/**
* Returns the last selected folder.
*
* @param lastSelectedFolder the last selected folder
* @return the last selected folder
*/
public String getLastSelectedFolder(LastSelectedFolder lastSelectedFolder) {
String result = null;
if (result == null) {
return null;
}
String folder = lastSelectedFolder.getLastSelectedFolder(SequenceDbDetailsDialog.lastFolderKey);
if (folder == null) {
folder = lastSelectedFolder.getLastSelectedFolder();
}
return folder;
}
/**
* Opens a file chooser where the user can select the database file.
*
* @param evt
*/
private void browseDatabaseSettingsActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_browseDatabaseSettingsActionPerformed
LastSelectedFolder lastSelectedFolder = peptideShakerGUI.getLastSelectedFolder();
File startLocation = null;
File utilitiesDbFolder = peptideShakerGUI.getUtilitiesUserPreferences().getDbFolder();
if (utilitiesDbFolder != null && utilitiesDbFolder.exists()) {
startLocation = utilitiesDbFolder;
}
if (startLocation == null) {
startLocation = new File(getLastSelectedFolder(lastSelectedFolder));
}
UtilitiesUserPreferences utilitiesUserPreferences =
UtilitiesUserPreferences.loadUserPreferences();
if (utilitiesUserPreferences.getDbFolder() != null
&& utilitiesUserPreferences.getDbFolder().exists()) {
startLocation = utilitiesUserPreferences.getDbFolder();
}
// First check whether a file has already been selected.
// If so, start from that file's parent.
if (databaseSettingsTxt.getText() != null && new File(databaseSettingsTxt.getText()).exists()) {
File temp = new File(databaseSettingsTxt.getText());
startLocation = temp.getParentFile();
}
JFileChooser fc = new JFileChooser(startLocation);
FileFilter filter =
new FileFilter() {
@Override
public boolean accept(File myFile) {
return myFile.getName().toLowerCase().endsWith("fasta")
|| myFile.getName().toLowerCase().endsWith("fas")
|| myFile.isDirectory();
}
@Override
public String getDescription() {
return "Supported formats: FASTA (.fasta or .fas)";
}
};
fc.setFileFilter(filter);
int result = fc.showOpenDialog(this);
if (result == JFileChooser.APPROVE_OPTION) {
File file = fc.getSelectedFile();
if (file.getName().contains(" ")) {
renameFastaFileName(file);
} else {
databaseSettingsTxt.setText(file.getAbsolutePath());
databaseSettingsTxt.setText(file.getAbsolutePath());
}
lastSelectedFolder.setLastSelectedFolder(
SequenceDbDetailsDialog.lastFolderKey, file.getAbsolutePath());
targetDecoySettingsButton.setEnabled(true);
// check if the database contains decoys
if (!file.getAbsolutePath()
.endsWith(
peptideShakerGUI.getUtilitiesUserPreferences().getTargetDecoyFileNameSuffix()
+ ".fasta")) {
int value =
JOptionPane.showConfirmDialog(
this,
"The selected FASTA file does not seem to contain decoy sequences.\n"
+ "Decoys are required by PeptideShaker. Add decoys?",
"Add Decoy Sequences?",
JOptionPane.YES_NO_OPTION);
if (value == JOptionPane.NO_OPTION) {
// do nothing
} else if (value == JOptionPane.YES_OPTION) {
targetDecoySettingsButtonActionPerformed(null);
}
}
validateParametersInput(false);
}
} // GEN-LAST:event_browseDatabaseSettingsActionPerformed
