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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.gui

File Preferences.java

 

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104
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Classes

Class Line # Actions
Preferences 83 406 87 524
0.0187265911.9%
Preferences.OptionsParam 1244 11 9 21
0.00%
Preferences.UrlListSelectionHandler 1299 13 4 20
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.gui;
22   
23    import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24    import jalview.bin.Cache;
25    import jalview.bin.Jalview;
26    import jalview.gui.Help.HelpId;
27    import jalview.gui.StructureViewer.ViewerType;
28    import jalview.io.FileFormatI;
29    import jalview.io.JalviewFileChooser;
30    import jalview.io.JalviewFileView;
31    import jalview.jbgui.GPreferences;
32    import jalview.jbgui.GSequenceLink;
33    import jalview.schemes.ColourSchemeI;
34    import jalview.schemes.ColourSchemes;
35    import jalview.schemes.ResidueColourScheme;
36    import jalview.urls.UrlLinkTableModel;
37    import jalview.urls.api.UrlProviderFactoryI;
38    import jalview.urls.api.UrlProviderI;
39    import jalview.urls.desktop.DesktopUrlProviderFactory;
40    import jalview.util.MessageManager;
41    import jalview.util.Platform;
42    import jalview.util.UrlConstants;
43    import jalview.ws.sifts.SiftsSettings;
44   
45    import java.awt.BorderLayout;
46    import java.awt.Color;
47    import java.awt.Component;
48    import java.awt.Dimension;
49    import java.awt.Font;
50    import java.awt.event.ActionEvent;
51    import java.awt.event.ActionListener;
52    import java.awt.event.MouseEvent;
53    import java.io.File;
54    import java.util.ArrayList;
55    import java.util.List;
56   
57    import javax.help.HelpSetException;
58    import javax.swing.JComboBox;
59    import javax.swing.JFileChooser;
60    import javax.swing.JInternalFrame;
61    import javax.swing.JPanel;
62    import javax.swing.ListSelectionModel;
63    import javax.swing.RowFilter;
64    import javax.swing.RowSorter;
65    import javax.swing.SortOrder;
66    import javax.swing.event.DocumentEvent;
67    import javax.swing.event.DocumentListener;
68    import javax.swing.event.ListSelectionEvent;
69    import javax.swing.event.ListSelectionListener;
70    import javax.swing.table.TableCellRenderer;
71    import javax.swing.table.TableColumn;
72    import javax.swing.table.TableModel;
73    import javax.swing.table.TableRowSorter;
74   
75    import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
76   
77    /**
78    * DOCUMENT ME!
79    *
80    * @author $author$
81    * @version $Revision$
82    */
 
83    public class Preferences extends GPreferences
84    {
85    public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
86   
87    public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
88   
89    public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
90   
91    public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
92   
93    public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
94   
95    public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
96   
97    public static final String ADD_SS_ANN = "ADD_SS_ANN";
98   
99    public static final String USE_RNAVIEW = "USE_RNAVIEW";
100   
101    public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
102   
103    public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
104   
105    public static final String CHIMERA_PATH = "CHIMERA_PATH";
106   
107    public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
108   
109    public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
110   
111    public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
112   
113    public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
114   
115    public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
116   
117    public static final String GAP_COLOUR = "GAP_COLOUR";
118   
119    public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
120   
121    private static final int MIN_FONT_SIZE = 1;
122   
123    private static final int MAX_FONT_SIZE = 30;
124   
125    /**
126    * Holds name and link separated with | character. Sequence ID must be
127    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
128    */
129    public static UrlProviderI sequenceUrlLinks;
130   
131    public static UrlLinkTableModel dataModel;
132   
133    /**
134    * Holds name and link separated with | character. Sequence IDS and Sequences
135    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
136    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
137    * for first and second token specified after a pipe character at end |,|.
138    * (TODO: proper escape for using | to separate ids or sequences
139    */
140   
141    public static List<String> groupURLLinks;
 
142  1 toggle static
143    {
144    // get links selected to be in the menu (SEQUENCE_LINKS)
145    // and links entered by the user but not selected (STORED_LINKS)
146  1 String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
147  1 String notInMenuString = Cache.getDefault("STORED_LINKS", "");
148  1 String defaultUrl = Cache.getDefault("DEFAULT_URL",
149    UrlConstants.DEFAULT_LABEL);
150   
151    // if both links lists are empty, add the DEFAULT_URL link
152    // otherwise we assume the default link is in one of the lists
153  1 if (inMenuString.isEmpty() && notInMenuString.isEmpty())
154    {
155  0 inMenuString = UrlConstants.DEFAULT_STRING;
156    }
157  1 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
158    inMenuString, notInMenuString);
159  1 sequenceUrlLinks = factory.createUrlProvider();
160  1 dataModel = new UrlLinkTableModel(sequenceUrlLinks);
161   
162    /**
163    * TODO: reformulate groupURL encoding so two or more can be stored in the
164    * .properties file as '|' separated strings
165    */
166   
167  1 groupURLLinks = new ArrayList<>();
168    }
169   
170    JInternalFrame frame;
171   
172    private WsPreferences wsPrefs;
173   
174    private OptionsParam promptEachTimeOpt = new OptionsParam(
175    MessageManager.getString("label.prompt_each_time"),
176    "Prompt each time");
177   
178    private OptionsParam lineArtOpt = new OptionsParam(
179    MessageManager.getString("label.lineart"), "Lineart");
180   
181    private OptionsParam textOpt = new OptionsParam(
182    MessageManager.getString("action.text"), "Text");
183   
184    /**
185    * Creates a new Preferences object.
186    */
 
