X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=ccca6a6e35250febcbdb134a4e2a00dd811d3c10;hb=72dbda1ebc7b6fe0ffbb486a3c3fb973a73483e7;hp=50c4cf5a3725b0770901db40aa1ecb55e2ef1cf2;hpb=f932cb5bb08dce9d7441c788d6996efaef53d15a;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 50c4cf5..ccca6a6 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -42,7 +42,7 @@ 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 dbRef = new JCheckBox(); protected JCheckBox fullScreen = new JCheckBox(); protected JCheckBox conservation = new JCheckBox(); protected JCheckBox identity = new JCheckBox(); @@ -79,6 +79,7 @@ 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(); @@ -90,6 +91,29 @@ public class GPreferences extends JPanel JPanel exportTab = new JPanel(); JLabel epsLabel = new JLabel(); protected JComboBox epsRendering = new JComboBox(); + JLabel jLabel1 = new JLabel(); + JLabel jLabel2 = new JLabel(); + protected JCheckBox pileupdb = new JCheckBox(); + protected JCheckBox fastadb = new JCheckBox(); + protected JCheckBox blcjv = new JCheckBox(); + protected JCheckBox pileupjv = new JCheckBox(); + protected JCheckBox msfdb = new JCheckBox(); + protected JCheckBox pfamdb = new JCheckBox(); + protected JCheckBox clustaljv = new JCheckBox(); + protected JCheckBox msfjv = new JCheckBox(); + protected JCheckBox blcdb = new JCheckBox(); + protected JCheckBox clustaldb = new JCheckBox(); + protected JCheckBox fastajv = new JCheckBox(); + protected JCheckBox pfamjv = new JCheckBox(); + JLabel jLabel10 = new JLabel(); + JLabel jLabel11 = new JLabel(); + FlowLayout flowLayout1 = new FlowLayout(); + protected JCheckBox pirdb = new JCheckBox(); + protected JCheckBox pirjv = new JCheckBox(); + JPanel jPanel11 = new JPanel(); + GridLayout gridLayout3 = new GridLayout(); + Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11); + protected JCheckBox seqLimit = new JCheckBox(); /** * Creates a new GPreferences object. */ @@ -130,36 +154,36 @@ 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"); 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)); + dbRef.setFont(verdana11); + dbRef.setHorizontalAlignment(SwingConstants.RIGHT); + dbRef.setHorizontalTextPosition(SwingConstants.LEFT); + dbRef.setMargin(new Insets(4, 2, 2, 0)); + dbRef.setText("DB prefix (DB|AccNo)"); + 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(new java.awt.Font("Verdana", Font.PLAIN, 11)); + 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.setFont(verdana11); 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.setFont(verdana11); annotations.setHorizontalAlignment(SwingConstants.RIGHT); annotations.setHorizontalTextPosition(SwingConstants.LEFT); annotations.setMargin(new Insets(2, 4, 2, 0)); @@ -172,32 +196,32 @@ public class GPreferences extends JPanel annotations_actionPerformed(e); } }); - gapLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + gapLabel.setFont(verdana11); gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); gapLabel.setText("Gap Symbol "); - colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - colour.setBounds(new Rectangle(148, 171, 154, 21)); - colourLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + colour.setFont(verdana11); + colour.setBounds(new Rectangle(170, 170, 155, 21)); + colourLabel.setFont(verdana11); colourLabel.setHorizontalAlignment(SwingConstants.RIGHT); colourLabel.setText("Colour "); - fontLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + fontLabel.setFont(verdana11); fontLabel.setHorizontalAlignment(SwingConstants.RIGHT); fontLabel.setText("Font "); - fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + fontSizeCB.setFont(verdana11); fontSizeCB.setBounds(new Rectangle(317, 111, 49, 21)); - fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + fontStyleCB.setFont(verdana11); fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21)); - fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - fontNameCB.setBounds(new Rectangle(148, 111, 169, 21)); - gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - gapSymbolCB.setBounds(new Rectangle(148, 141, 67, 21)); + fontNameCB.setFont(verdana11); + fontNameCB.setBounds(new Rectangle(170, 111, 147, 21)); + gapSymbolCB.setFont(verdana11); + gapSymbolCB.setBounds(new Rectangle(170, 141, 69, 21)); startupCheckbox.setText("Open file"); - 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(148, 232, 302, 20)); + startupFileTextfield.setFont(verdana11); + startupFileTextfield.setBounds(new Rectangle(170, 232, 271, 20)); startupFileTextfield.addMouseListener(new MouseAdapter() { public void mouseClicked(MouseEvent e) @@ -212,16 +236,16 @@ 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() { @@ -268,7 +292,7 @@ public class GPreferences extends JPanel linkNameList.