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Coverage Report

  1. Project Clover database Wed Nov 13 2024 16:21:17 GMT
  2. Package jalview.gui

File Preferences.java

 

Coverage histogram

../../img/srcFileCovDistChart1.png
56% of files have more coverage

Code metrics

132
569
45
3
1,628
1,216
140
0.25
12.64
15
3.11

Classes

Class Line # Actions
Preferences 90 545 127
0.0198581552%
Preferences.OptionsParam 1533 11 9
0.00%
Preferences.UrlListSelectionHandler 1588 13 4
0.00%
 

Contributing tests

This file is covered by 2 tests. .

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.io.File;
31    import java.util.ArrayList;
32    import java.util.List;
33    import java.util.concurrent.CompletableFuture;
34   
35    import javax.help.HelpSetException;
36    import javax.swing.JComboBox;
37    import javax.swing.JInternalFrame;
38    import javax.swing.JPanel;
39    import javax.swing.ListSelectionModel;
40    import javax.swing.RowFilter;
41    import javax.swing.RowSorter;
42    import javax.swing.SortOrder;
43    import javax.swing.event.DocumentEvent;
44    import javax.swing.event.DocumentListener;
45    import javax.swing.event.ListSelectionEvent;
46    import javax.swing.event.ListSelectionListener;
47    import javax.swing.table.TableCellRenderer;
48    import javax.swing.table.TableColumn;
49    import javax.swing.table.TableModel;
50    import javax.swing.table.TableRowSorter;
51   
52    //import edu.stanford.ejalbert.launching.IBrowserLaunching;
53    import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
54    import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
55    import jalview.bin.Cache;
56    import jalview.bin.Console;
57    import jalview.bin.MemorySetting;
58    import jalview.ext.pymol.PymolManager;
59    import jalview.gui.Help.HelpId;
60    import jalview.gui.StructureViewer.ViewerType;
61    import jalview.io.BackupFiles;
62    import jalview.io.BackupFilesPresetEntry;
63    import jalview.io.FileFormatI;
64    import jalview.io.JalviewFileChooser;
65    import jalview.io.JalviewFileView;
66    import jalview.jbgui.GPreferences;
67    import jalview.jbgui.GSequenceLink;
68    import jalview.schemes.ColourSchemeI;
69    import jalview.schemes.ColourSchemes;
70    import jalview.schemes.ResidueColourScheme;
71    import jalview.urls.UrlLinkTableModel;
72    import jalview.urls.api.UrlProviderFactoryI;
73    import jalview.urls.api.UrlProviderI;
74    import jalview.urls.desktop.DesktopUrlProviderFactory;
75    import jalview.util.MessageManager;
76    import jalview.util.Platform;
77    import jalview.util.UrlConstants;
78    import jalview.ws.sifts.SiftsSettings;
79   
80    /**
81    * DOCUMENT ME!
82    *
83    * @author $author$
84    * @version $Revision$
85    */
86    /*
87    * for merge with Jalview-JS
88    public class Preferences extends GPreferences implements ApplicationSingletonI
89    */
 
90    public class Preferences extends GPreferences
91    {
92    public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
93   
94    public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
95   
96    public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
97   
98    public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
99   
100    public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
101   
102    public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
103   
104    public static final String ADD_SS_ANN = "ADD_SS_ANN";
105   
106    public static final String USE_RNAVIEW = "USE_RNAVIEW";
107   
108    public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
109   
110    public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
111   
112    public static final String CHIMERA_PATH = "CHIMERA_PATH";
113   
114    public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
115   
116    public static final String PYMOL_PATH = "PYMOL_PATH";
117   
118    public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
119   
120    public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
121   
122    public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
123   
124    public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
125   
126    public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
127   
128    public static final String GAP_COLOUR = "GAP_COLOUR";
129   
130    public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
131   
132    private static final int MIN_FONT_SIZE = 1;
133   
134    private static final int MAX_FONT_SIZE = 30;
135   
136    private String previousProxyType;
137   
138    private static Preferences INSTANCE = null; // add "final"
139   
140    /**
141    * Holds name and link separated with | character. Sequence ID must be
142    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
143    */
144    public static UrlProviderI sequenceUrlLinks;
145   
146    public static UrlLinkTableModel dataModel;
147   
148    /**
149    * Holds name and link separated with | character. Sequence IDS and Sequences
150    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
151    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
152    * for first and second token specified after a pipe character at end |,|.
153    * (TODO: proper escape for using | to separate ids or sequences
154    */
155   
156    public static List<String> groupURLLinks;
 
157  10 toggle static
158    {
159    // don't populate with session properties
160  10 Cache.disableSessionProperties();
161   
162    // get links selected to be in the menu (SEQUENCE_LINKS)
163    // and links entered by the user but not selected (STORED_LINKS)
164  10 String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
165  10 String notInMenuString = Cache.getDefault("STORED_LINKS", "");
166  10 String defaultUrl = Cache.getDefault("DEFAULT_URL",
167    UrlConstants.DEFAULT_LABEL);
168   
169    // if both links lists are empty, add the DEFAULT_URL link
170    // otherwise we assume the default link is in one of the lists
171  10 if (inMenuString.isEmpty() && notInMenuString.isEmpty())
172    {
173  8 inMenuString = UrlConstants.DEFAULT_STRING;
174    }
175  10 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
176    inMenuString, notInMenuString);
177  10 sequenceUrlLinks = factory.createUrlProvider();
178  10 dataModel = new UrlLinkTableModel(sequenceUrlLinks);
179   
180    /**
181    * TODO: reformulate groupURL encoding so two or more can be stored in the
182    * .properties file as '|' separated strings
183    */
184   
185  10 groupURLLinks = new ArrayList<>();
186   
187    // reenable
188  10 Cache.enableSessionProperties();
189    }
190   
191    JInternalFrame frame;
192   
193    private WsPreferences wsPrefs;
194   
195    private OptionsParam promptEachTimeOpt = new OptionsParam(
196    MessageManager.getString("label.prompt_each_time"),
197    LineartOptions.PROMPT_EACH_TIME);
198   
199    private OptionsParam lineArtOpt = new OptionsParam(
200    MessageManager.getString("label.lineart"), "Lineart");
201   
202    private OptionsParam textOpt = new OptionsParam(
203    MessageManager.getString("action.text"), "Text");
204   
205    // get singleton Preferences instance
 
