X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=842ade9ec497fea3e418be714104cf5152ea920c;hb=88bc025708f1b7881bababb92d14351760e0f9da;hp=8c3f9379b9e079b25d6bad1c505bbc6aea9cc0e7;hpb=0dcafd41725e30848c8ce8a279e4d6f9bf2f5eba;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 8c3f937..842ade9 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -1,30 +1,29 @@ /* -* 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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.*; +import javax.swing.border.*; import javax.swing.event.*; - +import java.awt.Rectangle; /** * DOCUMENT ME! @@ -32,31 +31,31 @@ import javax.swing.event.*; * @author $author$ * @version $Revision$ */ -public class GPreferences extends JPanel +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 fullID = new JCheckBox(); - 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(); + 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(); @@ -79,6 +78,7 @@ public class GPreferences extends JPanel 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(); @@ -90,185 +90,209 @@ public class GPreferences extends 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(); + protected JCheckBox idItalics = new JCheckBox(); + protected JCheckBox openoverv = new JCheckBox(); /** - * Creates a new GPreferences object. - */ - public GPreferences() + * Creates a new GPreferences object. + */ + public GPreferences() + { + try { - try - { - jbInit(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } + jbInit(); } + catch (Exception ex) + { + ex.printStackTrace(); + } + } - /** - * DOCUMENT ME! - * - * @throws Exception DOCUMENT ME! - */ - private void jbInit() throws Exception + /** + * DOCUMENT ME! + * + * @throws Exception DOCUMENT ME! + */ + private void jbInit() + throws Exception + { + this.setLayout(borderLayout1); + ok.setText("OK"); + ok.addActionListener(new ActionListener() { - 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(new java.awt.Font("Verdana", Font.PLAIN, 11)); - quality.setHorizontalAlignment(SwingConstants.RIGHT); - quality.setHorizontalTextPosition(SwingConstants.LEFT); - quality.setSelected(true); - quality.setText("Quality"); + 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); - fullID.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fullID.setHorizontalAlignment(SwingConstants.RIGHT); - fullID.setHorizontalTextPosition(SwingConstants.LEFT); - fullID.setMargin(new Insets(4, 2, 2, 0)); - fullID.setText("Full Sequence ID"); - fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); - fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); - fullScreen.setMargin(new Insets(2, 2, 2, 0)); + fullScreen.setFont(verdana11); + fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); + fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); fullScreen.setText("Maximise Window"); conservation.setEnabled(false); - conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - conservation.setHorizontalAlignment(SwingConstants.RIGHT); - conservation.setHorizontalTextPosition(SwingConstants.LEFT); - conservation.setSelected(true); - conservation.setText("Conservation"); + conservation.setFont(verdana11); + conservation.setHorizontalAlignment(SwingConstants.RIGHT); + conservation.setHorizontalTextPosition(SwingConstants.LEFT); + conservation.setSelected(true); + conservation.setText("Conservation"); identity.setEnabled(false); - identity.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - identity.setHorizontalAlignment(SwingConstants.RIGHT); - identity.setHorizontalTextPosition(SwingConstants.LEFT); - identity.setSelected(true); - identity.setText("Consensus"); - annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - annotations.setHorizontalAlignment(SwingConstants.RIGHT); - annotations.setHorizontalTextPosition(SwingConstants.LEFT); - annotations.setMargin(new Insets(2, 4, 2, 0)); + 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.setSelected(true); - annotations.setText("Show Annotations"); + annotations.setText("Show Annotations"); annotations.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - annotations_actionPerformed(e); - } - }); - gapLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); - gapLabel.setText("Gap Symbol "); - colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - colour.setBounds(new Rectangle(147, 189, 154, 21)); - colourLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - colourLabel.setHorizontalAlignment(SwingConstants.RIGHT); - colourLabel.setText("Colour "); - fontLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fontLabel.setHorizontalAlignment(SwingConstants.RIGHT); - fontLabel.setText("Font "); - fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fontSizeCB.setBounds(new Rectangle(316, 124, 49, 21)); - fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fontStyleCB.setBounds(new Rectangle(364, 124, 70, 21)); - fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fontNameCB.setBounds(new Rectangle(147, 124, 169, 21)); - gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - gapSymbolCB.setBounds(new Rectangle(147, 156, 67, 21)); - startupCheckbox.setText("Open file"); - startupCheckbox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT); - startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT); - startupCheckbox.setSelected(true); - startupFileTextfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - startupFileTextfield.setBounds(new Rectangle(147, 255, 302, 20)); - startupFileTextfield.addMouseListener(new MouseAdapter() - { - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() > 1) - { - startupFileTextfield_mouseClicked(); - } - } - }); + { + 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, 225, 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, 204, 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, 273, 270, 20)); + startupFileTextfield.addMouseListener(new MouseAdapter() + { + public void mouseClicked(MouseEvent e) + { + if (e.getClickCount() > 1) + { + startupFileTextfield_mouseClicked(); + } + } + }); - connectTab.setLayout(gridBagLayout3); + connectTab.setLayout(gridBagLayout3); serverLabel.setText("Address"); serverLabel.setHorizontalAlignment(SwingConstants.RIGHT); - serverLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - proxyServerTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - proxyPortTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - portLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + 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(new java.awt.Font("Verdana", Font.PLAIN, 11)); + defaultBrowser.setFont(verdana11); defaultBrowser.setText(""); newLink.setText("New"); - newLink.