/*
- * 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.
*
*/
package jalview.jbgui;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.gui.JvSwingUtils;
-import jalview.gui.StructureViewer.Viewer;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Component;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
+import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
+import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JTabbedPane;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
+import javax.swing.border.EtchedBorder;
import javax.swing.border.TitledBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
*/
public class GPreferences extends JPanel
{
- private static final Font verdana11 = JvSwingUtils.getLabelFont();
+ private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
+
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
+ false, true);
/*
* Visual tab components
protected JCheckBox smoothFont = new JCheckBox();
+ protected JCheckBox scaleProteinToCdna = new JCheckBox();
+
protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
protected JCheckBox wrap = new JCheckBox();
protected JCheckBox showNpTooltip = new JCheckBox();
/*
- * Annotations tab components
+ * Structure tab and components
*/
+ protected JPanel structureTab;
+
protected JCheckBox structFromPdb = new JCheckBox();
protected JCheckBox useRnaView = new JCheckBox();
protected JComboBox<String> structViewer = new JComboBox<String>();
+ protected JTextField chimeraPath = new JTextField();
+
+ protected ButtonGroup mappingMethod = new ButtonGroup();
+
+ protected JRadioButton siftsMapping = new JRadioButton();
+
+ protected JRadioButton nwMapping = new JRadioButton();
+
/*
* Colours tab components
*/
protected JPanel maxColour = new JPanel();
- protected JComboBox<String> colour = new JComboBox<String>();
+ protected JComboBox<String> protColour = new JComboBox<String>();
+
+ protected JComboBox<String> nucColour = new JComboBox<String>();
/*
* Connections tab components
/*
* Output tab components
*/
- protected JComboBox<String> epsRendering = new JComboBox<String>();
+ protected JComboBox<Object> epsRendering = new JComboBox<Object>();
protected JLabel userIdWidthlabel = new JLabel();
protected JCheckBox modellerOutput = new JCheckBox();
+ protected JCheckBox embbedBioJSON = new JCheckBox();
+
/*
* Editing tab components
*/
*/
private void jbInit() throws Exception
{
- JTabbedPane tabbedPane = new JTabbedPane();
+ final JTabbedPane tabbedPane = new JTabbedPane();
this.setLayout(new BorderLayout());
JPanel okCancelPanel = initOkCancelPanel();
this.add(tabbedPane, BorderLayout.CENTER);
tabbedPane.add(initConnectionsTab(),
MessageManager.getString("label.connections"));
- tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
+ tabbedPane.add(initOutputTab(),
+ MessageManager.getString("label.output"));
- tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
+ tabbedPane.add(initEditingTab(),
+ MessageManager.getString("label.editing"));
/*
* See DasSourceBrowser for the real work of configuring this tab.
*/
dasTab.setLayout(new BorderLayout());
- tabbedPane
- .add(dasTab, MessageManager.getString("label.das_settings"));
+ tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
/*
* See WsPreferences for the real work of configuring this tab.
*/
wsTab.setLayout(new BorderLayout());
tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+
+ /*
+ * Handler to validate a tab before leaving it - currently only for
+ * Structure.
