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;
}
public void actionPerformed(ActionEvent e)
{
+ // TODO: new thread for this call with vis-delay
af.showProductsFor(sel, ds, isRegSel, dna, source);
}
}
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)
- {
- SequenceI[] sprods = new SequenceI[prods.getHeight()];
- for (int s=0; s<sprods.length;s++)
- {
- sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
- if (ds.getSequences()==null || !ds.getSequences().contains(sprods[s].getDatasetSequence()))
- ds.addSequence(sprods[s].getDatasetSequence());
- }
- Alignment al = new Alignment(sprods);
- AlignedCodonFrame[] cf = prods.getCodonFrames();
- for (int s=0; cf!=null && s<cf.length; s++)
+ final boolean fisRegSel = isRegSel;
+ final boolean fdna = dna;
+ final String fsrc = source;
+ final AlignFrame ths = this;
+ final SequenceI[] fsel = sel;
+ Runnable foo = new Runnable() {
+
+ public void run()
{
- al.addCodonFrame(cf[s]);
- cf[s] = null;
+ final long sttime = System.currentTimeMillis();
+ ths.setProgressBar("Searching for sequences from "+fsrc, sttime);
+ try {
+ Alignment ds = ths.getViewport().alignment.getDataset(); // update our local dataset reference
+ Alignment prods = CrossRef.findXrefSequences(fsel, fdna, fsrc, ds);
+ if (prods!=null)
+ {
+ SequenceI[] sprods = new SequenceI[prods.getHeight()];
+ for (int s=0; s<sprods.length;s++)
+ {
+ sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
+ if (ds.getSequences()==null || !ds.getSequences().contains(sprods[s].getDatasetSequence()))
+ ds.addSequence(sprods[s].getDatasetSequence());
+ sprods[s].updatePDBIds();
+ }
+ Alignment al = new Alignment(sprods);
+ AlignedCodonFrame[] cf = prods.getCodonFrames();
+ for (int s=0; cf!=null && s<cf.length; s++)
+ {
+ al.addCodonFrame(cf[s]);
+ cf[s] = null;
+ }
+ al.setDataset(ds);
+ AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ String newtitle =""+((fdna) ? "Proteins " : "Nucleotides ") + " for "+((fisRegSel) ? "selected region of " : "")
+ + getTitle();
+ Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ } else {
+ System.err.println("No Sequences generated for xRef type "+fsrc);
+ }
+ }
+ catch (Exception e)
+ {
+ jalview.bin.Cache.log.error("Exception when finding crossreferences",e);
+ }
+ catch (Error e)
+ {
+ jalview.bin.Cache.log.error("Error when finding crossreferences",e);
+ }
+ ths.setProgressBar("Finished searching for sequences from "+fsrc, sttime);
}
- al.setDataset(ds);
- AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- String newtitle =""+((dna) ? "Proteins " : "Nucleotides ") + " for "+((isRegSel) ? "selected region of " : "")
- + getTitle();
- Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- } else {
- System.err.println("No Sequences generated for xRef type "+source);
- }
+
+ };
+ Thread frunner = new Thread(foo);
+ frunner.start();
}
git://source.jalview.org / jalview.git / blobdiff