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package fun;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.Arrays;
public class Palindrome {
public static void main(String[] args){
ArrayList<String> sequences=new ArrayList<String>();
for(String s : args) {
if(s.equalsIgnoreCase("rcomp") || s.equalsIgnoreCase("rc")) {
rcomp=true;
}else if(Character.isDigit(s.charAt(0))) {
maxMismatches=Integer.parseInt(s);
}else if(s.startsWith("loop")) {
maxLoop=Integer.parseInt(s.split("=")[1]);
}else if(new File(args[0]).exists()) {
sequences.addAll(getSequence(args[0]));
}else {
sequences.add(s);
}
}
String longest="";
for(String s : sequences) {
String p;
if(maxLoop<1) {
p=longestPalindrome(s);
}else {
p=longestPalindrome(s, maxLoop);
}
if(p.length()>longest.length()) {
longest=p;
}
}
System.out.println("Longest palindrome is length "+longest.length()+":\n'"+longest+"'");
}
public static ArrayList<String> getSequence(String fname){
ArrayList<String> list=new ArrayList<String>();
try {
final BufferedReader reader=new BufferedReader(new FileReader(fname));
StringBuilder sb=new StringBuilder();
for(String line=reader.readLine(); line!=null; line=reader.readLine()) {
if(line.length()>0) {
if(line.charAt(0)=='>'){
if(sb.length()>0) {
list.add(sb.toString());
sb.setLength(0);
}
}else{
sb.append(line);
}
}
}
if(sb.length()>0) {list.add(sb.toString());}
reader.close();
}catch(Exception e){
}
return list;
}
public static String longestPalindrome(String s){
int longestLength=0;
int longestStart=0;
String p="";
for(int i=0; i<s.length(); i++){
int lenEven=palindromeLengthEven(s, i);
if(lenEven>longestLength){
longestLength=lenEven;
longestStart=i-lenEven/2+1;
int a=longestStart, b=longestStart+longestLength;
p=s.substring(a, b);
}
int lenOdd=palindromeLengthOdd(s, i);
if(lenOdd>longestLength){
longestLength=lenOdd;
longestStart=i-lenOdd/2;
p=s.substring(longestStart, longestStart+longestLength);
}
}
return p;
}
public static String longestPalindrome(String s, int maxloop){
int longestLength=0;
int longestStart=0;
String p="";
for(int loop=0; loop<=maxloop; loop++) {
for(int i=0; i<s.length(); i++){
if((loop&1)==1) {//odd
int lenOdd=palindromeLengthOdd(s, i, i+loop+1);
if(lenOdd>longestLength){
longestLength=lenOdd;
// longestStart=i-lenOdd/2;
// p=s.substring(longestStart, longestStart+longestLength-loop);
p=s.substring(a_, b_+1);
}
}else {//even
int lenEven=palindromeLengthEven(s, i, i+1+loop);
if(lenEven>longestLength){
longestLength=lenEven;
// longestStart=i-lenEven/2+1;
// int a=longestStart, b=longestStart+longestLength-loop;
// p=s.substring(a, b);
p=s.substring(a_, b_+1);
}
}
}
}
return p;
}
public static int palindromeLengthOdd(String s, int middle){
return palindromeLengthOdd(s, middle, middle);
}
public static int palindromeLengthOdd(String s, int a, int b){
int length=b-a-1;
int mismatches=0;
while(a>=0 && b<s.length() && mismatches<=maxMismatches){
if(!matches(s.charAt(a), s.charAt(b))){
mismatches++;
if(mismatches>maxMismatches) {break;}
}
length+=2;
a--;
b++;
}
if(a<0 || b>=s.length() || mismatches>maxMismatches) {a++; b--;}
a_=a;
b_=b;
if(length==1 && rcomp && maxMismatches<1) {return 0;}
return length<0 ? 0 : length;
// return b-a+1;
}
public static int palindromeLengthEven(String s, int middle){
return palindromeLengthEven(s, middle, middle+1);
}
public static int palindromeLengthEven(String s, int a, int b){
int length=b-a-1;
int mismatches=0;
while(a>=0 && b<s.length() && mismatches<=maxMismatches){
if(!matches(s.charAt(a), s.charAt(b))){
mismatches++;
if(mismatches>maxMismatches) {break;}
}
length+=2;
a--;
b++;
}
if(a<0 || b>=s.length() || mismatches>maxMismatches) {a++; b--;}
a_=a;
b_=b;
return length;
// return b-a+1;
}
static boolean matches(char a, char b) {
return a==(rcomp ? baseToComp[b] : b);
}
static char[] makeBaseToComp() {
char[] array=new char[128];
Arrays.fill(array, 'N');
array['A']=array['a']='T';
array['C']=array['c']='G';
array['G']=array['g']='C';
array['T']=array['t']=array['U']=array['u']='A';
return array;
}
static boolean rcomp=false;
static int maxMismatches=0;
static int maxLoop=0;
static final char[] baseToComp=makeBaseToComp();
static int a_, b_;
}
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