I have created hashtable to solve one of the problem on hackerearth using java.
link:https://www.hackerearth.com/practice/data-structures/hash-tables/basics-of-hash-tables/practice-problems/algorithm/mind-palaces-3/
My java solution is able to pass all the test cases.
Now with same logic ,I am creating solution in C.
But by solution in C does not pass all test cases.
I am learning C.
Please help me to find the problem in C code.
Thanks.
My Java Code:
package hashtable;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
public class MindPalces {
public static void main(String[] args) throws NumberFormatException,
IOException {
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
String string = br.readLine();
String strArr[] = string.split(" ");
int n = Integer.parseInt(strArr[0]);
int m = Integer.parseInt(strArr[1]);
SinglyLinkLists hashTable[] = new SinglyLinkLists[337];
long array[][] = new long[n][m];
for (int i = 0; i < n; i++) {
String string1 = br.readLine();
String[] innerArr = string1.split(" ");
for (int j = 0; j < m; j++) {
array[i][j] = Long.parseLong((innerArr[j]));
}
}
for (int i = 0; i < n; i++) {
for (int j = 0; j < m; j++) {
long data = array[i][j];
if (data < 0) {
data = data * -1;
}
int index = Hashs.hashFunction(data);
if (hashTable[index] == null) {
SinglyLinkLists linkList = new SinglyLinkLists();
linkList.insertAtEnd(i, j, array[i][j]);
hashTable[index] = linkList;
} else {
SinglyLinkLists linkList = hashTable[index];
linkList.insertAtEnd(i, j, array[i][j]);
}
}
}
int q = Integer.parseInt(br.readLine());
for (int i = 0; i < q; i++) {
long val = Long.parseLong(br.readLine());
long val1 = val;
if (val < 0) {
val = val * -1;
}
int index = Hashs.hashFunction(val);
if (hashTable[index] == null) {
System.out.println("-1" + " " + "-1");
} else {
SinglyLinkLists linkList = hashTable[index];
NOde list = linkList.getNode(val1);
if (null != list) {
System.out.println(list.getI1() + " " + list.getJ1());
} else {
System.out.println("-1" + " " + "-1");
}
}
}
}
}
class Hashs {
public static int hashFunction(long key) {
return (int) (key % 337);
}
}
class NOde {
int i1 = 0;
int j1 = 0;
NOde link = null;
long number = 0;
public NOde() {
link = null;
i1 = 0;
j1 = 0;
number = 0;
}
public NOde(NOde node, int i1, int j1, long number) {
this.i1 = i1;
this.j1 = j1;
link = node;
this.number = number;
}
public NOde getLink() {
return link;
}
public void setLink(NOde link) {
this.link = link;
}
public int getI1() {
return i1;
}
public void setI1(int i1) {
this.i1 = i1;
}
public int getJ1() {
return j1;
}
public void setJ1(int j1) {
this.j1 = j1;
}
public long getNumber() {
return number;
}
public void setNumber(long number) {
this.number = number;
}
}
class SinglyLinkLists {
NOde start = null;
NOde end = null;
int size = 0;
public SinglyLinkLists() {
start = null;
end = null;
size = 0;
}
public void insertAtEnd(int i1, int j1, long number) {
NOde nptr = new NOde(null, i1, j1, number);
size++;
if (start == null) {
start = nptr;
end = start;
} else {
end.setLink(nptr);
end = nptr;
}
}
// Function to display elements
public NOde getNode(long val) {
if (start.getNumber() == val) {
return start;
}
NOde ptr = start;
ptr = start.getLink();
while (null != ptr && ptr.getLink() != null) {
if (ptr.getNumber() == val) {
return ptr;
}
ptr = ptr.getLink();
}
if (null != ptr && ptr.getNumber() == val) {
return ptr;
}
return null;
}
}
My C Code:
#include<stdio.h>
