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cluster-common.h
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cluster-common.h
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#ifndef CLUSTER_COMMON_H
#define CLUSTER_COMMON_H
#include <eutils/evar.h>
#include <eutils/estr.h>
#include <eutils/ernd.h>
#include <eutils/ebasicarray.h>
#include <eutils/eintarray.h>
#include <eutils/ebasichashmap.h>
#include <eutils/estrhash.h>
#include <eutils/etimer.h>
#include <eutils/eblockarray.h>
#include <list>
#include <math.h>
#include <unistd.h>
#include <eutils/ethread.h>
#include "eseqcluster.h"
#include "eseqclustersingle.h"
#include "eseqclustercount.h"
#include "lookuptables.h"
extern float warnMemThres;
extern bool warnedMemThres;
extern float exitMemThres;
extern bool ignoreMemThres;
/*
extern char lt_gap_count[0x1u << 16];
extern char lt_nogap_count[0x1u << 16];
extern char lt_nogap_len[0x1u << 16];
*/
extern char lt_tamura_p[0x1u << 16];
extern char lt_tamura_q[0x1u << 16];
extern char lt_tamura_len[0x1u << 16];
extern char lt_tamura_gc[0x1u << 16];
//void gap_initLookupTable();
//void nogap_initLookupTable();
//void initLookupTable();
class eshortseq
{
public:
int b;
int e;
estr seq;
estr name;
void compress();
};
inline unsigned char nuc_compress(unsigned char c){
switch(c){
case 'A': return(0x00u);
case 'T': return(0x01u);
case 'U': return(0x01u);
case 'G': return(0x02u);
case 'C': return(0x03u);
case 'R': return(0x04u);
case 'Y': return(0x05u);
case 'S': return(0x06u);
case 'W': return(0x07u);
case 'K': return(0x08u);
case 'M': return(0x09u);
case 'B': return(0x0Au);
case 'D': return(0x0Bu);
case 'H': return(0x0Cu);
case 'V': return(0x0Du);
case 'N': return(0x0Eu);
case '-': return(0x0Fu);
case '.': return(0x0Fu);
}
ldie("unknown nucleotide: "+estr(c));
return(0x0F);
}
inline void getL2(int& l,int w,int x,int y)
{
if (y<x) { int t; t=x; x=y; y=t; }
--w;
if (x>w/2) { x=w-x; y-=1; l=x*w+y; return; }
y-=x+1;
l=x*w+y;
return;
}
inline void getL(int& l,int w,int x,int y)
{
--w;
if (x>w/2) { x=w-x; y-=1; l=x*w+y; return; }
y-=x+1;
l=x*w+y;
return;
}
inline void getXY(int l,int w,int& x,int& y)
{
--w;
x=(l/w);
y=(l%w);
if (y<w-x){ y+=x+1; return; }
y+=1;
x=w-x;
}
inline float dist_nogap(const estr& s1,const estr& s2,int gc1,int gc2)
{
int i;
int count=0;
int gcount=0;
for (i=0; i<s1._strlen; ++i){
if (s1._str[i]==s2._str[i]) { if (s1._str[i]=='-') ++gcount; else ++count; }
}
return((float)count/(float)(s1._strlen-gc1-gc2+gcount));
}
const long int b4_m0=0x0Fl;
const long int b4_m1=0x0F0l;
const long int b4_m2=0x0F00l;
const long int b4_m3=0x0F000l;
const long int b4_m4=0x0F0000l;
const long int b4_m5=0x0F00000l;
const long int b4_m6=0x0F000000l;
const long int b4_m7=0x0F0000000l;
const long int b4_m8=0x0F00000000l;
const long int b4_m9=0x0F000000000l;
const long int b4_m10=0x0F0000000000l;
const long int b4_m11=0x0F00000000000l;
const long int b4_m12=0x0F000000000000l;
const long int b4_m13=0x0F0000000000000l;
const long int b4_m14=0x0F00000000000000l;
const long int b4_m15=0x0F000000000000000l;
const long int b4_umask=0x1111111111111111;
const long int b8_m0=0x00000000000000FFl;
const long int b8_m1=0x000000000000FF00l;
const long int b8_m2=0x0000000000FF0000l;
const long int b8_m3=0x00000000FF000000l;
const long int b8_m4=0x000000FF00000000l;
const long int b8_m5=0x0000FF0000000000l;
const long int b8_m6=0x00FF000000000000l;
const long int b8_m7=0xFF00000000000000l;
const long int b8_d0='-';
const long int b8_d1=b8_d0 << 8;
const long int b8_d2=b8_d0 << 16;
const long int b8_d3=b8_d0 << 24;
const long int b8_d4=b8_d0 << 32;
const long int b8_d5=b8_d0 << 40;
const long int b8_d6=b8_d0 << 48;
const long int b8_d7=b8_d0 << 56;
