DBPrefix and JVSuffix added

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 209f939..382fcb6 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -36,7 +36,8 @@ public class AlignViewport
   int startSeq;\r
   int endSeq;\r
 \r
-  boolean showFullId = true;\r
+  boolean showDBPrefix = true;\r
+  boolean showJVSuffix = true;\r
   boolean showText = true;\r
   boolean showColourText = false;\r
   boolean showBoxes = true;\r
@@ -98,7 +99,7 @@ public class AlignViewport
       String param = applet.getParameter("showFullId");\r
       if (param != null)\r
       {\r
-        showFullId = Boolean.valueOf(param).booleanValue();\r
+        showJVSuffix = Boolean.valueOf(param).booleanValue();\r
       }\r
 \r
       param = applet.getParameter("showAnnotation");\r
@@ -596,14 +597,24 @@ public class AlignViewport
     return colourAppliesToAllGroups;\r
   }\r
 \r
-  public boolean getShowFullId()\r
+  public boolean getShowJVSuffix()\r
   {\r
-    return showFullId;\r
+    return showJVSuffix;\r
   }\r
 \r
-  public void setShowFullId(boolean b)\r
+  public void setShowJVSuffix(boolean b)\r
   {\r
-    showFullId = b;\r
+    showJVSuffix = b;\r
+  }\r
+\r
+  public boolean getShowDBPrefix()\r
+  {\r
+    return showDBPrefix;\r
+  }\r
+\r
+  public void setShowDBPrefix(boolean b)\r
+  {\r
+    showDBPrefix = b;\r
   }\r
 \r
   public boolean getShowAnnotation()\r

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 7332a1a..44370d4 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -204,14 +204,7 @@ public class AlignmentPanel
     while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
     {\r
       SequenceI s = al.getSequenceAt(i);\r
-      if (av.getShowFullId())\r
-      {\r
-        id = s.getDisplayId();\r
-      }\r
-      else\r
-      {\r
-        id = s.getName();\r
-      }\r
+      id = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
 \r
       if (fm.stringWidth(id) > idWidth)\r
       {\r

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index d581273..7686e8a 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -74,11 +74,7 @@ public class IdCanvas
       gg.setColor(Color.black);\r
     }\r
 \r
-    String string = s.getName();\r
-    if (av.getShowFullId())\r
-    {\r
-      string = s.getDisplayId();\r
-    }\r
+    String string = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
 \r
     gg.drawString(string, 0,\r
                   ((i - starty) * charHeight) + ypos +\r
@@ -266,11 +262,9 @@ public class IdCanvas
                     av.charHeight);\r
 \r
         gg.setColor(currentTextColor);\r
-        String string = av.alignment.getSequenceAt(i).getName();\r
-        if (av.getShowFullId())\r
-        {\r
-          string = av.alignment.getSequenceAt(i).getDisplayId();\r
-        }\r
+        String string = av.alignment.getSequenceAt(i)\r
+            .getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
+\r
         gg.drawString(string, 0,\r
                       ((i - starty) * av.charHeight) +\r
                       av.charHeight - (av.charHeight / 5));\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 9b1f10d..5314ade 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -93,15 +93,9 @@ public class IdCanvas extends JPanel
             gg.setColor(Color.black);\r
         }\r
 \r
-        String string = s.getName();\r
 \r
-        if (av.getShowFullId())\r
-        {\r
-            string = s.getDisplayId();\r
-        }\r
-\r
-        gg.drawString(string, 0,\r
-            (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
+        gg.drawString( s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix()),\r
+                      0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
     }\r
 \r
     /**\r
@@ -290,12 +284,8 @@ public class IdCanvas extends JPanel
 \r
                 gg.setColor(currentTextColor);\r
 \r
-                String string = av.alignment.getSequenceAt(i).getName();\r
-\r
-                if (av.getShowFullId())\r
-                {\r
