import jalview.bin.Cache;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GPreferences;
import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
import javax.swing.JColorChooser;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
/*
* Set Colours tab defaults
*/
- for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ protColour.addItem(ResidueColourScheme.NONE);
+ nucColour.addItem(ResidueColourScheme.NONE);
+ for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
{
- protColour.addItem(ColourSchemeProperty.getColourName(i));
- nucColour.addItem(ColourSchemeProperty.getColourName(i));
+ String name = cs.getSchemeName();
+ protColour.addItem(name);
+ nucColour.addItem(name);
}
- String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
protColour.setSelectedItem(newProp != null ? newProp : oldProp);
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
@Override
public void startupFileTextfield_mouseClicked()
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.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"));
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ JalviewFileChooser chooser = JalviewFileChooser.forRead(
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
.getString("label.select_startup_file"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- jalview.bin.Cache.applicationProperties.setProperty(
- "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
+ FileFormatI format = chooser.getSelectedFormat();
+ if (format != null)
+ {
+ Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+ format.getName());
+ }
startupFileTextfield.setText(chooser.getSelectedFile()
.getAbsolutePath());
}