/*
- * 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.ViewerType;
import jalview.util.MessageManager;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.border.*;
-import javax.swing.event.*;
+import jalview.util.Platform;
+
+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.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.AbstractButton;
+import javax.swing.AbstractCellEditor;
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.ButtonGroup;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+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.table.TableCellEditor;
+import javax.swing.table.TableCellRenderer;
+
+import net.miginfocom.swing.MigLayout;
/**
- * DOCUMENT ME!
+ * Base class for the Preferences panel.
*
* @author $author$
* @version $Revision$
*/
public class GPreferences extends JPanel
{
- JTabbedPane tabbedPane = new JTabbedPane();
+ private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
- JButton ok = new JButton();
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils
+ .getLabelFont(false, true);
- JButton cancel = new JButton();
+ /*
+ * Visual tab components
+ */
+ protected JCheckBox fullScreen = new JCheckBox();
- JPanel okCancelPanel = new JPanel();
+ protected JCheckBox openoverv = new JCheckBox();
- BorderLayout borderLayout1 = new BorderLayout();
+ protected JCheckBox seqLimit = new JCheckBox();
- protected JCheckBox quality = new JCheckBox();
+ protected JCheckBox rightAlign = new JCheckBox();
- JPanel visualTab = new JPanel();
+ protected JComboBox<String> fontSizeCB = new JComboBox<>();
- JPanel visual2Tab = new JPanel();
+ protected JComboBox<String> fontStyleCB = new JComboBox<>();
- protected JCheckBox fullScreen = new JCheckBox();
+ protected JComboBox<String> fontNameCB = new JComboBox<>();
- protected JCheckBox conservation = new JCheckBox();
+ protected JCheckBox showOccupancy = new JCheckBox();
- protected JCheckBox identity = new JCheckBox();
+ protected JCheckBox showUnconserved = new JCheckBox();
- protected JCheckBox annotations = new JCheckBox();
+ protected JCheckBox idItalics = new JCheckBox();
- protected JPanel minColour = new JPanel();
+ protected JCheckBox smoothFont = new JCheckBox();
- JLabel mincolourLabel = new JLabel();
+ protected JCheckBox scaleProteinToCdna = new JCheckBox();
- protected JPanel maxColour = new JPanel();
+ protected JComboBox<String> gapSymbolCB = new JComboBox<>();
- JLabel maxcolourLabel = new JLabel();
+ protected JCheckBox wrap = new JCheckBox();
- JLabel gapLabel = new JLabel();
+ protected JComboBox<String> sortby = new JComboBox<>();
- protected JComboBox colour = new JComboBox();
+ protected JComboBox<String> sortAnnBy = new JComboBox<>();
- JLabel colourLabel = new JLabel();
+ protected JComboBox<String> sortAutocalc = new JComboBox<>();
- JLabel fontLabel = new JLabel();
+ protected JCheckBox startupCheckbox = new JCheckBox();
- protected JComboBox fontSizeCB = new JComboBox();
+ protected JTextField startupFileTextfield = new JTextField();
- protected JComboBox fontStyleCB = new JComboBox();
+ // below are in the 'second column'
+ protected JCheckBox annotations = new JCheckBox();
- protected JComboBox fontNameCB = new JComboBox();
+ protected JCheckBox quality = new JCheckBox();
- protected JComboBox gapSymbolCB = new JComboBox();
+ protected JCheckBox conservation = new JCheckBox();
- protected JCheckBox startupCheckbox = new JCheckBox();
+ protected JCheckBox identity = new JCheckBox();
- protected JTextField startupFileTextfield = new JTextField();
+ protected JCheckBox showGroupConsensus = new JCheckBox();
- JPanel connectTab = new JPanel();
+ protected JCheckBox showGroupConservation = new JCheckBox();
- JLabel serverLabel = new JLabel();
+ protected JCheckBox showConsensHistogram = new JCheckBox();
- protected JList linkURLList = new JList();
+ protected JCheckBox showConsensLogo = new JCheckBox();
- protected JTextField proxyServerTB = new JTextField();
+ protected JCheckBox showInformationHistogram = new JCheckBox();
- protected JTextField proxyPortTB = new JTextField();
+ protected JCheckBox showHMMLogo = new JCheckBox();
- JLabel portLabel = new JLabel();
+ protected JCheckBox showDbRefTooltip = new JCheckBox();
- JLabel browserLabel = new JLabel();
+ protected JCheckBox showNpTooltip = new JCheckBox();
- protected JTextField defaultBrowser = new JTextField();
- JButton newLink = new JButton();
+ /*
+ * Structure tab and components
+ */
+ protected JPanel structureTab;
- JButton editLink = new JButton();
+ protected JCheckBox structFromPdb = new JCheckBox();
- JButton deleteLink = new JButton();
+ protected JCheckBox useRnaView = new JCheckBox();
- JScrollPane linkScrollPane = new JScrollPane();
+ protected JCheckBox addSecondaryStructure = new JCheckBox();
- JPanel linkPanel = new JPanel();
+ protected JCheckBox addTempFactor = new JCheckBox();
- BorderLayout borderLayout2 = new BorderLayout();
+ protected JComboBox<String> structViewer = new JComboBox<>();
- JPanel editLinkButtons = new JPanel();
+ protected JTextField chimeraPath = new JTextField();
- GridLayout gridLayout1 = new GridLayout();
+ protected ButtonGroup mappingMethod = new ButtonGroup();
- protected JList linkNameList = new JList();
+ protected JRadioButton siftsMapping = new JRadioButton();
- JPanel linkPanel2 = new JPanel();
+ protected JRadioButton nwMapping = new JRadioButton();
- BorderLayout borderLayout3 = new BorderLayout();
+ /*
+ * Colours tab components
+ */
+ protected JPanel minColour = new JPanel();
- protected JCheckBox useProxy = new JCheckBox();
+ protected JPanel maxColour = new JPanel();
- JPanel jPanel1 = new JPanel();
+ protected JComboBox<String> protColour = new JComboBox<>();
- TitledBorder titledBorder1 = new TitledBorder(
- MessageManager.getString("label.proxy_server"));
+ protected JComboBox<String> nucColour = new JComboBox<>();
- TitledBorder titledBorder2 = new TitledBorder(
- MessageManager.getString("label.file_output"));
+ /*
+ * Overview tab components
+ */
+ protected JPanel gapColour = new JPanel();
+
+ protected JPanel hiddenColour = new JPanel();
+
+ protected JCheckBox useLegacyGap;
+
+ protected JCheckBox showHiddenAtStart;
- GridBagLayout gridBagLayout2 = new GridBagLayout();
+ protected JLabel gapLabel;
- GridBagLayout gridBagLayout1 = new GridBagLayout();
+ /*
+ * Connections tab components
+ */
+ protected JTable linkUrlTable = new JTable();
+
+ protected JButton editLink = new JButton();
- GridBagLayout gridBagLayout3 = new GridBagLayout();
+ protected JButton deleteLink = new JButton();
- protected JComboBox sortby = new JComboBox();
+ protected JTextField filterTB = new JTextField();
- JLabel sortLabel = new JLabel();
+ protected JButton doReset = new JButton();
- JPanel jPanel2 = new JPanel();
+ protected JButton userOnly = new JButton();
- JPanel visual2panel = new JPanel();
+ protected JLabel portLabel = new JLabel();
- GridLayout gridLayout2 = new GridLayout();
+ protected JLabel serverLabel = new JLabel();
- GridLayout gridLayout4 = new GridLayout();
+ protected JTextField proxyServerTB = new JTextField();
- JPanel annsettingsPanel = new JPanel();
+ protected JTextField proxyPortTB = new JTextField();
- JPanel autoAnnotSettings1 = new JPanel();
+ protected JTextField defaultBrowser = new JTextField();
- JPanel autoAnnotSettings2 = new JPanel();
+ protected JCheckBox useProxy = new JCheckBox();
- JPanel autoAnnotSettings3 = new JPanel();
+ protected JCheckBox usagestats = new JCheckBox();
- JPanel exportTab = new JPanel();
+ protected JCheckBox questionnaire = new JCheckBox();
- JLabel epsLabel = new JLabel();
+ protected JCheckBox versioncheck = new JCheckBox();
- protected JComboBox epsRendering = new JComboBox();
+ /*
+ * Output tab components
+ */
+ protected JComboBox<Object> epsRendering = new JComboBox<>();
protected JLabel userIdWidthlabel = new JLabel();
protected JTextField userIdWidth = new JTextField();
- JLabel jLabel1 = new JLabel();
-
protected JCheckBox blcjv = new JCheckBox();
protected JCheckBox pileupjv = new JCheckBox();
protected JCheckBox pfamjv = new JCheckBox();
- FlowLayout flowLayout1 = new FlowLayout();
-
protected JCheckBox pirjv = new JCheckBox();
- JPanel jPanel11 = new JPanel();
-
- Font verdana11 = JvSwingUtils.getLabelFont();
-
- protected JCheckBox seqLimit = new JCheckBox();
-
- GridLayout gridLayout3 = new GridLayout();
-
- protected JCheckBox smoothFont = new JCheckBox();
+ protected JCheckBox modellerOutput = new JCheckBox();
- JPanel calcTab = new JPanel();
+ protected JCheckBox embbedBioJSON = new JCheckBox();
+ /*
+ * Editing tab components
+ */
protected JCheckBox autoCalculateConsCheck = new JCheckBox();
protected JCheckBox padGaps = new JCheckBox();
- protected JCheckBox modellerOutput = new JCheckBox();
-
- protected JPanel dasPanel = new JPanel();
-
- BorderLayout borderLayout4 = new BorderLayout();
-
- protected JPanel wsPanel = new JPanel();
-
- BorderLayout borderLayout5 = new BorderLayout();
-
- protected JCheckBox wrap = new JCheckBox();
-
- protected JCheckBox rightAlign = new JCheckBox();
-
- protected JCheckBox showUnconserved = new JCheckBox();
-
- protected JCheckBox showDbRefTooltip = new JCheckBox();
-
- protected JCheckBox showNpTooltip = new JCheckBox();
-
- protected JCheckBox idItalics = new JCheckBox();
-
- protected JCheckBox openoverv = new JCheckBox();
-
- protected JCheckBox usagestats = new JCheckBox();
-
- protected JCheckBox questionnaire = new JCheckBox();
+ protected JCheckBox sortByTree = new JCheckBox();
- protected JCheckBox versioncheck = new JCheckBox();
+ /*
+ * hmmer tab and components
+ */
+ protected JPanel hmmerTab;
- protected JLabel showGroupbits = new JLabel();
+ protected JCheckBox hmmrTrimTermini;
- protected JLabel showConsensbits = new JLabel();
+ protected AbstractButton hmmerBackgroundUniprot;
- protected JCheckBox showConsensLogo = new JCheckBox();
+ protected AbstractButton hmmerBackgroundAlignment;
- protected JCheckBox showConsensHistogram = new JCheckBox();
+ protected JTextField hmmerSequenceCount;
- protected JCheckBox showGroupConsensus = new JCheckBox();
+ protected JTextField hmmerPath;
- protected JCheckBox showGroupConservation = new JCheckBox();
+ protected JTextField cygwinPath;
- protected JCheckBox shareSelections = new JCheckBox();
+ /*
+ * Web Services tab
+ */
+ protected JPanel wsTab = new JPanel();
- protected JCheckBox followHighlight = new JCheckBox();
- protected JCheckBox sortByTree = new JCheckBox();
/**
* Creates a new GPreferences object.
}
/**
- * DOCUMENT ME!
+ * Construct the panel and its tabbed sub-panels.
*
* @throws Exception
- * DOCUMENT ME!
*/
private void jbInit() throws Exception
{
- this.setLayout(borderLayout1);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
+ final JTabbedPane tabbedPane = new JTabbedPane();
+ this.setLayout(new BorderLayout());
+ JPanel okCancelPanel = initOkCancelPanel();
+ this.add(tabbedPane, BorderLayout.CENTER);
+ this.add(okCancelPanel, BorderLayout.SOUTH);
+
+ tabbedPane.add(initVisualTab(),
+ MessageManager.getString("label.visual"));
+
+ tabbedPane.add(initColoursTab(),
+ MessageManager.getString("label.colours"));
+
+ tabbedPane.add(initOverviewTab(),
+ MessageManager.getString("label.overview"));
+
+ tabbedPane.add(initStructureTab(),
+ MessageManager.getString("label.structure"));
+
+ tabbedPane.add(initConnectionsTab(),
+ MessageManager.getString("label.connections"));
+
+ tabbedPane.add(initLinksTab(),
+ MessageManager.getString("label.urllinks"));
+
+ tabbedPane.add(initOutputTab(),
+ MessageManager.getString("label.output"));
+
+ tabbedPane.add(initEditingTab(),
+ MessageManager.getString("label.editing"));
+
+ tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+
+ /*
+ * 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()
{
- public void actionPerformed(ActionEvent e)
+ private Component lastTab;
+
+ @Override
+ public void stateChanged(ChangeEvent e)
{
- ok_actionPerformed(e);
+ if (lastTab == structureTab
+ && tabbedPane.getSelectedComponent() != structureTab)
+ {
+ if (!validateStructure())
+ {
+ tabbedPane.setSelectedComponent(structureTab);
+ return;
+ }
+ }
+ lastTab = tabbedPane.getSelectedComponent();
}
+
});
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
+ }
+
+ /**
+ * Initialises the Editing tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initEditingTab()
+ {
+ JPanel editingTab = new JPanel();
+ editingTab.setLayout(null);
+ autoCalculateConsCheck.setFont(LABEL_FONT);
+ autoCalculateConsCheck.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
+ padGaps.setFont(LABEL_FONT);
+ padGaps.setText(
+ MessageManager.getString("label.pad_gaps_when_editing"));
+ padGaps.setBounds(new Rectangle(22, 94, 168, 23));
+ sortByTree.setFont(LABEL_FONT);
+ sortByTree
+ .setText(MessageManager.getString("label.sort_with_new_tree"));
+ sortByTree.setToolTipText(MessageManager.getString(
+ "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
+ sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+ editingTab.add(autoCalculateConsCheck);
+ editingTab.add(padGaps);
+ editingTab.add(sortByTree);
+ return editingTab;
+ }
+
+ /**
+ * Initialises the hmmer tabbed panel
+ *
+ * @return
+ */
+ private JPanel initHMMERTab()
+ {
+ hmmerTab = new JPanel();
+ hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS));
+ hmmerTab.setLayout(new MigLayout("flowy"));
+
+ /*
+ * path to hmmer binaries folder
+ */
+ JPanel installationPanel = new JPanel(new MigLayout("flowy"));
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(installationPanel,
+ MessageManager.getString("label.installation"), true);
+ hmmerTab.add(installationPanel);
+ JLabel hmmerLocation = new JLabel(
+ MessageManager.getString("label.hmmer_location"));
+ hmmerLocation.setFont(LABEL_FONT);
+ final int pathFieldLength = 40;
+ hmmerPath = new JTextField(pathFieldLength);
+ hmmerPath.addMouseListener(new MouseAdapter()
{
- public void actionPerformed(ActionEvent e)
+ @Override
+ public void mouseClicked(MouseEvent e)
{
- cancel_actionPerformed(e);
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ hmmerPath.setText(chosen);
+ validateHmmerPath();
+ }
+ }
}
});
- quality.setEnabled(false);
- quality.setFont(verdana11);
- quality.setHorizontalAlignment(SwingConstants.RIGHT);
- quality.setHorizontalTextPosition(SwingConstants.LEFT);
- quality.setSelected(true);
- quality.setText(MessageManager.getString("label.quality"));
- visualTab.setBorder(new TitledBorder(MessageManager
- .getString("action.open_new_aligmnent")));
- visualTab.setLayout(null);
- visual2Tab.setBorder(new TitledBorder(MessageManager
- .getString("action.open_new_aligmnent")));
- visual2Tab.setLayout(new FlowLayout());
- fullScreen.setFont(verdana11);
- fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
- fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
- fullScreen.setText(MessageManager.getString("label.maximize_window"));
- conservation.setEnabled(false);
- conservation.setFont(verdana11);
- conservation.setHorizontalAlignment(SwingConstants.RIGHT);