206  0 toggle public static Preferences getInstance()
207    {
208  0 if (INSTANCE == null || INSTANCE.frame == null
209    || INSTANCE.frame.isClosed())
210    {
211  0 INSTANCE = new Preferences();
212    }
213  0 return INSTANCE;
214   
215    /*
216    * Replace code with the following for Jalvew-JS
217    Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
218    if (INSTANCE == null || INSTANCE.frame == null
219    || INSTANCE.frame.isClosed())
220    {
221    ApplicationSingletonProvider.remove(Preferences.class);
222    INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
223    }
224    return INSTANCE;
225    */
226    }
227   
 
228  0 toggle public static void openPreferences()
229    {
230  0 openPreferences(null, null);
231    }
232   
 
233  0 toggle public static void openPreferences(TabRef selectTab, String message)
234    {
235  0 Preferences p = getInstance();
236  0 if (selectTab != null)
237  0 p.selectTab(selectTab, message);
238  0 p.frame.show();
239  0 p.frame.moveToFront();
240  0 p.frame.grabFocus();
241    }
242   
 
243  0 toggle public void selectTab(TabRef selectTab, String message)
244    {
245  0 this.selectTab(selectTab);
246  0 if (message != null)
247  0 this.setMessage(message);
248  0 this.frame.show();
249    }
250   
251    /**
252    * Creates a new Preferences object.
253    */
 
254  0 toggle private Preferences()
255    {
256  0 super();
257    // don't populate with session properties
258  0 Cache.disableSessionProperties();
259   
260  0 frame = new JInternalFrame();
261  0 frame.setFrameIcon(null);
262  0 frame.setContentPane(this);
263  0 if (!Platform.isJS())
264    /**
265    * Java only
266    *
267    * @j2sIgnore
268    */
269    {
270  0 wsPrefs = new WsPreferences();
271  0 wsTab.add(wsPrefs, BorderLayout.CENTER);
272    }
273  0 int width = 500, height = 450;
274  0 if (Platform.isAMacAndNotJS())
275    {
276  0 width = 570;
277  0 height = 480;
278    }
279   
280  0 Desktop.addInternalFrame(frame,
281    MessageManager.getString("label.preferences"), width, height);
282  0 frame.setMinimumSize(new Dimension(width, height));
283   
284    /*
285    * Set Visual tab defaults
286    */
287  0 seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
288  0 rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
289  0 fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
290  0 annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
291   
292  0 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
293  0 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
294  0 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
295  0 ssConsensus.setSelected(Cache.getDefault("SHOW_SS_CONSENSUS", false));
296  0 openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
297  0 showUnconserved
298    .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
299  0 showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
300  0 showGroupConsensus
301    .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
302  0 showGroupConservation.setSelected(
303    Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
304  0 showConsensHistogram.setSelected(
305    Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
306  0 showConsensLogo
307    .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
308  0 showNpTooltip
309    .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
310  0 showDbRefTooltip
311    .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
312   
313  0 String[] fonts = java.awt.GraphicsEnvironment
314    .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
315  0 for (int i = 0; i < fonts.length; i++)
316    {
317  0 fontNameCB.addItem(fonts[i]);
318    }
319   
320  0 for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
321    {
322  0 fontSizeCB.addItem(i + "");
323    }
324   
325  0 fontStyleCB.addItem("plain");
326  0 fontStyleCB.addItem("bold");
327  0 fontStyleCB.addItem("italic");
328   
329  0 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
330  0 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
331  0 fontStyleCB.setSelectedItem(
332    Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
333   
334  0 smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
335  0 scaleProteinToCdna
336    .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
337   
338  0 idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
339   
340  0 wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
341   
342  0 gapSymbolCB.addItem("-");
343  0 gapSymbolCB.addItem(".");
344   
345  0 gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
346   
347  0 sortby.addItem("No sort");
348  0 sortby.addItem("Id");
349  0 sortby.addItem("Pairwise Identity");
350  0 sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
351   
352  0 sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
353  0 sortAnnBy
354    .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
355  0 sortAnnBy
356    .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
357  0 SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
358    .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
359    SequenceAnnotationOrder.NONE.name()));
360  0 sortAnnBy.setSelectedItem(savedSort.toString());
361   
362  0 sortAutocalc.addItem("Autocalculated first");
363  0 sortAutocalc.addItem("Autocalculated last");
364  0 final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
365  0 sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
366    : sortAutocalc.getItemAt(1));
367  0 startupCheckbox
368    .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
369  0 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
370    Cache.getDefault("www.jalview.org", "https://www.jalview.org")
371    + "/examples/exampleFile_2_7.jvp"));
372   
373    /*
374    * Set Colours tab defaults
375    */
376  0 protColour.addItem(ResidueColourScheme.NONE);
377  0 nucColour.addItem(ResidueColourScheme.NONE);
378  0 for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
379    {
380  0 String name = cs.getSchemeName();
381  0 protColour.addItem(name);
382  0 nucColour.addItem(name);
383    }
384  0 String oldProp = Cache.getDefault(DEFAULT_COLOUR,
385    ResidueColourScheme.NONE);
386  0 String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
387  0 protColour.setSelectedItem(newProp != null ? newProp : oldProp);
388  0 newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
389  0 nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
390  0 minColour.setBackground(
391    Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
392  0 maxColour.setBackground(
393    Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
394   
395    /*
396    * Set overview panel defaults
397    */
398  0 gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
399    OverviewCanvas.OVERVIEW_DEFAULT_GAP));
400  0 hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
401    OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN));
402  0 useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
403  0 gapLabel.setEnabled(!useLegacyGap.isSelected());
404  0 gapColour.setEnabled(!useLegacyGap.isSelected());
405  0 showHiddenAtStart
406    .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
407   
408    /*
409    * Set Structure tab defaults
410    */
411  0 final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
412  0 structFromPdb.setSelected(structSelected);
413  0 addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
414  0 addSecondaryStructure.setEnabled(structSelected);
415  0 addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
416  0 addTempFactor.setEnabled(structSelected);
417   
418    /*
419    * set choice of structure viewer, and path if saved as a preference;
420    * default to Jmol (first choice) if an unexpected value is found
421    */
422  0 String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
423    ViewerType.JMOL.name());
424  0 structViewer.setSelectedItem(viewerType);
425  0 String viewerPath = "";
426  0 ViewerType type = null;
427  0 try
428    {
429  0 type = ViewerType.valueOf(viewerType);
430  0 switch (type)
431    {
432  0 case JMOL:
433  0 break;
434  0 case CHIMERA:
435  0 viewerPath = Cache.getDefault(CHIMERA_PATH, "");
436  0 break;
437  0 case CHIMERAX:
438  0 viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
439  0 break;
440  0 case PYMOL:
441  0 viewerPath = Cache.getDefault(PYMOL_PATH, "");
442  0 break;
443    }
444    } catch (IllegalArgumentException e)
445    {
446  0 Console.error("Unknown structure viewer type: " + viewerType
447    + ", defaulting to Jmol");
448  0 type = ViewerType.JMOL;
449    }
450  0 structureViewerPath.setText(viewerPath);
451   
452  0 structureViewerPath.addActionListener(new ActionListener()
453    {
 
