selection removed, now SelectionGroup does same job as id select and residue select

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4209455..c679559 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -64,6 +64,7 @@ public class AlignFrame extends GAlignFrame
   protected void saveAs_actionPerformed(ActionEvent e)\r
   {\r
     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+    chooser.setFileView(new JalviewFileView());\r
     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
     chooser.setToolTipText("Save");\r
     int value = chooser.showSaveDialog(this);\r
@@ -222,7 +223,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void moveSelectedSequences(boolean up)\r
   {\r
-    SequenceGroup sg = viewport.getRubberbandGroup();\r
+    SequenceGroup sg = viewport.getSelectionGroup();\r
     if (sg == null)\r
       return;\r
 \r
@@ -266,10 +267,10 @@ public class AlignFrame extends GAlignFrame
 \r
   protected void copy_actionPerformed(ActionEvent e)\r
   {\r
-   if(viewport.getRubberbandGroup()==null)\r
+   if(viewport.getSelectionGroup()==null)\r
      return;\r
 \r
-   SequenceGroup sg = viewport.getRubberbandGroup();\r
+   SequenceGroup sg = viewport.getSelectionGroup();\r
 \r
      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
      StringBuffer buffer= new StringBuffer();\r
@@ -352,10 +353,10 @@ public class AlignFrame extends GAlignFrame
   protected void delete_actionPerformed(ActionEvent e)\r
   {\r
     addHistoryItem("Delete");\r
-    if (viewport.getRubberbandGroup() == null)\r
+    if (viewport.getSelectionGroup() == null)\r
       return;\r
 \r
-     SequenceGroup sg = viewport.getRubberbandGroup();\r
+     SequenceGroup sg = viewport.getSelectionGroup();\r
      for (int i=0;i < sg.sequences.size(); i++)\r
      {\r
        SequenceI seq = sg.getSequenceAt(i);\r
@@ -368,7 +369,7 @@ public class AlignFrame extends GAlignFrame
           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
      }\r
 \r
-     viewport.setRubberbandGroup(null);\r
+     viewport.setSelectionGroup(null);\r
      viewport.alignment.deleteGroup(sg);\r
      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
      if(viewport.getAlignment().getHeight()<1)\r
@@ -404,7 +405,7 @@ public class AlignFrame extends GAlignFrame
   protected void deleteGroups_actionPerformed(ActionEvent e)\r
   {\r
     viewport.alignment.deleteAllGroups();\r
-    viewport.getSelection().clear();\r
+    viewport.setSelectionGroup(null);\r
 \r
     alignPanel.RefreshPanels();\r
   }\r
@@ -413,29 +414,26 @@ public class AlignFrame extends GAlignFrame
 \r
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    Selection sel = viewport.getSelection();\r
+    SequenceGroup sg = new SequenceGroup();\r
     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
-      sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
+      sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
+    sg.setEndRes(viewport.alignment.getWidth());\r
+    viewport.setSelectionGroup(sg);\r
     PaintRefresher.Refresh(null);\r
   }\r
 \r
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    viewport.setRubberbandGroup(null);\r
-    viewport.getSelection().clear();\r
+    viewport.setSelectionGroup(null);\r
     PaintRefresher.Refresh(null);\r
   }\r
 \r
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    Selection sel = viewport.getSelection();\r
+    SequenceGroup sg = viewport.getSelectionGroup();\r
     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
-    {\r
-      if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
-        sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
-      else\r
-        sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
-    }\r
+      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
+\r
     PaintRefresher.Refresh(null);\r
   }\r
 \r
@@ -870,7 +868,7 @@ if ( viewport.getConservationSelected() )
 \r
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    if(viewport.getSelection().size()<2)\r
+    if(viewport.getSelectionGroup().getSize()<2)\r
       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
     else\r
     {\r
@@ -882,7 +880,8 @@ if ( viewport.getConservationSelected() )
 \r
   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
+\r
+    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
        || viewport.getAlignment().getHeight()<4)\r
     {\r
       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
@@ -938,9 +937,9 @@ if ( viewport.getConservationSelected() )
     }\r
 \r
     TreePanel tp=null;\r
-   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
+   if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
    {\r
-     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
+     tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
                          0, viewport.alignment.getWidth());\r
    }\r
    else\r