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No more dbprefix
[jalview.git] / src / jalview / jbgui / GPreferences.java
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 106f400..2001efd 100755 (executable)
--- 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();\r
     protected JCheckBox quality = new JCheckBox();\r
     JPanel visualTab = new JPanel();\r
-    protected JCheckBox dbRef = new JCheckBox();\r
-    protected JCheckBox fullScreen = new JCheckBox();\r
+  protected JCheckBox fullScreen = new JCheckBox();\r
     protected JCheckBox conservation = new JCheckBox();\r
     protected JCheckBox identity = new JCheckBox();\r
     protected JCheckBox annotations = new JCheckBox();\r
@@ -92,28 +91,18 @@ public class GPreferences extends JPanel
   JLabel epsLabel = new JLabel();\r
   protected JComboBox epsRendering = new JComboBox();\r
   JLabel jLabel1 = new JLabel();\r
-  JLabel jLabel2 = new JLabel();\r
-  protected JCheckBox pileupdb = new JCheckBox();\r
-  protected  JCheckBox fastadb = new JCheckBox();\r
   protected  JCheckBox blcjv = new JCheckBox();\r
   protected  JCheckBox pileupjv = new JCheckBox();\r
-  protected  JCheckBox msfdb = new JCheckBox();\r
-  protected  JCheckBox pfamdb = new JCheckBox();\r
   protected  JCheckBox clustaljv = new JCheckBox();\r
   protected  JCheckBox msfjv = new JCheckBox();\r
-  protected  JCheckBox blcdb = new JCheckBox();\r
-  protected  JCheckBox clustaldb = new JCheckBox();\r
   protected  JCheckBox fastajv = new JCheckBox();\r
   protected  JCheckBox pfamjv = new JCheckBox();\r
-  JLabel jLabel10 = new JLabel();\r
-  JLabel jLabel11 = new JLabel();\r
   FlowLayout flowLayout1 = new FlowLayout();\r
-  protected  JCheckBox pirdb = new JCheckBox();\r
   protected  JCheckBox pirjv = new JCheckBox();\r
   JPanel jPanel11 = new JPanel();\r
-  GridLayout gridLayout3 = new GridLayout();\r
   Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);\r
   protected JCheckBox seqLimit = new JCheckBox();\r
+  GridLayout gridLayout3 = new GridLayout();\r
   /**\r
      * Creates a new GPreferences object.\r
      */\r
@@ -161,11 +150,6 @@ public class GPreferences extends JPanel
         quality.setText("Quality");\r
     visualTab.setBorder(new TitledBorder("Open new alignment"));\r
     visualTab.setLayout(null);\r
-    dbRef.setFont(verdana11);\r
-    dbRef.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    dbRef.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    dbRef.setMargin(new Insets(4, 2, 2, 0));\r
-    dbRef.setText("DB refs (Uniprot|H456)");\r
     fullScreen.setFont(verdana11);\r
         fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
         fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
@@ -200,7 +184,7 @@ public class GPreferences extends JPanel
         gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         gapLabel.setText("Gap Symbol ");\r
     colour.setFont(verdana11);\r
-        colour.setBounds(new Rectangle(173, 169, 154, 21));\r
+        colour.setBounds(new Rectangle(170, 170, 155, 21));\r
         colourLabel.setFont(verdana11);\r
         colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         colourLabel.setText("Colour ");\r
@@ -212,9 +196,9 @@ public class GPreferences extends JPanel
         fontStyleCB.setFont(verdana11);\r
         fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21));\r
         fontNameCB.setFont(verdana11);\r
-        fontNameCB.setBounds(new Rectangle(169, 111, 148, 21));\r
+        fontNameCB.setBounds(new Rectangle(170, 111, 147, 21));\r
         gapSymbolCB.setFont(verdana11);\r
-        gapSymbolCB.setBounds(new Rectangle(171, 136, 67, 21));\r
+        gapSymbolCB.setBounds(new Rectangle(170, 141, 69, 21));\r
         startupCheckbox.setText("Open file");\r
     startupCheckbox.setFont(verdana11);\r
         startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
@@ -319,14 +303,14 @@ public class GPreferences extends JPanel
     jPanel1.setBorder(titledBorder1);\r
     jPanel1.setLayout(gridBagLayout1);\r
     sortby.setFont(verdana11);\r
-    sortby.setBounds(new Rectangle(171, 200, 272, 21));\r
+    sortby.setBounds(new Rectangle(170, 200, 155, 21));\r
     sortLabel.setFont(verdana11);\r
     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
     sortLabel.setText("Sort by ");\r
     jPanel2.setBounds(new Rectangle(7, 17, 158, 242));\r
     jPanel2.setLayout(gridLayout2);\r
     gridLayout2.setRows(8);\r
-    jPanel3.setBounds(new Rectangle(147, 46, 274, 26));\r
+    jPanel3.setBounds(new Rectangle(168, 47, 274, 26));\r
     exportTab.setLayout(null);\r
     epsLabel.setFont(verdana11);\r
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
@@ -336,74 +320,41 @@ public class GPreferences extends JPanel
     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));\r
     jLabel1.setFont(verdana11);\r
     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);\r
-    jLabel1.setText("/start-end suffix");\r
-    jLabel2.setFont(verdana11);\r
-    jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    jLabel2.setHorizontalTextPosition(SwingConstants.RIGHT);\r
-    jLabel2.setText("Database ref prefix");\r
+    jLabel1.setText("Append /start-end (/15-380)");\r
     jLabel1.setFont(verdana11);\r