#include <stdlib.h>
struct Node
{
int i1;
int j1;
long inputVal;
struct Node * next;
};
struct hash
{
struct Node * head;
};
struct hash *hashTable=NULL;
struct Node *createNode(int i,int j,long number)
{
struct Node *list;
list = (struct Node *) malloc(sizeof(struct Node));
list->i1 = i;
list->j1 = j;
list->inputVal=number;
list->next = NULL;
return list;
};
int main()
{
int m=0,n=0;
scanf("%d%d",&m,&n);
hashTable=(struct hash *)calloc(337,sizeof(struct Node));
for(int i=0; i<n; i++)
{
for(int j=0; j<m; j++)
{
long data=0;
long copy=0;
scanf("%ld",&data);
copy=data;
if(data<0)
{
data=data*-1;
}
int index=hashFunction(data);
struct Node *newnode = createNode(i,j,copy);
struct Node *myNode = hashTable[index].head;
if (!myNode)
{
hashTable[index].head=newnode;
}
else
{
newnode->next=hashTable[index].head;
hashTable[index].head=newnode;
}
}
}
int q=0;
scanf("%d",&q);
for(int i=0; i<q; i++)
{
long val=0;
long copy=0;
int boolean=0;
scanf("%ld",&val);
copy=val;
if(val<0)
{
val=val*-1;
}
int index=hashFunction(val);
struct Node *myNode = hashTable[index].head;
if(!myNode)
{
printf("%d %d\n",-1,-1);
}
else
{
while (myNode->next!= NULL)
{
if (myNode->inputVal==copy)
{
boolean=1;
printf("%d %d\n",myNode->i1,myNode->j1);
break;
}
myNode = myNode->next;
}
if(myNode->inputVal==copy &&!boolean)
{
boolean=1;
printf("%d %d\n",myNode->i1,myNode->j1);
}
if(!boolean)
{
printf("%d %d\n",-1,-1);
}
}
}
return 0;
}
int hashFunction(long data)
{
return (int)(data%337);
}
Sample Input:
5 5
-993655555 -758584352 -725954642 -696391700 -649643547
-591473088 -568010221 -432112275 -421496588 -351507172
-323741602 -232192004 -30134637 -369573 100246476
156824549 174266331 392354039 601294716 763826005
768378344 802829330 818988557 992012759 999272829
10
156824549
-758584352
-993655555
601294716
-696391700
802829330
-993655555
-232192004
392354039
-568010221
I'm a bit new to java, I'm having one error with my Java program that I can't seem to fix, very easy solution I just can't see it haha. How can I fix this? I tried a few things but it adds more errors on top of each other. Thank you all!
import java.io.*;
import java.util.*;
class Node {
public char ch;
public Node leftChild;
public Node rightChild;
Node(char c) {
ch = c;
}
public void displayNode() {
System.out.print(ch);
}
}
class Tree {
public Node root;
public Tree(Node nd) {
root = nd;
}
public void traverse(int traverseType) {
switch (traverseType) {
case 1:
System.out.print(" \n Preorder traversal : ");
preOrder(root);
break;
case 2:
System.out.print(" \n Inorder traversal : ");
inOrder(root);
break;
case 3:
System.out.print(" \n Postorder traversal : ");
postOrder(root);
break;
}
System.out.println();
}
private void preOrder(Node localRoot) {
if (localRoot != null) {
localRoot.displayNode();
preOrder(localRoot.leftChild);
preOrder(localRoot.rightChild);
}
}
private void inOrder(Node localRoot) {
if (localRoot != null) {
inOrder(localRoot.leftChild);
localRoot.displayNode();
inOrder(localRoot.rightChild);
}
}
private void postOrder(Node localRoot) {
if (localRoot != null) {
postOrder(localRoot.leftChild);
postOrder(localRoot.rightChild);
localRoot.displayNode();
}
}
public void displayTree() {
Stack globalStack = new Stack();
globalStack.push(root);
int nBlanks = 32;
boolean isRowEmpty = false;
System.out.println(" ...................................................... ");
while (isRowEmpty == false) {