454  0 toggle @Override
455    public void actionPerformed(ActionEvent e)
456    {
457  0 if (validateViewerPath())
458    {
459  0 String path = structureViewerPath.getText();
460  0 try
461    {
462  0 ViewerType type = ViewerType.valueOf(viewerType);
463  0 switch (type)
464    {
465  0 case JMOL:
466  0 break;
467  0 case CHIMERA:
468  0 Cache.setProperty(CHIMERA_PATH, path);
469  0 break;
470  0 case CHIMERAX:
471  0 Cache.setProperty(CHIMERAX_PATH, path);
472  0 break;
473  0 case PYMOL:
474  0 Cache.setProperty(PYMOL_PATH, path);
475  0 break;
476    }
477    } catch (IllegalArgumentException x)
478    {
479  0 Console.error("Failed to set path - unknown viewer type", x);
480    }
481    }
482    }
483    });
484   
485  0 if (Cache.getDefault("MAP_WITH_SIFTS", false))
486    {
487  0 siftsMapping.setSelected(true);
488    }
489    else
490    {
491  0 nwMapping.setSelected(true);
492    }
493   
494  0 SiftsSettings
495    .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
496   
497    /*
498    * Set Connections tab defaults
499    */
500   
501    // set up sorting
502  0 linkUrlTable.setModel(dataModel);
503  0 final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
504    linkUrlTable.getModel());
505  0 linkUrlTable.setRowSorter(sorter);
506  0 List<RowSorter.SortKey> sortKeys = new ArrayList<>();
507   
508  0 UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
509  0 sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
510    SortOrder.DESCENDING));
511  0 sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
512    SortOrder.DESCENDING));
513  0 sortKeys.add(
514    new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
515   
516  0 sorter.setSortKeys(sortKeys);
517    // BH 2018 setSortKeys will do the sort
518    // sorter.sort();
519   
520    // set up filtering
521  0 ActionListener onReset;
522  0 onReset = new ActionListener()
523    {
 
524  0 toggle @Override
525    public void actionPerformed(ActionEvent e)
526    {
527  0 filterTB.setText("");
528  0 sorter.setRowFilter(RowFilter.regexFilter(""));
529    }
530   
531    };
532  0 doReset.addActionListener(onReset);
533   
534    // filter to display only custom urls
535  0 final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
536    {
 
537  0 toggle @Override
538    public boolean include(
539    Entry<? extends TableModel, ? extends Object> entry)
540    {
541  0 return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
542    }
543    };
544   
545  0 final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
546    linkUrlTable.getModel());
547  0 customSorter.setRowFilter(customUrlFilter);
548   
549  0 ActionListener onCustomOnly;
550  0 onCustomOnly = new ActionListener()
551    {
 
552  0 toggle @Override
553    public void actionPerformed(ActionEvent e)
554    {
555  0 filterTB.setText("");
556  0 sorter.setRowFilter(customUrlFilter);
557    }
558    };
559  0 userOnly.addActionListener(onCustomOnly);
560   
561  0 filterTB.getDocument().addDocumentListener(new DocumentListener()
562    {
563    String caseInsensitiveFlag = "(?i)";
564   
 
565  0 toggle @Override
566    public void changedUpdate(DocumentEvent e)
567    {
568  0 sorter.setRowFilter(RowFilter
569    .regexFilter(caseInsensitiveFlag + filterTB.getText()));
570    }
571   
 
572  0 toggle @Override
573    public void removeUpdate(DocumentEvent e)
574    {
575  0 sorter.setRowFilter(RowFilter
576    .regexFilter(caseInsensitiveFlag + filterTB.getText()));
577    }
578   
 
