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/* This file is part of PhiPack.
Copyright (c)2005, Trevor Bruen
Foobar is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Foobar is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
You should have received a copy of the GNU General Public License
along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
*/
/*
Copyright (c)2005, Trevor Bruen
All rights reserved.
Any feedback is very welcome.
email: david.bryant@otago.ac.nz
*/
#include "global.h"
#include "mem.h"
#include "seqManip.h"
void get_polymorphic( align_type **alignment, site* site_desc, int *site_states, int num_taxa, int num_sites, int *new_num_sites, align_type ***new_alignment, int **new_site_states, site **new_site_desc)
{
int i,j;
int site_count=0,polymorphic_count=0;
for(i=0;i<num_sites;i++)
{
if((site_desc[i].poly)==polymorphic)
polymorphic_count++;
}
*new_num_sites=polymorphic_count;
*new_site_states=(int *)mcalloc(polymorphic_count , sizeof(int));
*new_site_desc=(site *)mcalloc(polymorphic_count , sizeof(site));
*new_alignment=(align_type **)mcalloc(num_taxa , sizeof(align_type *));
for(i=0;i<num_taxa;i++)
((*new_alignment)[i])=(align_type *)mcalloc(polymorphic_count , sizeof(align_type) );
for(j=0;j<num_sites;j++)
{
if((site_desc[j].poly)==polymorphic)
{
for(i=0;i<num_taxa;i++)
{
(*new_alignment)[i][site_count]=alignment[i][j];
}
(*new_site_states)[site_count]=site_states[j];
(*new_site_desc)[site_count].inf=site_desc[j].inf;
(*new_site_desc)[site_count].poly=site_desc[j].poly;
(*new_site_desc)[site_count].gap=site_desc[j].gap;
(*new_site_desc)[site_count].orig_index=site_desc[j].orig_index;
(*new_site_desc)[site_count].num_missing=site_desc[j].num_missing;
site_count++;
}
}
}
void extract( align_type **alignment, int num_taxa, int num_sites, int start, int end, align_type ***new_alignment)
{
int i,j;
int site_count=0,new_count=end-start;
*new_alignment=(align_type **)mcalloc(num_taxa , sizeof(align_type *));
for(i=0;i<num_taxa;i++)
((*new_alignment)[i])=(align_type *)mcalloc(new_count , sizeof(align_type) );
for(j=start;j<end;j++)
{
for(i=0;i<num_taxa;i++)
{
(*new_alignment)[i][site_count]=alignment[i][j];
}
site_count++;
}
}
void get_unambig( align_type **alignment, site* site_desc, int *site_states, int num_taxa, int num_sites, int *new_num_sites, align_type ***new_alignment, int **new_site_states, site **new_site_desc)
{
int i,j;
int site_count=0,nongapped_count=0;
for(i=0;i<num_sites;i++)
{
if((site_desc[i].gap)==nongapped && (site_desc[i].num_missing == 0))
nongapped_count++;
}
*new_num_sites=nongapped_count;
*new_site_states=(int *)mcalloc(nongapped_count , sizeof(int));
*new_site_desc=(site *)mcalloc(nongapped_count , sizeof(site));
*new_alignment=(align_type **)mcalloc(num_taxa , sizeof(align_type *));
for(i=0;i<num_taxa;i++)
((*new_alignment)[i])=(align_type *)mcalloc(nongapped_count , sizeof(align_type) );
for(j=0;j<num_sites;j++)
{
if(((site_desc[j].gap)==nongapped) && (site_desc[j].num_missing == 0))
{
for(i=0;i<num_taxa;i++)
{
(*new_alignment)[i][site_count]=alignment[i][j];
}
(*new_site_states)[site_count]=site_states[j];
(*new_site_desc)[site_count].inf=site_desc[j].inf;
(*new_site_desc)[site_count].poly=site_desc[j].poly;
(*new_site_desc)[site_count].gap=site_desc[j].gap;
(*new_site_desc)[site_count].orig_index=site_desc[j].orig_index;
(*new_site_desc)[site_count].num_missing=site_desc[j].num_missing;
site_count++;
}
}
}
/* In: alignment - alignment ordered by taxa
site_desc - a description of each site
site_states - the number of states at each site
num_taxa.. num_inf - number of taxa char, etc..