Stack localStack = new Stack();
isRowEmpty = true;
for (int j = 0; j < nBlanks; j++)
System.out.print(' ');
while (globalStack.isEmpty() == false) {
Node temp = (Node) globalStack.pop();
if (temp != null) {
temp.displayNode();
localStack.push(temp.leftChild);
localStack.push(temp.rightChild);
if (temp.leftChild != null || temp.rightChild != null)
isRowEmpty = false;
} else {
System.out.print("-");
localStack.push(null);
localStack.push(null);
}
for (int j = 0; j < nBlanks * 2 - 1; j++)
System.out.print(' ');
}
System.out.println();
nBlanks / = 2;
while (localStack.isEmpty() == false)
globalStack.push(localStack.pop());
}
System.out.println(" ...................................................... ");
}
}
class BottomUp {
private String inString;
private int strlen;
private Tree[] treeArray;
private Tree aTree;
private int numNodes;
BottomUp(String s) {
inString = s;
strlen = inString.length();
treeArray = new Tree[100];
for (int j = 0; j < strlen; j++) {
char ch = inString.charAt(j);
Node aNode = new Node(ch);
treeArray[j] = new Tree(aNode);
}
}
public Tree getTree() {
return aTree;
}
public void balanced() {
numNodes = strlen;
while (numNodes > 1) {
int i = 0;
int j = 0;
Tree[] tempArray = new Tree[100];
for (j = 0; j < strlen - 1; j++) {
Tree tree1 = treeArray[j];
Tree tree2 = treeArray[j + 1];
Node aNode = new Node('+');
aTree = new Tree(aNode);
aTree.root.leftChild = tree1.root;
aTree.root.rightChild = tree2.root;
tempArray[i++] = aTree;
numNodes--;
j++;
}
if (strlen % 2 == 1) {
Tree tree1 = treeArray[j];
Node aNode = new Node('+');
aTree = new Tree(aNode);
aTree.root.leftChild = tree1.root;
tempArray[i++] = aTree;
}
treeArray = tempArray;
strlen = numNodes;
}
aTree = treeArray[0];
}
}
class BottomUpApp {
public static void main(String[] args) throws IOException {
BottomUp bup;
Tree theTree = null;
int value;
String str;
while (true) {
System.out.print(" Enter first letter of ");
System.out.print(" balanced , show , or traverse : ");
int choice = getChar();
switch (choice) {
case 'b':
System.out.print(" Enter string : ");
str = getString();
bup = new BottomUp(str);
bup.balanced();
theTree = bup.getTree();
break;
case 's':
theTree.displayTree();
break;
case 't':
System.out.print(" Enter type 1, 2 or 3 : ");
value = getInt();
theTree.traverse(value);
break;
default:
System.out.print(" Invalid entry \n ");
}
}
}
public static String getString() throws IOException {
InputStreamReader isr = new InputStreamReader(System.in);
BufferedReader br = new BufferedReader(isr);
String s = br.readLine();
return s;
}
public static char getChar() throws IOException {
String s = getString();
return s.charAt(0);
}
public static int getInt() throws IOException {
String s = getString();
return Integer.parseInt(s);
}
}
ERROR CODE
Node.java:112: error: illegal start of expression
nBlanks / = 2 ;
^
1 error
The Java operator /= must be typed without spaces in between, or else it will be parsed as 2 separate operators, / and =, which is a syntax error. Try
nBlanks /= 2 ;
I have to implement the T9 Dictionary .
Essentially, when I am pressing any of the 9 keys, it should show me
the top 5 words that can be started with that combination of keys.
If I type '46', it can give 'hotel' or 'good' depending on whether I
intended 'g' or 'h' when I pressed 4.
The priority is based on which words are relatively popular - you can
use, say, the first 5000 words from the top 100 000 words.
