X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=de3e8fd29c7c941f7a954b41f444d20678c3c5cf;hb=6f72987ac17c0846a12b635c29fc1788b3c13b8c;hp=4641fdbb043fc9a3ecea14029f58b8baaad2c10c;hpb=8b4e92b5a422435311e2384f04b28f16b77206b6;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4641fdb..de3e8fd 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -60,6 +60,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
 
+  public String fileName = null;
+
   private int treeCount = 0;
 
   /**
@@ -177,7 +179,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 newap.av.viewName = "View " +
                     (Desktop.getViewCount(viewport.getSequenceSetId())+1);
 
-                addAlignmentPanel(newap, true);
+                addAlignmentPanel(newap, false);
 
                 tabbedPane.setSelectedIndex(tabbedPane.getTabCount()-1);
 
@@ -571,12 +573,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+    if(fileName==null || currentFileFormat==null)
+      saveAs_actionPerformed(null);
+    else
+      saveAlignment(fileName, currentFileFormat);
+  }
+
   /**
    * DOCUMENT ME!
    *
    * @param e DOCUMENT ME!
    */
-  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty( "LAST_DIRECTORY"),
@@ -597,7 +608,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
         currentFileFormat = chooser.getSelectedFormat();
-
         if (currentFileFormat == null)
         {
           JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -608,13 +618,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           return;
         }
 
+        fileName = chooser.getSelectedFile().getPath();
+
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
                                     currentFileFormat);
 
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
 
-      saveAlignment(choice, currentFileFormat);
+      saveAlignment(fileName, currentFileFormat);
     }
   }
 
@@ -632,6 +643,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       new Jalview2XML().SaveAlignment(this, file, shortName);
 
+      statusBar.setText("Successfully saved to file: "
+                          +fileName+" in "
+                          +format +" format.");
+
+
       // USE Jalview2XML to save this file
       return true;
     }
@@ -670,6 +686,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         out.print(output);
         out.close();
         this.setTitle(file);
+        statusBar.setText("Successfully saved to file: "
+                          +fileName+" in "
+                          +format +" format.");
         return true;
       }
       catch (Exception ex)
@@ -821,8 +840,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         }
       //  alignPanels = null;
       }
-      else
-        System.out.println("null one here");
+    //  else
+     //   System.out.println("null one here");
 
     //  alignPanel = null;
     //  viewport = null;
@@ -2054,8 +2073,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 viewport.getIgnoreGapsConsensus());
 
          sg.cs.setConsensus(AAFrequency.calculate(
-             sg.getSequences(true), 0,
-             sg.getWidth()));
+             sg.getSequences(true), sg.getStartRes(),
+             sg.getEndRes()+1));
        }
         else
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
@@ -2065,8 +2084,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.getSequences(true), 0,
-                                            viewport.alignment.getWidth() - 1);
+                                            sg.getSequences(true),
+                                            sg.getStartRes(),
+                                            sg.getEndRes()+1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           sg.cs.setConservation(c);