/*
- * 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.StructureViewer.Viewer;
+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 jalview.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.io.File;
-import java.util.Collection;
+import java.util.ArrayList;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
+import javax.help.HelpSetException;
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;
+
/**
* 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";
+
+ 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";
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
- public static Vector sequenceURLLinks;
+ public static Vector<String> sequenceURLLinks;
/**
* Holds name and link separated with | character. Sequence IDS and Sequences
* (TODO: proper escape for using | to separate ids or sequences
*/
- public static Vector groupURLLinks;
+ public static List<String> groupURLLinks;
static
{
String string = Cache
.getDefault(
"SEQUENCE_LINKS",
"EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
- sequenceURLLinks = new Vector();
+ sequenceURLLinks = new Vector<String>();
try
{
* .properties file as '|' separated strings
*/
- groupURLLinks = new Vector();
+ groupURLLinks = new ArrayList<String>();
}
- Vector nameLinks, urlLinks;
+ Vector<String> nameLinks, urlLinks;
JInternalFrame frame;
private WsPreferences wsPrefs;
+ private OptionsParam promptEachTimeOpt = new OptionsParam(
+ MessageManager.getString("label.prompt_each_time"),
+ "Prompt each time");
+
+ private OptionsParam lineArtOpt = new OptionsParam(
+ MessageManager.getString("label.lineart"), "Lineart");
+
+ private OptionsParam textOpt = new OptionsParam(
+ MessageManager.getString("action.text"), "Text");
+
/**
* Creates a new Preferences object.
*/
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;
+ new jalview.util.Platform();
+ 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));
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
*/
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",
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);
structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
- Viewer.JMOL.name()));
+ ViewerType.JMOL.name()));
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- if (chimeraPath.getText().trim().length() > 0)
- {
- File f = new File(chimeraPath.getText());
- if (!f.canExecute())
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.invalid_path"),
- MessageManager.getString("label.invalid_name"),
- JOptionPane.ERROR_MESSAGE);
- }
- }
+ validateChimeraPath();
}
});
+ if (Cache.getDefault("MAP_WITH_SIFTS", false))
+ {
+ siftsMapping.setSelected(true);
+ }
+ else
+ {
+ nwMapping.setSelected(true);
+ }
+
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
/*
* Set Connections tab defaults
*/
- nameLinks = new Vector();
- urlLinks = new Vector();
+ nameLinks = new Vector<String>();
+ urlLinks = new Vector<String>();
for (int i = 0; i < sequenceURLLinks.size(); i++)
{
String link = sequenceURLLinks.elementAt(i).toString();
/*
* Set Output tab defaults
*/
- epsRendering
- .addItem(MessageManager.getString("label.prompt_each_time"));
- epsRendering.addItem(MessageManager.getString("label.lineart"));
- epsRendering.addItem(MessageManager.getString("action.text"));
- epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
- "Prompt each time"));
+ epsRendering.addItem(promptEachTimeOpt);
+ epsRendering.addItem(lineArtOpt);
+ epsRendering.addItem(textOpt);
+ String defaultEPS = Cache.getDefault("EPS_RENDERING",
+ "Prompt each time");
+ if (defaultEPS.equalsIgnoreCase("Text"))
+ {
+ epsRendering.setSelectedItem(textOpt);
+ }
+ else if (defaultEPS.equalsIgnoreCase("Lineart"))
+ {
+ epsRendering.setSelectedItem(lineArtOpt);
+ }
+ else
+ {
+ epsRendering.setSelectedItem(promptEachTimeOpt);
+ }
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
*
* @param e
*/
+ @Override
public void ok_actionPerformed(ActionEvent e)
{
+ if (!validateSettings())
+ {
+ return;
+ }
+
/*
* Save Visual settings
*/
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",
}
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
*/
- 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.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
.getSelectedItem().toString());
Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+ Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+ Boolean.toString(siftsMapping.isSelected()));
+ SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
/*
* Save Output settings
*/
- if (epsRendering.getSelectedItem().equals("Prompt each time"))
- {
- Cache.applicationProperties.remove("EPS_RENDERING");
- }
- else
- {
- Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
- .getSelectedItem().toString());
- }
+ Cache.applicationProperties.setProperty("EPS_RENDERING",
+ ((OptionsParam) epsRendering.getSelectedItem()).getCode());
/*
* Save Connections settings
if (nameLinks.size() > 0)
{
StringBuffer links = new StringBuffer();
- sequenceURLLinks = new Vector();
+ sequenceURLLinks = new Vector<String>();
for (int i = 0; i < nameLinks.size(); i++)
{
sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
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",
dasSource.saveProperties(Cache.applicationProperties);
wsPrefs.updateAndRefreshWsMenuConfig(false);
-
Cache.saveProperties();
-
+ Desktop.instance.doConfigureStructurePrefs();
try
{
frame.setClosed(true);
}
/**
+ * Do any necessary validation before saving settings. Return focus to the
+ * first tab which fails validation.