The code I am doing is:
Import
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.Date;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
T9Dict class
public class T9Dict {
private static final Runtime s_runtime = Runtime.getRuntime();
public static void main(String[] args) throws Exception {
runGC();
long heap1 = usedMemory();
long start = new Date().getTime();
Trie trie = Trie.getInstance();
System.out.println("Creating Dictionary");
File f = new File("C:\\Users\\hp1\\Desktop\\100kfound.txt");
BufferedReader br = new BufferedReader(new FileReader(f));
String s = br.readLine();
int i = 0;
do {
i++;
trie.add(s);
s = br.readLine();
} while (s != null);
br.close();
long end = new Date().getTime();
long time = (end - start);
System.out.println("Loaded Dictionary with " + i + " words in " + time
+ " msec");
// runGC();
long heap2 = usedMemory(); // take an "after" heap snapshot:
System.out.println("Memory used = " + (heap2 - heap1));
String pattern = "4663";
start = new Date().getTime();
String word = trie.getWord(pattern);
end = new Date().getTime();
time = (end - start);
System.out.println("Found word : " + word + " in " + time + " msec");
}
private static void runGC() throws Exception {
// for whatever reason it helps to call Runtime.gc()
// using several method calls:
for (int r = 0; r < 4; ++r) {
_runGC();
}
}
private static void _runGC() throws Exception {
long usedMem1 = usedMemory();
long usedMem2 = Long.MAX_VALUE;
for (int i = 0; (usedMem1 < usedMem2) && (i < 1000); ++i) {
s_runtime.runFinalization();
s_runtime.gc();
Thread.currentThread().yield();
usedMem2 = usedMem1;
usedMem1 = usedMemory();
}
}
private static long usedMemory() {
return s_runtime.totalMemory() - s_runtime.freeMemory();
}
}
Trie class
class Trie {
private static final String regex = "[a-zA-Z]*";
private static Trie instance = null;
Node root = null;
Map<Character, Integer> map = new HashMap<Character, Integer>();
private Trie() {
map.put('a', 2);
map.put('b', 2);
map.put('c', 2);
map.put('d', 3);
map.put('e', 3);
map.put('f', 3);
map.put('g', 4);
map.put('h', 4);
map.put('i', 4);
map.put('j', 5);
map.put('k', 5);
map.put('l', 5);
map.put('m', 6);
map.put('n', 6);
map.put('o', 6);
map.put('p', 7);
map.put('q', 7);
map.put('r', 7);
map.put('s', 7);
map.put('t', 8);
map.put('u', 8);
map.put('v', 8);
map.put('w', 9);
map.put('x', 9);
map.put('y', 9);
map.put('z', 9);
}
private int getVal(char c) {
return map.get(c);
}
public static Trie getInstance() {
if (instance == null) {
synchronized (Trie.class) {
instance = new Trie();
}
}
return instance;
}
public String getWord(String pattern) {
String s = null;
Node node = root;
int i = 0;
int num = 0;
while (i < pattern.length()) {
num = pattern.charAt(i) - '0';
if (num == node.val) {
i++;
if (i == pattern.length()) {
s = node.list.get(0);
}
node = node.middle;
} else if (num < node.val) {
if (i == pattern.length()) {
s = node.list.get(0);
}
node = node.left;
} else {
if (i == pattern.length()) {
s = node.list.get(0);
}
node = node.right;
}
}
return s;
}
public void add(String s) {
if (s.length() > 0) {
s = s.toLowerCase();
System.out.println("Adding : " + s);
if (root == null) {
root = new Node(this.getVal(s.charAt(0)));
Node node = root;
Node temp = null;
for (int i = 1; i < s.length(); i++) {
temp = new Node(getVal(s.charAt(i)));
node.middle = temp;
node = temp;
if (i == s.length() - 1) {
temp.set(s);
}
}
} else {
Node node = root;
int i = 0;
Node temp = null;
int val = 0;
while (i < s.length()) {
val = getVal(s.charAt(i));
if (node.val == val) {
if (i == s.length() - 1) {
node.set(s);
i++;
} else {
i++;
if (node.middle == null) {
while (i < s.length()) {
val = getVal(s.charAt(i));
temp = new Node(val);
node.middle = temp;
node = temp;
if (i == s.length() - 1) {
temp.set(s);
}
i++;
}
} else {
node = node.middle;
}
}
} else if (val < node.val) {
if (node.left == null) {
temp = new Node(val);
node.left = temp;
node = temp;
if (i == s.length() - 1) {
temp.set(s);
} else {
i++;
while (i < s.length()) {
val = getVal(s.charAt(i));
temp = new Node(val);
node.middle = temp;
node = temp;
if (i == s.length() - 1) {
temp.set(s);
}
i++;
}
}
} else {
node = node.left;
}
} else {
if (node.right == null) {
temp = new Node(val);
node.right = temp;
node = temp;
if (i == s.length() - 1) {
temp.set(s);
} else {
i++;
while (i < s.length()) {
val = getVal(s.charAt(i));
temp = new Node(val);
node.middle = temp;
node = temp;
if (i == s.length() - 1) {
temp.set(s);
}
i++;
}
}
} else {
node = node.right;
}
}
}
}
}
}
}
Node class
class Node {
int val;
Node left;
Node middle;
Node right;
List<String> list = new LinkedList<String>();
public Node(int val) {
this.val = val;
}
public void set(String s) {
list.add(s);
}
public String toString() {
return String.valueOf(val);
}
}
This code is giving nullpointerexception when adding to Trie
I cannot find the solution please help
1 - You File doesn't contains characters. It is binary so you should use FileInputStream object to read it.
