import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
@SuppressWarnings("serial")
public class Preferences extends GPreferences
{
+
+ // original to develop
+
public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
private static final int MAX_FONT_SIZE = 30;
+ // new for applet
+
+ public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
+
+ public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
+
+ public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
+
+ public static final String ANTI_ALIAS = "ANTI_ALIAS";
+
+ public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
+
+ public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
+
+ public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
+
+ public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
+
+ public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
+
+ public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
+
+ public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
+
+ public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
+
+ public static final String FONT_NAME = "FONT_NAME";
+
+ public static final String FONT_SIZE = "FONT_SIZE";
+
+ public static final String FONT_STYLE = "FONT_STYLE";
+
+ public static final String GAP_SYMBOL = "GAP_SYMBOL";
+
+ public static final String HIDE_INTRONS = "HIDE_INTRONS";
+
+ public static final String ID_ITALICS = "ID_ITALICS";
+
+ public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
+
+ public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
+
+ public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
+
+ public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
+
+ public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
+
+ public static final String PAD_GAPS = "PAD_GAPS";
+
+ public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
+
+ public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
+
+ public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
+
+ public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
+
+ public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
+
+ public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
+
+ public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
+
+ public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
+
+ public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
+
+ public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
+
+ public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
+
+ public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
+
+ public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
+
+ public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
+
+ public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
+
+ public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
+
+ public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
+
+ public static final String SHOW_QUALITY = "SHOW_QUALITY";
+
+ public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
+
+ public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
+
+ public static final String SORT_BY_TREE = "SORT_BY_TREE";
+
+ public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
+
+ public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
+
+ public static final String USE_FULL_SO = "USE_FULL_SO";
+
+ public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+
+ public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
+
+
+ public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
+ 600, 600);
+
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
}
- int width = 500, height = 450;
+ int width = 700, height = 510; // BH 2019.07.12 added 60 to height and 40 to
+ // width (for Visual check boxes and Links
+ // "Double Click" header)
+ // BH 2019.09.24 added 20 to width
+ // (structure panel was too small anyway, and I added a default dimension
+ // for Jmol
if (Platform.isAMacAndNotJS())
{
width = 570;
- height = 480;
+ height = 540; // BH 2019.07.12 added 30
}
Desktop.addInternalFrame(frame,
/*
* Set Visual tab defaults
*/
- seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
- rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
- fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
- annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
- conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
- quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
- identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
- openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
+ seqLimit.setSelected(Cache.getDefault(SHOW_JVSUFFIX, true));