-                    string = av.alignment.getSequenceAt(i).getDisplayId();\r
-                }\r
+                String string = av.alignment.getSequenceAt(i).getDisplayId(\r
+                  av.getShowDBPrefix(), av.getShowJVSuffix());\r
 \r
                 gg.drawString(string, 0,\r
                     (((i - starty) * av.charHeight) + av.charHeight) -\r

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 9ab6419..f49878c 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -27,6 +27,7 @@ import java.io.*;
 import java.net.*;\r
 \r
 import java.util.*;\r
+\r
 import java.util.jar.*;\r
 \r
 import javax.swing.*;\r
@@ -393,7 +394,7 @@ public class Jalview2XML
         view.setShowBoxes(av.getShowBoxes());\r
         view.setShowColourText(av.getColourText());\r
         view.setShowConservation(av.showConservation);\r
-        view.setShowFullId(av.getShowFullId());\r
+        view.setShowFullId(av.getShowJVSuffix());\r
         view.setShowIdentity(av.showIdentity);\r
         view.setShowQuality(av.showQuality);\r
         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
@@ -700,8 +701,8 @@ public class Jalview2XML
         af.viewport.setConservationSelected(view.getConservationSelected());\r
         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 \r
-        af.viewport.setShowFullId(view.getShowFullId());\r
-        af.fullSeqId.setSelected(view.getShowFullId());\r
+        af.viewport.setShowJVSuffix(view.getShowFullId());\r
+        af.seqLimits.setSelected(view.getShowFullId());\r
 \r
         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
                 view.getFontStyle(), view.getFontSize()));\r

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 078eff1..8915f6f 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -79,7 +79,8 @@ public class Preferences extends GPreferences
         Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
         frame.setMinimumSize(new Dimension(480,390));\r
 \r
-        fullID.setSelected(      Cache.getDefault("SHOW_FULL_ID", true));\r
+        dbRef.setSelected(      Cache.getDefault("SHOW_DBREF", true));\r
+        seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));\r
         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 \r
@@ -196,7 +197,8 @@ public class Preferences extends GPreferences
     public void ok_actionPerformed(ActionEvent e)\r
     {\r
 \r
-      Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));\r
+      Cache.applicationProperties.setProperty("SHOW_DBREF", Boolean.toString(dbRef.isSelected()));\r
+      Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 \r
       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 201ff0c..257e9fa 100755 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -134,16 +134,11 @@ public class HTMLOutput
       seq = alignment.getSequenceAt(i);\r
       groups = alignment.findAllGroups(seq);\r
 \r
-      if (av.getShowFullId())\r
-      {\r
-        out.println("<tr><td nowrap>" + seq.getDisplayId() +\r
-                    "&nbsp;&nbsp;</td>");\r
-      }\r
-      else\r
-      {\r
-        out.println("<tr><td nowrap>" + seq.getName() +\r
+      String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
+\r
+      out.println("<tr><td nowrap>" + id +\r
                     "&nbsp;&nbsp;</td>");\r
-      }\r
+\r
 \r
       for (int res = 0; res < seq.getLength(); res++)\r
       {\r
@@ -229,16 +224,11 @@ public class HTMLOutput
         seq = al.getSequenceAt(s);\r
         groups = al.findAllGroups(seq);\r
 \r
-        if (av.getShowFullId())\r
-        {\r
-          out.println("<td nowrap>" + seq.getDisplayId() +\r
-                      "&nbsp;&nbsp;</td>");\r
-        }\r
-        else\r
-        {\r
-          out.println("<td nowrap>" + seq.getName() +\r
+        String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
+\r
+          out.println("<td nowrap>" + id +\r
                       "&nbsp;&nbsp;</td>");\r
-        }\r
+\r
 \r
         for (int res = startRes; res < endRes; res++)\r