2 - In reading file and adding string in your Trie you should verify that this string is not null, otherwise it can throws a NullPointerException. You can run your file like this:
When I run this I find that the exception occurs on this line:
root = new Node(this.getVal(s.charAt(0)));
Let's unroll this, you're passing the first character of the "word" (ie the String, s) to the getVal(), and this in turn will return an int if, and only if, that character is a lowercase letter, a-z.
When I run the file the "word" is 6724 yahoo - this is the first line of the dictionary text file you linked to. There is nothing in your code to clean up this line to get to the actual word itself, instead you are facing a series of spaces and then a number.
So the reason it fails is because you're effectively going this.getVal(" "). If you call map.get() and the key doesn't exist it'll return null (as described in the Map documentation).
One simple way of getting to the word itself and not the whitespace or frequency number is to first process the string:
s = s.trim(); // removes all leading and trailing whitespace
String word = s.substring(s.indexOf(" ")+1); // extract just the word after the space
And then you can pass the first character of word:
root = new Node(this.getVal(word.charAt(0)));
Java won't stop reading from input.
I understand that maybe this while loop might have something to do with it:
while(input.hasMoreTokens());
{
array1[counter] = input.nextToken();
counter++;
}
But I don't see why the loop should be a problem because I am already calling .nextToken() which should advance the token.
Here's the full source code:
import java.io.*;
import java.util.*;
class HelloWorld
{
static String ReadLn (int maxLg) // utility function to read from stdin
{
byte lin[] = new byte [maxLg];
int lg = 0, car = -1;
String line = "";
try
{
while (lg < maxLg)
{
car = System.in.read();
if ((car < 0) || (car == '\n')) break;
lin [lg++] += car;
}
}
catch (IOException e)
{
return (null);
}
if ((car < 0) && (lg == 0)) return (null); // eof
return (new String (lin, 0, lg));
}
public static void main (String args[]) // entry point from OS
{
HelloWorld myWork = new HelloWorld(); // create a dinamic instance
myWork.Begin(); // the true entry point
}
void Begin()
{
String idata;
StringTokenizer input;
while ((idata = HelloWorld.ReadLn (255)) != null)
{
input = new StringTokenizer (idata);
String[] array1 = {};
int counter = 0;
while(input.hasMoreTokens());
{
array1[counter] = input.nextToken();
counter++;
}
int[] array2 = {};
for(int a = 0; a < array1.length; a++)
{
array2[a] = Integer.parseInt(array1[a]);
}
int[] array3 = {};
for(int b = 0; b < array2.length; b++)
{
if ( array2[b] != 42)
{
array3[b] = array2[b];
}
else
{
break;
}
}
String string = "";
for( int c = 0; c < array3.length; c++)
{
if( c < array3.length - 1)
{
string += array3[c] + "\n";
}
else
{
string += array3[c];
}
}
System.out.println(string);
}
}
}
You have a stray semicolon at the end of the while:
while(input.hasMoreTokens());
^ REMOVE THIS
I am struggling with a "find supersequence" algorithm.
