X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=c37d2302ef47f8d3594f70fca163adbb156e56f0;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=d2d30911e80bda9f378546e2d816f01f1c947c70;hpb=99bd0585b045d25fa719ee007e3310d27e53ac88;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index d2d3091..c37d230 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -1,548 +1,896 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbgui; - -import java.awt.*; - -import javax.swing.*; -import javax.swing.border.TitledBorder; -import java.awt.event.*; -import javax.swing.event.*; -import java.awt.Font; -import java.awt.Rectangle; -import java.awt.Insets; - -/** - * DOCUMENT ME! - * - * @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(); - protected JCheckBox fullScreen = new JCheckBox(); - protected JCheckBox conservation = new JCheckBox(); - protected JCheckBox identity = new JCheckBox(); - protected JCheckBox annotations = new JCheckBox(); - JLabel gapLabel = new JLabel(); - protected JComboBox colour = new JComboBox(); - JLabel colourLabel = new JLabel(); - JLabel fontLabel = new JLabel(); - protected JComboBox fontSizeCB = new JComboBox(); - protected JComboBox fontStyleCB = new JComboBox(); - protected JComboBox fontNameCB = new JComboBox(); - protected JComboBox gapSymbolCB = 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(); - JButton deleteLink = new JButton(); - JScrollPane linkScrollPane = new JScrollPane(); - JPanel linkPanel = new JPanel(); - BorderLayout borderLayout2 = new BorderLayout(); - JPanel editLinkButtons = new JPanel(); - GridLayout gridLayout1 = new GridLayout(); - protected JList linkNameList = new JList(); - JPanel linkPanel2 = new JPanel(); - BorderLayout borderLayout3 = new BorderLayout(); - protected JCheckBox useProxy = new JCheckBox(); - JPanel jPanel1 = new JPanel(); - TitledBorder titledBorder1 = new TitledBorder("Proxy Server"); - TitledBorder titledBorder2 = new TitledBorder("File Output"); - GridBagLayout gridBagLayout2 = new GridBagLayout(); - GridBagLayout gridBagLayout1 = new GridBagLayout(); - GridBagLayout gridBagLayout3 = new GridBagLayout(); - protected JComboBox sortby = new JComboBox(); - JLabel sortLabel = new JLabel(); - JPanel jPanel2 = new JPanel(); - GridLayout gridLayout2 = new GridLayout(); - JPanel jPanel3 = new JPanel(); - JPanel exportTab = new JPanel(); - JLabel epsLabel = new JLabel(); - protected JComboBox epsRendering = new JComboBox(); - JLabel jLabel1 = new JLabel(); - protected JCheckBox blcjv = new JCheckBox(); - protected JCheckBox pileupjv = new JCheckBox(); - protected JCheckBox clustaljv = new JCheckBox(); - protected JCheckBox msfjv = new JCheckBox(); - protected JCheckBox fastajv = new JCheckBox(); - protected JCheckBox pfamjv = new JCheckBox(); - FlowLayout flowLayout1 = new FlowLayout(); - protected JCheckBox pirjv = new JCheckBox(); - JPanel jPanel11 = new JPanel(); - Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11); - protected JCheckBox seqLimit = new JCheckBox(); - GridLayout gridLayout3 = new GridLayout(); - protected JCheckBox smoothFont = new JCheckBox(); - JPanel calcTab = new JPanel(); - 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 JCheckBox wrap = new JCheckBox(); - protected JCheckBox rightAlign = new JCheckBox(); - /** - * Creates a new GPreferences object. - */ - public GPreferences() - { - try - { - jbInit(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - /** - * DOCUMENT ME! - * - * @throws Exception DOCUMENT ME! - */ - private void jbInit() throws Exception - { - this.setLayout(borderLayout1); - ok.setText("OK"); - ok.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - ok_actionPerformed(e); - } - }); - cancel.setText("Cancel"); - cancel.addActionListener(new ActionListener() - { - 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("Quality"); - visualTab.setBorder(new TitledBorder("Open new alignment")); - visualTab.setLayout(null); - fullScreen.setFont(verdana11); - fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); - fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); - fullScreen.setMargin(new Insets(2, 2, 2, 0)); - fullScreen.setText("Maximise Window"); - conservation.setEnabled(false); - conservation.setFont(verdana11); - conservation.setHorizontalAlignment(SwingConstants.RIGHT); - conservation.setHorizontalTextPosition(SwingConstants.LEFT); - conservation.setSelected(true); - conservation.setText("Conservation"); - identity.setEnabled(false); - identity.setFont(verdana11); - identity.setHorizontalAlignment(SwingConstants.RIGHT); - identity.setHorizontalTextPosition(SwingConstants.LEFT); - identity.setSelected(true); - identity.setText("Consensus"); - annotations.setFont(verdana11); - annotations.setHorizontalAlignment(SwingConstants.RIGHT); - annotations.setHorizontalTextPosition(SwingConstants.LEFT); - annotations.setMargin(new Insets(2, 2, 2, 0)); - annotations.setSelected(true); - annotations.setText("Show Annotations"); - annotations.