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;
{
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);
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);
}
}
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)
{
cap.setText(new FormatAdapter().formatSequences(
e.getActionCommand(),
viewport.alignment,
- omitHidden));
+ omitHidden, viewport.colSel));
}
/**
{
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);
+ }
}
}
{
ex.printStackTrace();
}
-
+
return tp;
}
}
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)
{
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);