X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=8f226efe2ceab17508b0532cd722870a8ceaccf5;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=bf01a01f31ab7aa2e12bbaf36e6abc2f7faffa54;hpb=057f733ab390518a3641f1dedebd36c028bf03d6;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index bf01a01..8f226ef 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -1,6 +1,6 @@ /* - * 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. * @@ -21,155 +21,168 @@ package jalview.jbgui; 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 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.FocusEvent; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; + +import javax.swing.BorderFactory; +import javax.swing.DefaultListCellRenderer; +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JFileChooser; +import javax.swing.JLabel; +import javax.swing.JList; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JTabbedPane; +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.TitledBorder; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; +import javax.swing.event.ListSelectionEvent; +import javax.swing.event.ListSelectionListener; /** - * DOCUMENT ME! + * Base class for the Preferences panel. * * @author $author$ * @version $Revision$ */ public class GPreferences extends JPanel { - JTabbedPane tabbedPane = new JTabbedPane(); - - JButton ok = new JButton(); - - JButton cancel = new JButton(); - - JPanel okCancelPanel = new JPanel(); - - BorderLayout borderLayout1 = new BorderLayout(); - - protected JCheckBox quality = new JCheckBox(); - - JPanel visualTab = new JPanel(); - - JPanel visual2Tab = new JPanel(); + private static final Font verdana11 = JvSwingUtils.getLabelFont(); + /* + * Visual tab components + */ protected JCheckBox fullScreen = new JCheckBox(); - protected JCheckBox conservation = new JCheckBox(); - - protected JCheckBox identity = new JCheckBox(); + protected JCheckBox openoverv = new JCheckBox(); - protected JCheckBox annotations = new JCheckBox(); + protected JCheckBox seqLimit = new JCheckBox(); - protected JPanel minColour = new JPanel(); + protected JCheckBox rightAlign = new JCheckBox(); - JLabel mincolourLabel = new JLabel(); + protected JComboBox fontSizeCB = new JComboBox(); - protected JPanel maxColour = new JPanel(); + protected JComboBox fontStyleCB = new JComboBox(); - JLabel maxcolourLabel = new JLabel(); + protected JComboBox fontNameCB = new JComboBox(); - JLabel gapLabel = new JLabel(); + protected JCheckBox showUnconserved = new JCheckBox(); - protected JComboBox colour = new JComboBox(); + protected JCheckBox idItalics = new JCheckBox(); - JLabel colourLabel = new JLabel(); + protected JCheckBox smoothFont = new JCheckBox(); - JLabel fontLabel = new JLabel(); + protected JComboBox gapSymbolCB = new JComboBox(); - protected JComboBox fontSizeCB = new JComboBox(); + protected JCheckBox wrap = new JCheckBox(); - protected JComboBox fontStyleCB = new JComboBox(); + protected JComboBox sortby = new JComboBox(); - protected JComboBox fontNameCB = new JComboBox(); + protected JComboBox sortAnnBy = new JComboBox(); - protected JComboBox gapSymbolCB = new JComboBox(); + protected JComboBox sortAutocalc = new JComboBox(); protected JCheckBox startupCheckbox = new JCheckBox(); protected JTextField startupFileTextfield = new JTextField(); - JPanel connectTab = new JPanel(); - - JLabel serverLabel = new JLabel(); - - protected JList linkURLList = new JList(); - - protected JTextField proxyServerTB = new JTextField(); - - protected JTextField proxyPortTB = new JTextField(); - - JLabel portLabel = new JLabel(); - - JLabel browserLabel = new JLabel(); - - protected JTextField defaultBrowser = new JTextField(); - - JButton newLink = new JButton(); - - JButton editLink = new JButton(); + // below are in the 'second column' + protected JCheckBox annotations = new JCheckBox(); - JButton deleteLink = new JButton(); + protected JCheckBox quality = new JCheckBox(); - JScrollPane linkScrollPane = new JScrollPane(); + protected JCheckBox conservation = new JCheckBox(); - JPanel linkPanel = new JPanel(); + protected JCheckBox identity = new JCheckBox(); - BorderLayout borderLayout2 = new BorderLayout(); + protected JCheckBox showGroupConsensus = new JCheckBox(); - JPanel editLinkButtons = new JPanel(); + protected JCheckBox showGroupConservation = new