579  0 toggle @Override
580    public void insertUpdate(DocumentEvent e)
581    {
582  0 sorter.setRowFilter(RowFilter
583    .regexFilter(caseInsensitiveFlag + filterTB.getText()));
584    }
585    });
586   
587    // set up list selection functionality
588  0 linkUrlTable.getSelectionModel()
589    .addListSelectionListener(new UrlListSelectionHandler());
590   
591    // set up radio buttons
592  0 int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
593    .getPrimaryColumn();
594  0 String onClickName = linkUrlTable.getColumnName(onClickCol);
595  0 linkUrlTable.getColumn(onClickName)
596    .setCellRenderer(new RadioButtonRenderer());
597  0 linkUrlTable.getColumn(onClickName)
598    .setCellEditor(new RadioButtonEditor());
599   
600    // get boolean columns and resize those to min possible
601  0 for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
602    {
603  0 if (linkUrlTable.getModel().getColumnClass(column)
604    .equals(Boolean.class))
605    {
606  0 TableColumn tableColumn = linkUrlTable.getColumnModel()
607    .getColumn(column);
608  0 int preferredWidth = tableColumn.getMinWidth();
609   
610  0 TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
611    column);
612  0 Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
613  0 int cwidth = c.getPreferredSize().width
614    + linkUrlTable.getIntercellSpacing().width;
615  0 preferredWidth = Math.max(preferredWidth, cwidth);
616   
617  0 tableColumn.setPreferredWidth(preferredWidth);
618    }
619    }
620   
621  0 String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
622  0 previousProxyType = proxyTypeString;
623  0 switch (proxyTypeString)
624    {
625  0 case Cache.PROXYTYPE_NONE:
626  0 proxyType.setSelected(noProxy.getModel(), true);
627  0 break;
628  0 case Cache.PROXYTYPE_SYSTEM:
629  0 proxyType.setSelected(systemProxy.getModel(), true);
630  0 break;
631  0 case Cache.PROXYTYPE_CUSTOM:
632  0 proxyType.setSelected(customProxy.getModel(), true);
633  0 break;
634  0 default:
635  0 Console.warn(
636    "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
637    + proxyTypeString);
638    }
639  0 proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
640  0 proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
641  0 proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
642  0 proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
643  0 proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
644  0 proxyAuthUsernameTB
645    .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
646    // we are not storing or retrieving proxy password from .jalview_properties
647  0 proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
648    : new String(Cache.proxyAuthPassword));
649  0 setCustomProxyEnabled();
650  0 applyProxyButtonEnabled(false);
651   
652  0 usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
653    // note antisense here: default is true
654  0 questionnaire
655    .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
656  0 versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
657   
658    /*
659    * Set Output tab defaults
660    */
661  0 setupOutputCombo(epsRendering, "EPS_RENDERING");
662  0 setupOutputCombo(htmlRendering, "HTML_RENDERING");
663  0 setupOutputCombo(svgRendering, "SVG_RENDERING");
664  0 autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
665  0 userIdWidth.setEnabled(!autoIdWidth.isSelected());
666  0 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
667  0 Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
668  0 userIdWidth.setText(wi == null ? "" : wi.toString());
669    // TODO: refactor to use common enum via FormatAdapter and allow extension
670    // for new flat file formats
671  0 blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
672  0 clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
673  0 fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
674  0 msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
675  0 pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
676  0 pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
677  0 pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
678  0 modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
679  0 embbedBioJSON
680    .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
681   
682    /*
683    * Set Editing tab defaults
684    */
685  0 autoCalculateConsCheck
686    .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
687  0 padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
688  0 sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
689   
690  0 annotations_actionPerformed(null); // update the display of the annotation
691    // settings
692   
693    /*
694    * Set Backups tab defaults
695    */
696  0 loadLastSavedBackupsOptions();
697   
698    /*
699    * Set Startup tab defaults
700    */
701   
702    // re-enable
703  0 Cache.enableSessionProperties();
704    }
705   
706    /**
707    * A helper method that sets the items and initial selection in a character
708    * rendering option list (Prompt each time/Lineart/Text)
709    *
710    * @param comboBox
711    * @param propertyKey
712    */
 
713  0 toggle protected void setupOutputCombo(JComboBox<Object> comboBox,
714    String propertyKey)
715    {
716  0 Cache.disableSessionProperties();
717   
718  0 comboBox.addItem(promptEachTimeOpt);
719  0 comboBox.addItem(lineArtOpt);
720  0 comboBox.addItem(textOpt);
721   
722    /*
723    * JalviewJS doesn't support Lineart so force it to Text
724    */
725  0 String defaultOption = Platform.isJS() ? "Text"
726    : Cache.getDefault(propertyKey, "Prompt each time");
727  0 if (defaultOption.equalsIgnoreCase("Text"))
728    {
729  0 comboBox.setSelectedItem(textOpt);
730    }
731  0 else if (defaultOption.equalsIgnoreCase("Lineart"))
732    {
733  0 comboBox.setSelectedItem(lineArtOpt);
734    }
735    else
736    {
737  0 comboBox.setSelectedItem(promptEachTimeOpt);
738    }
739   
740  0 Cache.enableSessionProperties();
741    }
742   
743    /**
744    * Save user selections on the Preferences tabs to the Cache and write out to
745    * file.
746    *
747    * @param e
748    */
 