187  0 toggle public Preferences()
188    {
189  0 super();
190  0 frame = new JInternalFrame();
191  0 frame.setContentPane(this);
192  0 if (!Jalview.isJS())
193    {
194  0 wsPrefs = new WsPreferences();
195  0 wsTab.add(wsPrefs, BorderLayout.CENTER);
196    }
197  0 int width = 500, height = 450;
198  0 if (Platform.isAMac())
199    {
200  0 width = 570;
201  0 height = 480;
202    }
203   
204  0 Desktop.addInternalFrame(frame,
205    MessageManager.getString("label.preferences"), width, height);
206  0 frame.setMinimumSize(new Dimension(width, height));
207   
208    /*
209    * Set Visual tab defaults
210    */
211  0 seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
212  0 rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
213  0 fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
214  0 annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
215   
216  0 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
217  0 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
218  0 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
219  0 openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
220  0 showUnconserved
221    .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
222  0 showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
223  0 showGroupConsensus
224    .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
225  0 showGroupConservation.setSelected(
226    Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
227  0 showConsensHistogram.setSelected(
228    Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
229  0 showConsensLogo
230    .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
231  0 showNpTooltip
232    .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
233  0 showDbRefTooltip
234    .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
235   
236  0 String[] fonts = java.awt.GraphicsEnvironment
237    .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
238  0 for (int i = 0; i < fonts.length; i++)
239    {
240  0 fontNameCB.addItem(fonts[i]);
241    }
242   
243  0 for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
244    {
245  0 fontSizeCB.addItem(i + "");
246    }
247   
248  0 fontStyleCB.addItem("plain");
249  0 fontStyleCB.addItem("bold");
250  0 fontStyleCB.addItem("italic");
251   
252  0 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
253  0 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
254  0 fontStyleCB.setSelectedItem(
255    Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
256   
257  0 smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
258  0 scaleProteinToCdna
259    .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
260   
261  0 idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
262   
263  0 wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
264   
265  0 gapSymbolCB.addItem("-");
266  0 gapSymbolCB.addItem(".");
267   
268  0 gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
269   
270  0 sortby.addItem("No sort");
271  0 sortby.addItem("Id");
272  0 sortby.addItem("Pairwise Identity");
273  0 sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
274   
275  0 sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
276  0 sortAnnBy
277    .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
278  0 sortAnnBy
279    .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
280  0 SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
281    .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
282    SequenceAnnotationOrder.NONE.name()));
283  0 sortAnnBy.setSelectedItem(savedSort.toString());
284   
285  0 sortAutocalc.addItem("Autocalculated first");
286  0 sortAutocalc.addItem("Autocalculated last");
287  0 final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
288  0 sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
289    : sortAutocalc.getItemAt(1));
290  0 startupCheckbox
291    .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
292  0 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
293    Cache.getDefault("www.jalview.org", "http://www.jalview.org")
294    + "/examples/exampleFile_2_3.jar"));
295   
296    /*
297    * Set Colours tab defaults
298    */
299  0 protColour.addItem(ResidueColourScheme.NONE);
300  0 nucColour.addItem(ResidueColourScheme.NONE);
301  0 for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
302    {
303  0 String name = cs.getSchemeName();
304  0 protColour.addItem(name);
305  0 nucColour.addItem(name);
306    }
307  0 String oldProp = Cache.getDefault(DEFAULT_COLOUR,
308    ResidueColourScheme.NONE);
309  0 String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
310  0 protColour.setSelectedItem(newProp != null ? newProp : oldProp);
311  0 newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
312  0 nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
313  0 minColour.setBackground(
314    Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
315  0 maxColour.setBackground(
316    Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
317   
318    /*
319    * Set overview panel defaults
320    */
321  0 gapColour.setBackground(
322    Cache.getDefaultColour(GAP_COLOUR,
323    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
324  0 hiddenColour.setBackground(
325    Cache.getDefaultColour(HIDDEN_COLOUR,
326    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
327  0 useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
328  0 gapLabel.setEnabled(!useLegacyGap.isSelected());
329  0 gapColour.setEnabled(!useLegacyGap.isSelected());
330  0 showHiddenAtStart
331    .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
332   
333    /*
334    * Set Structure tab defaults.
335    */
336  0 final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
337  0 structFromPdb.setSelected(structSelected);
338  0 useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
339  0 useRnaView.setEnabled(structSelected);
340  0 addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
341  0 addSecondaryStructure.setEnabled(structSelected);
342  0 addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
343  0 addTempFactor.setEnabled(structSelected);
344  0 structViewer.setSelectedItem(
345    Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
346  0 chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
347  0 chimeraPath.addActionListener(new ActionListener()
348    {
 
