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.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;
{
private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
- private static final Font LABEL_FONT_ITALIC = JvSwingUtils
- .getLabelFont(false, true);
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
+ false, true);
/*
* Visual tab components
protected JCheckBox wrap = new JCheckBox();
+ protected JCheckBox hideIntrons = new JCheckBox();
+
protected JComboBox<String> sortby = new JComboBox<String>();
protected JComboBox<String> sortAnnBy = 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
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.
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()
{
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("");
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();
defaultBrowser.addMouseListener(new MouseAdapter()
{
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() > 1)
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);
minColour.setPreferredSize(new Dimension(40, 20));
minColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
minColour_actionPerformed(minColour);
maxColour.setPreferredSize(new Dimension(40, 20));
maxColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
maxColour_actionPerformed(maxColour);
nucColourLabel.setFont(LABEL_FONT);
nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
nucColourLabel.setText(MessageManager
- .getString("label.nuc_alignment_colour")
- + " ");
+ .getString("label.nuc_alignment_colour") + " ");
JvSwingUtils.addtoLayout(coloursTab, MessageManager
.getString("label.default_colour_scheme_for_alignment"),
nucColourLabel, nucColour);
final int width = 400;
final int height = 22;
final int lineSpacing = 25;
- int ypos = 30;
+ int ypos = 15;
structFromPdb.setFont(LABEL_FONT);
- structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
+ structFromPdb
+ .setText(MessageManager.getString("label.struct_from_pdb"));
structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
structFromPdb.addActionListener(new ActionListener()
{
structureTab.add(chimeraPath);
ypos += lineSpacing;
- // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
- // scrl_pdbDocFieldConfig
- // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
- // scrl_pdbDocFieldConfig.setBounds();
+ 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;
PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
PreferenceSource.PREFERENCES);
- docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
+ docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
structureTab.add(docFieldPref);
-
-
-
return structureTab;
}
-
/**
* Action on choosing a structure viewer from combobox options.
*
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);
.getString("action.show_unconserved"));
showUnconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showunconserved_actionPerformed(e);
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
startupCheckbox.setSelected(true);
startupFileTextfield.setFont(LABEL_FONT);
- startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
+ startupFileTextfield.setBounds(new Rectangle(173, 328, 330, 20));
startupFileTextfield.addMouseListener(new MouseAdapter()
{
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() > 1)
}
}
});
-
+
sortby.setFont(LABEL_FONT);
- sortby.setBounds(new Rectangle(172, 260, 155, 21));
+ sortby.setBounds(new Rectangle(172, 280, 155, 20));
JLabel sortLabel = new JLabel();
sortLabel.setFont(LABEL_FONT);
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortLabel.setText(MessageManager.getString("label.sort_by"));
sortAnnBy.setFont(LABEL_FONT);
- sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
+ sortAnnBy.setBounds(new Rectangle(172, 305, 110, 20));
JLabel sortAnnLabel = new JLabel();
sortAnnLabel.setFont(LABEL_FONT);
sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
sortAutocalc.setFont(LABEL_FONT);
- sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
+ sortAutocalc.setBounds(new Rectangle(290, 305, 165, 20));
JPanel annsettingsPanel = new JPanel();
annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
wrap.setText(MessageManager.getString("label.wrap_alignment"));
+ hideIntrons.setFont(LABEL_FONT);
+ hideIntrons.setHorizontalAlignment(SwingConstants.TRAILING);
+ hideIntrons.setHorizontalTextPosition(SwingConstants.LEADING);
+ hideIntrons.setText(MessageManager.getString("label.hide_introns"));
+ hideIntrons.setToolTipText(MessageManager
+ .getString("label.hide_introns_tip"));
rightAlign.setFont(LABEL_FONT);
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
openoverv.setText(MessageManager.getString(("label.open_overview")));
JPanel jPanel2 = new JPanel();
- jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
- jPanel2.setLayout(new GridLayout(14, 1));
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 330));
+ jPanel2.setLayout(new GridLayout(15, 1));
jPanel2.add(fullScreen);
jPanel2.add(openoverv);
jPanel2.add(seqLimit);
jPanel2.add(scaleProteinToCdna);
jPanel2.add(gapLabel);
jPanel2.add(wrap);
+ jPanel2.add(hideIntrons);
jPanel2.add(sortLabel);
jPanel2.add(sortAnnLabel);
jPanel2.add(startupCheckbox);