X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=2001efd9fa775de198c783878568b511f4ba8781;hb=e21fb8306a9efaf170d7354daa10e7ee42d37c17;hp=106f400023a408668c6ea5b8244f66e63659eb4a;hpb=4e988b599b29712e28b5746d7594c33c67cd2f74;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 106f400..2001efd 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -42,8 +42,7 @@ public class GPreferences extends JPanel BorderLayout borderLayout1 = new BorderLayout(); protected JCheckBox quality = new JCheckBox(); JPanel visualTab = new JPanel(); - protected JCheckBox dbRef = 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(); @@ -92,28 +91,18 @@ public class GPreferences extends 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(); + GridLayout gridLayout3 = new GridLayout(); /** * Creates a new GPreferences object. */ @@ -161,11 +150,6 @@ public class GPreferences extends JPanel quality.setText("Quality"); visualTab.setBorder(new TitledBorder("Open new alignment")); visualTab.setLayout(null); - dbRef.setFont(verdana11); - dbRef.setHorizontalAlignment(SwingConstants.RIGHT); - dbRef.setHorizontalTextPosition(SwingConstants.LEFT); - dbRef.setMargin(new Insets(4, 2, 2, 0)); - dbRef.setText("DB refs (Uniprot|H456)"); fullScreen.setFont(verdana11); fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); @@ -200,7 +184,7 @@ public class GPreferences extends JPanel gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); gapLabel.setText("Gap Symbol "); colour.setFont(verdana11); - colour.setBounds(new Rectangle(173, 169, 154, 21)); + colour.setBounds(new Rectangle(170, 170, 155, 21)); colourLabel.setFont(verdana11); colourLabel.setHorizontalAlignment(SwingConstants.RIGHT); colourLabel.setText("Colour "); @@ -212,9 +196,9 @@ public class GPreferences extends JPanel fontStyleCB.setFont(verdana11); fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21)); fontNameCB.setFont(verdana11); - fontNameCB.setBounds(new Rectangle(169, 111, 148, 21)); + fontNameCB.setBounds(new Rectangle(170, 111, 147, 21)); gapSymbolCB.setFont(verdana11); - gapSymbolCB.setBounds(new Rectangle(171, 136, 67, 21)); + gapSymbolCB.setBounds(new Rectangle(170, 141, 69, 21)); startupCheckbox.setText("Open file"); startupCheckbox.setFont(verdana11); startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT); @@ -319,14 +303,14 @@ public class GPreferences extends JPanel jPanel1.setBorder(titledBorder1); jPanel1.setLayout(gridBagLayout1); sortby.setFont(verdana11); - sortby.setBounds(new Rectangle(171, 200, 272, 21)); + 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, 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(verdana11); epsLabel.setHorizontalAlignment(SwingConstants.RIGHT); @@ -336,74 +320,41 @@ public class GPreferences extends JPanel 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.setText("Append /start-end (/15-380)"); 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 "); + 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.CENTER); - pirdb.setFont(verdana11); - pirdb.setHorizontalAlignment(SwingConstants.RIGHT); - pirdb.setHorizontalTextPosition(SwingConstants.LEFT); - pirdb.setText("PIR "); + msfjv.setHorizontalAlignment(SwingConstants.LEFT); + pirjv.setText("PIR "); jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); jPanel11.setBorder(titledBorder2); - jPanel11.setBounds(new Rectangle(18, 72, 325, 182)); + jPanel11.setBounds(new Rectangle(30, 72, 196, 182)); jPanel11.setLayout(gridLayout3); - gridLayout3.setColumns(2); - gridLayout3.setRows(9); blcjv.setFont(verdana11); - blcjv.setHorizontalAlignment(SwingConstants.CENTER); + blcjv.setHorizontalAlignment(SwingConstants.LEFT); clustaljv.setFont(verdana11); - clustaljv.setHorizontalAlignment(SwingConstants.CENTER); + clustaljv.setHorizontalAlignment(SwingConstants.LEFT); pfamjv.setFont(verdana11); - pfamjv.setHorizontalAlignment(SwingConstants.CENTER); + pfamjv.setHorizontalAlignment(SwingConstants.LEFT); pileupjv.setFont(verdana11); - pileupjv.setHorizontalAlignment(SwingConstants.CENTER); + pileupjv.setHorizontalAlignment(SwingConstants.LEFT); pirjv.setFont(verdana11); - pirjv.setHorizontalAlignment(SwingConstants.CENTER); + pirjv.setHorizontalAlignment(SwingConstants.LEFT); seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + seqLimit.setHorizontalAlignment(SwingConstants.RIGHT); seqLimit.setHorizontalTextPosition(SwingConstants.LEADING); - seqLimit.setText("Sequence Limits (/1-350)"); - seqLimit.setBounds(new Rectangle(183, 81, 178, 23)); + seqLimit.setText("Full Sequence Id"); + gridLayout3.setRows(8); jPanel2.add(fullScreen); jPanel2.add(annotations); - jPanel2.add(dbRef); + jPanel2.add(seqLimit); jPanel2.add(fontLabel); jPanel2.add(gapLabel); jPanel2.add(colourLabel); @@ -411,11 +362,10 @@ public class GPreferences extends JPanel 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(startupFileTextfield); visualTab.add(fontNameCB); @@ -474,23 +424,13 @@ public class GPreferences extends JPanel tabbedPane.add(visualTab, "Visual"); 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);