X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=53b721d3d64ce7f1a57d0eb7ed66ffd82169a69d;hb=e5817172683acab3d5f51789fdf44f7a9106c8dd;hp=e870deaf4a6f3aa183c3eca359c28729dbca66fb;hpb=48fa14983ce103efe05661cbdd08a6811214625b;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e870dea..53b721d 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -59,9 +59,13 @@ public class AlignFrame
   Vector alignPanels = new Vector();
 
 
-  /** DOCUMENT ME!! */
+  /** 
+   * Last format used to load or save alignments in this window 
+   */
   String currentFileFormat = null;
-
+  /**
+   * Current filename for this alignment
+   */
   String fileName = null;
 
 
@@ -692,10 +696,8 @@ public class AlignFrame
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty( "LAST_DIRECTORY"),
-        new String[]
-        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","amsa","jar" },
-        new String[]
-        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" },
+        jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
+        jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
         currentFileFormat,
         false);
 
@@ -725,8 +727,11 @@ public class AlignFrame
                                     currentFileFormat);
 
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
-
-      saveAlignment(fileName, currentFileFormat.substring(0,currentFileFormat.indexOf(" ")));
+      if (currentFileFormat.indexOf(" ")>-1)
+      {
+        currentFileFormat = currentFileFormat.substring(0, currentFileFormat.indexOf(" "));
+      }
+      saveAlignment(fileName, currentFileFormat);
     }
   }
 
@@ -774,7 +779,7 @@ public class AlignFrame
       String output = f.formatSequences(
           format,
           (Alignment) viewport.alignment, // class cast exceptions will occur in the distant future
-          omitHidden, f.getCacheSuffixDefault(format));
+          omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
 
       if (output == null)
       {
@@ -846,7 +851,7 @@ public class AlignFrame
     cap.setText(new FormatAdapter().formatSequences(
         e.getActionCommand(),
         viewport.alignment,
-        omitHidden));
+        omitHidden, viewport.colSel));
   }
 
   /**
@@ -3320,21 +3325,28 @@ public class AlignFrame
     {
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-
+      jalview.io.NewickFile fin = null;
       try
       {
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
+        fin = new jalview.io.NewickFile(choice,
             "File");
         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
       }
       catch (Exception ex)
       {
         JOptionPane.showMessageDialog(Desktop.desktop,
-                                      "Problem reading tree file",
                                       ex.getMessage(),
+                                      "Problem reading tree file",
                                       JOptionPane.WARNING_MESSAGE);
         ex.printStackTrace();
       }
+      if (fin!=null && fin.hasWarningMessage())
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                fin.getWarningMessage(),
+                "Possible problem with tree file",
+                JOptionPane.WARNING_MESSAGE);
+      }
     }
   }
 
@@ -3399,7 +3411,7 @@ public class AlignFrame
     {
       ex.printStackTrace();
     }
-
+    
     return tp;
   }
 
@@ -3617,6 +3629,7 @@ public class AlignFrame
   }
 protected void showProductsFor(SequenceI[] sel, Alignment ds, boolean isRegSel, boolean dna, String source)
   {
+  ds = this.getViewport().alignment.getDataset(); // update our local dataset reference
   Alignment prods = CrossRef.findXrefSequences(sel, dna, source, ds);
   if (prods!=null)
   {
@@ -3624,7 +3637,7 @@ protected void showProductsFor(SequenceI[] sel, Alignment ds, boolean isRegSel,
     for (int s=0; s<sprods.length;s++)
     {
       sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
-      if (!ds.getSequences().contains(sprods[s].getDatasetSequence()))
+      if (ds.getSequences()==null || !ds.getSequences().contains(sprods[s].getDatasetSequence()))
         ds.addSequence(sprods[s].getDatasetSequence());
     }
     Alignment al = new Alignment(sprods);