         {\r

diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index 3c79599..69213af 100755 (executable)
--- a/src/jalview/io/VamsasDatastore.java
+++ b/src/jalview/io/VamsasDatastore.java
@@ -86,6 +86,30 @@ public class VamsasDatastore
               sequence.setStart(jal.getDataset().getSequenceAt(i).getStart());\r
               sequence.setEnd(jal.getDataset().getSequenceAt(i).getEnd());\r
 \r
+\r
+              if(jal.getDataset().getSequenceAt(i).getSequenceFeatures()!=null)\r
+              {\r
+                int sfSize = jal.getDataset().getSequenceAt(i).getSequenceFeatures().size();\r
+\r
+                for (int sf = 0; sf < sfSize; sf++)\r
+                {\r
+                  jalview.datamodel.SequenceFeature feature =\r
+                      (jalview.datamodel.SequenceFeature)\r
+                      jal.getDataset().getSequenceAt(i).getSequenceFeatures().elementAt(sf);\r
+\r
+                  DataSetAnnotations dsa = new DataSetAnnotations();\r
+                  dsa.setType(feature.getType());\r
+                  dsa.setBegin(feature.getBegin());\r
+                  dsa.setEnd(feature.getEnd());\r
+                  dsa.setDescription(feature.getDescription());\r
+                  dsa.setStatus(feature.getStatus());\r
+                  dsa.addProvenance(dummyProvenance());\r
+                  dsa.setSeqRef(sequence);\r
+                  dsa.setId("sf"+(time++));\r
+                  dataset.addDataSetAnnotations(dsa);\r
+                }\r
+              }\r
+\r
               if(jal.getDataset().getSequenceAt(i).getDBRef()!=null)\r
               {\r
                 java.util.Vector entries = jal.getDataset().getSequenceAt(i).getDBRef();\r
@@ -278,6 +302,23 @@ public class VamsasDatastore
                      dataset.getSequence(i).getEnd()  );\r
               seqs[i].setVamsasId(dataset.getSequence(i).getId());\r
 \r
+              if (dataset.getDataSetAnnotations() != null)\r
+              {\r
+                for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)\r
+                {\r
+                  if (dataset.getDataSetAnnotations(dsa).getSeqRef() ==\r
+                      dataset.getSequence(i))\r
+                  {\r
+                    seqs[i].addSequenceFeature(new jalview.datamodel.\r
+                                               SequenceFeature(\r
+                        dataset.getDataSetAnnotations(dsa).getType(),\r
+                        dataset.getDataSetAnnotations(dsa).getDescription(),\r
+                        dataset.getDataSetAnnotations(dsa).getStatus(),\r
+                        dataset.getDataSetAnnotations(dsa).getBegin(),\r
+                        dataset.getDataSetAnnotations(dsa).getEnd()));\r
+                  }\r
+                }\r
+              }\r
               dbref = dataset.getSequence(i).getDbRef();\r
 \r
               if(dbref.length>0)\r
@@ -291,7 +332,6 @@ public class VamsasDatastore
                            dbref[db].getAccessionId().toString()));\r
                 }\r
               }\r
-\r
             }\r
             jalview.datamodel.Alignment jdataset = new jalview.datamodel.Alignment(seqs);\r
             ////////////////////////////////////////////////\r
@@ -302,6 +342,8 @@ public class VamsasDatastore
             Alignment alignment = dataset.getAlignment(0);\r
             iSize = alignment.getAlignmentSequenceCount();\r
             seqs = new jalview.datamodel.Sequence[iSize];\r
+            String id;\r
+            int j, jSize = jdataset.getHeight();\r
             for (i = 0; i < iSize; i++)\r
             {\r
               seqs[i] = new jalview.datamodel.Sequence(\r
@@ -309,6 +351,17 @@ public class VamsasDatastore
                   alignment.getAlignmentSequence(i).getSequence(),\r
                   alignment.getAlignmentSequence(i).getStart(),\r
                   alignment.getAlignmentSequence(i).getEnd());\r
+\r
+              id = ( (Sequence) alignment.getAlignmentSequence(i).getRefid()).getId();\r
