--- a/chromeister/src/alignmentFunctions.c	Wed Dec 12 07:18:40 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,266 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-#include <inttypes.h>
-#include <math.h>
-#include <float.h>
-#include "structs.h"
-#include "alignmentFunctions.h"
-#include "commonFunctions.h"
-
-
-
-int64_t compare_letters(unsigned char a, unsigned char b){
-    if(a != (unsigned char) 'N' && a != (unsigned char) '>') return (a == b) ? POINT : -POINT;
-    return -POINT;
-}
-
-llpos * getNewLocationllpos(Mempool_l * mp, uint64_t * n_pools_used){
-
-    if(mp[*n_pools_used].current == POOL_SIZE){
-        *n_pools_used += 1;
-        if(*n_pools_used == MAX_MEM_POOLS) terror("Reached max pools");
-        init_mem_pool_llpos(&mp[*n_pools_used]);
-        
-    }
-
-    llpos * new_pos = mp[*n_pools_used].base + mp[*n_pools_used].current;
-    mp[*n_pools_used].current++;
-
-    
-    return new_pos;
-}
-
-void init_mem_pool_llpos(Mempool_l * mp){
-    mp->base = (llpos *) calloc(POOL_SIZE, sizeof(llpos));
-    if(mp->base == NULL) terror("Could not request memory pool");
-    mp->current = 0;
-}
-
-AVLTree * getNewLocationAVLTree(Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t key){
-
-    if(mp[*n_pools_used].current == POOL_SIZE){
-        *n_pools_used += 1;
-        if(*n_pools_used == MAX_MEM_POOLS) terror("Reached max pools");
-        init_mem_pool_AVL(&mp[*n_pools_used]);
-        
-    }
-
-    AVLTree * new_pos = mp[*n_pools_used].base + mp[*n_pools_used].current;
-    mp[*n_pools_used].current++;
-
-    new_pos->key = key;
-    new_pos->count = 1;
-    new_pos->height = 1;
-
-    return new_pos;
-}
-
-void init_mem_pool_AVL(Mempool_AVL * mp){
-    mp->base = (AVLTree *) calloc(POOL_SIZE, sizeof(AVLTree));
-    if(mp->base == NULL) terror("Could not request memory pool");
-    mp->current = 0;
-}
-
-
-
-/*
-// An AVL tree node
-typedef struct AVL_Node{
-    uint64_t key;
-    struct AVL_Node * left;
-    struct AVL_Node * right;
-    uint64_t height;
-    llpos * next;
-} AVLTree;
-*/
- 
-// A utility function to get height of the tree
-
-uint64_t height(AVLTree * N){
-    if (N == NULL)
-        return 0;
-    return N->height;
-}
-
-/* Substituted by (x == NULL) ? (0) : (x->height) */
- 
-/* Helper function that allocates a new node with the given key and
-    NULL left and right pointers. */
-
-/* This one is substituted by AVLTree * getNewLocationAVLTree(Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t key) */
- 
-// A utility function to right rotate subtree rooted with y
-// See the diagram given above.
-AVLTree * right_rotate(AVLTree * y){
-    AVLTree * x = y->left;
-    AVLTree * T2 = x->right;
- 
-    // Perform rotation
-    x->right = y;
-    y->left = T2;
- 
-    // Update heights
-    //x->height = MAX((x == NULL) ? (0) : (x->left->height), (x == NULL) ? (0) : (x->right->height))+1;
-    //y->height = MAX((y == NULL) ? (0) : (y->left->height), (y == NULL) ? (0) : (y->right->height))+1;
-    // Update heights
-    y->height = MAX(height(y->left), height(y->right))+1;
-    x->height = MAX(height(x->left), height(x->right))+1;
- 
-    // Return new root
-    return x;
-}
- 
-// A utility function to left rotate subtree rooted with x
-// See the diagram given above.
