/**
* Main method to control data flow. This function takes the command line parameter as input and
* uses it to read from the input file, executing and outputting commands along the way.
*
* @param args - the command line arguments
*/
public static void main(String[] args) {
// Check for proper usage
if (args.length != 1) {
System.out.println("Usage:");
System.out.println("P3 COMMAND_FILE");
System.exit(0);
}
String fileName = args[0];
tree = new DNATree();
dbm = new DatabaseManager();
// Main command line reading
try {
// Attempt to open the input file into a buffered reader
BufferedReader in = new BufferedReader(new FileReader(fileName));
// Keep reading in commands until we reach the EOF
String line;
while ((line = in.readLine()) != null) {
if (line.matches(INSERT_PATTERN)) {
// Parse out the sequence id and length from the command line
int begin = Math.max(line.indexOf("r"), line.indexOf("R")) + 2;
int end =
Math.max(
Math.max(
Math.max(line.lastIndexOf('A'), line.lastIndexOf('C')),
line.lastIndexOf('G')),
line.lastIndexOf('T'))
+ 1;
String sequence = line.substring(begin, end);
sequence = sequence.trim();
int length = Integer.parseInt(line.substring(end).trim());
if (length <= 0) {
System.out.println("Length less than zero.");
continue;
}
// Get the next line for the sequence
String entry = in.readLine();
// Add to the dbm
Handle handle = dbm.insert(entry, length);
// Add to tree
int result = tree.insert(sequence, handle);
if (result < 0) {
dbm.remove(handle);
System.out.println("Sequence " + sequence + " already in tree.");
} else {
System.out.println("Sequence " + sequence + " inserted at level " + result + ".");
}
System.out.println();
} else if (line.matches(REMOVE_PATTERN)) {
// Parse out the sequence id from the command line
int index = Math.max(line.indexOf("v"), line.indexOf("V")) + 2;
String sequence = line.substring(index);
sequence = sequence.trim();
// Remove sequence id from tree
Handle handle = tree.remove(sequence);
// Remove sequence from dbm
if (handle == null) {
System.out.println("Sequence " + sequence + " not found in tree.");
System.out.println();
} else {
dbm.remove(handle);
}
} else if (line.matches(PRINT_PATTERN)) {
// Output the tree
System.out.println(tree);
// Output free blocks
System.out.println(dbm);
System.out.println();
} else if (line.matches(SEARCH_PATTERN)) {
// Parse out the sequence id from the command line
int index = Math.max(line.indexOf("h"), line.indexOf("H")) + 1;
String sequence = line.substring(index);
sequence = sequence.trim();
// Search the tree for handles
String results = tree.search(sequence);
Scanner scan = new Scanner(results);
String output = scan.nextLine() + "\n";
// Augment output with results from dbm
String entry;
int offset, length;
Handle handle;
while (scan.hasNextLine()) {
entry = scan.nextLine();
if (entry.matches(KEY_PATTERN)) {
output += entry + "\n";
} else if (entry.matches(HANDLE_PATTERN)) {
// Parse out offset and length
offset =
Integer.parseInt(entry.substring(entry.indexOf('[') + 1, entry.indexOf(',')));
length =
Integer.parseInt(entry.substring(entry.indexOf(',') + 2, entry.indexOf(']')));
// Create handle and use it to query database
handle = new Handle(offset, length);
output += "Sequence:\n" + dbm.getEntry(handle) + "\n";
} else {
continue;
}
}
scan.close();
System.out.println(output.substring(0, output.length() - 1));
System.out.println();
} else {
continue;
}
}
in.close();
} catch (FileNotFoundException e) {
System.out.println("The input file could not be found.");
System.exit(0);
} catch (IOException e) {
System.out.println("Error reading from file.");
System.exit(0);
} catch (Exception e) {
System.out.println("Incorrect file formatting.");
e.printStackTrace();
System.exit(0);
}
}