749  0 toggle @Override
750    public void ok_actionPerformed(ActionEvent e)
751    {
752  0 Cache.disableSessionProperties();
753   
754  0 if (!validateSettings())
755    {
756  0 return;
757    }
758   
759    /*
760    * Set proxy settings first (to be before web services refresh)
761    */
762  0 saveProxySettings();
763   
764    /*
765    * Save Visual settings
766    */
767   
768  0 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
769    Boolean.toString(seqLimit.isSelected()));
770  0 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
771    Boolean.toString(rightAlign.isSelected()));
772  0 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
773    Boolean.toString(fullScreen.isSelected()));
774  0 Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
775    Boolean.toString(openoverv.isSelected()));
776  0 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
777    Boolean.toString(annotations.isSelected()));
778  0 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
779    Boolean.toString(conservation.isSelected()));
780  0 Cache.applicationProperties.setProperty("SHOW_QUALITY",
781    Boolean.toString(quality.isSelected()));
782  0 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
783    Boolean.toString(identity.isSelected()));
784   
785  0 Cache.applicationProperties.setProperty("SHOW_SS_CONSENSUS",
786    Boolean.toString(ssConsensus.isSelected()));
787   
788  0 Cache.applicationProperties.setProperty("GAP_SYMBOL",
789    gapSymbolCB.getSelectedItem().toString());
790   
791  0 Cache.applicationProperties.setProperty("FONT_NAME",
792    fontNameCB.getSelectedItem().toString());
793  0 Cache.applicationProperties.setProperty("FONT_STYLE",
794    fontStyleCB.getSelectedItem().toString());
795  0 Cache.applicationProperties.setProperty("FONT_SIZE",
796    fontSizeCB.getSelectedItem().toString());
797   
798  0 Cache.applicationProperties.setProperty("ID_ITALICS",
799    Boolean.toString(idItalics.isSelected()));
800  0 Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
801    Boolean.toString(showUnconserved.isSelected()));
802  0 Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
803    Boolean.toString(showOccupancy.isSelected()));
804  0 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
805    Boolean.toString(showGroupConsensus.isSelected()));
806  0 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
807    Boolean.toString(showGroupConservation.isSelected()));
808  0 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
809    Boolean.toString(showConsensHistogram.isSelected()));
810  0 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
811    Boolean.toString(showConsensLogo.isSelected()));
812  0 Cache.applicationProperties.setProperty("ANTI_ALIAS",
813    Boolean.toString(smoothFont.isSelected()));
814  0 Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
815    Boolean.toString(scaleProteinToCdna.isSelected()));
816  0 Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
817    Boolean.toString(showNpTooltip.isSelected()));
818  0 Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
819    Boolean.toString(showDbRefTooltip.isSelected()));
820   
821  0 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
822    Boolean.toString(wrap.isSelected()));
823   
824  0 Cache.applicationProperties.setProperty("STARTUP_FILE",
825    startupFileTextfield.getText());
826  0 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
827    Boolean.toString(startupCheckbox.isSelected()));
828   
829  0 Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
830    sortby.getSelectedItem().toString());
831   
832    // convert description of sort order to enum name for save
833  0 SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
834    .forDescription(sortAnnBy.getSelectedItem().toString());
835  0 if (annSortOrder != null)
836    {
837  0 Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
838    annSortOrder.name());
839    }
840   
841  0 final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
842  0 Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
843    Boolean.valueOf(showAutocalcFirst).toString());
844   
845    /*
846    * Save Colours settings
847    */
848  0 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
849    protColour.getSelectedItem().toString());
850  0 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
851    nucColour.getSelectedItem().toString());
852  0 Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
853    minColour.getBackground());
854  0 Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
855    maxColour.getBackground());
856   
857    /*
858    * Save Overview settings
859    */
860  0 Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
861  0 Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
862  0 Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
863    Boolean.toString(useLegacyGap.isSelected()));
864  0 Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
865    Boolean.toString(showHiddenAtStart.isSelected()));
866   
867    /*
868    * Save Structure settings
869    */
870  0 Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
871    Boolean.toString(addTempFactor.isSelected()));
872  0 Cache.applicationProperties.setProperty(ADD_SS_ANN,
873    Boolean.toString(addSecondaryStructure.isSelected()));
874  0 Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
875    Boolean.toString(structFromPdb.isSelected()));
876  0 String viewer = structViewer.getSelectedItem().toString();
877  0 String viewerPath = structureViewerPath.getText();
878  0 Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
879  0 if (viewer.equals(ViewerType.CHIMERA.name()))
880    {
881  0 Cache.setOrRemove(CHIMERA_PATH, viewerPath);
882    }
883  0 else if (viewer.equals(ViewerType.CHIMERAX.name()))
884    {
885  0 Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
886    }
887  0 else if (viewer.equals(ViewerType.PYMOL.name()))
888    {
889  0 Cache.setOrRemove(PYMOL_PATH, viewerPath);
890    }
891  0 Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
892    Boolean.toString(siftsMapping.isSelected()));
893  0 SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
894   
895    /*
896    * Save Output settings
897    */
898  0 Cache.applicationProperties.setProperty("EPS_RENDERING",
899    ((OptionsParam) epsRendering.getSelectedItem()).getCode());
900  0 Cache.applicationProperties.setProperty("HTML_RENDERING",
901    ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
902  0 Cache.applicationProperties.setProperty("SVG_RENDERING",
903    ((OptionsParam) svgRendering.getSelectedItem()).getCode());
904   
905    /*
906    * Save Connections settings
907    */
908    // Proxy settings set first (to catch web services)
909   
910    // save user-defined and selected links
911  0 String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
912  0 if (menuLinks.isEmpty())
913    {
914  0 Cache.applicationProperties.remove("SEQUENCE_LINKS");
915    }
916    else
917    {
918  0 Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
919    menuLinks.toString());
920    }
921   
922  0 String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
923  0 if (nonMenuLinks.isEmpty())
924    {
925  0 Cache.applicationProperties.remove("STORED_LINKS");
926    }
927    else
928    {
929  0 Cache.applicationProperties.setProperty("STORED_LINKS",
930    nonMenuLinks.toString());
931    }
932   
933  0 Cache.applicationProperties.setProperty("DEFAULT_URL",
934    sequenceUrlLinks.getPrimaryUrlId());
935   
936  0 Cache.setProperty("VERSION_CHECK",
937    Boolean.toString(versioncheck.isSelected()));
938  0 if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
939    {
940    // default is false - we only set this if the user has actively agreed
941  0 Cache.setProperty("USAGESTATS",
942    Boolean.toString(usagestats.isSelected()));
943    }
944  0 if (!questionnaire.isSelected())
945    {
946  0 Cache.setProperty("NOQUESTIONNAIRES", "true");
947    }
948    else
949    {
950    // special - made easy to edit a property file to disable questionnaires
951    // by just adding the given line
952  0 Cache.removeProperty("NOQUESTIONNAIRES");
953    }
954   
955    /*
956    * Save Output settings
957    */
958  0 Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
959    Boolean.toString(blcjv.isSelected()));
960  0 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
961    Boolean.toString(clustaljv.isSelected()));
962  0 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
963    Boolean.toString(fastajv.isSelected()));
964  0 Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
965    Boolean.toString(msfjv.isSelected()));
966  0 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
967    Boolean.toString(pfamjv.isSelected()));
968  0 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
969    Boolean.toString(pileupjv.isSelected()));
970  0 Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
971    Boolean.toString(pirjv.isSelected()));
972  0 Cache.applicationProperties.setProperty("PIR_MODELLER",
973    Boolean.toString(modellerOutput.isSelected()));
974  0 Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
975    Boolean.toString(embbedBioJSON.isSelected()));
976  0 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
977   
978  0 Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
979    Boolean.toString(autoIdWidth.isSelected()));
980  0 userIdWidth_actionPerformed();
981  0 Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
982    userIdWidth.getText());
983   
984    /*
985    * Save Editing settings
986    */
987  0 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
988    Boolean.toString(autoCalculateConsCheck.isSelected()));
989  0 Cache.applicationProperties.setProperty("SORT_BY_TREE",
990    Boolean.toString(sortByTree.isSelected()));
991  0 Cache.applicationProperties.setProperty("PAD_GAPS",
992    Boolean.toString(padGaps.isSelected()));
993   
994  0 if (!Platform.isJS())
995    {
996  0 wsPrefs.updateAndRefreshWsMenuConfig(false);
997    }
998   
999    /*
1000    * Save Backups settings
1001    */
1002  0 Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
1003    Boolean.toString(enableBackupFiles.isSelected()));
1004  0 int preset = getComboIntStringKey(backupfilesPresetsCombo);
1005  0 Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
1006    Integer.toString(preset));
1007   
1008  0 if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
1009    {
1010  0 BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
1011  0 BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1012    BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
1013  0 Cache.applicationProperties.setProperty(
1014    BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
1015    }
1016   
1017  0 BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1018    .get(preset);
1019  0 Cache.applicationProperties.setProperty(
1020    BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
1021   
1022    /*
1023    * Save Memory Settings
1024    */
1025  0 Cache.applicationProperties.setProperty(
1026    MemorySetting.CUSTOMISED_SETTINGS,
1027    Boolean.toString(customiseMemorySetting.isSelected()));
1028  0 Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC,
1029    Integer.toString(jvmMemoryPercentSlider.getValue()));
1030  0 Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX,
1031    jvmMemoryMaxTextField.getText());
1032   
1033    /*
1034    * save and close Preferences
1035    */
1036   
1037  0 Cache.saveProperties();
1038  0 Desktop.instance.doConfigureStructurePrefs();
1039  0 try
1040    {
1041  0 frame.setClosed(true);
1042    } catch (Exception ex)
1043    {
1044    }
1045   
1046  0 Cache.enableSessionProperties();
1047    }
1048   
 