JCheckBox(); - GridLayout gridLayout1 = new GridLayout(); + protected JCheckBox showConsensHistogram = new JCheckBox(); - protected JList linkNameList = new JList(); + protected JCheckBox showConsensLogo = new JCheckBox(); - JPanel linkPanel2 = new JPanel(); + protected JCheckBox showDbRefTooltip = new JCheckBox(); - BorderLayout borderLayout3 = new BorderLayout(); + protected JCheckBox showNpTooltip = new JCheckBox(); - protected JCheckBox useProxy = new JCheckBox(); + /* + * Structure tab and components + */ + protected JPanel structureTab; - JPanel jPanel1 = new JPanel(); + protected JCheckBox structFromPdb = new JCheckBox(); - TitledBorder titledBorder1 = new TitledBorder( - MessageManager.getString("label.proxy_server")); + protected JCheckBox useRnaView = new JCheckBox(); - TitledBorder titledBorder2 = new TitledBorder( - MessageManager.getString("label.file_output")); + protected JCheckBox addSecondaryStructure = new JCheckBox(); - GridBagLayout gridBagLayout2 = new GridBagLayout(); + protected JCheckBox addTempFactor = new JCheckBox(); - GridBagLayout gridBagLayout1 = new GridBagLayout(); + protected JComboBox structViewer = new JComboBox(); - GridBagLayout gridBagLayout3 = new GridBagLayout(); + protected JTextField chimeraPath = new JTextField(); - protected JComboBox sortby = new JComboBox(); + /* + * Colours tab components + */ + protected JPanel minColour = new JPanel(); - JLabel sortLabel = new JLabel(); + protected JPanel maxColour = new JPanel(); - JPanel jPanel2 = new JPanel(); + protected JComboBox colour = new JComboBox(); - JPanel visual2panel = new JPanel(); + /* + * Connections tab components + */ + protected JList linkURLList = new JList(); - GridLayout gridLayout2 = new GridLayout(); + protected JTextField proxyServerTB = new JTextField(); - GridLayout gridLayout4 = new GridLayout(); + protected JTextField proxyPortTB = new JTextField(); - JPanel annsettingsPanel = new JPanel(); + protected JTextField defaultBrowser = new JTextField(); - JPanel autoAnnotSettings1 = new JPanel(); + protected JList linkNameList = new JList(); - 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 epsRendering = new JComboBox(); protected JLabel userIdWidthlabel = new JLabel(); @@ -177,8 +190,6 @@ public class GPreferences extends JPanel protected JTextField userIdWidth = new JTextField(); - JLabel jLabel1 = new JLabel(); - protected JCheckBox blcjv = new JCheckBox(); protected JCheckBox pileupjv = new JCheckBox(); @@ -191,73 +202,28 @@ public class GPreferences extends JPanel 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(); - - JPanel calcTab = new JPanel(); + protected JCheckBox modellerOutput = 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 versioncheck = new JCheckBox(); - - protected JLabel showGroupbits = new JLabel(); - - protected JLabel showConsensbits = new JLabel(); - - protected JCheckBox showConsensLogo = new JCheckBox(); - - protected JCheckBox showConsensHistogram = new JCheckBox(); - - protected JCheckBox showGroupConsensus = new JCheckBox(); - - protected JCheckBox showGroupConservation = new JCheckBox(); - - protected JCheckBox shareSelections = new JCheckBox(); + protected JCheckBox sortByTree = new JCheckBox(); - protected JCheckBox followHighlight = new JCheckBox(); + /* + * DAS Settings tab + */ + protected JPanel dasTab = new JPanel(); - protected JCheckBox sortByTree = new JCheckBox(); + /* + * Web Services tab + */ + protected JPanel wsTab = new JPanel(); /** * Creates a new GPreferences object. @@ -274,237 +240,230 @@ public class GPreferences extends JPanel } /** - * 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(initStructureTab(), + MessageManager.getString("label.structure")); + + tabbedPane.add(initConnectionsTab(), + MessageManager.getString("label.connections")); + + tabbedPane.add(initOutputTab(), MessageManager.getString("label.output")); + + tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing")); + + /* + * See DasSourceBrowser for the real work of configuring this tab. + */ + dasTab.setLayout(new BorderLayout()); + tabbedPane + .add(dasTab, MessageManager.getString("label.das_settings")); + + /* + * See WsPreferences for the real work of configuring this tab. + */ + wsTab.setLayout(new BorderLayout()); + tabbedPane.add(wsTab, MessageManager.getString("label.web_services")); + + /* + * Handler to