+ *
+ * @return
+ */
+ private boolean validateSettings()
+ {
+ if (!validateStructure())
+ {
+ structureTab.requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ protected boolean validateStructure()
+ {
+ return validateChimeraPath();
+
+ }
+
+ /**
* DOCUMENT ME!
*/
+ @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("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);
* @param e
* DOCUMENT ME!
*/
+ @Override
public void cancel_actionPerformed(ActionEvent e)
{
try
* @param e
* DOCUMENT ME!
*/
+ @Override
public void annotations_actionPerformed(ActionEvent e)
{
conservation.setEnabled(annotations.isSelected());
&& (identity.isSelected() || showGroupConsensus.isSelected()));
}
+ @Override
public void newLink_actionPerformed(ActionEvent e)
{
}
}
+ @Override
public void editLink_actionPerformed(ActionEvent e)
{
GSequenceLink link = new GSequenceLink();
}
}
+ @Override
public void deleteLink_actionPerformed(ActionEvent e)
{
int index = linkNameList.getSelectedIndex();
linkURLList.setListData(urlLinks);
}
+ @Override
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);
* jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
protected void showunconserved_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
super.showunconserved_actionPerformed(e);
}
- public static Collection getGroupURLLinks()
+ public static List<String> getGroupURLLinks()
{
return groupURLLinks;
}
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("");
}
}
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
}
+ /**
+ * Returns true if chimera path is to a valid executable, else show an error
+ * dialog.
+ */
+ private boolean validateChimeraPath()
+ {
+ if (chimeraPath.getText().trim().length() > 0)
+ {
+ File f = new File(chimeraPath.getText());
+ if (!f.canExecute())
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.invalid_chimera_path"),
+ MessageManager.getString("label.invalid_name"),
+ JOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * If Chimera is selected, check it can be found on default or user-specified
+ * path, if not show a warning/help dialog.
+ */
+ @Override
+ protected void structureViewer_actionPerformed(String selectedItem)
+ {
+ if (!selectedItem.equals(ViewerType.CHIMERA.name()))
+ {
+ return;
+ }
+ boolean found = false;
+
+ /*
+ * Try user-specified and standard paths for Chimera executable.
+ */
+ List<String> paths = StructureManager.getChimeraPaths();
+ paths.add(0, chimeraPath.getText());
+ for (String path : paths)
+ {
+ if (new File(path.trim()).canExecute())
+ {
+ found = true;
+ break;
+ }
+ }
+ if (!found)
+ {
+ 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]);
+ if (showHelp == JOptionPane.NO_OPTION)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.StructureViewer);
+ } catch (HelpSetException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ public class OptionsParam
+ {
+ private String name;
+
+ private String code;
+
+ public OptionsParam(String name, String code)
+ {
+ this.name = name;
+ this.code = code;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ @Override
+ public String toString()
+ {
+ return name;
+ }
+
+ @Override
+ public boolean equals(Object that)
+ {
+ if (!(that instanceof OptionsParam))
+ {
+ return false;
+ }
+ return this.code.equalsIgnoreCase(((OptionsParam) that).code);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return name.hashCode() + code.hashCode();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff