Example 1 with FastaFileFilter
use of uk.ac.babraham.SeqMonk.Utilities.FileFilters.FastaFileFilter in project SeqMonk by s-andrews.
the class ManualGenomeBuilderPanel method actionPerformed.
public void actionPerformed(ActionEvent ae) {
if (ae.getActionCommand().equals("add")) {
String newName = (String) JOptionPane.showInputDialog(this, "Region name", "Add region", JOptionPane.QUESTION_MESSAGE, null, null, "");
if (newName != null) {
manualGenome.getChromosome(newName);
}
} else if (ae.getActionCommand().equals("gff")) {
JFileChooser chooser = new JFileChooser(SeqMonkPreferences.getInstance().getDataLocation());
chooser.setMultiSelectionEnabled(false);
chooser.setFileFilter(new GFFFileFilter());
int result = chooser.showOpenDialog(this);
/*
* There seems to be a bug in the file chooser which allows the user to
* select no files, but not cancel if the control+double click on a file
*/
if (result == JFileChooser.CANCEL_OPTION || chooser.getSelectedFile() == null) {
return;
}
SeqMonkPreferences.getInstance().setLastUsedDataLocation(chooser.getSelectedFile());
new SimpleGFFReader(chooser.getSelectedFile());
gffFiles.add(chooser.getSelectedFile());
} else if (ae.getActionCommand().equals("pseudo")) {
if (pseudoBox.isSelected()) {
int pseudoNumber = 25;
if (pseudoNumberField.getText().length() > 0) {
pseudoNumber = Integer.parseInt(pseudoNumberField.getText());
}
manualGenome.addPseudoGenome(pseudoNumber);
} else {
manualGenome.removePseudoGenome();
}
} else if (ae.getActionCommand().equals("fasta")) {
JFileChooser chooser = new JFileChooser(SeqMonkPreferences.getInstance().getDataLocation());
chooser.setMultiSelectionEnabled(true);
chooser.setFileFilter(new FastaFileFilter());
int result = chooser.showOpenDialog(this);
/*
* There seems to be a bug in the file chooser which allows the user to
* select no files, but not cancel if the control+double click on a file
*/
if (result == JFileChooser.CANCEL_OPTION || chooser.getSelectedFile() == null) {
return;
}
SeqMonkPreferences.getInstance().setLastUsedDataLocation(chooser.getSelectedFile());
new SimpleFastaReader(chooser.getSelectedFiles());
} else if (ae.getActionCommand().equals("remove")) {
int[] rows = manualChrTable.getSelectedRows();
ManualGenomeChromosome[] chrsToRemove = new ManualGenomeChromosome[rows.length];
for (int i = 0; i < rows.length; i++) {
chrsToRemove[i] = manualGenome.getChromosome(manualChrTable.convertRowIndexToModel(rows[i]));
}
manualGenome.removeChromosome(chrsToRemove);
} else if (ae.getActionCommand().equals("create")) {
// Check if the species name is set and make the folder if needs be
String speciesName = speciesField.getText().trim();
if (speciesName.length() == 0) {
reportError("Species name isn't filled in");
return;
}
// Check that the assembly name is set
String assemblyName = assemblyField.getText().trim();
if (assemblyName.length() == 0) {
reportError("Assembly name isn't filled in");
return;
}
// Check that we have some chromosomes
if (manualGenome.getRowCount() == 0) {
reportError("You need to define some chromosomes before creating your genome");
return;
}
// Check to see if they're making a silly number of chromosomes
if (manualGenome.getRowCount() > 100 && !pseudoBox.isSelected()) {
if (JOptionPane.showConfirmDialog(this, "<html>You're making a very large number of chromosomes which won't work well.<br>You should probably choose to make pseudo chromosomes for this genome.<br><br>Really continue?</html>", "That's a lot of chromosomes", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION)
return;
JOptionPane.showMessageDialog(this, "OK, but don't say we didn't warn you", "Going ahead", JOptionPane.WARNING_MESSAGE);
}
// See if the species folder exists already and make it if it doesn't
File speciesFolder = null;
try {
speciesFolder = new File(SeqMonkPreferences.getInstance().getGenomeBase().getAbsolutePath() + "/" + speciesName);
if (!speciesFolder.exists()) {
if (!speciesFolder.mkdir()) {
reportError("Failed to make " + speciesFolder + " folder");
return;
}
}
} catch (IOException ioe) {
throw new IllegalStateException(ioe);
}
// Make the assembly folder and bail out if it exists
File assemblyFolder = new File(speciesFolder.getAbsolutePath() + "/" + assemblyName);
if (assemblyFolder.exists()) {
reportError("There is already an assembly called " + speciesName + "/" + assemblyName + " you need to delete this manually before creating a new genome of the same name");
return;
}
if (!assemblyFolder.mkdir()) {
reportError("Failed to make " + assemblyFolder + " folder");
return;
}
// Copy over the gff files
try {
for (int f = 0; f < gffFiles.size(); f++) {
FileOutputStream fos = new FileOutputStream(new File(assemblyFolder.getAbsolutePath() + "/" + gffFiles.elementAt(f).getName()));
// PrintWriter pr = new PrintWriter(new File(assemblyFolder.getAbsolutePath()+"/"+gffFiles.elementAt(f).getName()));
FileInputStream fis = new FileInputStream(gffFiles.elementAt(f));
// BufferedReader br = new BufferedReader(new FileReader(gffFiles.elementAt(f)));
byte[] buffer = new byte[1024];
int noOfBytes = 0;
while ((noOfBytes = fis.read(buffer)) != -1) {
fos.write(buffer, 0, noOfBytes);
}
fis.close();
fos.close();
}
// Write out chromosome lengths along with aliases for pseudo chromosomes
manualGenome.writeGenomeFiles(assemblyFolder);
} catch (IOException ioe) {
throw new IllegalStateException(ioe);
}
JOptionPane.showMessageDialog(this, "Successfully created new custom genome", "Success", JOptionPane.INFORMATION_MESSAGE);
if (parent != null) {
parent.setVisible(false);
parent.dispose();
}
}
}
Also used :
GFFFileFilter(uk.ac.babraham.SeqMonk.Utilities.FileFilters.GFFFileFilter)
FastaFileFilter(uk.ac.babraham.SeqMonk.Utilities.FileFilters.FastaFileFilter)
IOException(java.io.IOException)
FileInputStream(java.io.FileInputStream)
JFileChooser(javax.swing.JFileChooser)
FileOutputStream(java.io.FileOutputStream)
File(java.io.File)
Aggregations
File (java.io.File)1
FileInputStream (java.io.FileInputStream)1
FileOutputStream (java.io.FileOutputStream)1
IOException (java.io.IOException)1
JFileChooser (javax.swing.JFileChooser)1
FastaFileFilter (uk.ac.babraham.SeqMonk.Utilities.FileFilters.FastaFileFilter)1
GFFFileFilter (uk.ac.babraham.SeqMonk.Utilities.FileFilters.GFFFileFilter)1