- conservation.setHorizontalTextPosition(SwingConstants.LEFT);
- conservation.setSelected(true);
- conservation.setText(MessageManager.getString("label.conservation"));
- identity.setEnabled(false);
- identity.setFont(verdana11);
- identity.setHorizontalAlignment(SwingConstants.RIGHT);
- identity.setHorizontalTextPosition(SwingConstants.LEFT);
- identity.setSelected(true);
- identity.setText(MessageManager.getString("label.consensus"));
- showGroupbits.setFont(verdana11);
- showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText(MessageManager.getString("action.show_group")
- + ":");
- showConsensbits.setFont(verdana11);
- showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensbits.setText(MessageManager.getString("label.consensus")
- + ":");
- showConsensHistogram.setEnabled(false);
- showConsensHistogram.setFont(verdana11);
- showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensHistogram.setSelected(true);
- showConsensHistogram.setText(MessageManager
- .getString("label.histogram"));
- showConsensLogo.setEnabled(false);
- showConsensLogo.setFont(verdana11);
- showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensLogo.setSelected(true);
- showConsensLogo.setText(MessageManager.getString("label.logo"));
- showGroupConsensus.setEnabled(false);
- showGroupConsensus.setFont(verdana11);
- showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupConsensus.setSelected(true);
- showGroupConsensus.setText(MessageManager.getString("label.consensus"));
- showGroupConservation.setEnabled(false);
- showGroupConservation.setFont(verdana11);
- showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupConservation.setSelected(true);
- showGroupConservation.setText(MessageManager
- .getString("label.conservation"));
- showNpTooltip.setEnabled(true);
- showNpTooltip.setFont(verdana11);
- 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.setHorizontalAlignment(SwingConstants.RIGHT);
- showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
- showDbRefTooltip.setSelected(true);
- showDbRefTooltip.setText(MessageManager
- .getString("label.database_references"));
- annotations.setFont(verdana11);
- annotations.setHorizontalAlignment(SwingConstants.RIGHT);
- annotations.setHorizontalTextPosition(SwingConstants.LEADING);
- annotations.setSelected(true);
- annotations.setText(MessageManager.getString("label.show_annotations"));
- annotations.setBounds(new Rectangle(169, 12, 200, 23));
- annotations.addActionListener(new ActionListener()
+ installationPanel.add(hmmerLocation);
+ installationPanel.add(hmmerPath);
+
+ /*
+ * path to Cygwin binaries folder (for Windows)
+ */
+ if (Platform.isWindows())
{
- public void actionPerformed(ActionEvent e)
+ JLabel cygwinLocation = new JLabel(
+ MessageManager.getString("label.cygwin_location"));
+ cygwinLocation.setFont(LABEL_FONT);
+ cygwinPath = new JTextField(pathFieldLength);
+ cygwinPath.addMouseListener(new MouseAdapter()
{
- annotations_actionPerformed(e);
- }
- });
- identity.addActionListener(new ActionListener()
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ cygwinPath.setText(chosen);
+ validateCygwinPath();
+ }
+ }
+ }
+ });
+ installationPanel.add(cygwinLocation);
+ installationPanel.add(cygwinPath);
+ }
+
+ /*
+ * preferences for hmmalign
+ */
+ JPanel alignOptionsPanel = new JPanel(new MigLayout());
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(alignOptionsPanel,
+ MessageManager.getString("label.hmmalign_options"), true);
+ hmmerTab.add(alignOptionsPanel);
+ hmmrTrimTermini = new JCheckBox();
+ hmmrTrimTermini.setFont(LABEL_FONT);
+ hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+ alignOptionsPanel.add(hmmrTrimTermini);
+
+ /*
+ * preferences for hmmsearch
+ */
+ JPanel searchOptions = new JPanel(new MigLayout());
+ // FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(searchOptions,
+ MessageManager.getString("label.hmmsearch_options"), true);
+ hmmerTab.add(searchOptions);
+ JLabel sequencesToKeep = new JLabel(
+ MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setFont(LABEL_FONT);
+ searchOptions.add(sequencesToKeep);
+ hmmerSequenceCount = new JTextField(5);
+ searchOptions.add(hmmerSequenceCount);
+
+ /*
+ * preferences for Information Content annotation
+ */
+ // JPanel dummy = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ JPanel annotationOptions = new JPanel(new MigLayout("left"));
+ JvSwingUtils.createTitledBorder(annotationOptions,
+ MessageManager.getString("label.information_annotation"), true);
+ // dummy.add(annotationOptions);
+ hmmerTab.add(annotationOptions);
+ ButtonGroup backgroundOptions = new ButtonGroup();
+ hmmerBackgroundUniprot = new JRadioButton(
+ MessageManager.getString("label.freq_uniprot"));
+ hmmerBackgroundUniprot.setFont(LABEL_FONT);
+ hmmerBackgroundAlignment = new JRadioButton(
+ MessageManager.getString("label.freq_alignment"));
+ hmmerBackgroundAlignment.setFont(LABEL_FONT);
+ backgroundOptions.add(hmmerBackgroundUniprot);
+ backgroundOptions.add(hmmerBackgroundAlignment);
+ backgroundOptions.setSelected(hmmerBackgroundUniprot.getModel(), true);
+ // disable buttons for now as annotation only uses Uniprot background
+ hmmerBackgroundAlignment.setEnabled(false);
+ hmmerBackgroundUniprot.setEnabled(false);
+ annotationOptions.add(hmmerBackgroundUniprot, "wrap");
+ annotationOptions.add(hmmerBackgroundAlignment);
+
+ return hmmerTab;
+ }
+
+ /**
+ * Initialises the Output tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initOutputTab()
+ {
+ JPanel outputTab = new JPanel();
+ outputTab.setLayout(null);
+ JLabel epsLabel = new JLabel();
+ 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(LABEL_FONT);
+ epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+ JLabel jLabel1 = new JLabel();
+ jLabel1.setFont(LABEL_FONT);
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+ jLabel1.setText(MessageManager.getString("label.append_start_end"));
+ jLabel1.setFont(LABEL_FONT);
+ fastajv.setFont(LABEL_FONT);
+ fastajv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setText(MessageManager.getString("label.clustal") + " ");
+ blcjv.setText(MessageManager.getString("label.blc") + " ");
+ fastajv.setText(MessageManager.getString("label.fasta") + " ");
+ msfjv.setText(MessageManager.getString("label.msf") + " ");
+ pfamjv.setText(MessageManager.getString("label.pfam") + " ");
+ pileupjv.setText(MessageManager.getString("label.pileup") + " ");
+ msfjv.setFont(LABEL_FONT);
+ msfjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setText(MessageManager.getString("label.pir") + " ");
+ JPanel jPanel11 = new JPanel();
+ jPanel11.setFont(LABEL_FONT);
+ TitledBorder titledBorder2 = new TitledBorder(
+ MessageManager.getString("label.file_output"));
+ jPanel11.setBorder(titledBorder2);
+ jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+ GridLayout gridLayout3 = new GridLayout();
+ jPanel11.setLayout(gridLayout3);
+ gridLayout3.setRows(8);
+ blcjv.setFont(LABEL_FONT);
+ blcjv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setFont(LABEL_FONT);
+ clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
+ pfamjv.setFont(LABEL_FONT);
+ pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pileupjv.setFont(LABEL_FONT);
+ pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setFont(LABEL_FONT);
+ pirjv.setHorizontalAlignment(SwingConstants.LEFT);
+ 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.setBounds(new Rectangle(228, 96, 188, 23));
+ autoIdWidth.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- annotations_actionPerformed(e);