+\r
+             for(j=0; j<jSize; j++)\r
+             {\r
+               if(jdataset.getSequenceAt(j).getVamsasId().equals(id))\r
+               {\r
+                 seqs[i].setDatasetSequence( jdataset.getSequenceAt(j) );\r
+                 break;\r
+               }\r
+             }\r
             }\r
             jalview.datamodel.Alignment jal = new jalview.datamodel.Alignment(seqs);\r
             jal.setDataset(jdataset);\r
@@ -326,7 +379,7 @@ public class VamsasDatastore
             {\r
               AlignmentAnnotations[] an = alignment.getAlignmentAnnotations();\r
 \r
-              for (int j = 0; j < an.length; j++)\r
+              for (j = 0; j < an.length; j++)\r
               {\r
                 boolean topaliBreakpoint = false;\r
 \r

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 5a0357e..6ec19e2 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -99,7 +99,7 @@ public class GAlignFrame
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
   JMenuItem createPNG = new JMenuItem();\r
   protected JMenuItem font = new JMenuItem();\r
-  public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
   JMenuItem epsFile = new JMenuItem();\r
   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
@@ -117,6 +117,7 @@ public class GAlignFrame
   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
   protected JTabbedPane tabbedPane = new JTabbedPane();\r
   protected JMenuItem featureSettings = new JMenuItem();\r
+  public JCheckBoxMenuItem seqDBRef = new JCheckBoxMenuItem();\r
 \r
   public GAlignFrame()\r
   {\r
@@ -826,13 +827,14 @@ public class GAlignFrame
         font_actionPerformed(e);\r
       }\r
     });\r
-    fullSeqId.setText("Show Full Sequence ID");\r
-    fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true));\r
-    fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
+\r
+    seqLimits.setText("Show Sequence Limits");\r
+    seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
+    seqLimits.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        fullSeqId_actionPerformed(e);\r
+        seqLimit_actionPerformed(e);\r
       }\r
     });\r
     epsFile.setText("EPS");\r
@@ -944,6 +946,15 @@ public class GAlignFrame
         featureSettings_actionPerformed(e);\r
       }\r
     });\r
+    seqDBRef.setState( jalview.bin.Cache.getDefault("SHOW_DBPREFIX",true));\r
+    seqDBRef.setText("Show Sequence DB Refs");\r
+    seqDBRef.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        seqDBRef_actionPerformed(e);\r
+      }\r
+    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -983,7 +994,8 @@ public class GAlignFrame
     viewMenu.add(font);\r
     viewMenu.addSeparator();\r
     viewMenu.add(wrapMenuItem);\r
-    viewMenu.add(fullSeqId);\r
+    viewMenu.add(seqDBRef);\r
+    viewMenu.add(seqLimits);\r
     viewMenu.add(scaleAbove);\r
     viewMenu.add(scaleLeft);\r
     viewMenu.add(scaleRight);\r
@@ -1270,10 +1282,16 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  protected void fullSeqId_actionPerformed(ActionEvent e)\r
+  protected void seqLimit_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
+  public void seqDBRef_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+\r
   public void createEPS(java.io.File f)\r
   {\r
   }\r
@@ -1354,4 +1372,5 @@ public class GAlignFrame
   {\r
 \r
   }\r
+\r
 }\r

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 1896e06..106f400 100755 (executable)
--- 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();\r
     protected JCheckBox quality = new JCheckBox();\r
     JPanel visualTab = new JPanel();\r
-    protected JCheckBox fullID = new JCheckBox();\r
+    protected JCheckBox dbRef = new JCheckBox();\r
     protected JCheckBox fullScreen = new JCheckBox();\r
     protected JCheckBox conservation = new JCheckBox();\r
     protected JCheckBox identity = new JCheckBox();\r
@@ -113,6 +113,7 @@ public class GPreferences extends JPanel
   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
   /**\r