+ rightAlign.setSelected(Cache.getDefault(RIGHT_ALIGN_IDS, false));
+ fullScreen.setSelected(Cache.getDefault(SHOW_FULLSCREEN, false));
+ annotations.setSelected(Cache.getDefault(SHOW_ANNOTATIONS, true));
+
+ conservation.setSelected(Cache.getDefault(SHOW_CONSERVATION, true));
+ quality.setSelected(Cache.getDefault(SHOW_QUALITY, true));
+ identity.setSelected(Cache.getDefault(SHOW_IDENTITY, true));
+ openoverv.setSelected(Cache.getDefault(SHOW_OVERVIEW, false));
showUnconserved
- .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ .setSelected(Cache.getDefault(SHOW_UNCONSERVED, false));
showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
showGroupConsensus
- .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+ .setSelected(Cache.getDefault(SHOW_GROUP_CONSENSUS, false));
showGroupConservation.setSelected(
- Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+ Cache.getDefault(SHOW_GROUP_CONSERVATION, false));
showConsensHistogram.setSelected(
- Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+ Cache.getDefault(SHOW_CONSENSUS_HISTOGRAM, true));
showConsensLogo
- .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ .setSelected(Cache.getDefault(SHOW_CONSENSUS_LOGO, false));
showNpTooltip
- .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ .setSelected(Cache.getDefault(SHOW_NPFEATS_TOOLTIP, true));
showDbRefTooltip
- .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+ .setSelected(Cache.getDefault(SHOW_DBREFS_TOOLTIP, true));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
fontStyleCB.addItem("bold");
fontStyleCB.addItem("italic");
- fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
- fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+ fontNameCB.setSelectedItem(Cache.getDefault(FONT_NAME, "SansSerif"));
+ fontSizeCB.setSelectedItem(Cache.getDefault(FONT_SIZE, "10"));
fontStyleCB.setSelectedItem(
- Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
+ Cache.getDefault(FONT_STYLE, Font.PLAIN + ""));
- smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+ smoothFont.setSelected(Cache.getDefault(ANTI_ALIAS, false));
scaleProteinToCdna
.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
- idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
+ idItalics.setSelected(Cache.getDefault(ID_ITALICS, true));
- wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+ wrap.setSelected(Cache.getDefault(WRAP_ALIGNMENT, false));
gapSymbolCB.addItem("-");
gapSymbolCB.addItem(".");
- gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
+ gapSymbolCB.setSelectedItem(Cache.getDefault(GAP_SYMBOL, "-"));
sortby.addItem("No sort");
sortby.addItem("Id");
sortby.addItem("Pairwise Identity");
- sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
+ sortby.setSelectedItem(Cache.getDefault(SORT_ALIGNMENT, "No sort"));
sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
sortAnnBy
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
minColour.setBackground(
- Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ Cache.getDefaultColour(ANNOTATIONCOLOUR_MIN, Color.orange));
maxColour.setBackground(
- Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ Cache.getDefaultColour(ANNOTATIONCOLOUR_MAX, Color.red));
/*
* Set overview panel defaults
addTempFactor.setEnabled(structSelected);
structViewer.setSelectedItem(
Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
+ Dimension d = Cache.getDefaultDim(STRUCTURE_DIMENSIONS,
+ DEFAULT_STRUCTURE_DIMENSIONS);
+ String s = d.width + "," + d.height;
+ structureDimensions.setText(s);
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
}
});
- if (Cache.getDefault("MAP_WITH_SIFTS", false))
+ if (Cache.getDefault(MAP_WITH_SIFTS, false))
{
siftsMapping.setSelected(true);
}
}
SiftsSettings
- .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+ .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false));
/*
* Set Connections tab defaults
usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
// note antisense here: default is true
questionnaire
- .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
+ .setSelected(Cache.getProperty(NOQUESTIONNAIRES) == null);
versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
/*
setupOutputCombo(epsRendering, "EPS_RENDERING");
setupOutputCombo(htmlRendering, "HTML_RENDERING");
setupOutputCombo(svgRendering, "SVG_RENDERING");
- autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+ autoIdWidth.setSelected(Cache.getDefault(FIGURE_AUTOIDWIDTH, false));
userIdWidth.setEnabled(!autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
- Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
+ Integer wi = Cache.getIntegerProperty(FIGURE_FIXEDIDWIDTH);