-    jLabel2.setFont(verdana11);\r
     fastajv.setFont(verdana11);\r
-    fastajv.setHorizontalAlignment(SwingConstants.CENTER);\r
-    jLabel10.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
-    jLabel10.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    jLabel10.setText("(Uniprot|P02055)");\r
-    jLabel11.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
-    jLabel11.setHorizontalAlignment(SwingConstants.CENTER);\r
-    jLabel11.setText("(/15-380)");\r
-    clustaldb.setFont(verdana11);\r
-    clustaldb.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    clustaldb.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    clustaldb.setText("Clustal     ");\r
-    blcdb.setFont(verdana11);\r
-    blcdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    blcdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    blcdb.setText("BLC     ");\r
-    fastadb.setFont(verdana11);\r
-    fastadb.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    fastadb.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    fastadb.setText("Fasta     ");\r
-    msfdb.setFont(verdana11);\r
-    msfdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    msfdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    msfdb.setText("MSF     ");\r
-    pfamdb.setFont(verdana11);\r
-    pfamdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    pfamdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    pfamdb.setText("PFAM     ");\r
-    pileupdb.setFont(verdana11);\r
-    pileupdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    pileupdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    pileupdb.setText("Pileup     ");\r
+    fastajv.setHorizontalAlignment(SwingConstants.LEFT);\r
+    clustaljv.setText("Clustal     ");\r
+    blcjv.setText("BLC     ");\r
+    fastajv.setText("Fasta     ");\r
+    msfjv.setText("MSF     ");\r
+    pfamjv.setText("PFAM     ");\r
+    pileupjv.setText("Pileup     ");\r
     msfjv.setFont(verdana11);\r
-    msfjv.setHorizontalAlignment(SwingConstants.CENTER);\r
-    pirdb.setFont(verdana11);\r
-    pirdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    pirdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    pirdb.setText("PIR     ");\r
+    msfjv.setHorizontalAlignment(SwingConstants.LEFT);\r
+    pirjv.setText("PIR     ");\r
     jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
     jPanel11.setBorder(titledBorder2);\r
-    jPanel11.setBounds(new Rectangle(18, 72, 325, 182));\r
+    jPanel11.setBounds(new Rectangle(30, 72, 196, 182));\r
     jPanel11.setLayout(gridLayout3);\r
-    gridLayout3.setColumns(2);\r
-    gridLayout3.setRows(9);\r
     blcjv.setFont(verdana11);\r
-    blcjv.setHorizontalAlignment(SwingConstants.CENTER);\r
+    blcjv.setHorizontalAlignment(SwingConstants.LEFT);\r
     clustaljv.setFont(verdana11);\r
-    clustaljv.setHorizontalAlignment(SwingConstants.CENTER);\r
+    clustaljv.setHorizontalAlignment(SwingConstants.LEFT);\r
     pfamjv.setFont(verdana11);\r
-    pfamjv.setHorizontalAlignment(SwingConstants.CENTER);\r
+    pfamjv.setHorizontalAlignment(SwingConstants.LEFT);\r
     pileupjv.setFont(verdana11);\r
-    pileupjv.setHorizontalAlignment(SwingConstants.CENTER);\r
+    pileupjv.setHorizontalAlignment(SwingConstants.LEFT);\r
     pirjv.setFont(verdana11);\r
-    pirjv.setHorizontalAlignment(SwingConstants.CENTER);\r
+    pirjv.setHorizontalAlignment(SwingConstants.LEFT);\r
     seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);\r
     seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);\r
-    seqLimit.setText("Sequence Limits (/1-350)");\r
-    seqLimit.setBounds(new Rectangle(183, 81, 178, 23));\r
+    seqLimit.setText("Full Sequence Id");\r
+    gridLayout3.setRows(8);\r
     jPanel2.add(fullScreen);\r
     jPanel2.add(annotations);\r
-    jPanel2.add(dbRef);\r
+    jPanel2.add(seqLimit);\r
     jPanel2.add(fontLabel);\r
     jPanel2.add(gapLabel);\r
     jPanel2.add(colourLabel);\r
@@ -411,11 +362,10 @@ public class GPreferences extends JPanel
     jPanel2.add(startupCheckbox);\r
     visualTab.add(gapSymbolCB);\r
     visualTab.add(colour);\r
-    visualTab.add(seqLimit);\r
     visualTab.add(jPanel3);\r
     jPanel3.add(conservation);\r
-    jPanel3.add(quality);\r
     jPanel3.add(identity);\r
+    jPanel3.add(quality);\r
     visualTab.add(sortby);\r
     visualTab.add(startupFileTextfield);\r
     visualTab.add(fontNameCB);\r
@@ -474,23 +424,13 @@ public class GPreferences extends JPanel
     tabbedPane.add(visualTab, "Visual");\r
     tabbedPane.add(connectTab,"Connections");\r
     tabbedPane.add(exportTab, "Output");\r
-    jPanel11.add(jLabel2);\r
     jPanel11.add(jLabel1);\r
-    jPanel11.add(jLabel10);\r
-    jPanel11.add(jLabel11);\r
-    jPanel11.add(blcdb);\r
     jPanel11.add(blcjv);\r
-    jPanel11.add(clustaldb);\r
     jPanel11.add(clustaljv);\r
-    jPanel11.add(fastadb);\r
     jPanel11.add(fastajv);\r
-    jPanel11.add(msfdb);\r
     jPanel11.add(msfjv);\r
-    jPanel11.add(pfamdb);\r
     jPanel11.add(pfamjv);\r
-    jPanel11.add(pileupdb);\r
     jPanel11.add(pileupjv);\r
-    jPanel11.add(pirdb);\r
     jPanel11.add(pirjv);\r
     exportTab.add(epsLabel);\r
     exportTab.add(epsRendering);\r