349  0 toggle @Override
350    public void actionPerformed(ActionEvent e)
351    {
352  0 validateChimeraPath();
353    }
354    });
355   
356  0 if (Cache.getDefault("MAP_WITH_SIFTS", false))
357    {
358  0 siftsMapping.setSelected(true);
359    }
360    else
361    {
362  0 nwMapping.setSelected(true);
363    }
364   
365  0 SiftsSettings
366    .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
367   
368    /*
369    * Set Connections tab defaults
370    */
371   
372    // set up sorting
373  0 linkUrlTable.setModel(dataModel);
374  0 final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
375    linkUrlTable.getModel());
376  0 linkUrlTable.setRowSorter(sorter);
377  0 List<RowSorter.SortKey> sortKeys = new ArrayList<>();
378   
379  0 UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
380  0 sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
381    SortOrder.DESCENDING));
382  0 sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
383    SortOrder.DESCENDING));
384  0 sortKeys.add(
385    new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
386   
387  0 sorter.setSortKeys(sortKeys);
388    // BH 2018 setSortKeys will do the sort
389    // sorter.sort();
390   
391    // set up filtering
392  0 ActionListener onReset;
393  0 onReset = new ActionListener()
394    {
 
395  0 toggle @Override
396    public void actionPerformed(ActionEvent e)
397    {
398  0 filterTB.setText("");
399  0 sorter.setRowFilter(RowFilter.regexFilter(""));
400    }
401   
402    };
403  0 doReset.addActionListener(onReset);
404   
405    // filter to display only custom urls
406  0 final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
407    {
 
408  0 toggle @Override
409    public boolean include(
410    Entry<? extends TableModel, ? extends Object> entry)
411    {
412  0 return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
413    }
414    };
415   
416  0 final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
417    linkUrlTable.getModel());
418  0 customSorter.setRowFilter(customUrlFilter);
419   
420  0 ActionListener onCustomOnly;
421  0 onCustomOnly = new ActionListener()
422    {
 
423  0 toggle @Override
424    public void actionPerformed(ActionEvent e)
425    {
426  0 filterTB.setText("");
427  0 sorter.setRowFilter(customUrlFilter);
428    }
429    };
430  0 userOnly.addActionListener(onCustomOnly);
431   
432  0 filterTB.getDocument().addDocumentListener(new DocumentListener()
433    {
434    String caseInsensitiveFlag = "(?i)";
435   
 
436  0 toggle @Override
437    public void changedUpdate(DocumentEvent e)
438    {
439  0 sorter.setRowFilter(RowFilter
440    .regexFilter(caseInsensitiveFlag + filterTB.getText()));
441    }
442   
 
443  0 toggle @Override
444    public void removeUpdate(DocumentEvent e)
445    {
446  0 sorter.setRowFilter(RowFilter
447    .regexFilter(caseInsensitiveFlag + filterTB.getText()));
448    }
449   
 
450  0 toggle @Override
451    public void insertUpdate(DocumentEvent e)
452    {
453  0 sorter.setRowFilter(RowFilter
454    .regexFilter(caseInsensitiveFlag + filterTB.getText()));
455    }
456    });
457   
458    // set up list selection functionality
459  0 linkUrlTable.getSelectionModel()
460    .addListSelectionListener(new UrlListSelectionHandler());
461   
462    // set up radio buttons
463  0 int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
464    .getPrimaryColumn();
465  0 String onClickName = linkUrlTable.getColumnName(onClickCol);
466  0 linkUrlTable.getColumn(onClickName)
467    .setCellRenderer(new RadioButtonRenderer());
468  0 linkUrlTable.getColumn(onClickName)
469    .setCellEditor(new RadioButtonEditor());
470   
471    // get boolean columns and resize those to min possible
472  0 for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
473    {
474  0 if (linkUrlTable.getModel().getColumnClass(column)
475    .equals(Boolean.class))
476    {
477  0 TableColumn tableColumn = linkUrlTable.getColumnModel()
478    .getColumn(column);
479  0 int preferredWidth = tableColumn.getMinWidth();
480   
481  0 TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
482    column);
483  0 Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
484  0 int cwidth = c.getPreferredSize().width
485    + linkUrlTable.getIntercellSpacing().width;
486  0 preferredWidth = Math.max(preferredWidth, cwidth);
487   
488  0 tableColumn.setPreferredWidth(preferredWidth);
489    }
490    }
491   
492  0 useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
493  0 useProxy_actionPerformed(); // make sure useProxy is correctly initialised
494  0 proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
495  0 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
496   
497  0 defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
498   
499  0 usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
500    // note antisense here: default is true
501  0 questionnaire
502    .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
503  0 versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
504   
505    /*
506    * Set Output tab defaults
507    */
508  0 setupOutputCombo(epsRendering, "EPS_RENDERING");
509  0 setupOutputCombo(htmlRendering, "HTML_RENDERING");
510  0 setupOutputCombo(svgRendering, "SVG_RENDERING");
511  0 autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
512  0 userIdWidth.setEnabled(!autoIdWidth.isSelected());
513  0 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
514  0 Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
515  0 userIdWidth.setText(wi == null ? "" : wi.toString());
516    // TODO: refactor to use common enum via FormatAdapter and allow extension
517    // for new flat file formats
518  0 blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
519  0 clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
520  0 fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
521  0 msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
522  0 pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
523  0 pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
524  0 pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
525  0 modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
526  0 embbedBioJSON
527    .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
528   
529    /*
530    * Set Editing tab defaults
531    */
532  0 autoCalculateConsCheck
533    .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
534  0 padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
535  0 sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
536   
537  0 annotations_actionPerformed(null); // update the display of the annotation
538    // settings
539    }
540   
541    /**
542    * A helper method that sets the items and initial selection in a character
543    * rendering option list (Prompt each time/Lineart/Text)
544    *
545    * @param comboBox
546    * @param propertyKey
547    */
 