validate a tab before leaving it - currently only for + * Structure. + */ + tabbedPane.addChangeListener(new ChangeListener() + { + private Component lastTab; + + @Override + public void stateChanged(ChangeEvent e) + { + if (lastTab == structureTab + && tabbedPane.getSelectedComponent() != structureTab) + { + if (!validateStructure()) + { + tabbedPane.setSelectedComponent(structureTab); + return; + } + } + lastTab = tabbedPane.getSelectedComponent(); + } + + }); + } + + /** + * Initialises the Editing tabbed panel. + * + * @return + */ + private JPanel initEditingTab() + { + JPanel editingTab = new JPanel(); + editingTab.setLayout(null); + autoCalculateConsCheck.setFont(verdana11); + autoCalculateConsCheck.setText(MessageManager + .getString("label.autocalculate_consensus")); + autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23)); + padGaps.setFont(verdana11); + padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing")); + padGaps.setBounds(new Rectangle(22, 94, 168, 23)); + sortByTree.setFont(verdana11); + 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 Output tabbed panel. + * + * @return + */ + private JPanel initOutputTab() + { + JPanel outputTab = new JPanel(); + outputTab.setLayout(null); + JLabel epsLabel = new JLabel(); + 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)); + JLabel jLabel1 = new JLabel(); + 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") + " "); + JPanel jPanel11 = new JPanel(); + jPanel11.setFont(verdana11); + 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(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); + autoIdWidth.setFont(verdana11); + 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) { - ok_actionPerformed(e); + autoIdWidth_actionPerformed(); } }); - cancel.setText(MessageManager.getString("action.cancel")); - cancel.addActionListener(new ActionListener() + userIdWidthlabel.setFont(verdana11); + 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) { - cancel_actionPerformed(e); - } - }); - 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() - { - public void actionPerformed(ActionEvent e) - { - annotations_actionPerformed(e); - } - }); - identity.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - annotations_actionPerformed(e); - } - }); - showGroupConsensus.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - annotations_actionPerformed(e); - } - }); - 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() - { - public void actionPerformed(ActionEvent e) - { - showunconserved_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); - mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT); - mincolourLabel.setText(MessageManager.getString("label.min_colour")); - minColour.setFont(verdana11); - minColour.setBorder(BorderFactory.createEtchedBorder()); - minColour.setPreferredSize(new Dimension(40, 20)); - minColour.addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent e) - { - minColour_actionPerformed(); - } - }); - maxcolourLabel.setFont(verdana11); - maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT); - maxcolourLabel.setText(MessageManager.getString("label.max_colour")); - maxColour.setFont(verdana11); - maxColour.setBorder(BorderFactory.createEtchedBorder()); - maxColour.setPreferredSize(new Dimension(40, 20)); - maxColour.addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent e) - { - maxColour_actionPerformed(); - } - }); - - 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() - { - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() > 1) - { - startupFileTextfield_mouseClicked(); - } + userIdWidth_actionPerformed(); } }); + 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(epsLabel); + outputTab.add(epsRendering); + outputTab.add(jPanel11); + modellerOutput.setFont(verdana11); + modellerOutput.setText(MessageManager + .getString("label.use_modeller_output")); + modellerOutput.setBounds(new Rectangle(228, 226, 168, 23)); + return outputTab; + } - connectTab.setLayout(gridBagLayout3); + /** + * Initialises the Connections tabbed panel. + * + * @return + */ + private JPanel initConnectionsTab() + { + JPanel connectTab = new JPanel(); + connectTab.setLayout(new GridBagLayout()); + JLabel serverLabel = new JLabel(); serverLabel.setText(MessageManager.getString("label.address")); serverLabel.setHorizontalAlignment(SwingConstants.RIGHT); serverLabel.setFont(verdana11); proxyServerTB.setFont(verdana11); proxyPortTB.setFont(verdana11); + JLabel