+ autoIdWidth_actionPerformed();
}
});
- showGroupConsensus.addActionListener(new ActionListener()
+ 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")));
+ userIdWidthlabel.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.setBounds(new Rectangle(232, 144, 84, 23));
+ userIdWidth.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- annotations_actionPerformed(e);
+ userIdWidth_actionPerformed();
}
});
- showUnconserved.setFont(verdana11);
- showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
- showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
- showUnconserved.setSelected(true);
- showUnconserved.setText(MessageManager
- .getString("action.show_unconserved"));
- showUnconserved.addActionListener(new ActionListener()
+ 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);
+ jPanel11.add(fastajv);
+ jPanel11.add(msfjv);
+ jPanel11.add(pfamjv);
+ jPanel11.add(pileupjv);
+ jPanel11.add(pirjv);
+ outputTab.add(autoIdWidth);
+ outputTab.add(userIdWidth);
+ outputTab.add(userIdWidthlabel);
+ outputTab.add(modellerOutput);
+ outputTab.add(embbedBioJSON);
+ outputTab.add(epsLabel);
+ outputTab.add(epsRendering);
+ outputTab.add(jPanel11);
+ return outputTab;
+ }
+
+ /**
+ * Initialises the Connections tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initConnectionsTab()
+ {
+ JPanel connectTab = new JPanel();
+ connectTab.setLayout(new GridBagLayout());
+
+ // Label for browser text box
+ JLabel browserLabel = new JLabel();
+ browserLabel.setFont(LABEL_FONT);
+ browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
+ browserLabel.setText(
+ MessageManager.getString("label.default_browser_unix"));
+ defaultBrowser.setFont(LABEL_FONT);
+ defaultBrowser.setText("");
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.double_click_to_browse"));
+ defaultBrowser.setToolTipText(tooltip);
+ defaultBrowser.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ defaultBrowser_mouseClicked(e);
+ }
+ }
+ });
+
+ JPanel proxyPanel = initConnTabProxyPanel();
+ initConnTabCheckboxes();
+
+ // Add default Browser text box
+ connectTab.add(browserLabel,
+ new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(10, 0, 5, 5), 5, 1));
+ defaultBrowser.setFont(LABEL_FONT);
+ defaultBrowser.setText("");
+
+ connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
+ 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
+ new Insets(10, 0, 5, 10), 30, 1));
+
+ // Add proxy server panel
+ connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
+ GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
+ new Insets(10, 0, 5, 12), 4, 10));
+
+ // Add usage stats, version check and questionnaire checkboxes
+ connectTab.add(usagestats,
+ new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
+ connectTab.add(questionnaire,
+ new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 10), 70, 1));
+ connectTab.add(versioncheck,
+ new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
+
+ // Add padding so the panel doesn't look ridiculous
+ JPanel spacePanel = new JPanel();
+ connectTab.add(spacePanel,
+ new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 5), 70, 1));
+
+ return connectTab;
+ }
+
+ /**
+ * Initialises the Links tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initLinksTab()
+ {
+ JPanel linkTab = new JPanel();
+ linkTab.setLayout(new GridBagLayout());
+
+ // Set up table for Url links
+ linkUrlTable.setFillsViewportHeight(true);
+ linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
+ linkUrlTable.setAutoCreateRowSorter(true);
+ linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ // adjust row height so radio buttons actually fit
+ // don't do this in the renderer, it causes the awt thread to activate
+ // constantly
+ JRadioButton temp = new JRadioButton();
+ linkUrlTable.setRowHeight(temp.getMinimumSize().height);
+
+ // Table in scrollpane so that the table is given a scrollbar
+ JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
+ linkScrollPane.setBorder(null);
+
+ // Panel for links functionality
+ JPanel linkPanel = new JPanel(new GridBagLayout());
+ linkPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.url_linkfrom_sequence_id")));
+
+ // Put the Url links panel together
+
+ // Buttons go at top right, resizing only resizes the blank space vertically
+ JPanel buttonPanel = initLinkTabUrlButtons();
+ GridBagConstraints linkConstraints1 = new GridBagConstraints();
+ linkConstraints1.insets = new Insets(0, 0, 5, 0);
+ linkConstraints1.gridx = 0;
+ linkConstraints1.gridy = 0;
+ linkConstraints1.weightx = 1.0;
+ linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
+ linkTab.add(buttonPanel, linkConstraints1);
+
+ // Links table goes at top left, resizing resizes the table
+ GridBagConstraints linkConstraints2 = new GridBagConstraints();
+ linkConstraints2.insets = new Insets(0, 0, 5, 5);
+ linkConstraints2.gridx = 0;
+ linkConstraints2.gridy = 1;
+ linkConstraints2.weightx = 1.0;
+ linkConstraints2.weighty = 1.0;
+ linkConstraints2.fill = GridBagConstraints.BOTH;
+ linkTab.add(linkScrollPane, linkConstraints2);
+
+ // Filter box and buttons goes at bottom left, resizing resizes the text box
+ JPanel filterPanel = initLinkTabFilterPanel();
+ GridBagConstraints linkConstraints3 = new GridBagConstraints();
+ linkConstraints3.insets = new Insets(0, 0, 0, 5);
+ linkConstraints3.gridx = 0;
+ linkConstraints3.gridy = 2;
+ linkConstraints3.weightx = 1.0;
+ linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
+ linkTab.add(filterPanel, linkConstraints3);
+
+ return linkTab;
+ }
+
+ private JPanel initLinkTabFilterPanel()
+ {
+ // Filter textbox and reset button
+ JLabel filterLabel = new JLabel(
+ MessageManager.getString("label.filter"));
+ filterLabel.setFont(LABEL_FONT);
+ filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ filterTB.setFont(LABEL_FONT);
+ filterTB.setText("");
+
+ doReset.setText(MessageManager.getString("action.showall"));
+ userOnly.setText(MessageManager.getString("action.customfilter"));
+
+ // Panel for filter functionality
+ JPanel filterPanel = new JPanel(new GridBagLayout());
+ filterPanel.setBorder(new TitledBorder("Filter"));
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+
+ filterPanel.add(filterLabel, gbc);
+
+ GridBagConstraints gbc1 = new GridBagConstraints();
+ gbc1.gridx = 1;
+ gbc1.gridwidth = 2;
+ gbc1.fill = GridBagConstraints.HORIZONTAL;
+ gbc1.anchor = GridBagConstraints.WEST;
+ gbc1.weightx = 1.0;
+ filterPanel.add(filterTB, gbc1);
+
+ GridBagConstraints gbc2 = new GridBagConstraints();
+ gbc2.gridx = 3;
+ gbc2.fill = GridBagConstraints.NONE;
+ gbc2.anchor = GridBagConstraints.WEST;
+ filterPanel.add(doReset, gbc2);
+
+ GridBagConstraints gbc3 = new GridBagConstraints();
+ gbc3.gridx = 4;
+ gbc3.fill = GridBagConstraints.NONE;
+ gbc3.anchor = GridBagConstraints.WEST;
+ filterPanel.add(userOnly, gbc3);
+
+ return filterPanel;
+ }
+
+ private JPanel initLinkTabUrlButtons()
+ {
+ // Buttons for new / edit / delete Url links
+ JButton newLink = new JButton();
+ newLink.setText(MessageManager.getString("action.new"));
+
+ editLink.setText(MessageManager.getString("action.edit"));
+
+ deleteLink.setText(MessageManager.getString("action.delete"));
+
+ // no current selection, so initially disable delete/edit buttons
+ editLink.setEnabled(false);
+ deleteLink.setEnabled(false);
+
+ newLink.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- showunconserved_actionPerformed(e);
+ newLink_actionPerformed(e);
}
});
- // / TODO: fit these in to preferences panel!!!!!