548  0 toggle protected void setupOutputCombo(JComboBox<Object> comboBox,
549    String propertyKey)
550    {
551  0 comboBox.addItem(promptEachTimeOpt);
552  0 comboBox.addItem(lineArtOpt);
553  0 comboBox.addItem(textOpt);
554   
555    /*
556    * JalviewJS doesn't support Lineart so force it to Text
557    */
558  0 String defaultOption = Jalview.isJS() ? "Text"
559    : Cache.getDefault(propertyKey, "Prompt each time");
560  0 if (defaultOption.equalsIgnoreCase("Text"))
561    {
562  0 comboBox.setSelectedItem(textOpt);
563    }
564  0 else if (defaultOption.equalsIgnoreCase("Lineart"))
565    {
566  0 comboBox.setSelectedItem(lineArtOpt);
567    }
568    else
569    {
570  0 comboBox.setSelectedItem(promptEachTimeOpt);
571    }
572    }
573   
574    /**
575    * Save user selections on the Preferences tabs to the Cache and write out to
576    * file.
577    *
578    * @param e
579    */
 
580  0 toggle @Override
581    public void ok_actionPerformed(ActionEvent e)
582    {
583  0 if (!validateSettings())
584    {
585  0 return;
586    }
587   
588    /*
589    * Save Visual settings
590    */
591  0 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
592    Boolean.toString(seqLimit.isSelected()));
593  0 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
594    Boolean.toString(rightAlign.isSelected()));
595  0 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
596    Boolean.toString(fullScreen.isSelected()));
597  0 Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
598    Boolean.toString(openoverv.isSelected()));
599  0 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
600    Boolean.toString(annotations.isSelected()));
601  0 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
602    Boolean.toString(conservation.isSelected()));
603  0 Cache.applicationProperties.setProperty("SHOW_QUALITY",
604    Boolean.toString(quality.isSelected()));
605  0 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
606    Boolean.toString(identity.isSelected()));
607   
608  0 Cache.applicationProperties.setProperty("GAP_SYMBOL",
609    gapSymbolCB.getSelectedItem().toString());
610   
611  0 Cache.applicationProperties.setProperty("FONT_NAME",
612    fontNameCB.getSelectedItem().toString());
613  0 Cache.applicationProperties.setProperty("FONT_STYLE",
614    fontStyleCB.getSelectedItem().toString());
615  0 Cache.applicationProperties.setProperty("FONT_SIZE",
616    fontSizeCB.getSelectedItem().toString());
617   
618  0 Cache.applicationProperties.setProperty("ID_ITALICS",
619    Boolean.toString(idItalics.isSelected()));
620  0 Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
621    Boolean.toString(showUnconserved.isSelected()));
622  0 Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
623    Boolean.toString(showOccupancy.isSelected()));
624  0 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
625    Boolean.toString(showGroupConsensus.isSelected()));
626  0 Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
627    Boolean.toString(showGroupConservation.isSelected()));
628  0 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
629    Boolean.toString(showConsensHistogram.isSelected()));
630  0 Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
631    Boolean.toString(showConsensLogo.isSelected()));
632  0 Cache.applicationProperties.setProperty("ANTI_ALIAS",
633    Boolean.toString(smoothFont.isSelected()));
634  0 Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
635    Boolean.toString(scaleProteinToCdna.isSelected()));
636  0 Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
637    Boolean.toString(showNpTooltip.isSelected()));
638  0 Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
639    Boolean.toString(showDbRefTooltip.isSelected()));
640   
641  0 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
642    Boolean.toString(wrap.isSelected()));
643   
644  0 Cache.applicationProperties.setProperty("STARTUP_FILE",
645    startupFileTextfield.getText());
646  0 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
647    Boolean.toString(startupCheckbox.isSelected()));
648   
649  0 Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
650    sortby.getSelectedItem().toString());
651   
652    // convert description of sort order to enum name for save
653  0 SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
654    .forDescription(sortAnnBy.getSelectedItem().toString());
655  0 if (annSortOrder != null)
656    {
657  0 Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
658    annSortOrder.name());
659    }
660   
661  0 final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
662  0 Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
663    Boolean.valueOf(showAutocalcFirst).toString());
664   
665    /*
666    * Save Colours settings
667    */
668  0 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
669    protColour.getSelectedItem().toString());
670  0 Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
671    nucColour.getSelectedItem().toString());
672  0 Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
673    minColour.getBackground());
674  0 Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
675    maxColour.getBackground());
676   
677    /*
678    * Save Overview settings
679    */
680  0 Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
681  0 Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
682  0 Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
683    Boolean.toString(useLegacyGap.isSelected()));
684  0 Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
685    Boolean.toString(showHiddenAtStart.isSelected()));
686   
687    /*
688    * Save Structure settings
689    */