-AVLTree * left_rotate(AVLTree * x){
-    AVLTree * y = x->right;
-    AVLTree * T2 = y->left;
- 
-    // Perform rotation
-    y->left = x;
-    x->right = T2;
- 
-    //  Update heights
-    //x->height = MAX((x == NULL) ? (0) : (x->left->height), (x == NULL) ? (0) : (x->right->height))+1;
-    //y->height = MAX((y == NULL) ? (0) : (y->left->height), (y == NULL) ? (0) : (y->right->height))+1;
-    x->height = MAX(height(x->left), height(x->right))+1;
-    y->height = MAX(height(y->left), height(y->right))+1;
- 
-    // Return new root
-    return y;
-}
- 
-// Get Balance factor of node N
-
-int64_t get_balance(AVLTree * N){
-    if (N == NULL)
-        return 0;
-    return height(N->left) - height(N->right);
-}
-
-/* Substituted by (node == NULL) ? (0) : ((int64_t) node->left->height - (int64_t) node->right->height) */
-
-AVLTree * find_AVLTree(AVLTree * node, uint64_t key){
-    AVLTree * found = NULL;
-    if(node == NULL) return NULL;
-
-    if (key < node->key) {
-        found = find_AVLTree(node->left, key);
-    } else if (key > node->key) {
-        found = find_AVLTree(node->right, key);
-    } else { 
-        return node;
-    }
-    return found;
-} 
-
-llpos * find_AVLTree_llpos(AVLTree * node, uint64_t key){
-    llpos * aux = NULL;
-    if(node == NULL) return NULL;
-
-    if (key < node->key) {
-        aux = find_AVLTree_llpos(node->left, key);
-    } else if (key > node->key) {
-        aux = find_AVLTree_llpos(node->right, key);
-    } else { 
-        return node->next;
-    }
-    return aux;
-}
-
-// Recursive function to insert key in subtree rooted
-// with node and returns new root of subtree.
-AVLTree * insert_AVLTree(AVLTree * node, uint64_t key, Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t pos, Mempool_l * mp_l, uint64_t * n_pools_used_l){
-    /* 1.  Perform the normal BST insertion */
-    if (node == NULL){
-        
-        AVLTree * n_node = getNewLocationAVLTree(mp, n_pools_used, key);
-        llpos * aux = getNewLocationllpos(mp_l, n_pools_used_l);
-        aux->pos = pos;
-        n_node->next = aux;
-        return n_node;
-    }
- 
-    if (key < node->key) {
-        node->left  = insert_AVLTree(node->left, key, mp, n_pools_used, pos, mp_l, n_pools_used_l);
-    } else if (key > node->key) {
-        node->right = insert_AVLTree(node->right, key, mp, n_pools_used, pos, mp_l, n_pools_used_l);
-    } else { 
-        // Equal keys are inserted as a linked list
-        if(node->count == 1){ // DO NOT INSERT MORE THAN 2. 1 is good 2 is repetition
-            llpos * aux = getNewLocationllpos(mp_l, n_pools_used_l);
-            aux->pos = pos;
-            aux->next = node->next;
-            node->next = aux;
-            ++(node->count);
-        }
-        
-        return node;
-    }
- 
-    /* 2. Update height of this ancestor node */
-    //node->height = 1 + MAX((node->left == NULL) ? (0) : (node->left->height), (node->right == NULL) ? (0) : (node->right->height));
-    node->height = 1 + MAX(height(node->left), height(node->right));
- 
-    /* 3. Get the balance factor of this ancestor
-          node to check whether this node became
-          unbalanced */
-    //int64_t balance = (node->left == NULL || node->right == NULL) ? (0) : ((int64_t) node->left->height - (int64_t) node->right->height);
-    int64_t balance = get_balance(node);
- 
-    // If this node becomes unbalanced, then
-    // there are 4 cases
- 
-    // Left Left Case
-    if (balance > 1 && key < node->left->key)
-        return right_rotate(node);
- 
-    // Right Right Case
-    if (balance < -1 && key > node->right->key)
-        return left_rotate(node);
- 
-    // Left Right Case
-    if (balance > 1 && key > node->left->key)
-    {
-        node->left =  left_rotate(node->left);
-        return right_rotate(node);
-    }
- 
-    // Right Left Case
-    if (balance < -1 && key < node->right->key)
-    {
-        node->right = right_rotate(node->right);
-        return left_rotate(node);
-    }
- 
-    /* return the (unchanged) node pointer */
-    return node;
-}
- 
-// A utility function to print preorder traversal
-// of the tree.
-// The function also prints height of every node
-
-void pre_order(AVLTree * root){
-    if(root != NULL){
-        printf("%"PRIu64" ", root->key);
-        llpos * aux = root->next;
-        while(aux != NULL){ printf("#%"PRIu64", ", aux->pos); aux = aux->next; }
-        pre_order(root->left);
-        pre_order(root->right);
-    }
-}
-
-
-uint64_t sum_of_all_tree(AVLTree * root){
-    uint64_t mysum = 0;
-    if(root != NULL){
-        
-        mysum = root->count;
-        mysum += sum_of_all_tree(root->left);
-        mysum += sum_of_all_tree(root->right);
-    }
-    return mysum;
-}
\ No newline at end of file