/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
import jalview.gui.Help.HelpId;
-import jalview.gui.StructureViewer.Viewer;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.io.PIRFile;
import jalview.jbgui.GPreferences;
import jalview.jbgui.GSequenceLink;
import jalview.schemes.ColourSchemeProperty;
+import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
*/
public class Preferences extends GPreferences
{
+ 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";
dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
- int width = 500, height = 420;
- if (new jalview.util.Platform().isAMac())
+ int width = 500, height = 450;
+ if (Platform.isAMac())
{
width = 570;
- height = 460;
+ height = 480;
}
Desktop.addInternalFrame(frame,
+ ""));
smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+ scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
+ false));
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
*/
for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
{
- colour.addItem(ColourSchemeProperty.getColourName(i));
+ protColour.addItem(ColourSchemeProperty.getColourName(i));
+ nucColour.addItem(ColourSchemeProperty.getColourName(i));
}
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");
- colour.setSelectedItem(string);
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+ String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
+ protColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
+ nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
Color.orange));
maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
addTempFactor.setEnabled(structSelected);
structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
- Viewer.JMOL.name()));
+ ViewerType.JMOL.name()));
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
Boolean.toString(showConsensLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
+ Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+ Boolean.toString(scaleProteinToCdna.isSelected()));
Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
Boolean.toString(showNpTooltip.isSelected()));
Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
/*
* Save Colours settings
*/
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
.getSelectedItem().toString());
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
*/
Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
- jalview.util.BrowserLauncher.resetBrowser();
+ BrowserLauncher.resetBrowser();
if (nameLinks.size() > 0)
{
Boolean.toString(pirjv.isSelected()));
Cache.applicationProperties.setProperty("PIR_MODELLER",
Boolean.toString(modellerOutput.isSelected()));
- jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+ PIRFile.useModellerOutput = modellerOutput.isSelected();
Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
public void startupFileTextfield_mouseClicked()
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ Cache.getProperty("LAST_DIRECTORY"),
new String[]
{ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
- jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+ Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- jalview.bin.Cache.applicationProperties.setProperty(
+ Cache.applicationProperties.setProperty(
"DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
startupFileTextfield.setText(chooser.getSelectedFile()
.getAbsolutePath());
@Override
protected void structureViewer_actionPerformed(String selectedItem)
{
- if (!selectedItem.equals(Viewer.CHIMERA.name()))
+ if (!selectedItem.equals(ViewerType.CHIMERA.name()))
{
return;
}