/*
- * 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("<html>"
- + JvSwingUtils
- .wrapTooltip("Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed")
- + "</html>");
- 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("<html>"
- + JvSwingUtils
- .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")
- + "</html>");
- userIdWidthlabel
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")
- + "</html>");
- 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