portLabel = new JLabel(); portLabel.setFont(verdana11); portLabel.setHorizontalAlignment(SwingConstants.RIGHT); portLabel.setText(MessageManager.getString("label.port")); + JLabel browserLabel = new JLabel(); browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); browserLabel.setHorizontalAlignment(SwingConstants.TRAILING); browserLabel.setText(MessageManager @@ -526,6 +485,7 @@ public class GPreferences extends JPanel versioncheck.setFont(verdana11); versioncheck.setHorizontalAlignment(SwingConstants.RIGHT); versioncheck.setHorizontalTextPosition(SwingConstants.LEADING); + JButton newLink = new JButton(); newLink.setText(MessageManager.getString("action.new")); newLink.addActionListener(new java.awt.event.ActionListener() { @@ -534,6 +494,7 @@ public class GPreferences extends JPanel newLink_actionPerformed(e); } }); + JButton editLink = new JButton(); editLink.setText(MessageManager.getString("action.edit")); editLink.addActionListener(new java.awt.event.ActionListener() { @@ -542,6 +503,7 @@ public class GPreferences extends JPanel editLink_actionPerformed(e); } }); + JButton deleteLink = new JButton(); deleteLink.setText(MessageManager.getString("action.delete")); deleteLink.addActionListener(new java.awt.event.ActionListener() { @@ -569,14 +531,20 @@ public class GPreferences extends JPanel } }); + JScrollPane linkScrollPane = new JScrollPane(); linkScrollPane.setBorder(null); + JPanel linkPanel = new JPanel(); linkPanel.setBorder(new TitledBorder(MessageManager .getString("label.url_linkfrom_sequence_id"))); - linkPanel.setLayout(borderLayout2); + linkPanel.setLayout(new BorderLayout()); + GridLayout gridLayout1 = new GridLayout(); + JPanel editLinkButtons = new JPanel(); editLinkButtons.setLayout(gridLayout1); gridLayout1.setRows(3); linkNameList.setFont(verdana11); linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); + BorderLayout borderLayout3 = new BorderLayout(); + JPanel linkPanel2 = new JPanel(); linkPanel2.setLayout(borderLayout3); linkURLList.setFont(verdana11); linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); @@ -602,229 +570,19 @@ public class GPreferences extends JPanel useProxy_actionPerformed(); } }); + 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); + JPanel jPanel1 = new JPanel(); + TitledBorder titledBorder1 = new TitledBorder( + MessageManager.getString("label.proxy_server")); 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); - seqLimit.setHorizontalAlignment(SwingConstants.RIGHT); - seqLimit.setHorizontalTextPosition(SwingConstants.LEFT); - seqLimit.setText(MessageManager.getString("label.full_sequence_id")); - gridLayout3.setRows(8); - smoothFont.setFont(verdana11); - 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)); - - 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() - { - - @Override - public void actionPerformed(ActionEvent e) - { - autoIdWidth_actionPerformed(); - } - }); - 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)); - - dasPanel.setLayout(borderLayout4); - wsPanel.setLayout(borderLayout5); - wrap.setFont(JvSwingUtils.getLabelFont()); - wrap.setHorizontalAlignment(SwingConstants.TRAILING); - wrap.setHorizontalTextPosition(SwingConstants.LEADING); - wrap.setText(MessageManager.getString("label.wrap_alignment")); - rightAlign.setFont(JvSwingUtils.getLabelFont()); - 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.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")); - openoverv.setHorizontalAlignment(SwingConstants.RIGHT); - openoverv.setHorizontalTextPosition(SwingConstants.LEFT); - openoverv.setText(MessageManager.getString(("label.open_overview"))); - jPanel2.add(fullScreen); - jPanel2.add(openoverv); - jPanel2.add(seqLimit); - jPanel2.add(rightAlign); - jPanel2.add(fontLabel); - jPanel2.add(showUnconserved); - jPanel2.add(idItalics); - jPanel2.add(smoothFont); - jPanel2.add(gapLabel); - jPanel2.add(wrap); - jPanel2.add(sortLabel); - jPanel2.add(startupCheckbox); - visualTab.add(annotations); - visualTab.add(startupFileTextfield); - visualTab.add(sortby); - 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.setLayout(new GridBagLayout()); 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)); @@ -840,6 +598,9 @@ public class GPreferences extends JPanel 