148    {
1149  0 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1150    }
1151    }
1152    }
1153   
1154    /*
1155    * (non-Javadoc)
1156    *
1157    * @see
1158    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1159    * .ActionEvent)
1160    */
 
1161  0 toggle @Override
1162    protected void showunconserved_actionPerformed(ActionEvent e)
1163    {
1164    // TODO Auto-generated method stub
1165  0 super.showunconserved_actionPerformed(e);
1166    }
1167   
 
1168  0 toggle public static List<String> getGroupURLLinks()
1169    {
1170  0 return groupURLLinks;
1171    }
1172   
 
1173  0 toggle @Override
1174    public void minColour_actionPerformed(JPanel panel)
1175    {
1176  0 JalviewColourChooser.showColourChooser(this,
1177    MessageManager.getString("label.select_colour_minimum_value"),
1178    panel);
1179    }
1180   
 
1181  0 toggle @Override
1182    public void maxColour_actionPerformed(JPanel panel)
1183    {
1184  0 JalviewColourChooser.showColourChooser(this,
1185    MessageManager.getString("label.select_colour_maximum_value"),
1186    panel);
1187    }
1188   
 
1189  0 toggle @Override
1190    public void gapColour_actionPerformed(JPanel gap)
1191    {
1192  0 if (!useLegacyGap.isSelected())
1193    {
1194  0 JalviewColourChooser.showColourChooser(this,
1195    MessageManager.getString("label.select_gap_colour"),
1196    gap);
1197    }
1198    }
1199   
 
1200  0 toggle @Override
1201    public void hiddenColour_actionPerformed(JPanel hidden)
1202    {
1203  0 JalviewColourChooser.showColourChooser(this,
1204    MessageManager.getString("label.select_hidden_colour"),
1205    hidden);
1206    }
1207   
 
1208  0 toggle @Override
1209    protected void useLegacyGaps_actionPerformed(ActionEvent e)
1210    {
1211  0 boolean enabled = useLegacyGap.isSelected();
1212  0 if (enabled)
1213    {
1214  0 gapColour.setBackground(
1215    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1216    }
1217    else
1218    {
1219  0 gapColour.setBackground(
1220    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1221    }
1222  0 gapColour.setEnabled(!enabled);
1223  0 gapLabel.setEnabled(!enabled);
1224    }
1225   
 
1226  0 toggle @Override
1227    protected void resetOvDefaults_actionPerformed(ActionEvent e)
1228    {
1229  0 useLegacyGap.setSelected(false);
1230  0 useLegacyGaps_actionPerformed(null);
1231  0 showHiddenAtStart.setSelected(false);
1232  0 hiddenColour.setBackground(
1233    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1234    }
1235   
 
1236  0 toggle @Override
1237    protected void userIdWidth_actionPerformed()
1238    {
1239  0 try
1240    {
1241  0 String val = userIdWidth.getText().trim();
1242  0 if (val.length() > 0)
1243    {
1244  0 Integer iw = Integer.parseInt(val);
1245  0 if (iw.intValue() < 12)
1246    {
1247  0 throw new NumberFormatException();
1248    }
1249  0 userIdWidth.setText(iw.toString());
1250    }
1251    } catch (NumberFormatException x)
1252    {
1253  0 userIdWidth.setText("");
1254  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1255    MessageManager
1256    .getString("warn.user_defined_width_requirements"),
1257    MessageManager.getString("label.invalid_id_column_width"),
1258    JvOptionPane.WARNING_MESSAGE);
1259    }
1260    }
1261   
 
1262  0 toggle @Override
1263    protected void autoIdWidth_actionPerformed()
1264    {
1265  0 userIdWidth.setEnabled(!autoIdWidth.isSelected());
1266  0 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1267    }
1268   
1269    /**
1270    * Returns true if structure viewer path is to a valid executable, else shows
1271    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1272    * (built in to Jalview) or when Jalview is left to try default paths.
1273    */
 
1274  0 toggle private boolean validateViewerPath()
1275    {
1276  0 if (structureViewerPath.getText().trim().length() > 0)
1277    {
1278  0 File f = new File(structureViewerPath.getText());
1279  0 if (!f.canExecute())
1280    {
1281  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1282    MessageManager.getString("label.invalid_viewer_path"),
1283    MessageManager.getString("label.invalid_viewer_path"),
1284    JvOptionPane.ERROR_MESSAGE);
1285  0 return false;
1286    }
1287    }
1288  0 return true;
1289    }
1290   
1291    /**
1292    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1293    * default or user-specified path, if not show a warning/help dialog
1294    */
 
1295  0 toggle @Override
1296    protected void structureViewer_actionPerformed(String selectedItem)
1297    {
1298  0 if (selectedItem.equals(ViewerType.JMOL.name()))
1299    {
1300  0 structureViewerPath.setEnabled(false);
1301  0 structureViewerPathLabel.setEnabled(false);
1302  0 return;
1303    }
1304  0 boolean found = false;
1305  0 structureViewerPath.setEnabled(true);
1306  0 structureViewerPathLabel.setEnabled(true);
1307  0 structureViewerPathLabel.setText(MessageManager
1308    .formatMessage("label.viewer_path", selectedItem));
1309   
1310    /*
1311    * Try user-specified and standard paths for structure viewer executable
1312    */
1313  0 String viewerPath = "";
1314  0 List<String> paths = null;
1315  0 try
1316    {
1317  0 ViewerType viewerType = ViewerType.valueOf(selectedItem);
1318  0 switch (viewerType)
1319    {
1320  0 case JMOL:
1321    // dealt with above
1322  0 break;
1323  0 case CHIMERA:
1324  0 viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1325  0 paths = StructureManager.getChimeraPaths(false);
1326  0 break;
1327  0 case CHIMERAX:
1328  0 viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1329  0 paths = StructureManager.getChimeraPaths(true);
1330  0 break;
1331  0 case PYMOL:
1332  0 viewerPath = Cache.getDefault(PYMOL_PATH, "");
1333  0 paths = PymolManager.getPymolPaths();
1334  0 break;
1335    }
1336    } catch (IllegalArgumentException e)
1337    {
1338    // only valid entries should be in the drop-down
1339    }
1340  0 structureViewerPath.setText(viewerPath);
1341   
1342  0 paths.add(0, structureViewerPath.getText());
1343  0 for (String path : paths)
1344    {
1345  0 if (new File(path.trim()).canExecute())
1346    {
1347  0 found = true;
1348  0 break;
1349    }
1350    }
1351   
1352  0 if (!found)
1353    {
1354  0 String[] options = { "OK", "Help" };
1355  0 int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1356    JvSwingUtils.wrapTooltip(true,
1357    MessageManager.getString("label.viewer_missing")),
1358    "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1359    null, options, options[0]);
1360  0 if (showHelp == JvOptionPane.NO_OPTION)
1361    {
1362  0 try
1363    {
1364  0 Help.showHelpWindow(HelpId.StructureViewer);
1365    } catch (HelpSetException e)
1366    {
1367  0 e.printStackTrace();
1368    }
1369    }
1370    }
1371    }
1372   
 
1373    public class OptionsParam
1374    {
1375    private String name;
1376   
1377    private String code;
1378   
 
1379  0 toggle public OptionsParam(String name, String code)
1380    {
1381  0 this.name = name;
1382  0 this.code = code;
1383    }
1384   
 
1385  0 toggle public String getName()
1386    {
1387  0 return name;
1388    }
1389   
 
1390  0 toggle public void setName(String name)
1391    {
1392  0 this.name = name;
1393    }
1394   
 
1395  0 toggle public String getCode()
1396    {
1397  0 return code;
1398    }
1399   
 
1400  0 toggle public void setCode(String code)
1401    {
1402  0 this.code = code;
1403    }
1404   
 
1405  0 toggle @Override
1406    public String toString()
1407    {
1408  0 return name;
1409    }
1410   
 
1411  0 toggle @Override
1412    public boolean equals(Object that)
1413    {
1414  0 if (!(that instanceof OptionsParam))
1415    {
1416  0 return false;
1417    }
1418  0 return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1419    }
1420   
 
1421  0 toggle @Override
1422    public int hashCode()
1423    {
1424  0 return name.hashCode() + code.hashCode();
1425    }
1426    }
1427   
 
1428    private class UrlListSelectionHandler implements ListSelectionListener
1429    {
1430   
 
1431  0 toggle @Override
1432    public void valueChanged(ListSelectionEvent e)
1433    {
1434  0 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1435   
1436  0 int index = lsm.getMinSelectionIndex();
1437  0 if (index == -1)
1438    {
1439    // no selection, so disable delete/edit buttons
1440  0 editLink.setEnabled(false);
1441  0 deleteLink.setEnabled(false);
1442  0 return;
1443    }
1444  0 int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1445   
1446    // enable/disable edit and delete link buttons
1447  0 if (((UrlLinkTableModel) linkUrlTable.getModel())
1448    .isRowDeletable(modelIndex))
1449    {
1450  0 deleteLink.setEnabled(true);
1451    }
1452    else
1453    {
1454  0 deleteLink.setEnabled(false);
1455    }
1456   
1457  0 if (((UrlLinkTableModel) linkUrlTable.getModel())
1458    .isRowEditable(modelIndex))
1459    {
1460  0 editLink.setEnabled(true);
1461    }
1462    else
1463    {
1464  0 editLink.setEnabled(false);
1465    }
1466    }
1467    }
1468    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.