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - annotations_actionPerformed(e); - } - }); - gapLabel.setFont(verdana11); - gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); - gapLabel.setText("Gap Symbol "); - colour.setFont(verdana11); - colour.setBounds(new Rectangle(172, 203, 155, 21)); - colourLabel.setFont(verdana11); - colourLabel.setHorizontalAlignment(SwingConstants.RIGHT); - colourLabel.setText("Colour "); - fontLabel.setFont(verdana11); - fontLabel.setHorizontalAlignment(SwingConstants.RIGHT); - fontLabel.setText("Font "); - fontSizeCB.setFont(verdana11); - fontSizeCB.setBounds(new Rectangle(319, 111, 49, 21)); - fontStyleCB.setFont(verdana11); - fontStyleCB.setBounds(new Rectangle(367, 111, 70, 21)); - fontNameCB.setFont(verdana11); - fontNameCB.setBounds(new Rectangle(172, 111, 147, 21)); - gapSymbolCB.setFont(verdana11); - gapSymbolCB.setBounds(new Rectangle(172, 179, 69, 21)); - startupCheckbox.setText("Open file"); - startupCheckbox.setFont(verdana11); - startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT); - startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT); - startupCheckbox.setSelected(true); - startupFileTextfield.setFont(verdana11); - startupFileTextfield.setBounds(new Rectangle(172, 249, 270, 20)); - startupFileTextfield.addMouseListener(new MouseAdapter() - { - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() > 1) - { - startupFileTextfield_mouseClicked(); - } - } - }); - - connectTab.setLayout(gridBagLayout3); - serverLabel.setText("Address"); - serverLabel.setHorizontalAlignment(SwingConstants.RIGHT); - serverLabel.setFont(verdana11); - proxyServerTB.setFont(verdana11); - proxyPortTB.setFont(verdana11); - portLabel.setFont(verdana11); - portLabel.setHorizontalAlignment(SwingConstants.RIGHT); - portLabel.setText("Port"); - browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); - browserLabel.setHorizontalAlignment(SwingConstants.TRAILING); - browserLabel.setText("Default Browser (Unix)"); - defaultBrowser.setFont(verdana11); - defaultBrowser.setText(""); - newLink.setText("New"); - newLink.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - newLink_actionPerformed(e); - } - }); - editLink.setText("Edit"); - editLink.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - editLink_actionPerformed(e); - } - }); - deleteLink.setText("Delete"); - deleteLink.addActionListener(new java.awt.event.ActionListener() { - 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("URL link from 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); - } - } - }); - useProxy.setFont(verdana11); - useProxy.setHorizontalAlignment(SwingConstants.RIGHT); - useProxy.setHorizontalTextPosition(SwingConstants.LEADING); - useProxy.setText("Use a proxy server"); - useProxy.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - useProxy_actionPerformed(); - } - }); - jPanel1.setBorder(titledBorder1); - jPanel1.setLayout(gridBagLayout1); - sortby.setFont(verdana11); - sortby.setBounds(new Rectangle(172, 225, 155, 21)); - sortLabel.setFont(verdana11); - sortLabel.setHorizontalAlignment(SwingConstants.RIGHT); - sortLabel.setText("Sort by "); - jPanel2.setBounds(new Rectangle(7, 17, 158, 257)); - jPanel2.setLayout(gridLayout2); - gridLayout2.setRows(11); - jPanel3.setBounds(new Rectangle(169, 39, 274, 26)); - exportTab.setLayout(null); - epsLabel.setFont(verdana11); - epsLabel.setHorizontalAlignment(SwingConstants.RIGHT); - epsLabel.setText("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("Append /start-end (/15-380)"); - jLabel1.setFont(verdana11); - fastajv.setFont(verdana11); - fastajv.setHorizontalAlignment(SwingConstants.LEFT); - clustaljv.setText("Clustal "); - blcjv.setText("BLC "); - fastajv.setText("Fasta "); - msfjv.setText("MSF "); - pfamjv.setText("PFAM "); - pileupjv.setText("Pileup "); - msfjv.setFont(verdana11); - msfjv.setHorizontalAlignment(SwingConstants.LEFT); - pirjv.setText("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.setMargin(new Insets(2, 2, 2, 0)); - seqLimit.setText("Full Sequence Id"); - gridLayout3.setRows(8); - smoothFont.setFont(verdana11); - smoothFont.setHorizontalAlignment(SwingConstants.RIGHT); - smoothFont.setHorizontalTextPosition(SwingConstants.LEADING); - smoothFont.setText("Smooth Font"); - calcTab.setLayout(null); - autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - autoCalculateConsCheck.setText("AutoCalculate Consensus"); - autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23)); - padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - padGaps.setText("Pad gaps when editing"); - padGaps.setBounds(new Rectangle(22, 94, 168, 23)); - modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - modellerOutput.setText("Use Modeller Output"); - modellerOutput.setBounds(new Rectangle(228, 226, 168, 23)); - dasPanel.setLayout(borderLayout4); - wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - wrap.setHorizontalAlignment(SwingConstants.TRAILING); - wrap.setHorizontalTextPosition(SwingConstants.LEADING); - wrap.setText("Wrap Alignment"); - rightAlign.setForeground(Color.black); - rightAlign.setHorizontalAlignment(SwingConstants.RIGHT); - rightAlign.setHorizontalTextPosition(SwingConstants.LEADING); - rightAlign.setText("Right Align Ids"); - jPanel2.add(fullScreen); - - jPanel2.add(annotations); - jPanel2.add(seqLimit); - jPanel2.add(rightAlign); - jPanel2.add(fontLabel); - jPanel2.add(smoothFont); - jPanel2.add(wrap); - jPanel2.add(gapLabel); - jPanel2.add(colourLabel); - jPanel2.add(sortLabel); - jPanel2.add(startupCheckbox); - visualTab.add(fontNameCB); - visualTab.add(fontSizeCB); - visualTab.add(fontStyleCB); - visualTab.add(startupFileTextfield); - visualTab.add(gapSymbolCB); - visualTab.add(colour); - visualTab.add(sortby); - visualTab.add(jPanel3); - jPanel3.add(conservation); - jPanel3.add(identity); - jPanel3.add(quality); - visualTab.add(jPanel2); - 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)); - - - 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, "Visual"); - tabbedPane.add(connectTab,"Connections"); - tabbedPane.add(exportTab, "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(modellerOutput); - tabbedPane.add(calcTab, "Editing"); - calcTab.add(autoCalculateConsCheck); - calcTab.add(padGaps); - tabbedPane.add(dasPanel, "DAS Settings"); - - exportTab.add(epsLabel); - exportTab.add(epsRendering); - exportTab.add(jPanel11); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void ok_actionPerformed(ActionEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void cancel_actionPerformed(ActionEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void annotations_actionPerformed(ActionEvent e) - { - } - - - /** - * DOCUMENT ME! - */ - public void startupFileTextfield_mouseClicked() - { - } - - - public void newLink_actionPerformed(ActionEvent e) { - - } - - public void editLink_actionPerformed(ActionEvent e) { - - } - - public void deleteLink_actionPerformed(ActionEvent e) { - - } - - public void defaultBrowser_mouseClicked(MouseEvent e) - { - - } - - public void linkURLList_keyTyped(KeyEvent e) - { - - } - - public void useProxy_actionPerformed() - { - proxyServerTB.setEnabled(useProxy.isSelected()); - proxyPortTB.setEnabled(useProxy.isSelected()); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + */ +package jalview.jbgui; + +import jalview.gui.JvSwingUtils; + +import java.awt.*; +import java.awt.event.*; + +import javax.swing.*; +import javax.swing.border.*; +import javax.swing.event.*; +import java.awt.Rectangle; + +/** + * DOCUMENT ME! + * + * @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(); + + protected JCheckBox fullScreen = new JCheckBox(); + + protected JCheckBox conservation = new JCheckBox(); + + protected JCheckBox identity = new JCheckBox(); + + protected JCheckBox annotations = new JCheckBox(); + + protected JPanel minColour = new JPanel(); + JLabel mincolourLabel = new JLabel(); + + protected JPanel maxColour = new JPanel(); + JLabel maxcolourLabel = new JLabel(); + + JLabel gapLabel = new JLabel(); + + protected JComboBox colour = new JComboBox(); + + JLabel colourLabel = new JLabel(); + + JLabel fontLabel = new JLabel(); + + protected JComboBox fontSizeCB = new JComboBox(); + + protected JComboBox fontStyleCB = new JComboBox(); + + protected