690  0 Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
691    Boolean.toString(addTempFactor.isSelected()));
692  0 Cache.applicationProperties.setProperty(ADD_SS_ANN,
693    Boolean.toString(addSecondaryStructure.isSelected()));
694  0 Cache.applicationProperties.setProperty(USE_RNAVIEW,
695    Boolean.toString(useRnaView.isSelected()));
696  0 Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
697    Boolean.toString(structFromPdb.isSelected()));
698  0 Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
699    structViewer.getSelectedItem().toString());
700  0 Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
701  0 Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
702    Boolean.toString(siftsMapping.isSelected()));
703  0 SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
704   
705    /*
706    * Save Output settings
707    */
708  0 Cache.applicationProperties.setProperty("EPS_RENDERING",
709    ((OptionsParam) epsRendering.getSelectedItem()).getCode());
710  0 Cache.applicationProperties.setProperty("HTML_RENDERING",
711    ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
712  0 Cache.applicationProperties.setProperty("SVG_RENDERING",
713    ((OptionsParam) svgRendering.getSelectedItem()).getCode());
714   
715    /*
716    * Save Connections settings
717    */
718  0 Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
719   
720  0 jalview.util.BrowserLauncher.resetBrowser();
721   
722    // save user-defined and selected links
723  0 String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
724  0 if (menuLinks.isEmpty())
725    {
726  0 Cache.applicationProperties.remove("SEQUENCE_LINKS");
727    }
728    else
729    {
730  0 Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
731    menuLinks.toString());
732    }
733   
734  0 String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
735  0 if (nonMenuLinks.isEmpty())
736    {
737  0 Cache.applicationProperties.remove("STORED_LINKS");
738    }
739    else
740    {
741  0 Cache.applicationProperties.setProperty("STORED_LINKS",
742    nonMenuLinks.toString());
743    }
744   
745  0 Cache.applicationProperties.setProperty("DEFAULT_URL",
746    sequenceUrlLinks.getPrimaryUrlId());
747   
748  0 Cache.applicationProperties.setProperty("USE_PROXY",
749    Boolean.toString(useProxy.isSelected()));
750   
751  0 Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
752   
753  0 Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
754   
755  0 if (useProxy.isSelected())
756    {
757  0 System.setProperty("http.proxyHost", proxyServerTB.getText());
758  0 System.setProperty("http.proxyPort", proxyPortTB.getText());
759    }
760    else
761    {
762  0 System.setProperty("http.proxyHost", "");
763  0 System.setProperty("http.proxyPort", "");
764    }
765  0 Cache.setProperty("VERSION_CHECK",
766    Boolean.toString(versioncheck.isSelected()));
767  0 if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
768    {
769    // default is false - we only set this if the user has actively agreed
770  0 Cache.setProperty("USAGESTATS",
771    Boolean.toString(usagestats.isSelected()));
772    }
773  0 if (!questionnaire.isSelected())
774    {
775  0 Cache.setProperty("NOQUESTIONNAIRES", "true");
776    }
777    else
778    {
779    // special - made easy to edit a property file to disable questionnaires
780    // by just adding the given line
781  0 Cache.removeProperty("NOQUESTIONNAIRES");
782    }
783   
784    /*
785    * Save Output settings
786    */
787  0 Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
788    Boolean.toString(blcjv.isSelected()));
789  0 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
790    Boolean.toString(clustaljv.isSelected()));
791  0 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
792    Boolean.toString(fastajv.isSelected()));
793  0 Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
794    Boolean.toString(msfjv.isSelected()));
795  0 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
796    Boolean.toString(pfamjv.isSelected()));
797  0 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
798    Boolean.toString(pileupjv.isSelected()));
799  0 Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
800    Boolean.toString(pirjv.isSelected()));
801  0 Cache.applicationProperties.setProperty("PIR_MODELLER",
802    Boolean.toString(modellerOutput.isSelected()));
803  0 Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
804    Boolean.toString(embbedBioJSON.isSelected()));
805  0 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
806   
807  0 Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
808    Boolean.toString(autoIdWidth.isSelected()));
809  0 userIdWidth_actionPerformed();
810  0 Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
811    userIdWidth.getText());
812   
813    /*
814    * Save Editing settings
815    */
816  0 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
817    Boolean.toString(autoCalculateConsCheck.isSelected()));
818  0 Cache.applicationProperties.setProperty("SORT_BY_TREE",
819    Boolean.toString(sortByTree.isSelected()));
820  0 Cache.applicationProperties.setProperty("PAD_GAPS",
821    Boolean.toString(padGaps.isSelected()));
822   
823  0 if (!Jalview.isJS())
824    {
825  0 wsPrefs.updateAndRefreshWsMenuConfig(false);
826    }
827  0 Cache.saveProperties();
828  0 Desktop.instance.doConfigureStructurePrefs();
829  0 try
830    {
831  0 frame.setClosed(true);
832    } catch (Exception ex)
833    {
834    }
835    }
836   
837    /**
838    * Do any necessary validation before saving settings. Return focus to the
839    * first tab which fails validation.
840    *
841    * @return
842    */
 