The input is for set of strings
String A = "caagccacctacatca";
String B = "cgagccatccgtaaagttg";
String C = "agaacctgctaaatgctaga";
the result would be properly aligned set of strings (and next step should be merge)
String E = "ca ag cca cc ta cat c a";
String F = "c gag ccat ccgtaaa g tt g";
String G = " aga acc tgc taaatgc t a ga";
Thank you for any advice (I am sitting on this task for more than a day)
after merge the superstring would be
cagagaccatgccgtaaatgcattacga
The definition of supersequence in "this case" would be something like
The string R is contained in supersequence S if and only if all characters in a string R are present in supersequence S in the order in which they occur in the input sequence R.
The "solution" i tried (and again its the wrong way of doing it) is:
public class Solution4
{
static boolean[][] map = null;
static int size = 0;
public static void main(String[] args)
{
String A = "caagccacctacatca";
String B = "cgagccatccgtaaagttg";
String C = "agaacctgctaaatgctaga";
Stack data = new Stack();
data.push(A);
data.push(B);
data.push(C);
Stack clone1 = data.clone();
Stack clone2 = data.clone();
int length = 26;
size = max_size(data);
System.out.println(size+" "+length);
map = new boolean[26][size];
char[] result = new char[size];
HashSet<String> chunks = new HashSet<String>();
while(!clone1.isEmpty())
{
String a = clone1.pop();
char[] residue = make_residue(a);
System.out.println("---");
System.out.println("OLD : "+a);
System.out.println("RESIDUE : "+String.valueOf(residue));
String[] r = String.valueOf(residue).split(" ");
for(int i=0; i<r.length; i++)
{
if(r[i].equals(" ")) continue;
//chunks.add(spaces.substring(0,i)+r[i]);
chunks.add(r[i]);
}
}
for(String chunk : chunks)
{
System.out.println("CHUNK : "+chunk);
}
}
static char[] make_residue(String candidate)
{
char[] result = new char[size];
for(int i=0; i<candidate.length(); i++)
{
int pos = find_position_for(candidate.charAt(i),i);
for(int j=i; j<pos; j++) result[j]=' ';
if(pos==-1) result[candidate.length()-1] = candidate.charAt(i);
else result[pos] = candidate.charAt(i);
}
return result;
}
static int find_position_for(char character, int offset)
{
character-=((int)'a');
for(int i=offset; i<size; i++)
{
// System.out.println("checking "+String.valueOf((char)(character+((int)'a')))+" at "+i);
if(!map[character][i])
{
map[character][i]=true;
return i;
}
}
return -1;
}
static String move_right(String a, int from)
{
return a.substring(0, from)+" "+a.substring(from);
}
static boolean taken(int character, int position)
{ return map[character][position]; }
static void take(char character, int position)
{
//System.out.println("taking "+String.valueOf(character)+" at "+position+" (char_index-"+(character-((int)'a'))+")");
map[character-((int)'a')][position]=true;
}
static int max_size(Stack stack)
{
int max=0;
while(!stack.isEmpty())
{
String s = stack.pop();
if(s.length()>max) max=s.length();
}
return max;
}
}
Finding any common supersequence is not a difficult task:
In your example possible solution would be something like:
public class SuperSequenceTest {
public static void main(String[] args) {
String A = "caagccacctacatca";
String B = "cgagccatccgtaaagttg";
String C = "agaacctgctaaatgctaga";
int iA = 0;
int iB = 0;
int iC = 0;
char[] a = A.toCharArray();
char[] b = B.toCharArray();
char[] c = C.toCharArray();
StringBuilder sb = new StringBuilder();
while (iA < a.length || iB < b.length || iC < c.length) {
if (iA < a.length && iB < b.length && iC < c.length && (a[iA] == b[iB]) && (a[iA] == c[iC])) {
sb.append(a[iA]);
iA++;
iB++;
iC++;
}
else if (iA < a.length && iB < b.length && a[iA] == b[iB]) {
sb.append(a[iA]);
iA++;
iB++;
}
else if (iA < a.length && iC < c.length && a[iA] == c[iC]) {
sb.append(a[iA]);
iA++;
iC++;
}
else if (iB < b.length && iC < c.length && b[iB] == c[iC]) {
sb.append(b[iB]);
iB++;
iC++;
} else {
if (iC < c.length) {
sb.append(c[iC]);
iC++;
}
else if (iB < b.length) {
sb.append(b[iB]);
iB++;
} else if (iA < a.length) {
sb.append(a[iA]);
iA++;
}
}
}
System.out.println("SUPERSEQUENCE " + sb.toString());
}
}
However the real problem to solve is to find the solution for the known problem of Shortest Common Supersequence http://en.wikipedia.org/wiki/Shortest_common_supersequence,
which is not that easy.
