X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=27a54d774e51e59eef3d5ad2d5ab3afd816570e9;hb=5672e0350c857fffd3932d7e3a385373ede46fd4;hp=ab1d4e7afb2b74b83939f40b5012b7e0d90e2db3;hpb=65310fba3ddf0942d5f868130bca9e093888ce7a;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index ab1d4e7..27a54d7 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* 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 @@ -24,7 +24,9 @@ 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! @@ -42,8 +44,7 @@ public class GPreferences extends 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 fullScreen = new JCheckBox(); protected JCheckBox conservation = new JCheckBox(); protected JCheckBox identity = new JCheckBox(); protected JCheckBox annotations = new JCheckBox(); @@ -79,11 +80,39 @@ 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(); 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. */ @@ -124,82 +153,69 @@ public class GPreferences extends JPanel } }); quality.setEnabled(false); - quality.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + quality.setFont(verdana11); quality.setHorizontalAlignment(SwingConstants.RIGHT); quality.setHorizontalTextPosition(SwingConstants.LEFT); quality.setSelected(true); quality.setText("Quality"); - quality.setBounds(new Rectangle(248, 53, 81, 23)); - visualTab.setBorder(new TitledBorder("Open new alignment")); - visualTab.setBounds(new Rectangle(9, 20, 442, 241)); - visualTab.setLayout(null); - fullID.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fullID.setHorizontalAlignment(SwingConstants.RIGHT); - fullID.setHorizontalTextPosition(SwingConstants.LEFT); - fullID.setText("Full Sequence ID"); - fullID.setBounds(new Rectangle(9, 78, 129, 23)); - fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + visualTab.setBorder(new TitledBorder("Open new alignment")); + visualTab.setLayout(null); + fullScreen.setFont(verdana11); fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); - fullScreen.setText("Maximise Window"); - fullScreen.setBounds(new Rectangle(5, 29, 132, 23)); - conservation.setEnabled(false); - conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + 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"); - conservation.setBounds(new Rectangle(137, 53, 113, 23)); - identity.setEnabled(false); - identity.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + identity.setEnabled(false); + identity.setFont(verdana11); identity.setHorizontalAlignment(SwingConstants.RIGHT); identity.setHorizontalTextPosition(SwingConstants.LEFT); identity.setSelected(true); identity.setText("Consensus"); - identity.setBounds(new Rectangle(326, 53, 99, 23)); - annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + annotations.setFont(verdana11); annotations.setHorizontalAlignment(SwingConstants.RIGHT); annotations.setHorizontalTextPosition(SwingConstants.LEFT); - annotations.setSelected(true); + annotations.setMargin(new Insets(2, 2, 2, 0)); + annotations.setSelected(true); annotations.setText("Show Annotations"); - annotations.setBounds(new Rectangle(10, 53, 128, 23)); - annotations.addActionListener(new ActionListener() + annotations.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { annotations_actionPerformed(e); } }); - gapLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + gapLabel.setFont(verdana11); gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); - gapLabel.setText("Gap Symbol"); - gapLabel.setBounds(new Rectangle(41, 142, 76, 15)); - colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - colour.setBounds(new Rectangle(121, 168, 154, 21)); - colourLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + 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"); - colourLabel.setBounds(new Rectangle(60, 172, 58, 15)); - fontLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + colourLabel.setText("Colour "); + fontLabel.setFont(verdana11); fontLabel.setHorizontalAlignment(SwingConstants.RIGHT); - fontLabel.setText("Font"); - fontLabel.setBounds(new Rectangle(83, 114, 34, 15)); - fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fontSizeCB.setBounds(new Rectangle(304, 109, 49, 21)); - fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fontStyleCB.setBounds(new Rectangle(353, 109, 80, 21)); - fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fontNameCB.setBounds(new Rectangle(121, 109, 183, 21)); - gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - gapSymbolCB.setBounds(new Rectangle(121, 140, 67, 21)); + 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.setBounds(new Rectangle(4, 200, 115, 23)); - startupCheckbox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + startupCheckbox.setFont(verdana11); 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(121, 200, 309, 20)); + startupFileTextfield.setFont(verdana11); + startupFileTextfield.setBounds(new Rectangle(171, 236, 270, 20)); startupFileTextfield.addMouseListener(new MouseAdapter() { public void mouseClicked(MouseEvent e) @@ -214,16 +230,16 @@ public class GPreferences extends JPanel 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() { @@ -267,10 +283,10 @@ public class GPreferences extends JPanel 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() @@ -283,7 +299,7 @@ public class GPreferences extends JPanel } } }); - 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"); @@ -296,34 +312,99 @@ 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(122, 232, 308, 21)); - sortLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + sortby.setFont(verdana11); + sortby.setBounds(new Rectangle(171, 213, 155, 21)); + sortLabel.setFont(verdana11); sortLabel.setHorizontalAlignment(SwingConstants.RIGHT); - sortLabel.setText("Sort by"); - sortLabel.setBounds(new Rectangle(53, 235, 64, 15)); - visualTab.add(annotations); - visualTab.add(conservation); - visualTab.add(quality); - visualTab.add(fullID); - visualTab.add(gapSymbolCB); - visualTab.add(fontLabel); - visualTab.add(fontNameCB); - visualTab.add(colourLabel); - visualTab.add(gapLabel); + 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(fontSizeCB); - visualTab.add(fontStyleCB); - visualTab.add(identity); - visualTab.add(fullScreen); - visualTab.add(startupCheckbox); + visualTab.add(fontNameCB); + visualTab.add(fontSizeCB); + visualTab.add(fontStyleCB); + visualTab.add(jPanel3); visualTab.add(startupFileTextfield); - visualTab.add(sortby); - visualTab.add(sortLabel); - - tabbedPane.add(visualTab, "Visual"); - tabbedPane.add(connectTab, "Connections"); - + 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); @@ -334,7 +415,7 @@ public class GPreferences extends JPanel linkPanel2.add(linkNameList, BorderLayout.WEST); okCancelPanel.add(ok); okCancelPanel.add(cancel); - this.add(tabbedPane, java.awt.BorderLayout.CENTER); + 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 @@ -362,6 +443,8 @@ public class GPreferences extends JPanel 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, @@ -370,7 +453,28 @@ public class GPreferences extends JPanel 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!