1049  0 toggle @Override
1050    public void saveProxySettings()
1051    {
1052  0 Cache.disableSessionProperties();
1053   
1054  0 String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
1055  0 : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
1056    : Cache.PROXYTYPE_SYSTEM;
1057  0 Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
1058  0 Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
1059  0 Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
1060  0 Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
1061  0 Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
1062  0 Cache.setOrRemove("PROXY_AUTH",
1063    Boolean.toString(proxyAuth.isSelected()));
1064  0 Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1065  0 Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1066  0 Cache.setProxyPropertiesFromPreferences(previousProxyType);
1067  0 if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1068    || !newProxyType.equals(previousProxyType))
1069    {
1070    // force a re-lookup of ws if proxytype is custom or has changed
1071  0 wsPrefs.update++;
1072    }
1073  0 previousProxyType = newProxyType;
1074   
1075  0 Cache.enableSessionProperties();
1076    }
1077   
1078    /**
1079    * Do any necessary validation before saving settings. Return focus to the
1080    * first tab which fails validation.
1081    *
1082    * @return
1083    */
 
1084  0 toggle private boolean validateSettings()
1085    {
1086  0 if (!validateStructure())
1087    {
1088  0 structureTab.requestFocusInWindow();
1089  0 return false;
1090    }
1091  0 return true;
1092    }
1093   
 
1094  0 toggle @Override
1095    protected boolean validateStructure()
1096    {
1097  0 return validateViewerPath();
1098   
1099    }
1100   
1101    /**
1102    * DOCUMENT ME!
1103    */
 
1104  0 toggle @Override
1105    public void startupFileTextfield_mouseClicked()
1106    {
1107  0 Cache.disableSessionProperties();
1108   
1109    // TODO: JAL-3048 not needed for Jalview-JS
1110    // default file format now determined by JalviewFileChooser
1111  0 JalviewFileChooser chooser = JalviewFileChooser
1112    .forRead(Cache.getProperty("LAST_DIRECTORY"), null);
1113  0 chooser.setFileView(new JalviewFileView());
1114  0 chooser.setDialogTitle(
1115    MessageManager.getString("label.select_startup_file"));
1116   
1117  0 int value = chooser.showOpenDialog(this);
1118   
1119  0 if (value == JalviewFileChooser.APPROVE_OPTION)
1120    {
1121  0 FileFormatI format = chooser.getSelectedFormat();
1122  0 if (format != null)
1123    {
1124  0 Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1125    format.getName());
1126    }
1127  0 startupFileTextfield
1128    .setText(chooser.getSelectedFile().getAbsolutePath());
1129    }
1130   
1131  0 Cache.enableSessionProperties();
1132    }
1133   
1134    /**
1135    * DOCUMENT ME!
1136    *
1137    * @param e
1138    * DOCUMENT ME!
1139    */
 
1140  0 toggle @Override
1141    public void cancel_actionPerformed(ActionEvent e)
1142    {
1143  0 try
1144    {
1145  0 if (!Platform.isJS())
1146    {
1147  0 wsPrefs.updateWsMenuConfig(true);
1148  0 wsPrefs.refreshWs_actionPerformed(e);
1149    }
1150  0 frame.setClosed(true);
1151    } catch (Exception ex)
1152    {
1153    }
1154    }
1155   
1156    /**
1157    * DOCUMENT ME!
1158    *
1159    * @param e
1160    * DOCUMENT ME!
1161    */
 
1162  0 toggle @Override
1163    public void annotations_actionPerformed(ActionEvent e)
1164    {
1165  0 conservation.setEnabled(annotations.isSelected());
1166  0 quality.setEnabled(annotations.isSelected());
1167  0 identity.setEnabled(annotations.isSelected());
1168  0 ssConsensus.setEnabled(annotations.isSelected());
1169  0 showOccupancy.setEnabled(annotations.isSelected());
1170  0 showGroupConsensus.setEnabled(annotations.isSelected());
1171  0 showGroupConservation.setEnabled(annotations.isSelected());
1172  0 showConsensHistogram.setEnabled(annotations.isSelected()
1173    && (identity.isSelected() || showGroupConsensus.isSelected()));
1174  0 showConsensLogo.setEnabled(annotations.isSelected()
1175    && (identity.isSelected() || showGroupConsensus.isSelected()));
1176    }
1177   
 
1178  0 toggle @Override
1179    public void newLink_actionPerformed(ActionEvent e)
1180    {
1181  0 GSequenceLink link = new GSequenceLink();
1182  0 boolean valid = false;
1183  0 while (!valid)
1184    {
1185  0 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1186    MessageManager.getString("label.new_sequence_url_link"),
1187    JvOptionPane.OK_CANCEL_OPTION, -1,
1188    null) == JvOptionPane.OK_OPTION)
1189    {
1190  0 if (link.checkValid())
1191    {
1192  0 if (((UrlLinkTableModel) linkUrlTable.getModel())
1193    .isUniqueName(link.getName()))
1194    {
1195  0 ((UrlLinkTableModel) linkUrlTable.getModel())
1196    .insertRow(link.getName(), link.getURL());
1197  0 valid = true;
1198    }
1199    else
1200    {
1201  0 link.notifyDuplicate();
1202  0 continue;
1203    }
1204    }
1205    }
1206    else
1207    {
1208  0 break;
1209    }
1210    }
1211    }
1212   
 
