@Override
protected List<AlignmentFile> getAlignmentFiles(int currentIter) {
// sort input file alphabetically to look nicer
File inputDirectory = new File(this.inputDirectory);
File[] listOfFiles = inputDirectory.listFiles();
Arrays.sort(listOfFiles, new NaturalOrderFilenameComparator());
List<AlignmentFile> alignmentDataList = new ArrayList<AlignmentFile>();
List<Feature> allFeatures = new ArrayList<Feature>();
// load feature data
for (int i = 0; i < listOfFiles.length; i++) {
if (listOfFiles[i].isFile()) {
File myFile = listOfFiles[i];
String filename = myFile.getName();
String path = myFile.getPath();
String extension = filename.substring(filename.lastIndexOf('.') + 1);
// ignore other crap files in the directory
if (!"txt".equals(extension)) {
continue;
}
List<Feature> features = new ArrayList<Feature>();
try {
features = this.loadFeatures(path);
} catch (ValidityException e) {
e.printStackTrace();
} catch (ParsingException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
AlignmentFile alignmentData = new AlignmentFile(i, myFile, features);
if (verbose) {
System.out.println(
"Load " + filename + " with " + alignmentData.getFeaturesCount() + " features");
}
alignmentDataList.add(alignmentData);
allFeatures.addAll(alignmentData.getFeatures());
}
}
this.alignmentFiles = alignmentDataList;
return alignmentDataList;
}