843  0 toggle private boolean validateSettings()
844    {
845  0 if (!validateStructure())
846    {
847  0 structureTab.requestFocusInWindow();
848  0 return false;
849    }
850  0 return true;
851    }
852   
 
853  0 toggle @Override
854    protected boolean validateStructure()
855    {
856  0 return validateChimeraPath();
857   
858    }
859   
860    /**
861    * DOCUMENT ME!
862    */
 
863  0 toggle @Override
864    public void startupFileTextfield_mouseClicked()
865    {
866    // TODO: JAL-3048 not needed for Jalview-JS
867  0 String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
868  0 JalviewFileChooser chooser = JalviewFileChooser
869    .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
870  0 chooser.setFileView(new JalviewFileView());
871  0 chooser.setDialogTitle(
872    MessageManager.getString("label.select_startup_file"));
873   
874  0 int value = chooser.showOpenDialog(this);
875   
876  0 if (value == JalviewFileChooser.APPROVE_OPTION)
877    {
878  0 FileFormatI format = chooser.getSelectedFormat();
879  0 if (format != null)
880    {
881  0 Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
882    format.getName());
883    }
884  0 startupFileTextfield
885    .setText(chooser.getSelectedFile().getAbsolutePath());
886    }
887    }
888   
889    /**
890    * DOCUMENT ME!
891    *
892    * @param e
893    * DOCUMENT ME!
894    */
 
895  0 toggle @Override
896    public void cancel_actionPerformed(ActionEvent e)
897    {
898  0 try
899    {
900  0 if (!Jalview.isJS())
901    {
902  0 wsPrefs.updateWsMenuConfig(true);
903  0 wsPrefs.refreshWs_actionPerformed(e);
904    }
905  0 frame.setClosed(true);
906    } catch (Exception ex)
907    {
908    }
909    }
910   
911    /**
912    * DOCUMENT ME!
913    *
914    * @param e
915    * DOCUMENT ME!
916    */
 
917  0 toggle @Override
918    public void annotations_actionPerformed(ActionEvent e)
919    {
920  0 conservation.setEnabled(annotations.isSelected());
921  0 quality.setEnabled(annotations.isSelected());
922  0 identity.setEnabled(annotations.isSelected());
923  0 showOccupancy.setEnabled(annotations.isSelected());
924  0 showGroupConsensus.setEnabled(annotations.isSelected());
925  0 showGroupConservation.setEnabled(annotations.isSelected());
926  0 showConsensHistogram.setEnabled(annotations.isSelected()
927    && (identity.isSelected() || showGroupConsensus.isSelected()));
928  0 showConsensLogo.setEnabled(annotations.isSelected()
929    && (identity.isSelected() || showGroupConsensus.isSelected()));
930    }
931   
 
932  0 toggle @Override
933    public void newLink_actionPerformed(ActionEvent e)
934    {
935  0 GSequenceLink link = new GSequenceLink();
936  0 boolean valid = false;
937  0 while (!valid)
938    {
939  0 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
940    MessageManager.getString("label.new_sequence_url_link"),
941    JvOptionPane.OK_CANCEL_OPTION, -1,
942    null) == JvOptionPane.OK_OPTION)
943    {
944  0 if (link.checkValid())
945    {
946  0 if (((UrlLinkTableModel) linkUrlTable.getModel())
947    .isUniqueName(link.getName()))
948    {
949  0 ((UrlLinkTableModel) linkUrlTable.getModel())
950    .insertRow(link.getName(), link.getURL());
951  0 valid = true;
952    }
953    else
954    {
955  0 link.notifyDuplicate();
956  0 continue;
957    }
958    }
959    }
960    else
961    {
962  0 break;
963    }
964    }
965    }
966   
 
967  0 toggle @Override
968    public void editLink_actionPerformed(ActionEvent e)
969    {
970  0 GSequenceLink link = new GSequenceLink();
971   
972  0 int index = linkUrlTable.getSelectedRow();
973  0 if (index == -1)
974    {
975    // button no longer enabled if row is not selected
976  0 Cache.log.debug("Edit with no row selected in linkUrlTable");
977  0 return;
978    }
979   
980  0 int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
981    .getNameColumn();
982  0 int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
983    .getUrlColumn();
984  0 String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
985  0 link.setName(oldName);
986  0 link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
987   
988  0 boolean valid = false;
989  0 while (!valid)
990    {
991  0 if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
992    MessageManager.getString("label.edit_sequence_url_link"),
993    JvOptionPane.OK_CANCEL_OPTION, -1,
994    null) == JvOptionPane.OK_OPTION)
995    {
996  0 if (link.checkValid())
997    {
998  0 if ((oldName.equals(link.getName()))
999    || (((UrlLinkTableModel) linkUrlTable.getModel())
1000    .isUniqueName(link.getName())))
1001    {
1002  0 linkUrlTable.setValueAt(link.getName(), index, nameCol);
1003  0 linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1004  0 valid = true;
1005    }
1006    else
1007    {
1008  0 link.notifyDuplicate();
1009  0 continue;
1010    }
1011    }
1012    }
1013    else
1014    {
1015  0 break;
1016    }
1017    }
1018    }
1019   
 
1020  0 toggle @Override
1021    public void deleteLink_actionPerformed(ActionEvent e)
1022    {
1023  0 int index = linkUrlTable.getSelectedRow();
1024  0 int modelIndex = -1;
1025  0 if (index == -1)
1026    {
1027    // button no longer enabled if row is not selected
1028  0 Cache.log.debug("Delete with no row selected in linkUrlTable");
1029  0 return;
1030    }
1031    else
1032    {
1033  0 modelIndex = linkUrlTable.convertRowIndexToModel(index);
1034    }
1035   
1036    // make sure we use the model index to delete, and not the table index
1037  0 ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1038    }
1039   
 
1040  0 toggle @Override
1041    public void defaultBrowser_mouseClicked(MouseEvent e)
1042    {
1043    // TODO: JAL-3048 not needed for j2s
1044    /*
1045    * @j2sNative
1046    */
1047    {
1048  0 JFileChooser chooser = new JFileChooser(".");
1049  0 chooser.setDialogTitle(
1050    MessageManager.getString("label.select_default_browser"));
1051   
1052  0 int value = chooser.showOpenDialog(this);
1053   
1054  0 if (value == JFileChooser.APPROVE_OPTION)
1055    {
1056  0 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1057    }
1058    }
1059    }
1060   
1061    /*
1062    * (non-Javadoc)
1063    *
1064    * @see
1065    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1066    * .ActionEvent)
1067    */
 
1068  0 toggle @Override
1069    protected void showunconserved_actionPerformed(ActionEvent e)
1070    {
1071    // TODO Auto-generated method stub
1072  0 super.showunconserved_actionPerformed(e);
1073    }
1074   
 
1075  0 toggle public static List<String> getGroupURLLinks()
1076    {
1077  0 return groupURLLinks;
1078    }
1079   
 
1080  0 toggle @Override
1081    public void minColour_actionPerformed(JPanel panel)
1082    {
1083  0 JalviewColourChooser.showColourChooser(this,
1084    MessageManager.getString("label.select_colour_minimum_value"),
1085    panel);
1086    }
1087   
 
1088  0 toggle @Override
1089    public void maxColour_actionPerformed(JPanel panel)
1090    {
1091  0 JalviewColourChooser.showColourChooser(this,
1092    MessageManager.getString("label.select_colour_maximum_value"),
1093    panel);
1094    }
1095   
 
1096  0 toggle @Override
1097    public void gapColour_actionPerformed(JPanel gap)
1098    {
1099  0 if (!useLegacyGap.isSelected())
1100    {
1101  0 JalviewColourChooser.showColourChooser(this,
1102    MessageManager.getString("label.select_gap_colour"),
1103    gap);
1104    }
1105    }
1106   
 
1107  0 toggle @Override
1108    public void hiddenColour_actionPerformed(JPanel hidden)
1109    {
1110  0 JalviewColourChooser.showColourChooser(this,
1111    MessageManager.getString("label.select_hidden_colour"),
1112    hidden);
1113    }
1114   
 
1115  0 toggle @Override
1116    protected void useLegacyGaps_actionPerformed(ActionEvent e)
1117    {
1118  0 boolean enabled = useLegacyGap.isSelected();
1119  0 if (enabled)
1120    {
1121  0 gapColour.setBackground(
1122    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1123    }
1124    else
1125    {
1126  0 gapColour.setBackground(
1127    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1128    }
1129  0 gapColour.setEnabled(!enabled);
1130  0 gapLabel.setEnabled(!enabled);
1131    }
1132   
 
1133  0 toggle @Override
1134    protected void resetOvDefaults_actionPerformed(ActionEvent e)
1135    {
1136  0 useLegacyGap.setSelected(false);
1137  0 useLegacyGaps_actionPerformed(null);
1138  0 showHiddenAtStart.setSelected(true);
1139  0 hiddenColour.setBackground(
1140    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1141    }
1142   
 