JComboBox fontNameCB = new JComboBox(); + + protected JComboBox gapSymbolCB = 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(); + + JButton deleteLink = new JButton(); + + JScrollPane linkScrollPane = new JScrollPane(); + + JPanel linkPanel = new JPanel(); + + BorderLayout borderLayout2 = new BorderLayout(); + + JPanel editLinkButtons = new JPanel(); + + GridLayout gridLayout1 = new GridLayout(); + + protected JList linkNameList = new JList(); + + JPanel linkPanel2 = new JPanel(); + + BorderLayout borderLayout3 = new BorderLayout(); + + protected JCheckBox useProxy = new JCheckBox(); + + JPanel jPanel1 = new JPanel(); + + TitledBorder titledBorder1 = new TitledBorder("Proxy Server"); + + TitledBorder titledBorder2 = new TitledBorder("File Output"); + + GridBagLayout gridBagLayout2 = new GridBagLayout(); + + GridBagLayout gridBagLayout1 = new GridBagLayout(); + + GridBagLayout gridBagLayout3 = new GridBagLayout(); + + protected JComboBox sortby = new JComboBox(); + + JLabel sortLabel = new JLabel(); + + JPanel jPanel2 = new JPanel(); + JPanel visual2panel = new JPanel(); + + GridLayout gridLayout2 = new GridLayout(); + + GridLayout gridLayout4 = new GridLayout(); + + JPanel annsettingsPanel = new JPanel(); + + JPanel autoAnnotSettings1 = new JPanel(); + + JPanel autoAnnotSettings2 = new JPanel(); + + JPanel autoAnnotSettings3 = new JPanel(); + + JPanel exportTab = new JPanel(); + + JLabel epsLabel = new JLabel(); + + protected JComboBox epsRendering = new JComboBox(); + + JLabel jLabel1 = new JLabel(); + + protected JCheckBox blcjv = new JCheckBox(); + + protected JCheckBox pileupjv = new JCheckBox(); + + protected JCheckBox clustaljv = new JCheckBox(); + + protected JCheckBox msfjv = new JCheckBox(); + + protected JCheckBox fastajv = 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(); + + JPanel calcTab = new JPanel(); + + 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 followHighlight = new JCheckBox(); + + protected JCheckBox sortByTree= new JCheckBox(); + + /** + * Creates a new GPreferences object. + */ + public GPreferences() + { + try + { + jbInit(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + /** + * DOCUMENT ME! + * + * @throws Exception + * DOCUMENT ME! + */ + private void jbInit() throws Exception + { + this.setLayout(borderLayout1); + ok.setText("OK"); + ok.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ok_actionPerformed(e); + } + }); + cancel.setText("Cancel"); + cancel.addActionListener(new ActionListener() + { + 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("Quality"); + visualTab.setBorder(new TitledBorder("Open new alignment")); + visualTab.setLayout(null); + visual2Tab.setBorder(new TitledBorder("Open new alignment")); + visual2Tab.setLayout(new FlowLayout()); + fullScreen.setFont(verdana11); + fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); + fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); + fullScreen.setText("Maximise Window"); + conservation.setEnabled(false); + conservation.setFont(verdana11); + conservation.setHorizontalAlignment(SwingConstants.RIGHT); + conservation.setHorizontalTextPosition(SwingConstants.LEFT); + conservation.setSelected(true); + conservation.setText("Conservation"); + identity.setEnabled(false); + identity.setFont(verdana11); + identity.setHorizontalAlignment(SwingConstants.RIGHT); + identity.setHorizontalTextPosition(SwingConstants.LEFT); + identity.setSelected(true); + identity.setText("Consensus"); + showGroupbits.setFont(verdana11); + showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT); + showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT); + showGroupbits.setText("Show group:"); + showConsensbits.setFont(verdana11); + showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT); + showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT); + showConsensbits.setText("Consensus:"); + showConsensHistogram.setEnabled(false); + showConsensHistogram.setFont(verdana11); + showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT); + showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT); + showConsensHistogram.setSelected(true); + showConsensHistogram.setText("Histogram"); + showConsensLogo.setEnabled(false); + showConsensLogo.setFont(verdana11); + showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT); + showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT); + showConsensLogo.setSelected