/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.gui.Help.HelpId;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GPreferences;
-import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-
/**
* DOCUMENT ME!
*
*/
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";
sortAutocalc.addItem("Autocalculated first");
sortAutocalc.addItem("Autocalculated last");
- final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
- true);
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
: sortAutocalc.getItemAt(1));
startupCheckbox
structFromPdb.setSelected(structSelected);
useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
useRnaView.setEnabled(structSelected);
- addSecondaryStructure
- .setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
addSecondaryStructure.setEnabled(structSelected);
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
addTempFactor.setEnabled(structSelected);
epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
"Prompt each time"));
autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
- userIdWidth.setEnabled(autoIdWidth.isSelected());
- userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
userIdWidth.setText(wi == null ? "" : wi.toString());
blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+ embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
+ true));
/*
* Set Editing tab defaults
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
- Boolean.valueOf(showAutocalcFirst).toString());
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
+ .valueOf(showAutocalcFirst).toString());
/*
* Save Colours settings
Boolean.toString(pirjv.isSelected()));
Cache.applicationProperties.setProperty("PIR_MODELLER",
Boolean.toString(modellerOutput.isSelected()));
+ Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+ Boolean.toString(embbedBioJSON.isSelected()));
jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
return validateChimeraPath();
}
+
/**
* DOCUMENT ME!
*/
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("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"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_startup_file"));
int value = chooser.showOpenDialog(this);
public void defaultBrowser_mouseClicked(MouseEvent e)
{
JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_default_browser"));
int value = chooser.showOpenDialog(this);
public void minColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"),
+ minColour.getBackground());
if (col != null)
{
panel.setBackground(col);
public void maxColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"),
+ maxColour.getBackground());
if (col != null)
{
panel.setBackground(col);
}
} catch (NumberFormatException x)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("warn.user_defined_width_requirements"),
- MessageManager.getString("label.invalid_id_column_width"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("warn.user_defined_width_requirements"),
+ MessageManager.getString("label.invalid_id_column_width"),
+ JOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
}
}
}
if (!found)
{
- String[] options =
- { "OK", "Help" };
+ String[] options = { "OK", "Help" };
int showHelp = JOptionPane.showInternalOptionDialog(
Desktop.desktop,
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
- "", JOptionPane.YES_NO_OPTION,
- JOptionPane.WARNING_MESSAGE, null, options, options[0]);
+ "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
if (showHelp == JOptionPane.NO_OPTION)
{
try