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { + 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.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.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); - } - }); + { + 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); - } - }); + { + 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(new java.awt.Font("Verdana", Font.ITALIC, 11)); + linkNameList.setFont(verdana11); linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); linkPanel2.setLayout(borderLayout3); - linkURLList.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + linkURLList.setFont(verdana11); linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); defaultBrowser.addMouseListener(new MouseAdapter() @@ -276,12 +300,12 @@ public class GPreferences extends JPanel public void mouseClicked(MouseEvent e) { if (e.getClickCount() > 1) - { - defaultBrowser_mouseClicked(e); - } + { + defaultBrowser_mouseClicked(e); + } } }); - useProxy.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + useProxy.setFont(verdana11); useProxy.setHorizontalAlignment(SwingConstants.RIGHT); useProxy.setHorizontalTextPosition(SwingConstants.LEADING); useProxy.setText("Use a proxy server"); @@ -294,43 +318,115 @@ public class GPreferences extends JPanel }); jPanel1.setBorder(titledBorder1); jPanel1.setLayout(gridBagLayout1); - sortby.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - sortby.setBounds(new Rectangle(147, 222, 302, 21)); - sortLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + 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, 19, 138, 270)); + jPanel2.setBounds(new Rectangle(7, 17, 158, 278)); jPanel2.setLayout(gridLayout2); - gridLayout2.setRows(8); - jPanel3.setBounds(new Rectangle(146, 53, 274, 26)); + gridLayout2.setRows(12); + jPanel3.setBounds(new Rectangle(173, 35, 274, 26)); exportTab.setLayout(null); - epsLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + epsLabel.setFont(verdana11); epsLabel.setHorizontalAlignment(SwingConstants.RIGHT); epsLabel.setText("EPS Rendering Style"); - epsLabel.setBounds(new Rectangle(3, 47, 134, 21)); - epsRendering.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - epsRendering.setBounds(new Rectangle(145, 47, 286, 21)); + 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(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.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + rightAlign.setForeground(Color.black); + rightAlign.setHorizontalAlignment(SwingConstants.RIGHT); + rightAlign.setHorizontalTextPosition(SwingConstants.LEFT); + rightAlign.setText("Right Align Ids"); + idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + idItalics.setHorizontalAlignment(SwingConstants.RIGHT); + idItalics.setHorizontalTextPosition(SwingConstants.LEADING); + idItalics.setText("Sequence Name Italics"); + openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + openoverv.setActionCommand("Open Overview"); + openoverv.setHorizontalAlignment(SwingConstants.RIGHT); + openoverv.setHorizontalTextPosition(SwingConstants.LEADING); + openoverv.setText("Open Overview Window"); + openoverv.setBounds(new Rectangle(169, 17, 200, 23)); jPanel2.add(fullScreen); jPanel2.add(annotations); - jPanel2.add(fullID); + jPanel2.add(seqLimit); + jPanel2.add(rightAlign); jPanel2.add(fontLabel); + jPanel2.add(idItalics); + jPanel2.add(smoothFont); + jPanel2.add(wrap); jPanel2.add(gapLabel); jPanel2.add(colourLabel); jPanel2.add(sortLabel); jPanel2.add(startupCheckbox); + visualTab.add(openoverv); + visualTab.add(startupFileTextfield); + visualTab.add(sortby); + visualTab.add(colour); + visualTab.add(gapSymbolCB); + visualTab.add(jPanel3); visualTab.add(fontNameCB); visualTab.add(fontSizeCB); visualTab.add(fontStyleCB); - visualTab.add(gapSymbolCB); - visualTab.add(colour); - visualTab.add(sortby); - visualTab.add(startupFileTextfield); - visualTab.add(jPanel3); jPanel3.add(conservation); - jPanel3.add(quality); jPanel3.add(identity); + jPanel3.add(quality); visualTab.add(jPanel2); - linkPanel.add(editLinkButtons, BorderLayout.EAST); editLinkButtons.add(newLink, null); editLinkButtons.add(editLink, null); @@ -339,11 +435,11 @@ public class GPreferences extends JPanel linkScrollPane.getViewport().add(linkPanel2, null); linkPanel2.add(linkURLList, BorderLayout.CENTER); linkPanel2.add(linkNameList, BorderLayout.WEST); - okCancelPanel.add(ok); - okCancelPanel.add(cancel); + okCancelPanel.add(ok); + okCancelPanel.add(cancel); this.add(tabbedPane, java.awt.BorderLayout.CENTER); - this.add(okCancelPanel, java.awt.BorderLayout.SOUTH); + 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)); @@ -370,68 +466,83 @@ public class GPreferences extends JPanel , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, new Insets(15, 0, 0, 15), 307, 1)); - exportTab.add(epsLabel); - exportTab.add(epsRendering); - 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); + dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER); + gapSymbolCB.setRenderer(dlcr); tabbedPane.add(visualTab, "Visual"); tabbedPane.add(connectTab, "Connections"); - tabbedPane.add(exportTab, "Export"); - } + 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"); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void ok_actionPerformed(ActionEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void cancel_actionPerformed(ActionEvent e) - { - } + exportTab.add(epsLabel); + exportTab.add(epsRendering); + exportTab.add(jPanel11); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void annotations_actionPerformed(ActionEvent e) - { - } + /** + * 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! - */ - public void startupFileTextfield_mouseClicked() - { - } + /** + * 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 newLink_actionPerformed(ActionEvent e) + { } - public void editLink_actionPerformed(ActionEvent e) { + public void editLink_actionPerformed(ActionEvent e) + { } - public void deleteLink_actionPerformed(ActionEvent e) { + public void deleteLink_actionPerformed(ActionEvent e) + { } @@ -447,7 +558,8 @@ public class GPreferences extends JPanel public void useProxy_actionPerformed() { - proxyServerTB.setEnabled(useProxy.isSelected()); - proxyPortTB.setEnabled(useProxy.isSelected()); + proxyServerTB.setEnabled(useProxy.isSelected()); + proxyPortTB.setEnabled(useProxy.isSelected()); } + }