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(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0, + GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, + 2, 5, 185), 2, -4)); 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)); @@ -858,43 +619,563 @@ public class GPreferences extends JPanel 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)); + return connectTab; + } - 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)); + /** + * 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() + { + public void actionPerformed(ActionEvent e) + { + ok_actionPerformed(e); + } + }); + JButton cancel = new JButton(); + cancel.setText(MessageManager.getString("action.cancel")); + cancel.addActionListener(new ActionListener() + { + 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(verdana11); + mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT); + mincolourLabel.setText(MessageManager.getString("label.min_colour")); + minColour.setFont(verdana11); + minColour.setBorder(BorderFactory.createEtchedBorder()); + minColour.setPreferredSize(new Dimension(40, 20)); + minColour.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent e) + { + minColour_actionPerformed(minColour); + } + }); + JLabel maxcolourLabel = new JLabel(); + maxcolourLabel.setFont(verdana11); + maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT); + maxcolourLabel.setText(MessageManager.getString("label.max_colour")); + maxColour.setFont(verdana11); + maxColour.setBorder(BorderFactory.createEtchedBorder()); + maxColour.setPreferredSize(new Dimension(40, 20)); + maxColour.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent e) + { + maxColour_actionPerformed(maxColour); + } + }); + colour.setFont(verdana11); + colour.setBounds(new Rectangle(172, 225, 155, 21)); + JLabel colourLabel = new JLabel(); + colourLabel.setFont(verdana11); + colourLabel.setHorizontalAlignment(SwingConstants.RIGHT); + colourLabel.setText(MessageManager.getString("label.alignment_colour") + + " "); + JvSwingUtils.addtoLayout(coloursTab, 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); + coloursTab.add(annotationShding); // , FlowLayout.LEFT); + return coloursTab; + } + + /** + * 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 = 23; + final int lineSpacing = 30; + int ypos = 30; + + structFromPdb.setFont(verdana11); + 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(verdana11); + useRnaView.setText(MessageManager.getString("label.use_rnaview")); + useRnaView.setBounds(new Rectangle(25, ypos, width, height)); + structureTab.add(useRnaView); + + ypos += lineSpacing; + addSecondaryStructure.setFont(verdana11); + addSecondaryStructure.setText(MessageManager + .getString("label.autoadd_secstr")); + addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height)); + structureTab.add(addSecondaryStructure); + + ypos += lineSpacing; + addTempFactor.setFont(verdana11); + addTempFactor.setText(MessageManager.getString("label.autoadd_temp")); + addTempFactor.setBounds(new Rectangle(25, ypos, width, height)); + structureTab.add(addTempFactor); + + ypos += lineSpacing; + JLabel viewerLabel = new JLabel(); + viewerLabel.setFont(verdana11); + viewerLabel.setHorizontalAlignment(SwingConstants.LEFT); + viewerLabel.setText(MessageManager.getString("label.structure_viewer")); + viewerLabel.setBounds(new Rectangle(10, ypos, 200, height)); + structureTab.add(viewerLabel); + + structViewer.setFont(verdana11); + structViewer.setBounds(new Rectangle(160, ypos, 120, height)); + structViewer.addItem(ViewerType.JMOL.name()); + structViewer.addItem(ViewerType.CHIMERA.name()); + structViewer.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + structureViewer_actionPerformed((String) structViewer + .getSelectedItem()); + } + }); + structureTab.add(structViewer); + + ypos += lineSpacing; + JLabel pathLabel = new JLabel(); + pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); + pathLabel.setHorizontalAlignment(SwingConstants.LEFT); + pathLabel.setText(MessageManager.getString("label.chimera_path")); + final String tooltip = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.chimera_path_tip")); + pathLabel.setToolTipText(tooltip); + pathLabel.setBounds(new Rectangle(10, ypos, 140, height)); + structureTab.add(pathLabel); + + chimeraPath.setFont(verdana11); + chimeraPath.setText(""); + chimeraPath.setBounds(new