userIdWidth.setText(wi == null ? "" : wi.toString());
// TODO: refactor to use common enum via FormatAdapter and allow extension
// for new flat file formats
* Set Editing tab defaults
*/
autoCalculateConsCheck
- .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
- padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
- sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+ .setSelected(Cache.getDefault(AUTO_CALC_CONSENSUS, true));
+ padGaps.setSelected(Cache.getDefault(PAD_GAPS, false));
+ sortByTree.setSelected(Cache.getDefault(SORT_BY_TREE, false));
annotations_actionPerformed(null); // update the display of the annotation
// settings
/*
* Set Backups tab defaults
*/
- loadLastSavedBackupsOptions();
+ if (!Platform.isJS())
+ {
+ loadLastSavedBackupsOptions();
+ }
+
}
/**
/*
* Save Visual settings
*/
- Cache.setPropertyNoSave("SHOW_JVSUFFIX",
+ Cache.setPropertyNoSave(SHOW_JVSUFFIX,
Boolean.toString(seqLimit.isSelected()));
- Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
+ Cache.setPropertyNoSave(RIGHT_ALIGN_IDS,
Boolean.toString(rightAlign.isSelected()));
- Cache.setPropertyNoSave("SHOW_FULLSCREEN",
+ Cache.setPropertyNoSave(SHOW_FULLSCREEN,
Boolean.toString(fullScreen.isSelected()));
- Cache.setPropertyNoSave("SHOW_OVERVIEW",
+ Cache.setPropertyNoSave(SHOW_OVERVIEW,
Boolean.toString(openoverv.isSelected()));
- Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
+ Cache.setPropertyNoSave(SHOW_ANNOTATIONS,
Boolean.toString(annotations.isSelected()));
- Cache.setPropertyNoSave("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave(SHOW_CONSERVATION,
Boolean.toString(conservation.isSelected()));
- Cache.setPropertyNoSave("SHOW_QUALITY",
+ Cache.setPropertyNoSave(SHOW_QUALITY,
Boolean.toString(quality.isSelected()));
- Cache.setPropertyNoSave("SHOW_IDENTITY",
+ Cache.setPropertyNoSave(SHOW_IDENTITY,
Boolean.toString(identity.isSelected()));
- Cache.setPropertyNoSave("GAP_SYMBOL",
+ Cache.setPropertyNoSave(GAP_SYMBOL,
gapSymbolCB.getSelectedItem().toString());
- Cache.setPropertyNoSave("FONT_NAME",
+ Cache.setPropertyNoSave(FONT_NAME,
fontNameCB.getSelectedItem().toString());
- Cache.setPropertyNoSave("FONT_STYLE",
+ Cache.setPropertyNoSave(FONT_STYLE,
fontStyleCB.getSelectedItem().toString());
- Cache.setPropertyNoSave("FONT_SIZE",
+ Cache.setPropertyNoSave(FONT_SIZE,
fontSizeCB.getSelectedItem().toString());
- Cache.setPropertyNoSave("ID_ITALICS",
+ Cache.setPropertyNoSave(ID_ITALICS,
Boolean.toString(idItalics.isSelected()));
- Cache.setPropertyNoSave("SHOW_UNCONSERVED",
+ Cache.setPropertyNoSave(SHOW_UNCONSERVED,
Boolean.toString(showUnconserved.isSelected()));
Cache.setPropertyNoSave(SHOW_OCCUPANCY,
Boolean.toString(showOccupancy.isSelected()));
- Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS,
Boolean.toString(showGroupConsensus.isSelected()));
- Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION,
Boolean.toString(showGroupConservation.isSelected()));
- Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
+ Cache.setPropertyNoSave(SHOW_CONSENSUS_HISTOGRAM,
Boolean.toString(showConsensHistogram.isSelected()));
- Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
+ Cache.setPropertyNoSave(SHOW_CONSENSUS_LOGO,
Boolean.toString(showConsensLogo.isSelected()));
- Cache.setPropertyNoSave("ANTI_ALIAS",
+ Cache.setPropertyNoSave(ANTI_ALIAS,
Boolean.toString(smoothFont.isSelected()));
Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
Boolean.toString(scaleProteinToCdna.isSelected()));
- Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
+ Cache.setPropertyNoSave(SHOW_NPFEATS_TOOLTIP,
Boolean.toString(showNpTooltip.isSelected()));
- Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
+ Cache.setPropertyNoSave(SHOW_DBREFS_TOOLTIP,
Boolean.toString(showDbRefTooltip.isSelected()));
- Cache.setPropertyNoSave("WRAP_ALIGNMENT",
+ Cache.setPropertyNoSave(WRAP_ALIGNMENT,
Boolean.toString(wrap.isSelected()));
- Cache.setPropertyNoSave("STARTUP_FILE",
- startupFileTextfield.getText());
+ Cache.setPropertyNoSave("STARTUP_FILE", startupFileTextfield.getText());
Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
Boolean.toString(startupCheckbox.isSelected()));
- Cache.setPropertyNoSave("SORT_ALIGNMENT",
+ Cache.setPropertyNoSave(SORT_ALIGNMENT,
sortby.getSelectedItem().toString());
// convert description of sort order to enum name for save
.forDescription(sortAnnBy.getSelectedItem().toString());
if (annSortOrder != null)
{
- Cache.setPropertyNoSave(SORT_ANNOTATIONS,
- annSortOrder.name());
+ Cache.setPropertyNoSave(SORT_ANNOTATIONS, annSortOrder.name());
