What is the DNA sequence matching code below do and how it is working?

public class Sequence_Match {

public static void main(String args[]){

int matchLength = 0;

String corpusSeq = null;

String patternSeq = null;

String maskSeq = null;

if (args.length < 3)

{

System.out.println("Syntax: java Sequence_Match " +

" " +

"[]");

return;

}

else

{

matchLength = Integer.parseInt(args[0]);

corpusSeq = SeqReader.readSeq(args[1]);

patternSeq = SeqReader.readSeq(args[2]);

Terminal.println("M = " + matchLength);

Terminal.println("CORPUS: " + corpusSeq.length() + " bases");

Terminal.println("PATTERN: " + patternSeq.length()+" bases");

}

if (args.length > 3)

{

maskSeq = SeqReader.readSeq(args[3]);

Terminal.println("MASK: "+maskSeq.length()+" bases");

}

}

matchLength = 1;

corpusSeq = SeqReader.readSeq("test-corpus.txt");

patternSeq = SeqReader.readSeq("test-pattern.txt");

//maskSeq = SeqReader.readSeq("test2-mask.txt");

//*/

StringTable table = createTable(patternSeq, matchLength);

if (maskSeq != null)

maskTable(table, maskSeq, matchLength);

// table.printTable(); System.out.println("");

findMatches(table, corpusSeq, matchLength);

}

public static StringTable createTable(String patternSeq, int matchLength)

{

StringTable table = new StringTable(patternSeq.length());

for (int j = 0; j < patternSeq.length() - matchLength + 1; j++)

{

String key = patternSeq.substring(j, j + matchLength);

Record rec = table.find(key);

if (rec == null) // not found -- need new Record

{

rec = new Record(key);

if (!table.insert(rec))

System.out.println("Error (insert): hash table is full! ");

}

rec.positions.add(new Integer(j));

}

return table;

}

// Remove all substrings in the mask sequence from a StringTable.

//

public static void maskTable(StringTable table, String maskSeq,

int matchLength)

{

for (int j = 0; j < maskSeq.length() - matchLength + 1; j++)

{

String key = maskSeq.substring(j, j + matchLength);

Record rec = table.find(key);

if (rec != null)

table.remove(rec);

}

}

// Find and print all matches between the corpus sequence and any

// string in a StringTable.

//

public static void findMatches(StringTable table, String corpusSeq,

int matchLength)

{

for (int j = 0; j < corpusSeq.length() - matchLength + 1; j++)

{

String key = corpusSeq.substring(j, j + matchLength);

Record rec = table.find(key);

if (rec != null)

{

for (int k = 0; k < rec.positions.size(); k++)

{

Terminal.println(j + " " +

rec.positions.get(k) +" "+

key);

}

}

/*

if(j==26669){

System.out.println("");

System.out.println("key = "+key+" StringTable.toHashKey(key) = "+StringTable.toHashKey(key));

System.out.println("rec.key = "+rec.key+" StringTable.toHashKey(rec.key) = "+StringTable.toHashKey(rec.

}

}

}