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/***************************************************************************
* PHAST: PHylogenetic Analysis with Space/Time models
* Copyright (c) 2002-2005 University of California, 2006-2010 Cornell
* University. All rights reserved.
*
* This source code is distributed under a BSD-style license. See the
* file LICENSE.txt for details.
***************************************************************************/
/** @file indel_history.h
Functions and structs to hold and interrogate the history of insertions / deletions
@ingroup phylo
*/
#ifndef IND_HIST
#define IND_HIST
#include <stdio.h>
#include <trees.h>
#include <msa.h>
/** Number of Indel types i.e. insert, delete, none */
#define NINDEL_CHARS 3
/** What type of change, insertion, deletion, none */
typedef enum {INS, /**< Insertion */
DEL, /**< Deletion */
BASE /**< No insertion or deletion */
} indel_char; /* note: order is used in places */
/** Information about an indel */
typedef struct {
indel_char type; /**< What type of change, insertion, deletion, none */
int start; /**< Site the indel starts at */
int len; /**< Length of indel */
} Indel;
/** Compact Indel history of a Multiple Sequence Alignment */
typedef struct {
TreeNode *tree; /**< Tree describing structure of data */
int ncols; /**< Number of sites from data */
List **indels; /**< List of each indel */
} CompactIndelHistory;
/** Indel history of a Multiple Sequence Alignment */
typedef struct {
TreeNode *tree; /**< Tree describing structure of data */
int ncols; /**< Number of sites from data */
char **indel_strings; /**< list of strings describing each indel */ /* make bin vector later */
} IndelHistory;
/** \name Indel History allocation functions
\{ */
/** Create an Indel History object for a dataset
@param tree Representing dataset structure
@param ncols Number of columns in dataset
@result New indel history object
*/
IndelHistory *ih_new(TreeNode *tree, int ncols);
/** Create a compact Indel history object for a dataset
@param tree Representing dataset structure
@param ncols Number of columns in dataset
@result New compact indel history object
*/
CompactIndelHistory *ih_new_compact(TreeNode *tree, int ncols);
/** Given an alignment and tree structure, extract indels
@param msa Multiple Sequence Alignment sequence data
@param tree Tree structure
@result New Indel history object from sequence and tree data
@note Includes sequences for ancestral nodes and leaves
*/
IndelHistory *ih_extract_from_alignment(MSA *msa, TreeNode *tree);
/** Reconstruct an indel history by parsimony from an alignment, given a tree
@param msa Multiple Sequence Alignment sequence data
@param tree Tree structure
@result Indel history object from sequence and tree data
*/
IndelHistory *ih_reconstruct(MSA *msa, TreeNode *tree);
/** \} \name Indel History cleanup functions
\{ */
/** Free an Indel History object
@param ih Indel History object to free */
void ih_free(IndelHistory *ih);
/** Free a Compact Indel History object
@param cih Compact Indel History object to free
*/
void ih_free_compact(CompactIndelHistory *cih);
/** \} \name Indel History convert between compact and normal functions
\{ */
/** Expand a compact indel history.
@param cih Compact indel history
@result Indel history
*/
IndelHistory *ih_expand(CompactIndelHistory *cih);
/** Compact an indel history
@param ih Indel history
@result Compact indel history
*/
CompactIndelHistory *ih_compact(IndelHistory *ih);
/** \} \name Indel History read/write file access functions
\{ */
/** Save an indel history to a file
@param ih Indel History to write to file
@param outf File descriptor to write Indel History into
@param msa_name Name of the Multiple Sequence Alignment
@param prog_name Name of program that generated indel history
@warning Make sure ancestral nodes have been labeled before calling
*/
void ih_print(IndelHistory *ih, FILE *outf, char *msa_name, char *prog_name);
/** Save a compact indel history to a file
@param cih Compact Indel History to write to file
@param outf File descriptor to write compact Indel History into
@param msa_name Name of the Multiple Sequence Alignment
@param prog_name Name of program that generated indel history
@warning Make sure ancestral nodes have been labeled before calling
*/
void ih_print_compact(CompactIndelHistory *cih, FILE *outf, char *msa_name,
char *prog_name);
/** Read a compact indel history object from a file.
@param inf Input file to read compact indel history from
@result Compact indel history data read from file
*/
CompactIndelHistory *ih_read_compact(FILE *inf);
/** Read a indel history from a file.
@param inf Input file to read indel history from
@result Indel history data read from file
*/
IndelHistory *ih_new_from_file(FILE* inf);
/** \} \name Indel History Misc. functions
\{ */
/** Convert an indel history into an alignment.
Alignment includes sequences for ancestral nodes as
well as leaf nodes, and with '^' characters in place of '-' for
insertions and '.' characters in place of '-' for deletions.
@param ih Indel History to use as template to create modified MSA
@param msa Multiple Sequence Alignment
@result MSA modified at sites where indels occurred
*/
MSA *ih_as_alignment(IndelHistory *ih, MSA *msa);
/** Convert names in an alignment from the convention used by
inferAncestors to the convention used in PHAST, based on a given
tree.
@param[in,out] msa Multiple Sequence Alignment sequence data
@param[in] tree Tree structure
*/
void ih_convert_ia_names(MSA *msa, TreeNode *tree);
#endif
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