Out: new_num_sites - the new number of sites
new_alignment - alignment ordered by taxa with only informative
new_site_states - number of states at each informative site
new_site_desc - description of states at each informative site
*/
void get_informative( align_type **alignment, site* site_desc, int *site_states, int num_taxa, int num_sites, int* new_num_sites, align_type ***new_alignment, int **new_site_states, site **new_site_desc)
{
int i,j;
int site_count=0,informative_count=0;
for(i=0;i<num_sites;i++)
{
if((site_desc[i].inf)==informative)
informative_count++;
}
*new_num_sites=informative_count;
*new_site_states=(int *)mcalloc(informative_count , sizeof(int));
*new_site_desc=(site *)mcalloc(informative_count , sizeof(site));
*new_alignment=(align_type **)mcalloc(num_taxa , sizeof(align_type *));
for(i=0;i<num_taxa;i++)
((*new_alignment)[i])=(align_type *)mcalloc(informative_count , sizeof(align_type) );
for(j=0;j<num_sites;j++)
{
if((site_desc[j].inf)==informative)
{
for(i=0;i<num_taxa;i++)
{
(*new_alignment)[i][site_count]=alignment[i][j];
}
(*new_site_states)[site_count]=site_states[j];
(*new_site_desc)[site_count].inf=site_desc[j].inf;
(*new_site_desc)[site_count].poly=site_desc[j].poly;
(*new_site_desc)[site_count].gap=site_desc[j].gap;
(*new_site_desc)[site_count].orig_index=site_desc[j].orig_index;
(*new_site_desc)[site_count].num_missing=site_desc[j].num_missing;
site_count++;
}
}
}
/* Check validity of alignment */
cbool validate_alignment(align_type **alignment, alignmentClass alignKind,int num_taxa, int num_sites)
{
int i,j;
signed char ch;
char s[MAX_SIZE+1];
for(i=0;i<num_taxa;i++)
{
for(j=0;j<num_sites;j++)
{
ch=alignment[i][j];
if(!(validState(alignKind,ch) || missing_ambig_State(alignKind,ch) || (ch == (GLOBAL_GAP-CHAR_START))))
{
sprintf(s,"Error %c (%d) is not a valid state for this type of sequence\n",ch+CHAR_START,(int)ch+CHAR_START);
error(s);
}
}
}
return TRUE;
}
/* Estimate diversity using pairwise deletion */
void get_seq_div(align_type **alignment, alignmentClass alignKind, int num_taxa, int num_sites, double *div)
{
int i,j,l,count=0,num=0;
double val=0;
/* fprintf(stdout,"Looking at alignment %d \n",alignKind);*/
for(i=0;i<(num_taxa-1);i++)
{
for(j=(i+1);j<num_taxa;j++)
{
count=0;
num=0;
for(l=0;l<num_sites;l++)
{
if(validState(alignKind,alignment[i][l]) && validState(alignKind,alignment[j][l]))
/* if((alignment[i][l] < MAX_STATE) && (alignment[j][l] <MAX_STATE)) */
{
if(alignment[i][l]!=alignment[j][l])
count++;
num++;
}
}
val=val+((double)count)/((double)num);
}
}
*div=(val*2)/(num_taxa*(num_taxa-1));
//fprintf(stdout,"Found %lf\n",*div);
}
/* In: alignment - ordered by taxa
num_taxa - number of taxa
num_sites - number of sites
Out: site_states - number of states at every site
site_desc - type of every site
*/
void find_states( align_type **alignment, alignmentClass alignKind, cbool stateMissing, int num_taxa, int num_sites, site** site_desc, int** site_states)
{
int state_count,big_states, char_A,i,j;
int state_map[MAX_STATE];
int missing_ambig_count=0;
