SequenceFetcher new class

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 5a0357e..2909727 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
@@ -116,7 +116,9 @@ public class GAlignFrame
   JMenuItem vamsasStore = new JMenuItem();\r
   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
   protected JTabbedPane tabbedPane = new JTabbedPane();\r
-  protected JMenuItem featureSettings = new JMenuItem();\r
+  public JMenuItem featureSettings = new JMenuItem();\r
+  public JCheckBoxMenuItem seqDBRef = new JCheckBoxMenuItem();\r
+  JMenuItem fetchSequence = new JMenuItem();\r
 \r
   public GAlignFrame()\r
   {\r
@@ -826,13 +828,14 @@ 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 +947,23 @@ public class GAlignFrame
         featureSettings_actionPerformed(e);\r
       }\r
     });\r
+    seqDBRef.setState( jalview.bin.Cache.getDefault("SHOW_DBPREFIX",true));\r
+    seqDBRef.setText("Show Full Sequence Id");\r
+    seqDBRef.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        seqDBRef_actionPerformed(e);\r
+      }\r
+    });\r
+    fetchSequence.setText("Fetch Sequence...");\r
+    fetchSequence.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        fetchSequence_actionPerformed(e);\r
+      }\r
+    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -951,6 +971,7 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);\r
     alignFrameMenuBar.add(calculateMenu);\r
     alignFrameMenuBar.add(webService);\r
+    fileMenu.add(fetchSequence);\r
     fileMenu.add(vamsasStore);\r
     fileMenu.add(saveAlignmentMenu);\r
     fileMenu.add(jMenu2);\r
@@ -983,7 +1004,8 @@ 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 +1292,16 @@ 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 +1382,10 @@ public class GAlignFrame
   {\r
 \r
   }\r
+\r
+  public void fetchSequence_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
 }\r