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
{
- public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ // 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";
+
+ public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+ public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+ public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
+ public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+
+ public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
+
+ public static final String GAP_COLOUR = "GAP_COLOUR";
+
+ public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
+ private static final int MIN_FONT_SIZE = 1;
+
+ 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 AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
- public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
+ public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
- public static final String CHIMERA_PATH = "CHIMERA_PATH";
+ public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
- public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
-
- public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
-
- public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
-
- public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
-
public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
public static final String FONT_STYLE = "FONT_STYLE";
- public static final String GAP_COLOUR = "GAP_COLOUR";
-
public static final String GAP_SYMBOL = "GAP_SYMBOL";
- public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
-
public static final String HIDE_INTRONS = "HIDE_INTRONS";
public static final String ID_ITALICS = "ID_ITALICS";
public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
- public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
-
public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
- public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
-
public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
- public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
+ public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
- public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
+ public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
- public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+ public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
- public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+ public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
- public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
-
public static final String SORT_BY_TREE = "SORT_BY_TREE";
- public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
-
- public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
-
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 USE_LEGACY_GAP = "USE_LEGACY_GAP";
-
- public static final String USE_RNAVIEW = "USE_RNAVIEW";
-
public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
- private static final int MIN_FONT_SIZE = 1;
-
- private static final int MAX_FONT_SIZE = 30;
+ public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
+ 600, 600);
/**
* Holds name and link separated with | character. Sequence ID must be
public static final List<String> groupURLLinks; // not implemented
- public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
-
- public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
-
- public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
-
- public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
- 600, 600);
-
static
{
// get links selected to be in the menu (SEQUENCE_LINKS)
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(modellerOutput.isSelected()));
Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
Boolean.toString(embbedBioJSON.isSelected()));
- Cache.setPropertyNoSave(FIGURE_AUTOIDWIDTH,
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
+ Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH", userIdWidth.getText());
if (!Platform.isJS())
{
wsPrefs.updateAndRefreshWsMenuConfig(false);
+ }
+
/*
* Save Backups settings
*/
- Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
- Boolean.toString(backupfilesConfirmDelete.isSelected()));
- Cache.setPropertyNoSave(BackupFiles.ENABLED,
+ 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)));
- Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET", Integer
- .toString(getComboIntStringKey(backupfilesPresetsCombo)));
+ int preset = getComboIntStringKey(backupfilesPresetsCombo);
+ Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET",
+ 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();
try
}
/**
- * 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