There is a lot of researches which concern the topic.
See for instance:
http://www.csd.uwo.ca/~lila/pdfs/Towards%20a%20DNA%20solution%20to%20the%20Shortest%20Common%20Superstring%20Problem.pdf
http://www.ncbi.nlm.nih.gov/pubmed/14534185
You can try finding the shortest combination like this
static final char[] CHARS = "acgt".toCharArray();
public static void main(String[] ignored) {
String A = "caagccacctacatca";
String B = "cgagccatccgtaaagttg";
String C = "agaacctgctaaatgctaga";
String expected = "cagagaccatgccgtaaatgcattacga";
List<String> ABC = new Combination(A, B, C).findShortest();
System.out.println("expected: " + expected.length());
System.out.println("Merged: " + ABC.get(0).length() + " " + ABC);
}
static class Combination {
int shortest = Integer.MAX_VALUE;
List<String> shortestStr = new ArrayList<>();
char[][] chars;
int[] pos;
int count = 0;
Combination(String... strs) {
chars = new char[strs.length][];
pos = new int[strs.length];
for (int i = 0; i < strs.length; i++) {
chars[i] = strs[i].toCharArray();
}
}
public List<String> findShortest() {
findShortest0(new StringBuilder(), pos);
return shortestStr;
}
private void findShortest0(StringBuilder sb, int[] pos) {
if (allDone(pos)) {
if (sb.length() < shortest) {
shortestStr.clear();
shortest = sb.length();
}
if (sb.length() <= shortest)
shortestStr.add(sb.toString());
count++;
if (++count % 100 == 1)
System.out.println("Searched " + count + " shortest " + shortest);
return;
}
if (sb.length() + maxLeft(pos) > shortest)
return;
int[] pos2 = new int[pos.length];
int i = sb.length();
sb.append(' ');
for (char c : CHARS) {
if (!tryChar(pos, pos2, c)) continue;
sb.setCharAt(i, c);
findShortest0(sb, pos2);
}
sb.setLength(i);
}
private int maxLeft(int[] pos) {
int maxLeft = 0;
for (int i = 0; i < pos.length; i++) {
int left = chars[i].length - pos[i];
if (left > maxLeft)
maxLeft = left;
}
return maxLeft;
}
private boolean allDone(int[] pos) {
for (int i = 0; i < chars.length; i++)
if (pos[i] < chars[i].length)
return false;
return true;
}
private boolean tryChar(int[] pos, int[] pos2, char c) {
boolean matched = false;
for (int i = 0; i < chars.length; i++) {
pos2[i] = pos[i];
if (pos[i] >= chars[i].length) continue;
if (chars[i][pos[i]] == c) {
pos2[i]++;
matched = true;
}
}
return matched;
}
}
prints many solutions which are shorter than the one suggested.