+ */
+ tabbedPane.addChangeListener(new ChangeListener()
+ {
+ private Component lastTab;
+
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ if (lastTab == structureTab
+ && tabbedPane.getSelectedComponent() != structureTab)
+ {
+ if (!validateStructure())
+ {
+ tabbedPane.setSelectedComponent(structureTab);
+ return;
+ }
+ }
+ lastTab = tabbedPane.getSelectedComponent();
+ }
+
+ });
}
/**
{
JPanel editingTab = new JPanel();
editingTab.setLayout(null);
- autoCalculateConsCheck.setFont(verdana11);
+ autoCalculateConsCheck.setFont(LABEL_FONT);
autoCalculateConsCheck.setText(MessageManager
.getString("label.autocalculate_consensus"));
autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
- padGaps.setFont(verdana11);
+ padGaps.setFont(LABEL_FONT);
padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
padGaps.setBounds(new Rectangle(22, 94, 168, 23));
- sortByTree.setFont(verdana11);
+ sortByTree.setFont(LABEL_FONT);
sortByTree
.setText(MessageManager.getString("label.sort_with_new_tree"));
sortByTree
JPanel outputTab = new JPanel();
outputTab.setLayout(null);
JLabel epsLabel = new JLabel();
- epsLabel.setFont(verdana11);
+ epsLabel.setFont(LABEL_FONT);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
- epsRendering.setFont(verdana11);
+ epsRendering.setFont(LABEL_FONT);
epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
JLabel jLabel1 = new JLabel();
- jLabel1.setFont(verdana11);
+ jLabel1.setFont(LABEL_FONT);
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
jLabel1.setText(MessageManager.getString("label.append_start_end"));
- jLabel1.setFont(verdana11);
- fastajv.setFont(verdana11);
+ jLabel1.setFont(LABEL_FONT);
+ fastajv.setFont(LABEL_FONT);
fastajv.setHorizontalAlignment(SwingConstants.LEFT);
clustaljv.setText(MessageManager.getString("label.clustal") + " ");
blcjv.setText(MessageManager.getString("label.blc") + " ");
msfjv.setText(MessageManager.getString("label.msf") + " ");
pfamjv.setText(MessageManager.getString("label.pfam") + " ");
pileupjv.setText(MessageManager.getString("label.pileup") + " ");
- msfjv.setFont(verdana11);
+ msfjv.setFont(LABEL_FONT);
msfjv.setHorizontalAlignment(SwingConstants.LEFT);
pirjv.setText(MessageManager.getString("label.pir") + " ");
JPanel jPanel11 = new JPanel();
- jPanel11.setFont(verdana11);
+ jPanel11.setFont(LABEL_FONT);
TitledBorder titledBorder2 = new TitledBorder(
MessageManager.getString("label.file_output"));
jPanel11.setBorder(titledBorder2);
GridLayout gridLayout3 = new GridLayout();
jPanel11.setLayout(gridLayout3);
gridLayout3.setRows(8);
- blcjv.setFont(verdana11);
+ blcjv.setFont(LABEL_FONT);
blcjv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setFont(verdana11);
+ clustaljv.setFont(LABEL_FONT);
clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
- pfamjv.setFont(verdana11);
+ pfamjv.setFont(LABEL_FONT);
pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
- pileupjv.setFont(verdana11);
+ pileupjv.setFont(LABEL_FONT);
pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setFont(verdana11);
+ pirjv.setFont(LABEL_FONT);
pirjv.setHorizontalAlignment(SwingConstants.LEFT);
- autoIdWidth.setFont(verdana11);
+ autoIdWidth.setFont(LABEL_FONT);
autoIdWidth.setText(MessageManager
.getString("label.automatically_set_id_width"));
- autoIdWidth
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
+ autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager
+ .getString("label.adjusts_width_generated_eps_png")));
autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
autoIdWidth.addActionListener(new ActionListener()
{
autoIdWidth_actionPerformed();
}
});
- userIdWidthlabel.setFont(verdana11);
+ userIdWidthlabel.setFont(LABEL_FONT);
userIdWidthlabel.setText(MessageManager
.getString("label.figure_id_column_width"));
userIdWidth
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.manually_specify_width_left_column")));
userIdWidthlabel
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.manually_specify_width_left_column")));
userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
userIdWidth.setText("");
userIdWidth_actionPerformed();
}
});
+ modellerOutput.setFont(LABEL_FONT);
+ modellerOutput.setText(MessageManager
+ .getString("label.use_modeller_output"));
+ modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ embbedBioJSON.setFont(LABEL_FONT);
+ embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
+ embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
+
jPanel11.add(jLabel1);
jPanel11.add(blcjv);
jPanel11.add(clustaljv);
outputTab.add(userIdWidth);
outputTab.add(userIdWidthlabel);
outputTab.add(modellerOutput);
+ outputTab.add(embbedBioJSON);
outputTab.add(epsLabel);
outputTab.add(epsRendering);
outputTab.add(jPanel11);
- modellerOutput.setFont(verdana11);
- modellerOutput.setText(MessageManager
- .getString("label.use_modeller_output"));
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
return outputTab;
