/**
* Removes duplicate adjacent {@link #getPositions() positions} from this route, leaving only
* distinct neighbours
*/
public void removeDuplicates() {
List<P> positions = getPositions();
P previous = null;
int index = 0;
while (index < positions.size()) {
P next = positions.get(index);
if (previous != null && (!next.hasCoordinates() || next.calculateDistance(previous) <= 0.0)) {
positions.remove(index);
} else index++;
previous = next;
}
}
private static List<String> importGenomeData(
File genome_text_file, String target_organism, int sex) throws IOException {
List<String> temp_genome_data =
new ArrayList<String>(); // The genome data array that contains the sizes of each chromosome
// int haploid_number; // Used to determine the size of the first dimension in the
// temp_genome_data array
boolean found_target_organism =
false; // Used to determine what action to take when a new header line in the file is found;
// close if true, keep reading if false
boolean end_of_genome = false; // True when the Y chromosome has been dealt with
// Construct BufferedReader from FileReader; search for header line of target organism and
// obtain the haploid number then create a two dimensional array, size of the first dimension
// equals the haploid number, size of second dimension equals two (two chromosomes to form
// deploid organism)
// At this point, the next lines correspond to the size of each chromosome so populate the newly
// created array
// with this information. Stop reading when no more new lines or when a new header line is found
BufferedReader genome_file_reader = new BufferedReader(new FileReader(genome_text_file));
String line = null;
StringBuilder organism_name;
while ((line = genome_file_reader.readLine()) != null) {
String[] split_line = line.split(" ");
if (split_line[0].equals(">")) // If this is a first header line
{
organism_name =
new StringBuilder()
.append(split_line[1])
.append(" ")
.append(
split_line[
2]); // Recreate the genus and species of the organism from the strings that
// were separated during the splitting of the line
if (organism_name
.toString()
.equals(target_organism)) // If this line refers to the organism of interest
{
found_target_organism = true;
haploid_number =
Integer.parseInt(split_line[4]); // Get the haploid number stored in the header line
} else {
found_target_organism = false;
continue; // This is a header line but it is not the organism of interest
}
} else if (found_target_organism
&& !end_of_genome) // This is not a header line and we probably want to import this line
{
// boolean autosome = true;
switch (sex) {
case 1: // Female
{
if (split_line[0].equals("chrX")) {
temp_genome_data.add(split_line[1] + "," + split_line[1]);
} else if (split_line[0].equals("chrY")) {
end_of_genome = true;
} // Ignore the Y chromosome
else
temp_genome_data.add(
split_line[1] + "," + split_line[1]); // The current line is an autosome
}
break;
case 2: // Male
{
if (split_line[0].equals("chrX")) {
temp_genome_data.add(split_line[1] + ",");
} else if (split_line[0].equals("chrY")) {
String temp =
temp_genome_data.get(
temp_genome_data.size() - 1); // Store the value already there
temp_genome_data.remove(temp_genome_data.size() - 1);
temp = temp + split_line[1];
temp_genome_data.add(temp);
end_of_genome = true;
} else
temp_genome_data.add(
split_line[1] + "," + split_line[1]); // The current line is an autosome
}
break;
}
}
} // while ((line = genome_file_reader.readLine()) != null)
genome_file_reader.close();
return temp_genome_data;
} // importGenomeData
public P remove(int index) {
List<P> positions = getPositions();
return positions.remove(index);
}