- shareSelections.setFont(verdana11);
- shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
- shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
- shareSelections.setSelected(true);
- shareSelections.setText(MessageManager
- .getString("label.share_selection_across_views"));
- followHighlight.setFont(verdana11);
- followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
- followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
- // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
- followHighlight.setSelected(true);
- followHighlight.setText(MessageManager
- .getString("label.scroll_highlighted_regions"));
-
- gapLabel.setFont(verdana11);
- gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
- colour.setFont(verdana11);
- colour.setBounds(new Rectangle(172, 225, 155, 21));
- colourLabel.setFont(verdana11);
- colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText(MessageManager.getString("label.alignment_colour")
- + " ");
- fontLabel.setFont(verdana11);
- fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- fontLabel.setText(MessageManager.getString("label.font"));
- fontSizeCB.setFont(verdana11);
- fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
- fontStyleCB.setFont(verdana11);
- fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
- fontNameCB.setFont(verdana11);
- fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
- gapSymbolCB.setFont(verdana11);
- gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
- mincolourLabel.setFont(verdana11);
+
+ 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);
+ }
+ });
+
+ JPanel buttonPanel = new JPanel(new GridBagLayout());
+ buttonPanel.setBorder(new TitledBorder("Edit links"));
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.NONE;
+ buttonPanel.add(newLink, gbc);
+
+ GridBagConstraints gbc1 = new GridBagConstraints();
+ gbc1.gridx = 1;
+ gbc1.gridy = 0;
+ gbc1.fill = GridBagConstraints.NONE;
+ buttonPanel.add(editLink, gbc1);
+
+ GridBagConstraints gbc2 = new GridBagConstraints();
+ gbc2.gridx = 2;
+ gbc2.gridy = 0;
+ gbc2.fill = GridBagConstraints.NONE;
+ buttonPanel.add(deleteLink, gbc2);
+
+ GridBagConstraints gbc3 = new GridBagConstraints();
+ gbc3.gridx = 3;
+ gbc3.gridy = 0;
+ gbc3.fill = GridBagConstraints.HORIZONTAL;
+ gbc3.weightx = 1.0;
+ JPanel spacePanel = new JPanel();
+ spacePanel.setBorder(null);
+ buttonPanel.add(spacePanel, gbc3);
+
+ return buttonPanel;
+ }
+
+ /**
+ * Initialises the proxy server panel in the Connections tab
+ *
+ * @return the proxy server panel
+ */
+ private JPanel initConnTabProxyPanel()
+ {
+ // Label for server text box
+ serverLabel.setText(MessageManager.getString("label.address"));
+ serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ serverLabel.setFont(LABEL_FONT);
+
+ // Proxy server and port text boxes
+ proxyServerTB.setFont(LABEL_FONT);
+ proxyPortTB.setFont(LABEL_FONT);
+
+ // Label for Port text box
+ portLabel.setFont(LABEL_FONT);
+ portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ portLabel.setText(MessageManager.getString("label.port"));
+
+ // Use proxy server checkbox
+ 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();
+ }
+ });
+
+ // Make proxy server panel
+ JPanel proxyPanel = new JPanel();
+ TitledBorder titledBorder1 = new TitledBorder(
+ MessageManager.getString("label.proxy_server"));
+ proxyPanel.setBorder(titledBorder1);
+ proxyPanel.setLayout(new GridBagLayout());
+ proxyPanel.add(serverLabel,
+ new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 2, 2, 0), 5, 0));
+ proxyPanel.add(portLabel,
+ new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 0, 2, 0), 11, 0));
+ proxyPanel.add(useProxy,
+ new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 2, 5, 185), 2, -4));
+ proxyPanel.add(proxyPortTB,
+ new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 2), 54, 1));
+ proxyPanel.add(proxyServerTB,
+ new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 0), 263, 1));
+
+ return proxyPanel;
+ }
+
+ /**
+ * Initialises the checkboxes in the Connections tab
+ */
+ private void initConnTabCheckboxes()
+ {
+ // Usage stats checkbox label
+ usagestats.setText(
+ MessageManager.getString("label.send_usage_statistics"));
+ usagestats.setFont(LABEL_FONT);
+ usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
+ usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ // Questionnaire checkbox label
+ questionnaire.setText(
+ MessageManager.getString("label.check_for_questionnaires"));
+ questionnaire.setFont(LABEL_FONT);
+ questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
+ questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ // Check for latest version checkbox label
+ versioncheck.setText(
+ MessageManager.getString("label.check_for_latest_version"));
+ versioncheck.setFont(LABEL_FONT);
+ versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
+ versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
+ }
+
+ /**
+ * Initialises the parent panel which contains the tabbed sections.
+ *
+ * @return
+ */
+ private JPanel initOkCancelPanel()
+ {
+ JButton ok = new JButton();
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ JButton cancel = new JButton();
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+ JPanel okCancelPanel = new JPanel();
+ okCancelPanel.add(ok);
+ okCancelPanel.add(cancel);
+ return okCancelPanel;
+ }
+
+ /**
+ * Initialises the Colours tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initColoursTab()
+ {
+ JPanel coloursTab = new JPanel();
+ coloursTab.setBorder(new TitledBorder(
+ MessageManager.getString("action.open_new_alignment")));
+ coloursTab.setLayout(new FlowLayout());
+ JLabel mincolourLabel = new JLabel();
+ 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_actionPerformed(minColour);
}
});
- maxcolourLabel.setFont(verdana11);
+ JLabel maxcolourLabel = new JLabel();
+ 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_actionPerformed(maxColour);
}
});
- startupCheckbox.setText(MessageManager.getString("action.open_file"));
- startupCheckbox.setFont(verdana11);
- startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
- startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
- startupCheckbox.setSelected(true);
- startupFileTextfield.setFont(verdana11);
- startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
- startupFileTextfield.addMouseListener(new MouseAdapter()
+ 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") + " ");
+ GPreferences.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") + " ");
+ GPreferences.addtoLayout(coloursTab,
+ MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
+ nucColourLabel, nucColour);
+
+ JPanel annotationShding = new JPanel();
+ annotationShding.setBorder(new TitledBorder(
+ MessageManager.getString("label.annotation_shading_default")));
+ annotationShding.setLayout(new GridLayout(1, 2));
+ GPreferences.addtoLayout(annotationShding,
+ MessageManager.getString(
+ "label.default_minimum_colour_annotation_shading"),
+ mincolourLabel, minColour);
+ GPreferences.addtoLayout(annotationShding,
+ MessageManager.getString(
+ "label.default_maximum_colour_annotation_shading"),
+ maxcolourLabel, maxColour);
+ coloursTab.add(annotationShding); // , FlowLayout.LEFT);
+ return coloursTab;
+ }
+
+ /**
+ * Initialises the Overview tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initOverviewTab()
+ {
+ JPanel overviewPanel = new JPanel();
+ overviewPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.overview_settings")));
+
+ gapColour.setFont(LABEL_FONT);
+ // fixing the border colours stops apparent colour bleed from the panel
+ gapColour.setBorder(
+ BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
+ gapColour.setPreferredSize(new Dimension(40, 20));
+ gapColour.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ gapColour_actionPerformed(gapColour);
+ }
+ });
+
+ hiddenColour.setFont(LABEL_FONT);
+ // fixing the border colours stops apparent colour bleed from the panel
+ hiddenColour.setBorder(
+ BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
+ hiddenColour.setPreferredSize(new Dimension(40, 20));
+ hiddenColour.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ hiddenColour_actionPerformed(hiddenColour);
+ }
+ });
+
+ useLegacyGap = new JCheckBox(
+ MessageManager.getString("label.ov_legacy_gap"));
+ useLegacyGap.setFont(LABEL_FONT);
+ useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
+ useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
+ gapLabel = new JLabel(
+ MessageManager.getString("label.gap_colour"));
+ gapLabel.setFont(LABEL_FONT);
+ gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ gapLabel.setVerticalTextPosition(SwingConstants.TOP);
+ showHiddenAtStart = new JCheckBox(
+ MessageManager.getString("label.ov_show_hide_default"));
+ showHiddenAtStart.setFont(LABEL_FONT);
+ showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
+ showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
+ JLabel hiddenLabel = new JLabel(
+ MessageManager.getString("label.hidden_colour"));
+ hiddenLabel.setFont(LABEL_FONT);
+ hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
+
+ useLegacyGap.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ useLegacyGaps_actionPerformed(e);
+ }
+ });
+
+ overviewPanel.setLayout(new GridBagLayout());
+ GridBagConstraints c1 = new GridBagConstraints();
+
