Sends gapChar to seqData

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 5a404eb..8aa5159 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,6 +23,7 @@ import java.awt.event.*;
 import javax.swing.*;\r
 \r
 import jalview.schemes.*;\r
+import java.awt.BorderLayout;\r
 \r
 public class GAlignFrame\r
     extends JInternalFrame\r
@@ -113,15 +114,11 @@ public class GAlignFrame
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
   protected ButtonGroup colours = new ButtonGroup();\r
   JMenuItem vamsasStore = new JMenuItem();\r
-  protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
+  protected JMenuItem showTranslation = new JMenuItem();\r
   public JMenuItem featureSettings = new JMenuItem();\r
   JMenuItem fetchSequence = new JMenuItem();\r
   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
   JMenuItem annotationColour = new JMenuItem();\r
-  JMenuItem fetchSeqFeatures = new JMenuItem();\r
-\r
-\r
-\r
   JMenuItem associatedData = new JMenuItem();\r
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
   JMenu addSequenceMenu = new JMenu();\r
@@ -130,6 +127,16 @@ public class GAlignFrame
   JMenuItem addFromURL = new JMenuItem();\r
   JMenuItem exportAnnotations = new JMenuItem();\r
   JMenuItem exportFeatures = new JMenuItem();\r
+  protected JPanel statusPanel = new JPanel();\r
+  GridLayout gridLayout1 = new GridLayout();\r
+  JMenu jMenu3 = new JMenu();\r
+  JMenuItem showAllSeqs = new JMenuItem();\r
+  JMenuItem showAllColumns = new JMenuItem();\r
+  JMenu jMenu4 = new JMenu();\r
+  JMenuItem hideSelSequences = new JMenuItem();\r
+  JMenuItem hideSelColumns = new JMenuItem();\r
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
+\r
   public GAlignFrame()\r
   {\r
 \r
@@ -140,7 +147,7 @@ public class GAlignFrame
       setJMenuBar(alignFrameMenuBar);\r
 \r
       // dynamically fill save as menu with available formats\r
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)\r
       {\r
         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
                              elementAt(\r
@@ -968,14 +975,6 @@ public class GAlignFrame
         annotationColour_actionPerformed(e);\r
       }\r
     });\r
-    fetchSeqFeatures.setText("Fetch Sequence Features");\r
-    fetchSeqFeatures.addActionListener(new ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        fetchSeqFeatures_actionPerformed(e);\r
-      }\r
-    });\r
     associatedData.setText("Load Features / Annotations");\r
     associatedData.addActionListener(new ActionListener()\r
     {\r
@@ -1034,6 +1033,51 @@ public class GAlignFrame
         exportAnnotations_actionPerformed(e);\r
       }\r
     });\r
+    statusPanel.setLayout(gridLayout1);\r
+    jMenu3.setText("Show");\r
+    showAllSeqs.setText("All Sequences");\r
+    showAllSeqs.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showAllSeqs_actionPerformed(e);\r
+      }\r
+    });\r
+    showAllColumns.setText("All Columns");\r
+    showAllColumns.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showAllColumns_actionPerformed(e);\r
+      }\r
+    });\r
+    jMenu4.setText("Hide");\r
+    hideSelSequences.setText("Selected Sequences");\r
+    hideSelSequences.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        hideSelSequences_actionPerformed(e);\r
+      }\r
+    });\r
+    hideSelColumns.setText("Selected Columns");\r
+    hideSelColumns.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        hideSelColumns_actionPerformed(e);\r
+      }\r
+    });\r
+    hiddenMarkers.setText("Hidden Markers");\r
+    hiddenMarkers.setState(true);\r
+    hiddenMarkers.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        hiddenMarkers_actionPerformed(e);\r
+      }\r
+    });\r
+\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -1079,6 +1123,10 @@ public class GAlignFrame
     viewMenu.add(font);\r
     viewMenu.add(smoothFont);\r
     viewMenu.addSeparator();\r
+    viewMenu.add(jMenu3);\r
+    viewMenu.add(jMenu4);\r
+    viewMenu.add(hiddenMarkers);\r
+    viewMenu.addSeparator();\r
     viewMenu.add(wrapMenuItem);\r
     viewMenu.add(seqLimits);\r
     viewMenu.add(scaleAbove);\r
@@ -1090,7 +1138,6 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(annotationPanelMenuItem);\r
     viewMenu.addSeparator();\r
-    viewMenu.add(fetchSeqFeatures);\r
     viewMenu.add(showSeqFeatures);\r
     viewMenu.add(featureSettings);\r
     viewMenu.addSeparator();\r
@@ -1125,9 +1172,7 @@ public class GAlignFrame
     calculateMenu.add(showTranslation);\r
     calculateMenu.add(autoCalculate);\r
     webServiceNoServices=new JMenuItem("<No Services>");\r
-    webService.add(webServiceNoServices);\r
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
-    jMenu1.add(pasteNew);\r
+    webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
     jMenu1.add(pasteThis);\r
     sort.add(sortIDMenuItem);\r
     sort.add(sortGroupMenuItem);\r
@@ -1142,6 +1187,12 @@ public class GAlignFrame
     addSequenceMenu.add(addFromFile);\r
     addSequenceMenu.add(addFromText);\r
     addSequenceMenu.add(addFromURL);\r
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
+    statusPanel.add(statusBar, null);\r
+    jMenu3.add(showAllColumns);\r
+    jMenu3.add(showAllSeqs);\r
+    jMenu4.add(hideSelColumns);\r
+    jMenu4.add(hideSelSequences);\r
   }\r
 \r
   protected void outputText_actionPerformed(ActionEvent e)\r
@@ -1481,17 +1532,53 @@ public class GAlignFrame
 \r
   }\r
 \r
-  public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
+\r
+  public void associatedData_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
-  public void associatedData_actionPerformed(ActionEvent e)\r
+  public void autoCalculate_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
-  public void autoCalculate_actionPerformed(ActionEvent e)\r
+  public void showAllSeqs_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void showAllColumns_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void hideSelSequences_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void hideSelColumns_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void hiddenMarkers_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void findPdbId_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void enterPdbId_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void pdbFile_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r