}
JLabel serverLabel = new JLabel();
serverLabel.setText(MessageManager.getString("label.address"));
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- serverLabel.setFont(verdana11);
- proxyServerTB.setFont(verdana11);
- proxyPortTB.setFont(verdana11);
+ serverLabel.setFont(LABEL_FONT);
+ proxyServerTB.setFont(LABEL_FONT);
+ proxyPortTB.setFont(LABEL_FONT);
JLabel portLabel = new JLabel();
- portLabel.setFont(verdana11);
+ portLabel.setFont(LABEL_FONT);
portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
portLabel.setText(MessageManager.getString("label.port"));
JLabel browserLabel = new JLabel();
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
browserLabel.setText(MessageManager
.getString("label.default_browser_unix"));
- defaultBrowser.setFont(verdana11);
+ defaultBrowser.setFont(LABEL_FONT);
defaultBrowser.setText("");
usagestats.setText(MessageManager
.getString("label.send_usage_statistics"));
- usagestats.setFont(verdana11);
+ usagestats.setFont(LABEL_FONT);
usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
questionnaire.setText(MessageManager
.getString("label.check_for_questionnaires"));
- questionnaire.setFont(verdana11);
+ questionnaire.setFont(LABEL_FONT);
questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
versioncheck.setText(MessageManager
.getString("label.check_for_latest_version"));
- versioncheck.setFont(verdana11);
+ versioncheck.setFont(LABEL_FONT);
versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
JButton newLink = new JButton();
newLink.setText(MessageManager.getString("action.new"));
newLink.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
newLink_actionPerformed(e);
editLink.setText(MessageManager.getString("action.edit"));
editLink.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
editLink_actionPerformed(e);
deleteLink.setText(MessageManager.getString("action.delete"));
deleteLink.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
deleteLink_actionPerformed(e);
linkURLList.addListSelectionListener(new ListSelectionListener()
{
+ @Override
public void valueChanged(ListSelectionEvent e)
{
int index = linkURLList.getSelectedIndex();
linkNameList.addListSelectionListener(new ListSelectionListener()
{
+ @Override
public void valueChanged(ListSelectionEvent e)
{
int index = linkNameList.getSelectedIndex();
JPanel editLinkButtons = new JPanel();
editLinkButtons.setLayout(gridLayout1);
gridLayout1.setRows(3);
- linkNameList.setFont(verdana11);
+ linkNameList.setFont(LABEL_FONT);
linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
BorderLayout borderLayout3 = new BorderLayout();
JPanel linkPanel2 = new JPanel();
linkPanel2.setLayout(borderLayout3);
- linkURLList.setFont(verdana11);
+ linkURLList.setFont(LABEL_FONT);
linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
defaultBrowser.addMouseListener(new MouseAdapter()
{
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() > 1)
}
}
});
- useProxy.setFont(verdana11);
+ useProxy.setFont(LABEL_FONT);
useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
useProxy.setText(MessageManager.getString("label.use_proxy_server"));
useProxy.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
useProxy_actionPerformed();
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
.getString("action.open_new_alignment")));
coloursTab.setLayout(new FlowLayout());
JLabel mincolourLabel = new JLabel();
- mincolourLabel.setFont(verdana11);
+ mincolourLabel.setFont(LABEL_FONT);
mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
mincolourLabel.setText(MessageManager.getString("label.min_colour"));
- minColour.setFont(verdana11);
+ minColour.setFont(LABEL_FONT);
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
minColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
minColour_actionPerformed(minColour);
}
});
JLabel maxcolourLabel = new JLabel();
- maxcolourLabel.setFont(verdana11);
+ maxcolourLabel.setFont(LABEL_FONT);
maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
- maxColour.setFont(verdana11);
+ maxColour.setFont(LABEL_FONT);
maxColour.setBorder(BorderFactory.createEtchedBorder());
maxColour.setPreferredSize(new Dimension(40, 20));
maxColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
maxColour_actionPerformed(maxColour);
}
});
- colour.setFont(verdana11);
- colour.setBounds(new Rectangle(172, 225, 155, 21));
- JLabel colourLabel = new JLabel();
- colourLabel.setFont(verdana11);
- colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText(MessageManager.getString("label.alignment_colour")
- + " ");
+
+ protColour.setFont(LABEL_FONT);
+ protColour.setBounds(new Rectangle(172, 225, 155, 21));
+ JLabel protColourLabel = new JLabel();
+ protColourLabel.setFont(LABEL_FONT);
+ protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ protColourLabel.setText(MessageManager
+ .getString("label.prot_alignment_colour") + " ");