1213  0 toggle @Override
1214    public void editLink_actionPerformed(ActionEvent e)
1215    {
1216  0 GSequenceLink link = new GSequenceLink();
1217   
1218  0 int index = linkUrlTable.getSelectedRow();
1219  0 if (index == -1)
1220    {
1221    // button no longer enabled if row is not selected
1222  0 Console.debug("Edit with no row selected in linkUrlTable");
1223  0 return;
1224    }
1225   
1226  0 int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1227    .getNameColumn();
1228  0 int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1229    .getUrlColumn();
1230  0 String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1231  0 link.setName(oldName);
1232  0 link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1233   
1234  0 boolean valid = false;
1235  0 while (!valid)
1236    {
1237  0 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1238    MessageManager.getString("label.edit_sequence_url_link"),
1239    JvOptionPane.OK_CANCEL_OPTION, -1,
1240    null) == JvOptionPane.OK_OPTION)
1241    {
1242  0 if (link.checkValid())
1243    {
1244  0 if ((oldName.equals(link.getName()))
1245    || (((UrlLinkTableModel) linkUrlTable.getModel())
1246    .isUniqueName(link.getName())))
1247    {
1248  0 linkUrlTable.setValueAt(link.getName(), index, nameCol);
1249  0 linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1250  0 valid = true;
1251    }
1252    else
1253    {
1254  0 link.notifyDuplicate();
1255  0 continue;
1256    }
1257    }
1258    }
1259    else
1260    {
1261  0 break;
1262    }
1263    }
1264    }
1265   
 
1266  0 toggle @Override
1267    public void deleteLink_actionPerformed(ActionEvent e)
1268    {
1269  0 int index = linkUrlTable.getSelectedRow();
1270  0 int modelIndex = -1;
1271  0 if (index == -1)
1272    {
1273    // button no longer enabled if row is not selected
1274  0 Console.debug("Delete with no row selected in linkUrlTable");
1275  0 return;
1276    }
1277    else
1278    {
1279  0 modelIndex = linkUrlTable.convertRowIndexToModel(index);
1280    }
1281   
1282    // make sure we use the model index to delete, and not the table index
1283  0 ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1284    }
1285   
1286    /*
1287    * (non-Javadoc)
1288    *
1289    * @see
1290    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1291    * .ActionEvent)
1292    */
 
1293  0 toggle @Override
1294    protected void showunconserved_actionPerformed(ActionEvent e)
1295    {
1296    // TODO Auto-generated method stub
1297  0 super.showunconserved_actionPerformed(e);
1298    }
1299   
 
1300  0 toggle public static List<String> getGroupURLLinks()
1301    {
1302  0 return groupURLLinks;
1303    }
1304   
 
1305  0 toggle @Override
1306    public void minColour_actionPerformed(JPanel panel)
1307    {
1308  0 JalviewColourChooser.showColourChooser(this,
1309    MessageManager.getString("label.select_colour_minimum_value"),
1310    panel);
1311    }
1312   
 
1313  0 toggle @Override
1314    public void maxColour_actionPerformed(JPanel panel)
1315    {
1316  0 JalviewColourChooser.showColourChooser(this,
1317    MessageManager.getString("label.select_colour_maximum_value"),
1318    panel);
1319    }
1320   
 
1321  0 toggle @Override
1322    public void gapColour_actionPerformed(JPanel gap)
1323    {
1324  0 if (!useLegacyGap.isSelected())
1325    {
1326  0 JalviewColourChooser.showColourChooser(this,
1327    MessageManager.getString("label.select_gap_colour"), gap);
1328    }
1329    }
1330   
 
1331  0 toggle @Override
1332    public void hiddenColour_actionPerformed(JPanel hidden)
1333    {
1334  0 JalviewColourChooser.showColourChooser(this,
1335    MessageManager.getString("label.select_hidden_colour"), hidden);
1336    }
1337   
 
1338  0 toggle @Override
1339    protected void useLegacyGaps_actionPerformed(ActionEvent e)
1340    {
1341  0 boolean enabled = useLegacyGap.isSelected();
1342  0 if (enabled)
1343    {
1344  0 gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP);
1345    }
1346    else
1347    {
1348  0 gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP);
1349    }
1350  0 gapColour.setEnabled(!enabled);
1351  0 gapLabel.setEnabled(!enabled);
1352    }
1353   
 
1354  0 toggle @Override
1355    protected void resetOvDefaults_actionPerformed(ActionEvent e)
1356    {
1357  0 useLegacyGap.setSelected(false);
1358  0 useLegacyGaps_actionPerformed(null);
1359  0 showHiddenAtStart.setSelected(false);
1360  0 hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN);
1361    }
1362   
 
1363  0 toggle @Override
1364    protected void userIdWidth_actionPerformed()
1365    {
1366  0 try
1367    {
1368  0 String val = userIdWidth.getText().trim();
1369  0 if (val.length() > 0)
1370    {
1371  0 Integer iw = Integer.parseInt(val);
1372  0 if (iw.intValue() < 12)
1373    {
1374  0 throw new NumberFormatException();
1375    }
1376  0 userIdWidth.setText(iw.toString());
1377    }
1378    } catch (NumberFormatException x)
1379    {
1380  0 userIdWidth.setText("");
1381  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1382    MessageManager
1383    .getString("warn.user_defined_width_requirements"),
1384    MessageManager.getString("label.invalid_id_column_width"),
1385    JvOptionPane.WARNING_MESSAGE);
1386    }
1387    }
1388   
 
1389  0 toggle @Override
1390    protected void autoIdWidth_actionPerformed()
1391    {
1392  0 userIdWidth.setEnabled(!autoIdWidth.isSelected());
1393  0 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1394    }
1395   
1396    /**
1397    * Returns true if structure viewer path is to a valid executable, else shows
1398    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1399    * (built in to Jalview) or when Jalview is left to try default paths.
1400    */
 
1401  0 toggle private boolean validateViewerPath()
1402    {
1403  0 if (structureViewerPath.getText().trim().length() > 0)
1404    {
1405  0 File f = new File(structureViewerPath.getText());
1406  0 if (!f.canExecute())
1407    {
1408  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1409    MessageManager.getString("label.invalid_viewer_path"),
1410    MessageManager.getString("label.invalid_viewer_path"),
1411    JvOptionPane.ERROR_MESSAGE);
1412  0 return false;
1413    }
1414    }
1415  0 return true;
1416    }
1417   
1418    /**
1419    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1420    * default or user-specified path, if not show a warning/help dialog
1421    */
 