expected: 28
Merged: 27 [acgaagccatccgctaaatgctatcga, acgaagccatccgctaaatgctatgca, acgaagccatccgctaacagtgctaga, acgaagccatccgctaacatgctatga, acgaagccatccgctaacatgcttaga, acgaagccatccgctaacatgtctaga, acgaagccatccgctacaagtgctaga, acgaagccatccgctacaatgctatga, acgaagccatccgctacaatgcttaga, acgaagccatccgctacaatgtctaga, acgaagccatcgcgtaaatgctatcga, acgaagccatcgcgtaaatgctatgca, acgaagccatcgcgtaacagtgctaga, acgaagccatcgcgtaacatgctatga, acgaagccatcgcgtaacatgcttaga, acgaagccatcgcgtaacatgtctaga, acgaagccatcgcgtacaagtgctaga, acgaagccatcgcgtacaatgctatga, acgaagccatcgcgtacaatgcttaga, acgaagccatcgcgtacaatgtctaga, acgaagccatgccgtaaatgctatcga, acgaagccatgccgtaaatgctatgca, acgaagccatgccgtaacagtgctaga, acgaagccatgccgtaacatgctatga, acgaagccatgccgtaacatgcttaga, acgaagccatgccgtaacatgtctaga, acgaagccatgccgtacaagtgctaga, acgaagccatgccgtacaatgctatga, acgaagccatgccgtacaatgcttaga, acgaagccatgccgtacaatgtctaga, cagaagccatccgctaaatgctatcga, cagaagccatccgctaaatgctatgca, cagaagccatccgctaacagtgctaga, cagaagccatccgctaacatgctatga, cagaagccatccgctaacatgcttaga, cagaagccatccgctaacatgtctaga, cagaagccatccgctacaagtgctaga, cagaagccatccgctacaatgctatga, cagaagccatccgctacaatgcttaga, cagaagccatccgctacaatgtctaga, cagaagccatcgcgtaaatgctatcga, cagaagccatcgcgtaaatgctatgca, cagaagccatcgcgtaacagtgctaga, cagaagccatcgcgtaacatgctatga, cagaagccatcgcgtaacatgcttaga, cagaagccatcgcgtaacatgtctaga, cagaagccatcgcgtacaagtgctaga, cagaagccatcgcgtacaatgctatga, cagaagccatcgcgtacaatgcttaga, cagaagccatcgcgtacaatgtctaga, cagaagccatgccgtaaatgctatcga, cagaagccatgccgtaaatgctatgca, cagaagccatgccgtaacagtgctaga, cagaagccatgccgtaacatgctatga, cagaagccatgccgtaacatgcttaga, cagaagccatgccgtaacatgtctaga, cagaagccatgccgtacaagtgctaga, cagaagccatgccgtacaatgctatga, cagaagccatgccgtacaatgcttaga, cagaagccatgccgtacaatgtctaga, cagagaccatccgctaaatgctatcga, cagagaccatccgctaaatgctatgca, cagagaccatccgctaacagtgctaga, cagagaccatccgctaacatgctatga, cagagaccatccgctaacatgcttaga, cagagaccatccgctaacatgtctaga, cagagaccatccgctacaagtgctaga, cagagaccatccgctacaatgctatga, cagagaccatccgctacaatgcttaga, cagagaccatccgctacaatgtctaga, cagagaccatcgcgtaaatgctatcga, cagagaccatcgcgtaaatgctatgca, cagagaccatcgcgtaacagtgctaga, cagagaccatcgcgtaacatgctatga, cagagaccatcgcgtaacatgcttaga, cagagaccatcgcgtaacatgtctaga, cagagaccatcgcgtacaagtgctaga, cagagaccatcgcgtacaatgctatga, cagagaccatcgcgtacaatgcttaga, cagagaccatcgcgtacaatgtctaga, cagagaccatgccgtaaatgctatcga, cagagaccatgccgtaaatgctatgca, cagagaccatgccgtaacagtgctaga, cagagaccatgccgtaacatgctatga, cagagaccatgccgtaacatgcttaga, cagagaccatgccgtaacatgtctaga, cagagaccatgccgtacaagtgctaga, cagagaccatgccgtacaatgctatga, cagagaccatgccgtacaatgcttaga, cagagaccatgccgtacaatgtctaga, cagagccatcctagctaaagtgctaga, cagagccatcctagctaaatgctatga, cagagccatcctagctaaatgcttaga, cagagccatcctagctaaatgtctaga, cagagccatcctgactaaagtgctaga, cagagccatcctgactaaatgctatga, cagagccatcctgactaaatgcttaga, cagagccatcctgactaaatgtctaga, cagagccatcctgctaaatgctatcga, cagagccatcctgctaaatgctatgca, cagagccatcctgctaacagtgctaga, cagagccatcctgctaacatgctatga, cagagccatcctgctaacatgcttaga, cagagccatcctgctaacatgtctaga, cagagccatcctgctacaagtgctaga, cagagccatcctgctacaatgctatga, cagagccatcctgctacaatgcttaga, cagagccatcctgctacaatgtctaga]