+ c1.fill = GridBagConstraints.HORIZONTAL;
+ c1.gridx = 0;
+ c1.gridy = 0;
+ c1.weightx = 1;
+ c1.ipady = 20;
+ c1.anchor = GridBagConstraints.FIRST_LINE_START;
+ overviewPanel.add(useLegacyGap, c1);
+
+ GridBagConstraints c2 = new GridBagConstraints();
+ c2.fill = GridBagConstraints.HORIZONTAL;
+ c2.gridx = 1;
+ c2.gridy = 0;
+ c2.insets = new Insets(0, 15, 0, 10);
+ overviewPanel.add(gapLabel, c2);
+
+ GridBagConstraints c3 = new GridBagConstraints();
+ c3.fill = GridBagConstraints.HORIZONTAL;
+ c3.gridx = 2;
+ c3.gridy = 0;
+ c3.insets = new Insets(0, 0, 0, 15);
+ overviewPanel.add(gapColour, c3);
+
+ GridBagConstraints c4 = new GridBagConstraints();
+ c4.fill = GridBagConstraints.HORIZONTAL;
+ c4.gridx = 0;
+ c4.gridy = 1;
+ c4.weightx = 1;
+ overviewPanel.add(showHiddenAtStart, c4);
+
+ GridBagConstraints c5 = new GridBagConstraints();
+ c5.fill = GridBagConstraints.HORIZONTAL;
+ c5.gridx = 1;
+ c5.gridy = 1;
+ c5.insets = new Insets(0, 15, 0, 10);
+ overviewPanel.add(hiddenLabel, c5);
+
+ GridBagConstraints c6 = new GridBagConstraints();
+ c6.fill = GridBagConstraints.HORIZONTAL;
+ c6.gridx = 2;
+ c6.gridy = 1;
+ c6.insets = new Insets(0, 0, 0, 15);
+ overviewPanel.add(hiddenColour, c6);
+
+ JButton resetButton = new JButton(
+ MessageManager.getString("label.reset_to_defaults"));
+
+ resetButton.addActionListener(new ActionListener()
{
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ resetOvDefaults_actionPerformed(e);
+ }
+ });
+
+ GridBagConstraints c7 = new GridBagConstraints();
+ c7.fill = GridBagConstraints.NONE;
+ c7.gridx = 0;
+ c7.gridy = 2;
+ c7.insets = new Insets(10, 0, 0, 0);
+ c7.anchor = GridBagConstraints.WEST;
+ overviewPanel.add(resetButton, c7);
+
+ // Add padding so the panel doesn't look ridiculous
+ JPanel spacePanel = new JPanel();
+ overviewPanel.add(spacePanel,
+ new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 5), 0, 0));
+
+ return overviewPanel;
+ }
+
+ /**
+ * Initialises the Structure tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initStructureTab()
+ {
+ structureTab = new JPanel();
+
+ structureTab.setBorder(new TitledBorder(
+ MessageManager.getString("label.structure_options")));
+ structureTab.setLayout(null);
+ final int width = 400;
+ final int height = 22;
+ final int lineSpacing = 25;
+ int ypos = 15;
+
+ structFromPdb.setFont(LABEL_FONT);
+ structFromPdb
+ .setText(MessageManager.getString("label.struct_from_pdb"));
+ structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
+ structFromPdb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean selected = structFromPdb.isSelected();
+ // enable other options only when the first is checked
+ useRnaView.setEnabled(selected);
+ addSecondaryStructure.setEnabled(selected);
+ addTempFactor.setEnabled(selected);
+ }
+ });
+ structureTab.add(structFromPdb);
+
+ // indent checkboxes that are conditional on the first one
+ ypos += lineSpacing;
+ 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(LABEL_FONT);
+ addSecondaryStructure
+ .setText(MessageManager.getString("label.autoadd_secstr"));
+ addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(addSecondaryStructure);
+
+ ypos += lineSpacing;
+ 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(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(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"));
+ pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
+ structureTab.add(pathLabel);
+
+ chimeraPath.setFont(LABEL_FONT);
+ chimeraPath.setText("");
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_path_tip"));
+ chimeraPath.setToolTipText(tooltip);
+ chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
+ chimeraPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
public void mouseClicked(MouseEvent e)
{
- if (e.getClickCount() > 1)
+ if (e.getClickCount() == 2)
{
- startupFileTextfield_mouseClicked();
+ String chosen = openFileChooser(false);
+ 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;
+ }
- connectTab.setLayout(gridBagLayout3);
- serverLabel.setText(MessageManager.getString("label.address"));
- serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- serverLabel.setFont(verdana11);
- proxyServerTB.setFont(verdana11);
- proxyPortTB.setFont(verdana11);
- portLabel.setFont(verdana11);
- portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- portLabel.setText(MessageManager.getString("label.port"));
- browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
- browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText(MessageManager
- .getString("label.default_browser_unix"));
- defaultBrowser.setFont(verdana11);
- defaultBrowser.setText("");
- usagestats.setText(MessageManager
- .getString("label.send_usage_statistics"));
- usagestats.setFont(verdana11);
- usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
- usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
- questionnaire.setText(MessageManager
- .getString("label.check_for_questionnaires"));
- questionnaire.setFont(verdana11);
- questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
- questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
- versioncheck.setText(MessageManager
- .getString("label.check_for_latest_version"));
- versioncheck.setFont(verdana11);
- versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
- versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
- newLink.setText(MessageManager.getString("action.new"));
- newLink.addActionListener(new java.awt.event.ActionListener()
+ /**
+ * 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(boolean forFolder)
+ {
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
+
+ // 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;
+ }
+
+ protected boolean validateStructure()
+ {
+ return false;
+ }
+
+ /**
+ * Initialises the Visual tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initVisualTab()
+ {
+ JPanel visualTab = new JPanel();
+ visualTab.setBorder(new TitledBorder(
+ MessageManager.getString("action.open_new_alignment")));
+ visualTab.setLayout(null);
+ fullScreen.setFont(LABEL_FONT);
+ fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+ fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+ fullScreen.setText(MessageManager.getString("label.maximize_window"));
+ quality.setEnabled(false);
+ 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(LABEL_FONT);
+ conservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ conservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ conservation.setSelected(true);
+ conservation.setText(MessageManager.getString("label.conservation"));
+ identity.setEnabled(false);
+ identity.setFont(LABEL_FONT);
+ identity.setHorizontalAlignment(SwingConstants.RIGHT);
+ identity.setHorizontalTextPosition(SwingConstants.LEFT);
+ identity.setSelected(true);
+ identity.setText(MessageManager.getString("label.consensus"));
+ showOccupancy.setFont(LABEL_FONT);
+ showOccupancy.setEnabled(false);
+ showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
+ showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
+ showOccupancy.setSelected(true);
+ showOccupancy.setText(MessageManager.getString("label.occupancy"));
+
+ JLabel showGroupbits = new JLabel();
+ 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(LABEL_FONT);
+ showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensbits
+ .setText(MessageManager.getString("label.consensus") + ":");
+ showConsensHistogram.setEnabled(false);
+ 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(LABEL_FONT);
+ showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensLogo.setSelected(true);
+ showConsensLogo.setText(MessageManager.getString("label.logo"));
+ showGroupConsensus.setEnabled(false);
+ 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(LABEL_FONT);
+ showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConservation.setSelected(true);
+ showGroupConservation
+ .setText(MessageManager.getString("label.conservation"));
+ showNpTooltip.setEnabled(true);
+ 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(LABEL_FONT);
+ showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showDbRefTooltip.setSelected(true);
+ showDbRefTooltip
+ .setText(MessageManager.getString("label.database_references"));
+ annotations.setFont(LABEL_FONT);
+ annotations.setHorizontalAlignment(SwingConstants.RIGHT);
+ annotations.setHorizontalTextPosition(SwingConstants.LEFT);
+ annotations.setSelected(true);
+ annotations.setText(MessageManager.getString("label.show_annotations"));
+ // annotations.setBounds(new Rectangle(169, 12, 200, 23));
+ annotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- newLink_actionPerformed(e);
+ annotations_actionPerformed(e);
}
});
- editLink.setText(MessageManager.getString("action.edit"));
- editLink.addActionListener(new java.awt.event.ActionListener()
+ identity.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- editLink_actionPerformed(e);
+ annotations_actionPerformed(e);
}
});
- deleteLink.setText(MessageManager.getString("action.delete"));
- deleteLink.addActionListener(new java.awt.event.ActionListener()
+ showGroupConsensus.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- deleteLink_actionPerformed(e);
- }
- });
-
- linkURLList.addListSelectionListener(new ListSelectionListener()
- {
- public void valueChanged(ListSelectionEvent e)
- {