char s[250];
cbool gap_char;
*site_desc=(site *)mcalloc(num_sites , sizeof(site));
*site_states=(int *)mcalloc(num_sites , sizeof(int));
for(j=0;j<num_sites;j++)
{
for(i=0;i<MAX_STATE;i++)
state_map[i]=0;
state_count=0;
gap_char=FALSE;
missing_ambig_count=0;
for(i=0;i<num_taxa;i++)
{
char_A=(int)alignment[i][j];
if(validState(alignKind,char_A))
/* if(char_A <=MAX_STATE) */
{
if(state_map[char_A]<=0)
{
state_count++;
state_map[char_A]++;
}
else
state_map[char_A]++;
}
else if(missing_ambig_State(alignKind,char_A))
{
missing_ambig_count++;
}
else if(valid_gap(alignKind,char_A))
{
gap_char=TRUE;
}
else
{
sprintf(s,"Invalid state %c\n",(char_A+CHAR_START));
error(s);
}
}
/* Add current index to description */
((*site_desc)[j]).orig_index=j;
if(stateMissing && (missing_ambig_count > 0))
state_count++;
/*Add state count */
(*site_states)[j]=state_count;
((*site_desc)[j]).num_states=state_count;
/* Add missing count */
((*site_desc)[j]).num_missing=missing_ambig_count;
/* Check if gapped */
if(gap_char)
{
((*site_desc)[j]).gap=gapped;
}
else
{
((*site_desc)[j]).gap=nongapped;
}
/* Check if informative */
big_states=0;
if(state_count >= 2)
{
for(i=0;i<MAX_STATE;i++)
if(state_map[i]>= 2)
big_states++;
if(stateMissing && (missing_ambig_count >=2))
big_states++;
}
if(state_count>=2)
{
((*site_desc)[j]).poly=polymorphic;
if(big_states>=2)
{
((*site_desc)[j]).inf=informative;
}
else
{
((*site_desc)[j]).inf=uninformative;
}
}
else
{
((*site_desc)[j]).inf=uninformative;
(*site_desc)[j].poly=constant;
}
}
}
/* In: alignment - ordered by taxa
site_states - number of states at each site
num_sites - number of sites
num_taxa - number of taxa...
Out:
new_alignment - ordered by character
where each character goes from
0..k, for k states, with NEGATIVE
states for missing/gaps...
*/
void reorder_chars( align_type **alignment, alignmentClass alignKind, cbool stateMissing,int num_sites, int num_taxa, align_type ***new_alignment)
{
int state_map[MAX_STATE];
int state_count,cur_state;
int i,j,k,char_A;
*new_alignment=(align_type **)mcalloc(num_sites , sizeof(align_type *));
for(i=0;i<num_sites;i++)
((*new_alignment)[i])=(align_type *)mcalloc(num_taxa , sizeof(align_type));
for(j=0;j<num_sites;j++)
{
for(k=0;k<MAX_STATE;k++)
state_map[k]=-1;
state_count=0;
for(i=0;i<num_taxa;i++)
{
char_A=(int)alignment[i][j];
/* Figure out which positive state 0..k */
/* if(char_A <=MAX_STATE)*/
if(validState(alignKind,char_A))
{
if(state_map[char_A]<0)
{
state_map[char_A]=state_count;
cur_state=state_count;
state_count++;
}
else
{
cur_state=state_map[char_A];
}
}
else if(missing_ambig_State(alignKind,char_A) && (stateMissing == TRUE))
{
if(state_map[MISSING_STATE]<0)
{
state_map[MISSING_STATE]=state_count;
cur_state=state_count;
state_count++;
}
else
{
cur_state=state_map[MISSING_STATE];
}
}
/* Otherwise - state that should be ignored - use ignore state */
else
{
cur_state=IGNORE_STATE;
}
/* Add taxa */
(*new_alignment)[j][i]=(align_type)cur_state;
}
}
}
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