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); 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() @@ -281,7 +305,7 @@ 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"); @@ -294,43 +318,110 @@ 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(148, 200, 302, 21)); - sortLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + sortby.setFont(verdana11); + sortby.setBounds(new Rectangle(170, 200, 155, 21)); + sortLabel.setFont(verdana11); sortLabel.setHorizontalAlignment(SwingConstants.RIGHT); sortLabel.setText("Sort by "); - jPanel2.setBounds(new Rectangle(7, 17, 138, 242)); + jPanel2.setBounds(new Rectangle(7, 17, 158, 242)); jPanel2.setLayout(gridLayout2); gridLayout2.setRows(8); - jPanel3.setBounds(new Rectangle(147, 46, 274, 26)); + jPanel3.setBounds(new Rectangle(168, 47, 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("/start-end suffix"); + jLabel2.setFont(verdana11); + jLabel2.setHorizontalAlignment(SwingConstants.RIGHT); + jLabel2.setHorizontalTextPosition(SwingConstants.RIGHT); + jLabel2.setText("Database ref prefix"); + jLabel1.setFont(verdana11); + jLabel2.setFont(verdana11); + fastajv.setFont(verdana11); + fastajv.setHorizontalAlignment(SwingConstants.CENTER); + jLabel10.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); + jLabel10.setHorizontalAlignment(SwingConstants.RIGHT); + jLabel10.setText("(Uniprot|P02055)"); + jLabel11.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); + jLabel11.setHorizontalAlignment(SwingConstants.CENTER); + jLabel11.setText("(/15-380)"); + clustaldb.setFont(verdana11); + clustaldb.setHorizontalAlignment(SwingConstants.RIGHT); + clustaldb.setHorizontalTextPosition(SwingConstants.LEFT); + clustaldb.setText("Clustal "); + blcdb.setFont(verdana11); + blcdb.setHorizontalAlignment(SwingConstants.RIGHT); + blcdb.setHorizontalTextPosition(SwingConstants.LEFT); + blcdb.setText("BLC "); + fastadb.setFont(verdana11); + fastadb.setHorizontalAlignment(SwingConstants.RIGHT); + fastadb.setHorizontalTextPosition(SwingConstants.LEFT); + fastadb.setText("Fasta "); + msfdb.setFont(verdana11); + msfdb.setHorizontalTextPosition(SwingConstants.LEFT); + msfdb.setHorizontalAlignment(SwingConstants.RIGHT); + msfdb.setText("MSF "); + pfamdb.setFont(verdana11); + pfamdb.setHorizontalAlignment(SwingConstants.RIGHT); + pfamdb.setHorizontalTextPosition(SwingConstants.LEFT); + pfamdb.setText("PFAM "); + pileupdb.setFont(verdana11); + pileupdb.setHorizontalAlignment(SwingConstants.RIGHT); + pileupdb.setHorizontalTextPosition(SwingConstants.LEFT); + pileupdb.setText("Pileup "); + msfjv.setFont(verdana11); + msfjv.setHorizontalAlignment(SwingConstants.CENTER); + pirdb.setFont(verdana11); + pirdb.setHorizontalAlignment(SwingConstants.RIGHT); + pirdb.setHorizontalTextPosition(SwingConstants.LEFT); + pirdb.setText("PIR "); + jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + jPanel11.setBorder(titledBorder2); + jPanel11.setBounds(new Rectangle(18, 72, 325, 182)); + jPanel11.setLayout(gridLayout3); + gridLayout3.setColumns(2); + gridLayout3.setRows(9); + blcjv.setFont(verdana11); + blcjv.setHorizontalAlignment(SwingConstants.CENTER); + clustaljv.setFont(verdana11); + clustaljv.setHorizontalAlignment(SwingConstants.CENTER); + pfamjv.setFont(verdana11); + pfamjv.setHorizontalAlignment(SwingConstants.CENTER); + pileupjv.setFont(verdana11); + pileupjv.setHorizontalAlignment(SwingConstants.CENTER); + pirjv.setFont(verdana11); + pirjv.setHorizontalAlignment(SwingConstants.CENTER); + seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + seqLimit.setHorizontalTextPosition(SwingConstants.LEADING); + seqLimit.setText("Sequence Limits (/1-350)"); + seqLimit.setBounds(new Rectangle(172, 82, 195, 23)); jPanel2.add(fullScreen); jPanel2.add(annotations); - jPanel2.add(fullID); + jPanel2.add(dbRef); jPanel2.add(fontLabel); jPanel2.add(gapLabel); jPanel2.add(colourLabel); jPanel2.add(sortLabel); jPanel2.add(startupCheckbox); + visualTab.add(gapSymbolCB); + visualTab.add(colour); + visualTab.add(seqLimit); visualTab.add(jPanel3); jPanel3.add(conservation); - jPanel3.add(quality); jPanel3.add(identity); + jPanel3.add(quality); visualTab.add(sortby); - visualTab.add(colour); visualTab.add(startupFileTextfield); visualTab.add(fontNameCB); visualTab.add(fontSizeCB); visualTab.add(fontStyleCB); - visualTab.add(gapSymbolCB); visualTab.add(jPanel2); - linkPanel.add(editLinkButtons, BorderLayout.EAST); editLinkButtons.add(newLink, null); editLinkButtons.add(editLink, null); @@ -370,8 +461,6 @@ 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, @@ -383,8 +472,29 @@ public class GPreferences extends JPanel gapSymbolCB.setRenderer(dlcr); tabbedPane.add(visualTab, "Visual"); - tabbedPane.add(connectTab, "Connections"); - tabbedPane.add(exportTab, "Export"); + tabbedPane.add(connectTab,"Connections"); + tabbedPane.add(exportTab, "Output"); + jPanel11.add(jLabel2); + jPanel11.add(jLabel1); + jPanel11.add(jLabel10); + jPanel11.add(jLabel11); + jPanel11.add(blcdb); + jPanel11.add(blcjv); + jPanel11.add(clustaldb); + jPanel11.add(clustaljv); + jPanel11.add(fastadb); + jPanel11.add(fastajv); + jPanel11.add(msfdb); + jPanel11.add(msfjv); + jPanel11.add(pfamdb); + jPanel11.add(pfamjv); + jPanel11.add(pileupdb); + jPanel11.add(pileupjv); + jPanel11.add(pirdb); + jPanel11.add(pirjv); + exportTab.add(epsLabel); + exportTab.add(epsRendering); + exportTab.add(jPanel11); } /**