X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;fp=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=38d28f297de568c306c608cc0926fdb0a239f003;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=8b10c5f170a55b5818385b3cb4bd2079801131ab;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 8b10c5f..38d28f2 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -1,511 +1,542 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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.*; - - -/** - * 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(); - /** - * 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, 4, 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(171, 180, 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(318, 100, 49, 21)); - fontStyleCB.setFont(verdana11); - fontStyleCB.setBounds(new Rectangle(366, 100, 70, 21)); - fontNameCB.setFont(verdana11); - fontNameCB.setBounds(new Rectangle(171, 100, 147, 21)); - gapSymbolCB.setFont(verdana11); - gapSymbolCB.setBounds(new Rectangle(171, 153, 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(171, 236, 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(171, 208, 155, 21)); - sortLabel.setFont(verdana11); - sortLabel.setHorizontalAlignment(SwingConstants.RIGHT); - sortLabel.setText("Sort by "); - jPanel2.setBounds(new Rectangle(7, 17, 158, 245)); - jPanel2.setLayout(gridLayout2); - gridLayout2.setRows(9); - jPanel3.setBounds(new Rectangle(167, 41, 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.setText("Full Sequence Id"); - gridLayout3.setRows(8); - smoothFont.setFont(verdana11); - smoothFont.setHorizontalAlignment(SwingConstants.RIGHT); - smoothFont.setHorizontalTextPosition(SwingConstants.LEADING); - smoothFont.setText("Smooth Font"); - jPanel2.add(fullScreen); - - jPanel2.add(annotations); - jPanel2.add(seqLimit); - jPanel2.add(fontLabel); - jPanel2.add(smoothFont); - jPanel2.add(gapLabel); - jPanel2.add(colourLabel); - jPanel2.add(sortLabel); - jPanel2.add(startupCheckbox); - visualTab.add(colour); - visualTab.add(gapSymbolCB); - visualTab.add(startupFileTextfield); - visualTab.add(sortby); - visualTab.add(fontNameCB); - visualTab.add(fontSizeCB); - visualTab.add(fontStyleCB); - 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(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 +* 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(); + /** + * 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, 188, 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(317, 92, 49, 21)); + fontStyleCB.setFont(verdana11); + fontStyleCB.setBounds(new Rectangle(364, 92, 70, 21)); + fontNameCB.setFont(verdana11); + fontNameCB.setBounds(new Rectangle(171, 92, 147, 21)); + gapSymbolCB.setFont(verdana11); + gapSymbolCB.setBounds(new Rectangle(172, 163, 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(171, 236, 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(171, 213, 155, 21)); + sortLabel.setFont(verdana11); + sortLabel.setHorizontalAlignment(SwingConstants.RIGHT); + sortLabel.setText("Sort by "); + jPanel2.setBounds(new Rectangle(7, 17, 158, 245)); + jPanel2.setLayout(gridLayout2); + gridLayout2.setRows(10); + 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"); + jPanel2.add(fullScreen); + + jPanel2.add(annotations); + jPanel2.add(seqLimit); + jPanel2.add(fontLabel); + jPanel2.add(smoothFont); + jPanel2.add(wrap); + jPanel2.add(gapLabel); + jPanel2.add(colourLabel); + jPanel2.add(sortLabel); + jPanel2.add(startupCheckbox); + visualTab.add(sortby); + visualTab.add(gapSymbolCB); + visualTab.add(colour); + visualTab.add(fontNameCB); + visualTab.add(fontSizeCB); + visualTab.add(fontStyleCB); + visualTab.add(jPanel3); + visualTab.add(startupFileTextfield); + 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()); + } +}