- int index = linkURLList.getSelectedIndex();
- linkNameList.setSelectedIndex(index);
- }
- });
-
- linkNameList.addListSelectionListener(new ListSelectionListener()
- {
- public void valueChanged(ListSelectionEvent e)
- {
- int index = linkNameList.getSelectedIndex();
- linkURLList.setSelectedIndex(index);
- }
- });
-
- linkScrollPane.setBorder(null);
- linkPanel.setBorder(new TitledBorder(MessageManager
- .getString("label.url_linkfrom_sequence_id")));
- linkPanel.setLayout(borderLayout2);
- editLinkButtons.setLayout(gridLayout1);
- gridLayout1.setRows(3);
- linkNameList.setFont(verdana11);
- linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- linkPanel2.setLayout(borderLayout3);
- linkURLList.setFont(verdana11);
- linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
- defaultBrowser.addMouseListener(new MouseAdapter()
- {
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() > 1)
- {
- defaultBrowser_mouseClicked(e);
- }
+ annotations_actionPerformed(e);
}
});
- useProxy.setFont(verdana11);
- useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
- useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
- useProxy.setText(MessageManager.getString("label.use_proxy_server"));
- useProxy.addActionListener(new ActionListener()
+ showUnconserved.setFont(LABEL_FONT);
+ showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
+ showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
+ showUnconserved.setSelected(true);
+ showUnconserved
+ .setText(MessageManager.getString("action.show_unconserved"));
+ showUnconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- useProxy_actionPerformed();
+ showunconserved_actionPerformed(e);
}
});
- jPanel1.setBorder(titledBorder1);
- jPanel1.setLayout(gridBagLayout1);
- sortby.setFont(verdana11);
- sortby.setBounds(new Rectangle(172, 249, 155, 21));
- sortLabel.setFont(verdana11);
- sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- sortLabel.setText(MessageManager.getString("label.sort_by"));
- jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
- jPanel2.setLayout(gridLayout2);
- gridLayout2.setRows(12);
- exportTab.setLayout(null);
- epsLabel.setFont(verdana11);
- epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
- epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
- epsRendering.setFont(verdana11);
- epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
- jLabel1.setFont(verdana11);
- jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText(MessageManager.getString("label.append_start_end"));
- jLabel1.setFont(verdana11);
- fastajv.setFont(verdana11);
- fastajv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setText(MessageManager.getString("label.clustal") + " ");
- blcjv.setText(MessageManager.getString("label.blc") + " ");
- fastajv.setText(MessageManager.getString("label.fasta") + " ");
- msfjv.setText(MessageManager.getString("label.msf") + " ");
- pfamjv.setText(MessageManager.getString("label.pfam") + " ");
- pileupjv.setText(MessageManager.getString("label.pileup") + " ");
- msfjv.setFont(verdana11);
- msfjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setText(MessageManager.getString("label.pir") + " ");
- jPanel11.setFont(verdana11);
- jPanel11.setBorder(titledBorder2);
- jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
- jPanel11.setLayout(gridLayout3);
- blcjv.setFont(verdana11);
- blcjv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setFont(verdana11);
- clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
- pfamjv.setFont(verdana11);
- pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
- pileupjv.setFont(verdana11);
- pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setFont(verdana11);
- pirjv.setHorizontalAlignment(SwingConstants.LEFT);
- seqLimit.setFont(verdana11);
+
+ // TODO these are not yet added to / action from Preferences
+ // JCheckBox shareSelections = new JCheckBox();
+ // shareSelections.setFont(verdana11);
+ // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
+ // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
+ // shareSelections.setSelected(true);
+ // shareSelections.setText(MessageManager
+ // .getString("label.share_selection_across_views"));
+ // JCheckBox followHighlight = new JCheckBox();
+ // followHighlight.setFont(verdana11);
+ // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
+ // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
+ // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ // followHighlight.setSelected(true);
+ // followHighlight.setText(MessageManager
+ // .getString("label.scroll_highlighted_regions"));
+
+ seqLimit.setFont(LABEL_FONT);
seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
- gridLayout3.setRows(8);
- smoothFont.setFont(verdana11);
+ smoothFont.setFont(LABEL_FONT);
smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
smoothFont.setText(MessageManager.getString("label.smooth_font"));
- calcTab.setLayout(null);
- autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
- autoCalculateConsCheck.setText(MessageManager
- .getString("label.autocalculate_consensus"));
- autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
- padGaps.setFont(JvSwingUtils.getLabelFont());
- padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
- padGaps.setBounds(new Rectangle(22, 94, 168, 23));
- sortByTree.setFont(JvSwingUtils.getLabelFont());
- sortByTree
- .setText(MessageManager.getString("label.sort_with_new_tree"));
- sortByTree
- .setToolTipText(MessageManager
- .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
- sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+ 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(LABEL_FONT);
+ gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
+ JLabel fontLabel = new JLabel();
+ fontLabel.setFont(LABEL_FONT);
+ fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ fontLabel.setText(MessageManager.getString("label.font"));
+ 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);
- autoIdWidth.setFont(JvSwingUtils.getLabelFont());
- autoIdWidth.setText(MessageManager
- .getString("label.automatically_set_id_width"));
- 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()
+ startupCheckbox.setText(MessageManager.getString("action.open_file"));
+ startupCheckbox.setFont(LABEL_FONT);
+ startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
+ startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
+ startupCheckbox.setSelected(true);
+ startupFileTextfield.setFont(LABEL_FONT);
+ startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.double_click_to_browse"));
+ startupFileTextfield.setToolTipText(tooltip);
+ startupFileTextfield.addMouseListener(new MouseAdapter()
{
-
@Override
- public void actionPerformed(ActionEvent e)
+ public void mouseClicked(MouseEvent e)
{
- autoIdWidth_actionPerformed();
+ if (e.getClickCount() > 1)
+ {
+ startupFileTextfield_mouseClicked();
+ }
}
});
- userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
- userIdWidthlabel.setText(MessageManager
- .getString("label.figure_id_column_width"));
- userIdWidth
- .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")));
- userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
- userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
- userIdWidth.setText("");
- userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
- userIdWidth.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userIdWidth_actionPerformed();
- }
- });
- modellerOutput.setFont(JvSwingUtils.getLabelFont());
- modellerOutput.setText(MessageManager
- .getString("label.use_modeller_output"));
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ sortby.setFont(LABEL_FONT);
+ sortby.setBounds(new Rectangle(172, 260, 155, 21));
+ 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));
+ 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));
+
+ JPanel annsettingsPanel = new JPanel();
+ annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
+ annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
+ annsettingsPanel.setBorder(new EtchedBorder());
+ visualTab.add(annsettingsPanel);
+ Border jb = new EmptyBorder(1, 1, 4, 5);
+ annotations.setBorder(jb);
+ showOccupancy.setBorder(jb);
+ quality.setBorder(jb);
+ conservation.setBorder(jb);
+ identity.setBorder(jb);
+ showConsensbits.setBorder(jb);
+ showGroupbits.setBorder(jb);
+ showGroupConsensus.setBorder(jb);
+ showGroupConservation.setBorder(jb);
+ showConsensHistogram.setBorder(jb);
+ showConsensLogo.setBorder(jb);
+
+ JPanel autoAnnotSettings = new JPanel();
+ annsettingsPanel.add(autoAnnotSettings);
+ autoAnnotSettings.setLayout(new GridLayout(0, 2));
+ autoAnnotSettings.add(annotations);
+ autoAnnotSettings.add(quality);
+ // second row of autoannotation box
+ autoAnnotSettings = new JPanel();
+ annsettingsPanel.add(autoAnnotSettings);
+
+ autoAnnotSettings.setLayout(new GridLayout(0, 3));
+ autoAnnotSettings.add(conservation);
+ autoAnnotSettings.add(identity);
+ autoAnnotSettings.add(showOccupancy);
+ autoAnnotSettings.add(showGroupbits);
+ autoAnnotSettings.add(showGroupConservation);
+ autoAnnotSettings.add(showGroupConsensus);
+ autoAnnotSettings.add(showConsensbits);
+ autoAnnotSettings.add(showConsensHistogram);
+ autoAnnotSettings.add(showConsensLogo);
- dasPanel.setLayout(borderLayout4);
- wsPanel.setLayout(borderLayout5);
- wrap.setFont(JvSwingUtils.getLabelFont());