Rectangle(160, ypos, 300, height)); + chimeraPath.addMouseListener(new MouseAdapter() + { + @Override + public void mouseClicked(MouseEvent e) + { + if (e.getClickCount() == 2) + { + String chosen = openFileChooser(); + if (chosen != null) + { + chimeraPath.setText(chosen); + } + } + } + }); + structureTab.add(chimeraPath); + + return structureTab; + } + + /** + * Action on choosing a structure viewer from combobox options. + * + * @param selectedItem + */ + protected void structureViewer_actionPerformed(String selectedItem) + { + } + + /** + * Show a dialog for the user to choose a file. Returns the chosen path, or + * null on Cancel. + * + * @return + */ + protected String openFileChooser() + { + String choice = null; + JFileChooser chooser = new JFileChooser(); + + // chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager + .getString("label.open_local_file")); + chooser.setToolTipText(MessageManager.getString("action.open")); + + int value = chooser.showOpenDialog(this); + + if (value == JFileChooser.APPROVE_OPTION) + { + choice = chooser.getSelectedFile().getPath(); + } + return choice; + } + + /** + * Validate the structure tab preferences; if invalid, set focus on this tab. + * + * @param e + */ + protected boolean validateStructure(FocusEvent e) + { + if (!validateStructure()) + { + e.getComponent().requestFocusInWindow(); + return false; + } + return true; + } + + protected boolean validateStructure() + { + return false; + } + + /** + * Initialises the Visual tabbed panel. + * + * @return + */ + private JPanel initVisualTab() + { + JPanel visualTab = new JPanel(); + visualTab.setBorder(new TitledBorder(MessageManager + .getString("action.open_new_alignment"))); + visualTab.setLayout(null); + fullScreen.setFont(verdana11); + fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); + fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); + fullScreen.setText(MessageManager.getString("label.maximize_window")); + quality.setEnabled(false); + quality.setFont(verdana11); + quality.setHorizontalAlignment(SwingConstants.RIGHT); + quality.setHorizontalTextPosition(SwingConstants.LEFT); + quality.setSelected(true); + quality.setText(MessageManager.getString("label.quality")); + 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")); + JLabel showGroupbits = new JLabel(); + showGroupbits.setFont(verdana11); + showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT); + showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT); + showGroupbits.setText(MessageManager.getString("action.show_group") + + ":"); + JLabel showConsensbits = new JLabel(); + 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() + { + public void actionPerformed(ActionEvent e) + { + annotations_actionPerformed(e); + } + }); + identity.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + annotations_actionPerformed(e); + } + }); + showGroupConsensus.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + annotations_actionPerformed(e); + } + }); + 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() + { + public void actionPerformed(ActionEvent e) + { + showunconserved_actionPerformed(e); + } + }); + + // 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(verdana11); + seqLimit.setHorizontalAlignment(SwingConstants.RIGHT); + seqLimit.setHorizontalTextPosition(SwingConstants.LEFT); + seqLimit.setText(MessageManager.getString("label.full_sequence_id")); + smoothFont.setFont(verdana11); + smoothFont.setHorizontalAlignment(SwingConstants.RIGHT); + smoothFont.setHorizontalTextPosition(SwingConstants.LEADING); + smoothFont.setText(MessageManager.getString("label.smooth_font")); + JLabel gapLabel = new JLabel(); + gapLabel.setFont(verdana11); + gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); + gapLabel.setText(MessageManager.getString("label.gap_symbol") + " "); + JLabel fontLabel = new JLabel(); + fontLabel.setFont(verdana11); + fontLabel.setHorizontalAlignment(SwingConstants.RIGHT); + fontLabel.setText(MessageManager.getString("label.font")); + fontSizeCB.setFont(verdana11); + fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23)); + fontStyleCB.setFont(verdana11); + fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23)); + fontNameCB.setFont(verdana11); + fontNameCB.setBounds(new Rectangle(172, 104, 147, 23)); + gapSymbolCB.setFont(verdana11); + gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23)); 