(true); + showConsensLogo.setText("Logo"); + showGroupConsensus.setEnabled(false); + showGroupConsensus.setFont(verdana11); + showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT); + showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT); + showGroupConsensus.setSelected(true); + showGroupConsensus.setText("Consensus"); + showGroupConservation.setEnabled(false); + showGroupConservation.setFont(verdana11); + showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT); + showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT); + showGroupConservation.setSelected(true); + showGroupConservation.setText("Conservation"); + showNpTooltip.setEnabled(true); + showNpTooltip.setFont(verdana11); + showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT); + showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT); + showNpTooltip.setSelected(true); + showNpTooltip.setText("Non-positional Features"); + showDbRefTooltip.setEnabled(true); + showDbRefTooltip.setFont(verdana11); + showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT); + showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT); + showDbRefTooltip.setSelected(true); + showDbRefTooltip.setText("Database References"); + annotations.setFont(verdana11); + annotations.setHorizontalAlignment(SwingConstants.RIGHT); + annotations.setHorizontalTextPosition(SwingConstants.LEADING); + annotations.setSelected(true); + annotations.setText("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("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("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("Scroll to highlighted regions"); + + gapLabel.setFont(verdana11); + gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); + gapLabel.setText("Gap Symbol "); + colour.setFont(verdana11); + colour.setBounds(new Rectangle(172, 225, 155, 21)); + colourLabel.setFont(verdana11); + colourLabel.setHorizontalAlignment(SwingConstants.RIGHT); + colourLabel.setText("Alignment Colour "); + fontLabel.setFont(verdana11); + fontLabel.setHorizontalAlignment(SwingConstants.RIGHT); + fontLabel.setText("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("Minimum 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("Maximum 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("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(); + } + } + }); + + connectTab.setLayout(gridBagLayout3); + serverLabel.setText("Address"); + serverLabel.setHorizontalAlignment(SwingConstants.RIGHT); + serverLabel.setFont(verdana11); + proxyServerTB.setFont(verdana11); + proxyPortTB.setFont(verdana11); + portLabel.setFont(verdana11); + portLabel.setHorizontalAlignment(SwingConstants.RIGHT); + portLabel.setText("Port"); + browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); + browserLabel.setHorizontalAlignment(SwingConstants.TRAILING); + browserLabel.setText("Default Browser (Unix)"); + defaultBrowser.setFont(verdana11); + defaultBrowser.setText(""); + usagestats.setText("Send usage statistics"); + usagestats.setFont(verdana11); + usagestats.setHorizontalAlignment(SwingConstants.RIGHT); + usagestats.setHorizontalTextPosition(SwingConstants.LEADING); + questionnaire.setText("Check for questionnaires"); + questionnaire.setFont(verdana11); + questionnaire.setHorizontalAlignment(SwingConstants.RIGHT); + questionnaire.setHorizontalTextPosition(SwingConstants.LEADING); + versioncheck.setText("Check for latest version"); + versioncheck.setFont(verdana11); + versioncheck.setHorizontalAlignment(SwingConstants.RIGHT); + versioncheck.setHorizontalTextPosition(SwingConstants.LEADING); + newLink.setText("New"); + newLink.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + newLink_actionPerformed(e); + } + }); + editLink.setText("Edit"); + editLink.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + editLink_actionPerformed(e); + } + }); + deleteLink.setText("Delete"); + deleteLink.addActionListener(new java.awt.event.ActionListener() + { + 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("URL link from 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); + } + } + }); + useProxy.setFont(verdana11); + useProxy.setHorizontalAlignment(SwingConstants.RIGHT); + useProxy.setHorizontalTextPosition(SwingConstants.LEADING); + useProxy.setText("Use a proxy server"); + useProxy.