+ JvSwingUtils.addtoLayout(coloursTab, MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
+ protColourLabel, protColour);
+
+ nucColour.setFont(LABEL_FONT);
+ nucColour.setBounds(new Rectangle(172, 240, 155, 21));
+ JLabel nucColourLabel = new JLabel();
+ nucColourLabel.setFont(LABEL_FONT);
+ nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ nucColourLabel.setText(MessageManager
+ .getString("label.nuc_alignment_colour") + " ");
JvSwingUtils.addtoLayout(coloursTab, MessageManager
.getString("label.default_colour_scheme_for_alignment"),
- colourLabel, colour);
+ nucColourLabel, nucColour);
+
JPanel annotationShding = new JPanel();
annotationShding.setBorder(new TitledBorder(MessageManager
.getString("label.annotation_shading_default")));
*/
private JPanel initStructureTab()
{
- JPanel structureTab = new JPanel();
+ structureTab = new JPanel();
+
structureTab.setBorder(new TitledBorder(MessageManager
.getString("label.structure_options")));
structureTab.setLayout(null);
final int width = 400;
- final int height = 23;
- final int lineSpacing = 30;
- int ypos = 30;
+ final int height = 22;
+ final int lineSpacing = 25;
+ int ypos = 15;
- structFromPdb.setFont(verdana11);
- structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
+ structFromPdb.setFont(LABEL_FONT);
+ structFromPdb
+ .setText(MessageManager.getString("label.struct_from_pdb"));
structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
structFromPdb.addActionListener(new ActionListener()
{
// indent checkboxes that are conditional on the first one
ypos += lineSpacing;
- useRnaView.setFont(verdana11);
+ useRnaView.setFont(LABEL_FONT);
useRnaView.setText(MessageManager.getString("label.use_rnaview"));
useRnaView.setBounds(new Rectangle(25, ypos, width, height));
structureTab.add(useRnaView);
ypos += lineSpacing;
- addSecondaryStructure.setFont(verdana11);
+ addSecondaryStructure.setFont(LABEL_FONT);
addSecondaryStructure.setText(MessageManager
.getString("label.autoadd_secstr"));
addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
structureTab.add(addSecondaryStructure);
ypos += lineSpacing;
- addTempFactor.setFont(verdana11);
+ addTempFactor.setFont(LABEL_FONT);
addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
structureTab.add(addTempFactor);
ypos += lineSpacing;
JLabel viewerLabel = new JLabel();
- viewerLabel.setFont(verdana11);
+ viewerLabel.setFont(LABEL_FONT);
viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
structureTab.add(viewerLabel);
- structViewer.setFont(verdana11);
- structViewer.setBounds(new Rectangle(150, ypos, 120, height));
- structViewer.addItem(Viewer.JMOL.name());
- structViewer.addItem(Viewer.CHIMERA.name());
+ structViewer.setFont(LABEL_FONT);
+ structViewer.setBounds(new Rectangle(160, ypos, 120, height));
+ structViewer.addItem(ViewerType.JMOL.name());
+ structViewer.addItem(ViewerType.CHIMERA.name());
+ structViewer.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ structureViewer_actionPerformed((String) structViewer
+ .getSelectedItem());
+ }
+ });
structureTab.add(structViewer);
+ ypos += lineSpacing;
+ JLabel pathLabel = new JLabel();
+ pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+ pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ pathLabel.setText(MessageManager.getString("label.chimera_path"));
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_path_tip"));
+ pathLabel.setToolTipText(tooltip);
+ pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
+ structureTab.add(pathLabel);
+
+ chimeraPath.setFont(LABEL_FONT);
+ chimeraPath.setText("");
+ chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
+ chimeraPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser();
+ if (chosen != null)
+ {
+ chimeraPath.setText(chosen);
+ }
+ }
+ }
+ });
+ structureTab.add(chimeraPath);
+
+ ypos += lineSpacing;
+ nwMapping.setFont(LABEL_FONT);
+ nwMapping.setText(MessageManager.getString("label.nw_mapping"));
+ siftsMapping.setFont(LABEL_FONT);
+ siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
+ mappingMethod.add(nwMapping);
+ mappingMethod.add(siftsMapping);
+ JPanel mappingPanel = new JPanel();
+ mappingPanel.setFont(LABEL_FONT);
+ TitledBorder mmTitledBorder = new TitledBorder(
+ MessageManager.getString("label.mapping_method"));
+ mmTitledBorder.setTitleFont(LABEL_FONT);
+ mappingPanel.setBorder(mmTitledBorder);
+ mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
+ // GridLayout mappingLayout = new GridLayout();
+ mappingPanel.setLayout(new GridLayout());
+ mappingPanel.add(nwMapping);
+ mappingPanel.add(siftsMapping);
+ structureTab.add(mappingPanel);
+
+ ypos += lineSpacing;
+ ypos += lineSpacing;
+ FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
+ PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
+ docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
+ structureTab.add(docFieldPref);
+
return structureTab;
}
/**
+ * Action on choosing a structure viewer from combobox options.
