/**
* ************************** readDataFile **************************** * Reads the input file and
* gets the number of taxa and alignment * length * *
* *********************************************************************
*/
public static void getHeader(String infilenameComplete) {
// needs the complete path to the file
try {
TextInputStream in = new TextInputStream(infilenameComplete);
String line = in.readLine();
in.close();
StringTokenizer reader = new StringTokenizer(line);
options.setNumTaxa(Integer.parseInt(reader.nextToken()));
options.setNumSites(Integer.parseInt(reader.nextToken()));
} catch (FileNotFoundException e) {
JOptionPane.showMessageDialog(
new JFrame(),
"Could not read the input alignment",
"jModelTest error",
JOptionPane.ERROR_MESSAGE);
}
if (options.getNumTaxa() <= 4)
JOptionPane.showMessageDialog(
new JFrame(),
"The number of taxa does not seem to be correct: " + options.getNumTaxa(),
"jModelTest error",
JOptionPane.ERROR_MESSAGE);
if (options.getNumSites() <= 1)
JOptionPane.showMessageDialog(
new JFrame(),
"The number of sites does not seem to be correct: " + options.getNumTaxa(),
"jModelTest error",
JOptionPane.ERROR_MESSAGE);
}
public abstract class AlignmentReader {
private static ApplicationOptions options = ApplicationOptions.getInstance();;
/**
* ************************** readDataFile **************************** * Reads the input file and
* gets the number of taxa and alignment * length * *
* *********************************************************************
*/
public static void getHeader(String infilenameComplete) {
// needs the complete path to the file
try {
TextInputStream in = new TextInputStream(infilenameComplete);
String line = in.readLine();
in.close();
StringTokenizer reader = new StringTokenizer(line);
options.setNumTaxa(Integer.parseInt(reader.nextToken()));
options.setNumSites(Integer.parseInt(reader.nextToken()));
} catch (FileNotFoundException e) {
JOptionPane.showMessageDialog(
new JFrame(),
"Could not read the input alignment",
"jModelTest error",
JOptionPane.ERROR_MESSAGE);
}
if (options.getNumTaxa() <= 4)
JOptionPane.showMessageDialog(
new JFrame(),
"The number of taxa does not seem to be correct: " + options.getNumTaxa(),
"jModelTest error",
JOptionPane.ERROR_MESSAGE);
if (options.getNumSites() <= 1)
JOptionPane.showMessageDialog(
new JFrame(),
"The number of sites does not seem to be correct: " + options.getNumTaxa(),
"jModelTest error",
JOptionPane.ERROR_MESSAGE);
}
/**
* Creates an alignment instance.
*
* @param out the out
* @param pr the pushback reader which contains the alignment
* @param debug the debug state
* @return the alignment
* @throws AlignmentParseException the alignment parse exception
* @throws IOException Signals that an I/O exception has occured.
*/
public static Alignment createAlignment(PrintWriter out, PushbackReader pr, boolean debug)
throws AlignmentParseException, IOException {
if (debug) {
out.println("");
out.println("**********************************************************");
out.println(" Reading alignment...");
}
Alignment alignment = null;
try {
alignment = new ReadAlignment(pr);
} catch (pal.alignment.AlignmentParseException e) {
throw new AlignmentParseException(e.getMessage());
}
List<String> seqNames = new ArrayList<String>(alignment.getSequenceCount());
for (int i = 0; i < alignment.getSequenceCount(); i++) {
seqNames.add(alignment.getIdentifier(i).getName());
}
String currString;
int size = alignment.getSequenceCount();
for (int i = 0; i < size; i++) {
currString = seqNames.get(i);
for (int j = i + 1; j < size; j++) {
if (seqNames.get(j).equals(currString)) {
throw new AlignmentParseException(
"ERROR: There are duplicated taxa names in the alignment: " + currString);
}
}
}
if (debug) {
for (int i = 0; i < alignment.getSequenceCount(); i++) {
out.println(" Sequence #" + (i + 1) + ": " + alignment.getIdentifier(i).getName());
}
out.println(
" Alignment contains "
+ alignment.getSequenceCount()
+ " sequences of length "
+ alignment.getSiteCount());
out.println("");
out.println("**********************************************************");
out.println("");
}
return alignment;
}
} // class AlignmentReader