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
protColour.getSelectedItem().toString());
Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
nucColour.getSelectedItem().toString());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ Cache.setColourPropertyNoSave(ANNOTATIONCOLOUR_MIN,
minColour.getBackground());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ Cache.setColourPropertyNoSave(ANNOTATIONCOLOUR_MAX,
maxColour.getBackground());
/*
* Save Overview settings
*/
- Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
- Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+ Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourPropertyNoSave(HIDDEN_COLOUR,
+ hiddenColour.getBackground());
Cache.setPropertyNoSave(USE_LEGACY_GAP,
Boolean.toString(useLegacyGap.isSelected()));
Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
Boolean.toString(structFromPdb.isSelected()));
Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
structViewer.getSelectedItem().toString());
+ Cache.setPropertyNoSave(STRUCTURE_DIMENSIONS,
+ structureDimensions.getText()); // BH 2019.07.12
Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
- Cache.setPropertyNoSave("MAP_WITH_SIFTS",
+ Cache.setPropertyNoSave(MAP_WITH_SIFTS,
Boolean.toString(siftsMapping.isSelected()));
SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
}
else
{
- Cache.setPropertyNoSave("SEQUENCE_LINKS",
- menuLinks.toString());
+ Cache.setPropertyNoSave("SEQUENCE_LINKS", menuLinks.toString());
}
String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
}
else
{
- Cache.setPropertyNoSave("STORED_LINKS",
- nonMenuLinks.toString());
+ Cache.setPropertyNoSave("STORED_LINKS", nonMenuLinks.toString());
}
Cache.setPropertyNoSave("DEFAULT_URL",
}
if (!questionnaire.isSelected())
{
- Cache.setProperty("NOQUESTIONNAIRES", "true");
+ Cache.setProperty(NOQUESTIONNAIRES, "true");
}
else
{
// special - made easy to edit a property file to disable questionnaires
// by just adding the given line
- Cache.removeProperty("NOQUESTIONNAIRES");
+ Cache.removeProperty(NOQUESTIONNAIRES);
}
/*
Boolean.toString(modellerOutput.isSelected()));
Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
Boolean.toString(embbedBioJSON.isSelected()));
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
- Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
- userIdWidth.getText());
+ Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH", userIdWidth.getText());
/*
* Save Editing settings
*/
- Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
+ Cache.setPropertyNoSave(AUTO_CALC_CONSENSUS,
Boolean.toString(autoCalculateConsCheck.isSelected()));
- Cache.setPropertyNoSave("SORT_BY_TREE",
+ Cache.setPropertyNoSave(SORT_BY_TREE,
Boolean.toString(sortByTree.isSelected()));
- Cache.setPropertyNoSave("PAD_GAPS",
+ Cache.setPropertyNoSave(PAD_GAPS,
Boolean.toString(padGaps.isSelected()));
if (!Platform.isJS())
wsPrefs.updateAndRefreshWsMenuConfig(false);
}
- /*
- * Save Backups settings
- */
- Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
- Boolean.toString(backupfilesConfirmDelete.isSelected()));
+ /*
+ * Save Backups settings
+ */
Cache.setPropertyNoSave(BackupFiles.ENABLED,
- Boolean.toString(enableBackupFiles.isSelected()));
- Cache.setPropertyNoSave(BackupFiles.NO_MAX,
- Boolean.toString(backupfilesKeepAll.isSelected()));
- Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
- Boolean.toString(suffixReverse.isSelected()));
- Cache.setPropertyNoSave(BackupFiles.SUFFIX,
- suffixTemplate.getText());
- Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
- Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
- Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
- Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
+ Boolean.toString(enableBackupFiles.isSelected()));
+ int preset = getComboIntStringKey(backupfilesPresetsCombo);
Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET",
- Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
+ Integer.toString(preset));
+
+ if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+ {
+ BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
+ Cache.setPropertyNoSave(BackupFilesPresetEntry.CUSTOMCONFIG,
+ customBFPE.toString());
+ }
+
+ BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(preset);
+ Cache.setPropertyNoSave(BackupFilesPresetEntry.SAVEDCONFIG,
+ savedBFPE.toString());
Cache.saveProperties();
Desktop.getInstance().doConfigureStructurePrefs();
}
}
+ public static void setAppletDefaults()
+ {
+
+ // http://www.jalview.org/old/v2_8/examples/appletParameters.html
+
+ // showConservation true or false Default is true.