+ *
+ * @param selectedItem
+ */
+ protected void structureViewer_actionPerformed(String selectedItem)
+ {
+ }
+
+ /**
+ * Show a dialog for the user to choose a file. Returns the chosen path, or
+ * null on Cancel.
+ *
+ * @return
+ */
+ protected String openFileChooser()
+ {
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+
+ // chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager
+ .getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
+ /**
+ * Validate the structure tab preferences; if invalid, set focus on this tab.
+ *
+ * @param e
+ */
+ protected boolean validateStructure(FocusEvent e)
+ {
+ if (!validateStructure())
+ {
+ e.getComponent().requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ protected boolean validateStructure()
+ {
+ return false;
+ }
+
+ /**
* Initialises the Visual tabbed panel.
*
* @return
visualTab.setBorder(new TitledBorder(MessageManager
.getString("action.open_new_alignment")));
visualTab.setLayout(null);
- fullScreen.setFont(verdana11);
+ fullScreen.setFont(LABEL_FONT);
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
fullScreen.setText(MessageManager.getString("label.maximize_window"));
quality.setEnabled(false);
- quality.setFont(verdana11);
+ quality.setFont(LABEL_FONT);
quality.setHorizontalAlignment(SwingConstants.RIGHT);
quality.setHorizontalTextPosition(SwingConstants.LEFT);
quality.setSelected(true);
quality.setText(MessageManager.getString("label.quality"));
conservation.setEnabled(false);
- conservation.setFont(verdana11);
+ conservation.setFont(LABEL_FONT);
conservation.setHorizontalAlignment(SwingConstants.RIGHT);
conservation.setHorizontalTextPosition(SwingConstants.LEFT);
conservation.setSelected(true);
conservation.setText(MessageManager.getString("label.conservation"));
identity.setEnabled(false);
- identity.setFont(verdana11);
+ identity.setFont(LABEL_FONT);
identity.setHorizontalAlignment(SwingConstants.RIGHT);
identity.setHorizontalTextPosition(SwingConstants.LEFT);
identity.setSelected(true);
identity.setText(MessageManager.getString("label.consensus"));
JLabel showGroupbits = new JLabel();
- showGroupbits.setFont(verdana11);
+ showGroupbits.setFont(LABEL_FONT);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupbits.setText(MessageManager.getString("action.show_group")
+ ":");
JLabel showConsensbits = new JLabel();
- showConsensbits.setFont(verdana11);
+ showConsensbits.setFont(LABEL_FONT);
showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensbits.setText(MessageManager.getString("label.consensus")
+ ":");
showConsensHistogram.setEnabled(false);
- showConsensHistogram.setFont(verdana11);
+ showConsensHistogram.setFont(LABEL_FONT);
showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensHistogram.setSelected(true);
showConsensHistogram.setText(MessageManager
.getString("label.histogram"));
showConsensLogo.setEnabled(false);
- showConsensLogo.setFont(verdana11);
+ showConsensLogo.setFont(LABEL_FONT);
showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensLogo.setSelected(true);
showConsensLogo.setText(MessageManager.getString("label.logo"));
showGroupConsensus.setEnabled(false);
- showGroupConsensus.setFont(verdana11);
+ showGroupConsensus.setFont(LABEL_FONT);
showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConsensus.setSelected(true);
showGroupConsensus.setText(MessageManager.getString("label.consensus"));
showGroupConservation.setEnabled(false);
- showGroupConservation.setFont(verdana11);
+ showGroupConservation.setFont(LABEL_FONT);
showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConservation.setSelected(true);
showGroupConservation.setText(MessageManager
.getString("label.conservation"));
showNpTooltip.setEnabled(true);
- showNpTooltip.setFont(verdana11);
+ showNpTooltip.setFont(LABEL_FONT);
showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showNpTooltip.setSelected(true);
showNpTooltip.setText(MessageManager
.getString("label.non_positional_features"));
showDbRefTooltip.setEnabled(true);