1422  0 toggle @Override
1423    protected void structureViewer_actionPerformed(String selectedItem)
1424    {
1425  0 if (selectedItem.equals(ViewerType.JMOL.name()))
1426    {
1427  0 structureViewerPath.setEnabled(false);
1428  0 structureViewerPathLabel.setEnabled(false);
1429  0 return;
1430    }
1431  0 boolean found = false;
1432  0 structureViewerPath.setEnabled(true);
1433  0 structureViewerPathLabel.setEnabled(true);
1434  0 structureViewerPathLabel.setText(MessageManager
1435    .formatMessage("label.viewer_path", selectedItem));
1436   
1437    /*
1438    * Try user-specified and standard paths for structure viewer executable
1439    */
1440  0 String viewerPath = "";
1441  0 List<String> paths = null;
1442  0 Cache.disableSessionProperties();
1443  0 try
1444    {
1445  0 ViewerType viewerType = ViewerType.valueOf(selectedItem);
1446  0 switch (viewerType)
1447    {
1448  0 case JMOL:
1449    // dealt with above
1450  0 break;
1451  0 case CHIMERA:
1452  0 viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1453  0 paths = StructureManager.getChimeraPaths(false);
1454  0 break;
1455  0 case CHIMERAX:
1456  0 viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1457  0 paths = StructureManager.getChimeraPaths(true);
1458  0 break;
1459  0 case PYMOL:
1460  0 viewerPath = Cache.getDefault(PYMOL_PATH, "");
1461  0 paths = PymolManager.getPymolPaths();
1462  0 break;
1463    }
1464    } catch (IllegalArgumentException e)
1465    {
1466    // only valid entries should be in the drop-down
1467    }
1468  0 Cache.enableSessionProperties();
1469  0 structureViewerPath.setText(viewerPath);
1470   
1471  0 jalview.bin.Console
1472  0 .debug("Found " + (paths == null ? null : paths.size())
1473    + " paths to look for " + selectedItem.toString());
1474  0 if (paths == null)
1475    {
1476  0 paths = new ArrayList<>();
1477    }
1478  0 paths.add(0, structureViewerPath.getText());
1479  0 for (String path : paths)
1480    {
1481  0 jalview.bin.Console.debug("Looking for " + selectedItem.toString()
1482    + " in " + path.trim());
1483  0 if (new File(path.trim()).canExecute())
1484    {
1485  0 jalview.bin.Console.debug(
1486    "Found " + selectedItem.toString() + " in " + path.trim());
1487  0 found = true;
1488  0 break;
1489    }
1490    }
1491   
1492  0 if (!found)
1493    {
1494  0 String[] options = { "OK", "Help" };
1495  0 int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1496    JvSwingUtils.wrapTooltip(true,
1497    MessageManager.getString("label.viewer_missing")),
1498    "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1499    null, options, options[0]);
1500   
1501  0 if (showHelp == JvOptionPane.NO_OPTION)
1502    {
1503  0 this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1504  0 try
1505    {
1506  0 Help.showHelpWindow(HelpId.StructureViewer);
1507    } catch (HelpSetException e)
1508    {
1509  0 e.printStackTrace();
1510    }
1511    }
1512  0 else if (showHelp == JvOptionPane.OK_OPTION)
1513    {
1514  0 this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1515  0 CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
1516  0 try
1517    {
1518  0 for (int i = 0; i < 3; i++)
1519    {
1520  0 structureViewerPath.setBackground(Color.PINK);
1521  0 Thread.sleep(500);
1522  0 structureViewerPath.setBackground(Color.WHITE);
1523  0 Thread.sleep(500);
1524    }
1525    } catch (InterruptedException e)
1526    {
1527    }
1528    });
1529    }
1530    }
1531    }
1532   
 
1533    public class OptionsParam
1534    {
1535    private String name;
1536   
1537    private String code;
1538   
 
1539  0 toggle public OptionsParam(String name, String code)
1540    {
1541  0 this.name = name;
1542  0 this.code = code;
1543    }
1544   
 
1545  0 toggle public String getName()
1546    {
1547  0 return name;
1548    }
1549   
 
1550  0 toggle public void setName(String name)
1551    {
1552  0 this.name = name;
1553    }
1554   
 
1555  0 toggle public String getCode()
1556    {
1557  0 return code;
1558    }
1559   
 
1560  0 toggle public void setCode(String code)
1561    {
1562  0 this.code = code;
1563    }
1564   
 
1565  0 toggle @Override
1566    public String toString()
1567    {
1568  0 return name;
1569    }
1570   
 
1571  0 toggle @Override
1572    public boolean equals(Object that)
1573    {
1574  0 if (!(that instanceof OptionsParam))
1575    {
1576  0 return false;
1577    }
1578  0 return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1579    }
1580   
 
1581  0 toggle @Override
1582    public int hashCode()
1583    {
1584  0 return name.hashCode() + code.hashCode();
1585    }
1586    }
1587   
 
1588    private class UrlListSelectionHandler implements ListSelectionListener
1589    {
1590   
 
1591  0 toggle @Override
1592    public void valueChanged(ListSelectionEvent e)
1593    {
1594  0 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1595   
1596  0 int index = lsm.getMinSelectionIndex();
1597  0 if (index == -1)
1598    {
1599    // no selection, so disable delete/edit buttons
1600  0 editLink.setEnabled(false);
1601  0 deleteLink.setEnabled(false);
1602  0 return;
1603    }
1604  0 int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1605   
1606    // enable/disable edit and delete link buttons
1607  0 if (((UrlLinkTableModel) linkUrlTable.getModel())
1608    .isRowDeletable(modelIndex))
1609    {
1610  0 deleteLink.setEnabled(true);
1611    }
1612    else
1613    {
1614  0 deleteLink.setEnabled(false);
1615    }
1616   
1617  0 if (((UrlLinkTableModel) linkUrlTable.getModel())
1618    .isRowEditable(modelIndex))
1619    {
1620  0 editLink.setEnabled(true);
1621    }
1622    else
1623    {
1624  0 editLink.setEnabled(false);
1625    }
1626    }
1627    }
1628    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 13 2024 16:28:33 GMT using coverage data from Wed Nov 13 2024 16:28:18 GMT.
  • OpenClover is free and open-source software.