+ // showQuality true or false Default is true.
+ // showConsensus true or false Default is true.
+ // showFeatureSettings true or false Shows the feature settings window when
+ // startin
+ // showTreeBootstraps true or false (default is true) show or hide branch
+ // bootstraps
+ // showTreeDistances true or false (default is true) show or hide branch
+ // lengths
+ // showUnlinkedTreeNodes true or false (default is false) indicate if
+ // unassociated nodes should be highlighted in the tree view
+ // showUnconserved true of false (default is false) When true, only gaps and
+ // symbols different to the consensus sequence ions of the alignment
+ // showGroupConsensus true of false (default is false) When true, shows
+ // consensus annotation row for any groups on the alignment. (since 2.7)
+ // showGroupConservation true of false (default is false) When true, shows
+ // amino-acid property conservation annotation row for any groups on the
+ // showConsensusHistogram true of false (default is true) When true, shows
+ // the percentage occurence of the consensus symbol for each column as a
+ // showSequenceLogo true of false (default is false) When true, shows a
+ // sequence logo above the consensus sequence (overlaid above the Consensus
+
+ Cache.setPropertyNoSave(SHOW_CONSERVATION, "true");
+ Cache.setPropertyNoSave(SHOW_QUALITY, "false");
+ Cache.setPropertyNoSave(SHOW_CONSENSUS, "true");
+ Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false");
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false");
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false");
+
+ // TODO -- just a start here
+ }
+
/**
* Do any necessary validation before saving settings. Return focus to the
* first tab which fails validation.
}
/**
- * DOCUMENT ME!
+ * Opens a file browser, and if a file is chosen, sets its path as the text of
+ * the 'startup file' text field
*/
@Override
public void startupFileTextfield_mouseClicked()
FileFormatI format = chooser.getSelectedFormat();
if (format != null)
{
- Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
- format.getName());
+ /*
+ * saving properties to file is deferred to the 'OK' action
+ */
+ Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT", format.getName());
}
startupFileTextfield
.setText(chooser.getSelectedFile().getAbsolutePath());
{
ListSelectionModel lsm = (ListSelectionModel) e.getSource();
- int index = lsm.getMinSelectionIndex();
- if (index == -1)
- {
- // no selection, so disable delete/edit buttons
- editLink.setEnabled(false);
- deleteLink.setEnabled(false);
- return;
- }
- int modelIndex = linkUrlTable.convertRowIndexToModel(index);
+ updateValueChanged(lsm.getMinSelectionIndex());
+ }
+ }
- // enable/disable edit and delete link buttons
- if (((UrlLinkTableModel) linkUrlTable.getModel())
- .isRowDeletable(modelIndex))
- {
- deleteLink.setEnabled(true);
- }
- else
- {
- deleteLink.setEnabled(false);
- }
+ public void updateValueChanged(int index)
+ {
+ if (index == -1)
+ {
+ // no selection, so disable delete/edit buttons
+ editLink.setEnabled(false);
+ deleteLink.setEnabled(false);
+ return;
+ }
+ int modelIndex = linkUrlTable.convertRowIndexToModel(index);
- if (((UrlLinkTableModel) linkUrlTable.getModel())
- .isRowEditable(modelIndex))
- {
- editLink.setEnabled(true);
- }
- else
- {
- editLink.setEnabled(false);
- }
+ // enable/disable edit and delete link buttons
+ if (((UrlLinkTableModel) linkUrlTable.getModel())
+ .isRowDeletable(modelIndex))
+ {
+ deleteLink.setEnabled(true);
+ }
+ else
+ {
+ deleteLink.setEnabled(false);
+ }
+
+ if (((UrlLinkTableModel) linkUrlTable.getModel())
+ .isRowEditable(modelIndex))
+ {
+ editLink.setEnabled(true);
+ }
+ else
+ {
+ editLink.setEnabled(false);
}
}
}
git://source.jalview.org / jalview.git / blobdiff