- showDbRefTooltip.setFont(verdana11);
+ showDbRefTooltip.setFont(LABEL_FONT);
showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showDbRefTooltip.setSelected(true);
showDbRefTooltip.setText(MessageManager
.getString("label.database_references"));
- annotations.setFont(verdana11);
+ annotations.setFont(LABEL_FONT);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
annotations.setHorizontalTextPosition(SwingConstants.LEADING);
annotations.setSelected(true);
annotations.setBounds(new Rectangle(169, 12, 200, 23));
annotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
});
identity.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
});
showGroupConsensus.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
}
});
- showUnconserved.setFont(verdana11);
+ showUnconserved.setFont(LABEL_FONT);
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
showUnconserved.setSelected(true);
.getString("action.show_unconserved"));
showUnconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showunconserved_actionPerformed(e);
// followHighlight.setText(MessageManager
// .getString("label.scroll_highlighted_regions"));
- seqLimit.setFont(verdana11);
+ seqLimit.setFont(LABEL_FONT);
seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
- smoothFont.setFont(verdana11);
+ smoothFont.setFont(LABEL_FONT);
smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
smoothFont.setText(MessageManager.getString("label.smooth_font"));
+ scaleProteinToCdna.setFont(LABEL_FONT);
+ scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
+ scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
+ scaleProteinToCdna.setText(MessageManager
+ .getString("label.scale_protein_to_cdna"));
+ scaleProteinToCdna.setToolTipText(MessageManager
+ .getString("label.scale_protein_to_cdna_tip"));
JLabel gapLabel = new JLabel();
- gapLabel.setFont(verdana11);
+ gapLabel.setFont(LABEL_FONT);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
JLabel fontLabel = new JLabel();
- fontLabel.setFont(verdana11);
+ fontLabel.setFont(LABEL_FONT);
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
fontLabel.setText(MessageManager.getString("label.font"));
- fontSizeCB.setFont(verdana11);
- fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23));
- fontStyleCB.setFont(verdana11);
- fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23));
- fontNameCB.setFont(verdana11);
- fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
- gapSymbolCB.setFont(verdana11);
- gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
+ fontSizeCB.setFont(LABEL_FONT);
+ fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
+ fontStyleCB.setFont(LABEL_FONT);
+ fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
+ fontNameCB.setFont(LABEL_FONT);
+ fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
+ gapSymbolCB.setFont(LABEL_FONT);
+ gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
gapSymbolCB.setRenderer(dlcr);
startupCheckbox.setText(MessageManager.getString("action.open_file"));
- startupCheckbox.setFont(verdana11);
+ startupCheckbox.setFont(LABEL_FONT);
startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
startupCheckbox.setSelected(true);
- startupFileTextfield.setFont(verdana11);
- startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20));
+ startupFileTextfield.setFont(LABEL_FONT);
+ startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
startupFileTextfield.addMouseListener(new MouseAdapter()
{
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() > 1)
}
}
});
-
- sortby.setFont(verdana11);
- sortby.setBounds(new Rectangle(172, 240, 155, 21));
+
+ sortby.setFont(LABEL_FONT);
+ sortby.setBounds(new Rectangle(172, 260, 155, 21));
JLabel sortLabel = new JLabel();
- sortLabel.setFont(verdana11);
+ sortLabel.setFont(LABEL_FONT);
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortLabel.setText(MessageManager.getString("label.sort_by"));
- sortAnnBy.setFont(verdana11);
- sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21));
+ sortAnnBy.setFont(LABEL_FONT);
+ sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
JLabel sortAnnLabel = new JLabel();
- sortAnnLabel.setFont(verdana11);
+ sortAnnLabel.setFont(LABEL_FONT);
sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
- sortAutocalc.setFont(verdana11);
- sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21));
+ sortAutocalc.setFont(LABEL_FONT);
+ sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
+
JPanel annsettingsPanel = new JPanel();
- annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
+ annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
- JPanel autoAnnotSettings1 = new JPanel();
- autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
- annsettingsPanel.add(autoAnnotSettings1);
- JPanel autoAnnotSettings2 = new JPanel();
- autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
- annsettingsPanel.add(autoAnnotSettings2);
- JPanel autoAnnotSettings3 = new JPanel();
- autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
- annsettingsPanel.add(autoAnnotSettings3);
+ annsettingsPanel.setBorder(new EtchedBorder());
visualTab.add(annsettingsPanel);
Border jb = new EmptyBorder(1, 1, 4, 5);
quality.setBorder(jb);
showConsensHistogram.setBorder(jb);
showConsensLogo.setBorder(jb);
- autoAnnotSettings2.add(conservation);
- autoAnnotSettings1.add(quality);
- autoAnnotSettings3.add(identity);
- autoAnnotSettings1.add(showGroupbits);
- autoAnnotSettings3.add(showGroupConsensus);
- autoAnnotSettings2.add(showGroupConservation);
- autoAnnotSettings1.add(showConsensbits);
- autoAnnotSettings2.add(showConsensHistogram);
- autoAnnotSettings3.add(showConsensLogo);
+ JPanel autoAnnotSettings = new JPanel();
+ autoAnnotSettings.setLayout(new GridLayout(3, 3));
+ annsettingsPanel.add(autoAnnotSettings);
+ autoAnnotSettings.add(quality);
+ autoAnnotSettings.add(conservation);
+ autoAnnotSettings.add(identity);
+ autoAnnotSettings.add(showGroupbits);
+ autoAnnotSettings.add(showGroupConservation);
+ autoAnnotSettings.add(showGroupConsensus);
+ autoAnnotSettings.add(showConsensbits);
+ autoAnnotSettings.add(showConsensHistogram);
+ autoAnnotSettings.add(showConsensLogo);
JPanel tooltipSettings = new JPanel();
tooltipSettings.setBorder(new TitledBorder(MessageManager
.getString("label.sequence_id_tooltip")));
- tooltipSettings.setBounds(173, 130, 200, 62);
+ tooltipSettings.setBounds(173, 140, 220, 62);
tooltipSettings.setLayout(new GridLayout(2, 1));
tooltipSettings.add(showDbRefTooltip);
tooltipSettings.add(showNpTooltip);
visualTab.add(tooltipSettings);
- wrap.setFont(verdana11);
+ wrap.setFont(LABEL_FONT);
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
wrap.setText(MessageManager.getString("label.wrap_alignment"));
- rightAlign.setFont(verdana11);
+ rightAlign.setFont(LABEL_FONT);
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
rightAlign.setText(MessageManager.getString("label.right_align_ids"));
- idItalics.setFont(verdana11);
+ idItalics.setFont(LABEL_FONT_ITALIC);
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
idItalics.setText(MessageManager
.getString("label.sequence_name_italics"));
- openoverv.setFont(verdana11);
+ openoverv.setFont(LABEL_FONT);
openoverv.setActionCommand(MessageManager
.getString("label.open_overview"));
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
- openoverv.setText(MessageManager.getString(("label.open_overview")));
+ openoverv.setText(MessageManager.getString("label.open_overview"));
JPanel jPanel2 = new JPanel();
- jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
- GridLayout gridLayout2 = new GridLayout();
- jPanel2.setLayout(gridLayout2);
- gridLayout2.setRows(13);
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
+ jPanel2.setLayout(new GridLayout(14, 1));
jPanel2.add(fullScreen);
jPanel2.add(openoverv);
jPanel2.add(seqLimit);
jPanel2.add(showUnconserved);
jPanel2.add(idItalics);
jPanel2.add(smoothFont);
+ jPanel2.add(scaleProteinToCdna);
jPanel2.add(gapLabel);
jPanel2.add(wrap);
jPanel2.add(sortLabel);
git://source.jalview.org / jalview.git / blobdiff