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); + 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, 290, 270, 20)); + startupFileTextfield.addMouseListener(new MouseAdapter() + { + public void mouseClicked(MouseEvent e) + { + if (e.getClickCount() > 1) + { + startupFileTextfield_mouseClicked(); + } + } + }); + + sortby.setFont(verdana11); + sortby.setBounds(new Rectangle(172, 240, 155, 21)); + JLabel sortLabel = new JLabel(); + sortLabel.setFont(verdana11); + sortLabel.setHorizontalAlignment(SwingConstants.RIGHT); + sortLabel.setText(MessageManager.getString("label.sort_by")); + sortAnnBy.setFont(verdana11); + sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21)); + JLabel sortAnnLabel = new JLabel(); + sortAnnLabel.setFont(verdana11); + sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT); + sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by")); + sortAutocalc.setFont(verdana11); + sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21)); + JPanel annsettingsPanel = new JPanel(); + annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61)); + annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0)); + JPanel autoAnnotSettings1 = new JPanel(); + autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0)); + annsettingsPanel.add(autoAnnotSettings1); + JPanel autoAnnotSettings2 = new JPanel(); + autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0)); + annsettingsPanel.add(autoAnnotSettings2); + JPanel autoAnnotSettings3 = new JPanel(); + autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0)); + annsettingsPanel.add(autoAnnotSettings3); + 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); - tabbedPane - .add(dasPanel, MessageManager.getString("label.das_settings")); - tabbedPane.add(wsPanel, MessageManager.getString("label.web_services")); + 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); - exportTab.add(epsLabel); - exportTab.add(epsRendering); - exportTab.add(jPanel11); + wrap.setFont(verdana11); + wrap.setHorizontalAlignment(SwingConstants.TRAILING); + wrap.setHorizontalTextPosition(SwingConstants.LEADING); + wrap.setText(MessageManager.getString("label.wrap_alignment")); + rightAlign.setFont(verdana11); + rightAlign.setForeground(Color.black); + rightAlign.setHorizontalAlignment(SwingConstants.RIGHT); + rightAlign.setHorizontalTextPosition(SwingConstants.LEFT); + rightAlign.setText(MessageManager.getString("label.right_align_ids")); + idItalics.setFont(verdana11); + idItalics.setHorizontalAlignment(SwingConstants.RIGHT); + idItalics.setHorizontalTextPosition(SwingConstants.LEADING); + idItalics.setText(MessageManager + .getString("label.sequence_name_italics")); + openoverv.setFont(verdana11); + openoverv.setActionCommand(MessageManager + .getString("label.open_overview")); + openoverv.setHorizontalAlignment(SwingConstants.RIGHT); + openoverv.setHorizontalTextPosition(SwingConstants.LEFT); + openoverv.setText(MessageManager.getString(("label.open_overview"))); + JPanel jPanel2 = new JPanel(); + jPanel2.setBounds(new Rectangle(7, 17, 158, 297)); + GridLayout gridLayout2 = new GridLayout(); + jPanel2.setLayout(gridLayout2); + gridLayout2.setRows(13); + jPanel2.add(fullScreen); + jPanel2.add(openoverv); + jPanel2.add(seqLimit); + jPanel2.add(rightAlign); + jPanel2.add(fontLabel); + jPanel2.add(showUnconserved); + jPanel2.add(idItalics); + jPanel2.add(smoothFont); + jPanel2.add(gapLabel); + jPanel2.add(wrap); + jPanel2.add(sortLabel); + jPanel2.add(sortAnnLabel); + jPanel2.add(startupCheckbox); + visualTab.add(jPanel2); + visualTab.add(annotations); + visualTab.add(startupFileTextfield); + visualTab.add(sortby); + visualTab.add(sortAnnBy); + visualTab.add(sortAutocalc); + visualTab.add(gapSymbolCB); + visualTab.add(fontNameCB); + visualTab.add(fontSizeCB); + visualTab.add(fontStyleCB); + return visualTab; } protected void autoIdWidth_actionPerformed() @@ -909,16 +1190,12 @@ public class GPreferences extends JPanel } - protected void maxColour_actionPerformed() + protected void maxColour_actionPerformed(JPanel panel) { - // TODO Auto-generated method stub - } - protected void minColour_actionPerformed() + protected void minColour_actionPerformed(JPanel panel) { - // TODO Auto-generated method stub - } protected void showunconserved_actionPerformed(ActionEvent e)