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + useProxy_actionPerformed(); + } + }); + 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("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("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("Append /start-end (/15-380)"); + jLabel1.setFont(verdana11); + fastajv.setFont(verdana11); + fastajv.setHorizontalAlignment(SwingConstants.LEFT); + clustaljv.setText("Clustal "); + blcjv.setText("BLC "); + fastajv.setText("Fasta "); + msfjv.setText("MSF "); + pfamjv.setText("PFAM "); + pileupjv.setText("Pileup "); + msfjv.setFont(verdana11); + msfjv.setHorizontalAlignment(SwingConstants.LEFT); + pirjv.setText("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("Full Sequence Id"); + gridLayout3.setRows(8); + smoothFont.setFont(verdana11); + smoothFont.setHorizontalAlignment(SwingConstants.RIGHT); + smoothFont.setHorizontalTextPosition(SwingConstants.LEADING); + smoothFont.setText("Smooth Font"); + calcTab.setLayout(null); + autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont()); + autoCalculateConsCheck.setText("AutoCalculate Consensus"); + autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23)); + padGaps.setFont(JvSwingUtils.getLabelFont()); + padGaps.setText("Pad Gaps When Editing"); + padGaps.setBounds(new Rectangle(22, 94, 168, 23)); + sortByTree.setFont(JvSwingUtils.getLabelFont()); + sortByTree.setText("Sort With New Tree"); + sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment."); + sortByTree.setBounds(new Rectangle(22, 136, 168, 23)); + modellerOutput.setFont(JvSwingUtils.getLabelFont()); + modellerOutput.setText("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("Wrap Alignment"); + rightAlign.setFont(JvSwingUtils.getLabelFont()); + rightAlign.setForeground(Color.black); + rightAlign.setHorizontalAlignment(SwingConstants.RIGHT); + rightAlign.setHorizontalTextPosition(SwingConstants.LEFT); + rightAlign.setText("Right Align Ids"); + idItalics.setFont(JvSwingUtils.getLabelFont()); + idItalics.setHorizontalAlignment(SwingConstants.RIGHT); + idItalics.setHorizontalTextPosition(SwingConstants.LEADING); + idItalics.setText("Sequence Name Italics"); + openoverv.setFont(JvSwingUtils.getLabelFont()); + openoverv.setActionCommand("Open Overview"); + openoverv.setHorizontalAlignment(SwingConstants.RIGHT); + openoverv.setHorizontalTextPosition(SwingConstants.LEFT); + openoverv.setText("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("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, "Default Colourscheme for alignment", colourLabel, colour); + JPanel annotationShding=new JPanel(); + annotationShding.setBorder(new TitledBorder("Annotation Shading Default")); + annotationShding.setLayout(new GridLayout(1,2)); + JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour); + JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for 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, "Visual"); + tabbedPane.add(visual2Tab,"Colours"); + tabbedPane.add(connectTab, "Connections"); + tabbedPane.add(exportTab, "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(modellerOutput); + tabbedPane.add(calcTab, "Editing"); + calcTab.add(autoCalculateConsCheck); + calcTab.add(padGaps); + calcTab.add(sortByTree); + + tabbedPane.add(dasPanel, "DAS Settings"); + tabbedPane.add(wsPanel, "Web Services"); + + exportTab.add(epsLabel); + exportTab.add(epsRendering); + exportTab.add(jPanel11); + } + + protected void maxColour_actionPerformed() + { + // TODO Auto-generated method stub + + } + + protected void minColour_actionPerformed() + { + // TODO Auto-generated method stub + + } + + protected void showunconserved_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void ok_actionPerformed(ActionEvent e) + { + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void cancel_actionPerformed(ActionEvent e) + { + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void annotations_actionPerformed(ActionEvent e) + { + } + + /** + * DOCUMENT ME! + */ + public void startupFileTextfield_mouseClicked() + { + } + + public void newLink_actionPerformed(ActionEvent e) + { + + } + + public void editLink_actionPerformed(ActionEvent e) + { + + } + + public void deleteLink_actionPerformed(ActionEvent e) + { + + } + + public void defaultBrowser_mouseClicked(MouseEvent e) + { + + } + + public void linkURLList_keyTyped(KeyEvent e) + { + + } + + public void useProxy_actionPerformed() + { + proxyServerTB.setEnabled(useProxy.isSelected()); + proxyPortTB.setEnabled(useProxy.isSelected()); + } + +}