1143  0 toggle @Override
1144    protected void userIdWidth_actionPerformed()
1145    {
1146  0 try
1147    {
1148  0 String val = userIdWidth.getText().trim();
1149  0 if (val.length() > 0)
1150    {
1151  0 Integer iw = Integer.parseInt(val);
1152  0 if (iw.intValue() < 12)
1153    {
1154  0 throw new NumberFormatException();
1155    }
1156  0 userIdWidth.setText(iw.toString());
1157    }
1158    } catch (NumberFormatException x)
1159    {
1160  0 userIdWidth.setText("");
1161  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1162    MessageManager
1163    .getString("warn.user_defined_width_requirements"),
1164    MessageManager.getString("label.invalid_id_column_width"),
1165    JvOptionPane.WARNING_MESSAGE);
1166    }
1167    }
1168   
 
1169  0 toggle @Override
1170    protected void autoIdWidth_actionPerformed()
1171    {
1172  0 userIdWidth.setEnabled(!autoIdWidth.isSelected());
1173  0 userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1174    }
1175   
1176    /**
1177    * Returns true if chimera path is to a valid executable, else show an error
1178    * dialog.
1179    */
 
1180  0 toggle private boolean validateChimeraPath()
1181    {
1182  0 if (chimeraPath.getText().trim().length() > 0)
1183    {
1184  0 File f = new File(chimeraPath.getText());
1185  0 if (!f.canExecute())
1186    {
1187  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1188    MessageManager.getString("label.invalid_chimera_path"),
1189    MessageManager.getString("label.invalid_name"),
1190    JvOptionPane.ERROR_MESSAGE);
1191  0 return false;
1192    }
1193    }
1194  0 return true;
1195    }
1196   
1197    /**
1198    * If Chimera is selected, check it can be found on default or user-specified
1199    * path, if not show a warning/help dialog.
1200    */
 
1201  0 toggle @Override
1202    protected void structureViewer_actionPerformed(String selectedItem)
1203    {
1204  0 if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1205    {
1206  0 return;
1207    }
1208  0 boolean found = false;
1209   
1210    /*
1211    * Try user-specified and standard paths for Chimera executable.
1212    */
1213  0 List<String> paths = StructureManager.getChimeraPaths();
1214  0 paths.add(0, chimeraPath.getText());
1215  0 for (String path : paths)
1216    {
1217  0 if (new File(path.trim()).canExecute())
1218    {
1219  0 found = true;
1220  0 break;
1221    }
1222    }
1223  0 if (!found)
1224    {
1225  0 String[] options = { "OK", "Help" };
1226  0 int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1227    JvSwingUtils.wrapTooltip(true,
1228    MessageManager.getString("label.chimera_missing")),
1229    "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1230    null, options, options[0]);
1231  0 if (showHelp == JvOptionPane.NO_OPTION)
1232    {
1233  0 try
1234    {
1235  0 Help.showHelpWindow(HelpId.StructureViewer);
1236    } catch (HelpSetException e)
1237    {
1238  0 e.printStackTrace();
1239    }
1240    }
1241    }
1242    }
1243   
 
1244    public class OptionsParam
1245    {
1246    private String name;
1247   
1248    private String code;
1249   
 
1250  0 toggle public OptionsParam(String name, String code)
1251    {
1252  0 this.name = name;
1253  0 this.code = code;
1254    }
1255   
 
1256  0 toggle public String getName()
1257    {
1258  0 return name;
1259    }
1260   
 
1261  0 toggle public void setName(String name)
1262    {
1263  0 this.name = name;
1264    }
1265   
 
1266  0 toggle public String getCode()
1267    {
1268  0 return code;
1269    }
1270   
 
1271  0 toggle public void setCode(String code)
1272    {
1273  0 this.code = code;
1274    }
1275   
 
1276  0 toggle @Override
1277    public String toString()
1278    {
1279  0 return name;
1280    }
1281   
 
1282  0 toggle @Override
1283    public boolean equals(Object that)
1284    {
1285  0 if (!(that instanceof OptionsParam))
1286    {
1287  0 return false;
1288    }
1289  0 return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1290    }
1291   
 
1292  0 toggle @Override
1293    public int hashCode()
1294    {
1295  0 return name.hashCode() + code.hashCode();
1296    }
1297    }
1298   
 
1299    private class UrlListSelectionHandler implements ListSelectionListener
1300    {
1301   
 
1302  0 toggle @Override
1303    public void valueChanged(ListSelectionEvent e)
1304    {
1305  0 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1306   
1307  0 int index = lsm.getMinSelectionIndex();
1308  0 if (index == -1)
1309    {
1310    // no selection, so disable delete/edit buttons
1311  0 editLink.setEnabled(false);
1312  0 deleteLink.setEnabled(false);
1313  0 return;
1314    }
1315  0 int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1316   
1317    // enable/disable edit and delete link buttons
1318  0 if (((UrlLinkTableModel) linkUrlTable.getModel())
1319    .isRowDeletable(modelIndex))
1320    {
1321  0 deleteLink.setEnabled(true);
1322    }
1323    else
1324    {
1325  0 deleteLink.setEnabled(false);
1326    }
1327   
1328  0 if (((UrlLinkTableModel) linkUrlTable.getModel())
1329    .isRowEditable(modelIndex))
1330    {
1331  0 editLink.setEnabled(true);
1332    }
1333    else
1334    {
1335  0 editLink.setEnabled(false);
1336    }
1337    }
1338    }
1339    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.