a flauss changes

diff --git a/src/jalview/jbappletgui/GAlignFrame.java b/src/jalview/jbappletgui/GAlignFrame.java
index 42b2d63..4c95334 100755 (executable)
--- a/src/jalview/jbappletgui/GAlignFrame.java
+++ b/src/jalview/jbappletgui/GAlignFrame.java
@@ -215,7 +215,7 @@ public class GAlignFrame extends Frame
         viewTextMenuItem_actionPerformed(null);\r
       }\r
     });\r
-    sortPairwiseMenuItem.setLabel("By Pairwise Identity");\r
+    sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -223,7 +223,7 @@ public class GAlignFrame extends Frame
         sortPairwiseMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    sortIDMenuItem.setLabel("By ID");\r
+    sortIDMenuItem.setLabel("by ID");\r
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -231,7 +231,7 @@ public class GAlignFrame extends Frame
         sortIDMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    sortGroupMenuItem.setLabel("By Group");\r
+    sortGroupMenuItem.setLabel("by Group");\r
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -433,7 +433,7 @@ public class GAlignFrame extends Frame
         redoMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    conservationMenuItem.setLabel("By Conservation");\r
+    conservationMenuItem.setLabel("by Conservation");\r
     conservationMenuItem.addItemListener(new java.awt.event.ItemListener()\r
     {\r
       public void itemStateChanged(ItemEvent e)\r
@@ -682,13 +682,13 @@ public class GAlignFrame extends Frame
     editMenu.add(removeRedundancyMenuItem);\r
     searchMenu.add(findMenuItem);\r
     viewMenu.add(font);\r
-    viewMenu.add(fullSeqId);\r
     viewMenu.addSeparator();\r
     viewMenu.add(wrapMenuItem);\r
     viewMenu.add(scaleAbove);\r
     viewMenu.add(scaleLeft);\r
     viewMenu.add(scaleRight);\r
     viewMenu.addSeparator();\r
+    viewMenu.add(fullSeqId);\r
     viewMenu.add(viewBoxesMenuItem);\r
     viewMenu.add(viewTextMenuItem);\r
     viewMenu.add(colourTextMenuItem);\r
@@ -697,8 +697,8 @@ public class GAlignFrame extends Frame
     viewMenu.addSeparator();\r
     viewMenu.add(overviewMenuItem);\r
     colourMenu.add(applyToAllGroups);\r
-    colourMenu.add(noColourmenuItem);\r
     colourMenu.addSeparator();\r
+    colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(BLOSUM62Colour);\r
     colourMenu.add(PIDColour);\r

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 7370995..b4cd276 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -274,7 +274,7 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    sortPairwiseMenuItem.setText("By Pairwise Identity");\r
+    sortPairwiseMenuItem.setText("by Pairwise Identity");\r
     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -282,7 +282,7 @@ public class GAlignFrame extends JInternalFrame
         sortPairwiseMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    sortIDMenuItem.setText("By ID");\r
+    sortIDMenuItem.setText("by ID");\r
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -290,7 +290,7 @@ public class GAlignFrame extends JInternalFrame
         sortIDMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    sortGroupMenuItem.setText("By Group");\r
+    sortGroupMenuItem.setText("by Group");\r
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -691,6 +691,7 @@ public class GAlignFrame extends JInternalFrame
       }\r
     });\r
     fullSeqId.setText("Show Full Sequence ID");\r
+    fullSeqId.setState(true);\r
     fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -810,13 +811,12 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeRedundancyMenuItem);\r
     searchMenu.add(findMenuItem);\r
     viewMenu.add(font);\r
-    viewMenu.add(fullSeqId);\r
     viewMenu.addSeparator();\r
     viewMenu.add(wrapMenuItem);\r
+    viewMenu.add(fullSeqId);\r
     viewMenu.add(scaleAbove);\r
     viewMenu.add(scaleLeft);\r
     viewMenu.add(scaleRight);\r
-    viewMenu.addSeparator();\r
     viewMenu.add(viewBoxesMenuItem);\r
     viewMenu.add(viewTextMenuItem);\r
     viewMenu.add(colourTextMenuItem);\r
@@ -826,8 +826,8 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.addSeparator();\r
     viewMenu.add(overviewMenuItem);\r
     colourMenu.add(applyToAllGroups);\r
-    colourMenu.add(noColourmenuItem);\r
     colourMenu.addSeparator();\r
+    colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(BLOSUM62Colour);\r
     colourMenu.add(PIDColour);\r

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 1be96fb..2642d9c 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -50,7 +50,7 @@ public class GDesktop extends JFrame
     FileMenu.setText("File");\r
     HelpMenu.setText("Help");\r
     inputLocalFileMenuItem.setMnemonic('L');\r
-    inputLocalFileMenuItem.setText("Local File");\r
+    inputLocalFileMenuItem.setText("from File");\r
     inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -59,7 +59,7 @@ public class GDesktop extends JFrame
       }\r
     });\r
     inputURLMenuItem.setMnemonic('U');\r
-    inputURLMenuItem.setText("From URL");\r
+    inputURLMenuItem.setText("from URL");\r
     inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -68,7 +68,7 @@ public class GDesktop extends JFrame
       }\r
     });\r
     inputTextboxMenuItem.setMnemonic('C');\r
-    inputTextboxMenuItem.setText("Cut & Paste Textbox");\r
+    inputTextboxMenuItem.setText("from Textbox");\r
     inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r