      * Creates a new GPreferences object.\r
      */\r
@@ -160,11 +161,11 @@ public class GPreferences extends JPanel
         quality.setText("Quality");\r
     visualTab.setBorder(new TitledBorder("Open new alignment"));\r
     visualTab.setLayout(null);\r
-        fullID.setFont(verdana11);\r
-        fullID.setHorizontalAlignment(SwingConstants.RIGHT);\r
-        fullID.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    fullID.setMargin(new Insets(4, 2, 2, 0));\r
-    fullID.setText("Full Sequence ID");\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
@@ -199,7 +200,7 @@ public class GPreferences extends JPanel
         gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         gapLabel.setText("Gap Symbol ");\r
     colour.setFont(verdana11);\r
-        colour.setBounds(new Rectangle(148, 171, 154, 21));\r
+        colour.setBounds(new Rectangle(173, 169, 154, 21));\r
         colourLabel.setFont(verdana11);\r
         colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         colourLabel.setText("Colour ");\r
@@ -211,16 +212,16 @@ 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(148, 111, 169, 21));\r
+        fontNameCB.setBounds(new Rectangle(169, 111, 148, 21));\r
         gapSymbolCB.setFont(verdana11);\r
-        gapSymbolCB.setBounds(new Rectangle(148, 141, 67, 21));\r
+        gapSymbolCB.setBounds(new Rectangle(171, 136, 67, 21));\r
         startupCheckbox.setText("Open file");\r
     startupCheckbox.setFont(verdana11);\r
         startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
         startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
         startupCheckbox.setSelected(true);\r
         startupFileTextfield.setFont(verdana11);\r
-        startupFileTextfield.setBounds(new Rectangle(148, 232, 302, 20));\r
+        startupFileTextfield.setBounds(new Rectangle(170, 232, 271, 20));\r
         startupFileTextfield.addMouseListener(new MouseAdapter()\r
             {\r
                 public void mouseClicked(MouseEvent e)\r
@@ -318,11 +319,11 @@ public class GPreferences extends JPanel
     jPanel1.setBorder(titledBorder1);\r
     jPanel1.setLayout(gridBagLayout1);\r
     sortby.setFont(verdana11);\r
-    sortby.setBounds(new Rectangle(148, 200, 302, 21));\r
+    sortby.setBounds(new Rectangle(171, 200, 272, 21));\r
     sortLabel.setFont(verdana11);\r
     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
     sortLabel.setText("Sort by ");\r
-    jPanel2.setBounds(new Rectangle(7, 17, 138, 242));\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
@@ -396,27 +397,31 @@ public class GPreferences extends JPanel
     pileupjv.setHorizontalAlignment(SwingConstants.CENTER);\r
     pirjv.setFont(verdana11);\r
     pirjv.setHorizontalAlignment(SwingConstants.CENTER);\r
+    seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);\r
+    seqLimit.setText("Sequence Limits (/1-350)");\r
+    seqLimit.setBounds(new Rectangle(183, 81, 178, 23));\r
     jPanel2.add(fullScreen);\r
     jPanel2.add(annotations);\r
-    jPanel2.add(fullID);\r
+    jPanel2.add(dbRef);\r
     jPanel2.add(fontLabel);\r
     jPanel2.add(gapLabel);\r
     jPanel2.add(colourLabel);\r
     jPanel2.add(sortLabel);\r
     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
     visualTab.add(sortby);\r
-    visualTab.add(colour);\r
     visualTab.add(startupFileTextfield);\r
     visualTab.add(fontNameCB);\r
     visualTab.add(fontSizeCB);\r
     visualTab.add(fontStyleCB);\r
-    visualTab.add(gapSymbolCB);\r
     visualTab.add(jPanel2);\r
-\r
     linkPanel.add(editLinkButtons, BorderLayout.EAST);\r
     editLinkButtons.add(newLink, null);\r
     editLinkButtons.add(editLink, null);\r
@@ -468,7 +473,7 @@ public class GPreferences extends JPanel
 \r
     tabbedPane.add(visualTab, "Visual");\r
     tabbedPane.add(connectTab,"Connections");\r
-    tabbedPane.add(exportTab, "File");\r
+    tabbedPane.add(exportTab, "Output");\r
     jPanel11.add(jLabel2);\r
     jPanel11.add(jLabel1);\r
     jPanel11.add(jLabel10);\r