+ JPanel tooltipSettings = new JPanel();
+ tooltipSettings.setBorder(new TitledBorder(
+ MessageManager.getString("label.sequence_id_tooltip")));
+ tooltipSettings.setBounds(173, 140, 220, 62);
+ tooltipSettings.setLayout(new GridLayout(2, 1));
+ tooltipSettings.add(showDbRefTooltip);
+ tooltipSettings.add(showNpTooltip);
+ visualTab.add(tooltipSettings);
+
+ wrap.setFont(LABEL_FONT);
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
wrap.setText(MessageManager.getString("label.wrap_alignment"));
- rightAlign.setFont(JvSwingUtils.getLabelFont());
+ 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(JvSwingUtils.getLabelFont());
+ idItalics.setFont(LABEL_FONT_ITALIC);
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
- idItalics.setText(MessageManager
- .getString("label.sequence_name_italics"));
- openoverv.setFont(JvSwingUtils.getLabelFont());
- openoverv.setActionCommand(MessageManager
- .getString("label.open_overview"));
+ idItalics.setText(
+ MessageManager.getString("label.sequence_name_italics"));
+ 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, 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);
+ jPanel2.add(sortAnnLabel);
jPanel2.add(startupCheckbox);
- visualTab.add(annotations);
+ visualTab.add(jPanel2);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
+ visualTab.add(sortAnnBy);
+ visualTab.add(sortAutocalc);
visualTab.add(gapSymbolCB);
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
- annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
- annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
- annsettingsPanel.add(autoAnnotSettings1);
- annsettingsPanel.add(autoAnnotSettings2);
- annsettingsPanel.add(autoAnnotSettings3);
- autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
- autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
- autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
- visualTab.add(annsettingsPanel);
- Border jb = new EmptyBorder(1, 1, 4, 5);
- quality.setBorder(jb);
- conservation.setBorder(jb);
- identity.setBorder(jb);
- showConsensbits.setBorder(jb);
- showGroupbits.setBorder(jb);
- showGroupConsensus.setBorder(jb);
- showGroupConservation.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 tooltipSettings = new JPanel();
- tooltipSettings.setBorder(new TitledBorder(MessageManager
- .getString("label.sequence_id_tooltip")));
- tooltipSettings.setBounds(173, 130, 200, 62);
- tooltipSettings.setLayout(new GridLayout(2, 1));
- tooltipSettings.add(showDbRefTooltip);
- tooltipSettings.add(showNpTooltip);
- visualTab.add(tooltipSettings);
- visualTab.add(jPanel2);
- JvSwingUtils.addtoLayout(visual2Tab, MessageManager
- .getString("label.default_colour_scheme_for_alignment"),
- colourLabel, colour);
- JPanel annotationShding = new JPanel();
- annotationShding.setBorder(new TitledBorder(MessageManager
- .getString("label.annotation_shading_default")));
- annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding, MessageManager
- .getString("label.default_minimum_colour_annotation_shading"),
- mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding, MessageManager
- .getString("label.default_maximum_colour_annotation_shading"),
- maxcolourLabel, maxColour);
- visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
-
- // visual2panel.add(minColour);
- // visual2panel.add(maxColour);
- // visual2Tab.add(visual2panel);
-
- linkPanel.add(editLinkButtons, BorderLayout.EAST);
- editLinkButtons.add(newLink, null);
- editLinkButtons.add(editLink, null);
- editLinkButtons.add(deleteLink, null);
- linkPanel.add(linkScrollPane, BorderLayout.CENTER);
- linkScrollPane.getViewport().add(linkPanel2, null);
- linkPanel2.add(linkURLList, BorderLayout.CENTER);
- linkPanel2.add(linkNameList, BorderLayout.WEST);
- okCancelPanel.add(ok);
- okCancelPanel.add(cancel);
- this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-
- this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
- jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 4, 0), 5, 0));
- jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 0, 4, 0), 11, 6));
- connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 16, 0, 0, 12), 359, -17));
- connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 21, 0, 35, 12), 4, 6));
- connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(16, 0, 0, 0), 5, 1));
- jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 54, 1));
- jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 0), 263, 1));
- connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(15, 0, 0, 15), 307, 1));
- connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
-
- jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 5, 185), 2, -4));
- DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
- dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
- gapSymbolCB.setRenderer(dlcr);
-
- tabbedPane.add(visualTab, MessageManager.getString("label.visual"));
- tabbedPane.add(visual2Tab, MessageManager.getString("label.colours"));
- tabbedPane.add(connectTab,
- MessageManager.getString("label.connections"));
- tabbedPane.add(exportTab, MessageManager.getString("label.output"));
- jPanel11.add(jLabel1);
- jPanel11.add(blcjv);
- jPanel11.add(clustaljv);
- jPanel11.add(fastajv);
- jPanel11.add(msfjv);
- jPanel11.add(pfamjv);
- jPanel11.add(pileupjv);
- jPanel11.add(pirjv);
- exportTab.add(autoIdWidth);
- exportTab.add(userIdWidth);
- exportTab.add(userIdWidthlabel);
- exportTab.add(modellerOutput);
- tabbedPane.add(calcTab, MessageManager.getString("label.editing"));
- calcTab.add(autoCalculateConsCheck);
- calcTab.add(padGaps);
- calcTab.add(sortByTree);
-
- tabbedPane
- .add(dasPanel, MessageManager.getString("label.das_settings"));
- tabbedPane.add(wsPanel, MessageManager.getString("label.web_services"));
-
- exportTab.add(epsLabel);
- exportTab.add(epsRendering);
- exportTab.add(jPanel11);
+ return visualTab;
}
protected void autoIdWidth_actionPerformed()
}
- protected void maxColour_actionPerformed()
+ protected void maxColour_actionPerformed(JPanel panel)
{
- // TODO Auto-generated method stub
+ }
+ protected void minColour_actionPerformed(JPanel panel)
+ {
}
- protected void minColour_actionPerformed()
+ protected void gapColour_actionPerformed(JPanel panel)
{
- // TODO Auto-generated method stub
+ }
+ protected void hiddenColour_actionPerformed(JPanel panel)
+ {
}
protected void showunconserved_actionPerformed(ActionEvent e)
}
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void resetOvDefaults_actionPerformed(ActionEvent e)
+ {
+ }
+
/**
* DOCUMENT ME!
*
public void useProxy_actionPerformed()
{
- proxyServerTB.setEnabled(useProxy.isSelected());
- proxyPortTB.setEnabled(useProxy.isSelected());
+ boolean enabled = useProxy.isSelected();
+ portLabel.setEnabled(enabled);
+ serverLabel.setEnabled(enabled);
+ proxyServerTB.setEnabled(enabled);
+ proxyPortTB.setEnabled(enabled);
+ }
+
+ /**
+ * Customer renderer for JTable: supports column of radio buttons
+ */
+ public class RadioButtonRenderer extends JRadioButton
+ implements TableCellRenderer
+ {
+ public RadioButtonRenderer()
+ {
+ setHorizontalAlignment(CENTER);
+ setToolTipText(MessageManager.getString("label.urltooltip"));
+ }
+
+ @Override
+ public Component getTableCellRendererComponent(JTable table,
+ Object value, boolean isSelected, boolean hasFocus, int row,
+ int column)
+ {
+ setSelected((boolean) value);
+
+ // set colours to match rest of table
+ if (isSelected)
+ {
+ setBackground(table.getSelectionBackground());
+ setForeground(table.getSelectionForeground());
+ }
+ else
+ {
+ setBackground(table.getBackground());
+ setForeground(table.getForeground());
+ }
+ return this;
+ }
+ }
+
+ /**
+ * Customer cell editor for JTable: supports column of radio buttons in
+ * conjunction with renderer
+ */
+ public class RadioButtonEditor extends AbstractCellEditor
+ implements TableCellEditor
+ {
+ private JRadioButton button = new JRadioButton();
+
+ public RadioButtonEditor()
+ {
+ button.setHorizontalAlignment(SwingConstants.CENTER);
+ this.button.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fireEditingStopped();
+ }
+ });
+ }
+
+ @Override
+ public Component getTableCellEditorComponent(JTable table, Object value,
+ boolean isSelected, int row, int column)
+ {
+ button.setSelected((boolean) value);
+ return button;
+ }
+
+ @Override
+ public Object getCellEditorValue()
+ {
+ return button.isSelected();
+ }
+
+ }
+
+ protected void validateHmmerPath()
+ {
}
+ protected void validateCygwinPath()
+ {
+ }
+
+ /**
+ * A helper method to add a panel containing a label and a component to a
+ * panel
+ *
+ * @param panel
+ * @param tooltip
+ * @param label
+ * @param valBox
+ */
+ protected static void addtoLayout(JPanel panel, String tooltip,
+ JComponent label, JComponent valBox)
+ {
+ JPanel laypanel = new JPanel(new GridLayout(1, 2));
+ JPanel labPanel = new JPanel(new BorderLayout());
+ JPanel valPanel = new JPanel();
+ labPanel.setBounds(new Rectangle(7, 7, 158, 23));
+ valPanel.setBounds(new Rectangle(172, 7, 270, 23));
+ labPanel.add(label, BorderLayout.WEST);
+ valPanel.add(valBox);
+ laypanel.add(labPanel);
+ laypanel.add(valPanel);
+ valPanel.setToolTipText(tooltip);
+ labPanel.setToolTipText(tooltip);
+ valBox.setToolTipText(tooltip);
+ panel.add(laypanel);
+ panel.validate();
+ }
}
git://source.jalview.org / jalview.git / blobdiff