inline void dist_inc(long int a1,long int a2,long int mask,int& count){
if ((a1&mask)==(a2&mask))
++count;
}
inline void dist_nogap_inc2(long int a1,long int a2,long int mask,int& count,int& len){
if ((a1&a2&mask)==mask)
--len;
else if ((a1&mask)==(a2&mask))
++count;
// if ((a1&mask)==(a2&mask)){
// if ((a1&mask)!=mask)
// ++count;
// else
// --len;
// }
}
inline void dist_nogap_inc3(long int a1,long int a2,long int mask,int& count,int& len){
if ((a1&a2&mask)==mask)
++len;
if ((a1&mask)==(a2&mask))
++count;
// if ((a1&mask)==(a2&mask)){
// if ((a1&mask)!=mask)
// ++count;
// else
// --len;
// }
}
//inline void dist_nogap_inc(long int a1,long int a2,long int mask,int& count,int& len){
// if (!((a1&mask)==mask || (a2&mask)==mask)){
// if ((a1&mask)==(a2&mask)) ++count;
// ++len;
// }
//}
inline void dist_nogapsingle_inc(long int a1,long int a2,long int mask,int& count,int& len,int& gapmiss){
if ((a1&mask)==mask && (a2&mask)==mask)
{ --len; return; }
if ((a1&mask)==(a2&mask))
{ ++count; gapmiss=0; return; }
if ((a1&mask)==mask) {
if (gapmiss==1) { --len; return; }
gapmiss=1;
return;
}
if ((a2&mask)==mask) {
if (gapmiss==2) { --len; return; }
gapmiss=2;
return;
}
}
inline void dist_tamura_inc(long int a1,long int a2,long int mask,int& P,int& Q,int& GC1,int& GC2,int& len){
if ((a1&mask)==mask || (a2&mask)==mask)
--len;
else if (((a1^a2)&mask)==((0x02*b4_umask)&mask))
++P;
else if (((a1^a2)&mask)==((0x03*b4_umask)&mask))
++Q;
if ((a1&mask)==((0x02*b4_umask)&mask) || (a1&mask)==((0x03*b4_umask)&mask))
++GC1;
if ((a2&mask)==((0x02*b4_umask)&mask) || (a2&mask)==((0x03*b4_umask)&mask))
++GC2;
}
inline float dist_tamura_compressed(const estr& s1,const estr& s2,int seqlen)
{
int len=seqlen;
int P=0; // transitions
int Q=0; // transversions
int GC1=0; // GC content seq1
int GC2=0; // GC content seq2
long int *ep1=(long int*)(s1._str)+(s1._strlen/8);
long int *p1=(long int*)s1._str;
long int *p2=(long int*)s2._str;
for (; p1!=ep1; ++p1,++p2){
dist_tamura_inc(*p1,*p2,b4_m0,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m1,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m2,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m3,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m4,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m5,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m6,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m7,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m8,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m9,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m10,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m11,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m12,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m13,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m14,P,Q,GC1,GC2,len);
dist_tamura_inc(*p1,*p2,b4_m15,P,Q,GC1,GC2,len);
}
switch (seqlen%16){
case 15:
dist_tamura_inc(*p1,*p2,b4_m14,P,Q,GC1,GC2,len);
case 14:
dist_tamura_inc(*p1,*p2,b4_m13,P,Q,GC1,GC2,len);
case 13:
dist_tamura_inc(*p1,*p2,b4_m12,P,Q,GC1,GC2,len);
case 12:
dist_tamura_inc(*p1,*p2,b4_m11,P,Q,GC1,GC2,len);
case 11:
dist_tamura_inc(*p1,*p2,b4_m10,P,Q,GC1,GC2,len);
case 10:
dist_tamura_inc(*p1,*p2,b4_m9,P,Q,GC1,GC2,len);
case 9:
dist_tamura_inc(*p1,*p2,b4_m8,P,Q,GC1,GC2,len);
case 8:
dist_tamura_inc(*p1,*p2,b4_m7,P,Q,GC1,GC2,len);
case 7:
dist_tamura_inc(*p1,*p2,b4_m6,P,Q,GC1,GC2,len);
case 6:
dist_tamura_inc(*p1,*p2,b4_m5,P,Q,GC1,GC2,len);
case 5:
dist_tamura_inc(*p1,*p2,b4_m4,P,Q,GC1,GC2,len);
case 4:
dist_tamura_inc(*p1,*p2,b4_m3,P,Q,GC1,GC2,len);
case 3:
dist_tamura_inc(*p1,*p2,b4_m2,P,Q,GC1,GC2,len);
case 2:
dist_tamura_inc(*p1,*p2,b4_m1,P,Q,GC1,GC2,len);
case 1:
dist_tamura_inc(*p1,*p2,b4_m0,P,Q,GC1,GC2,len);
}
float C=GC1/seqlen + GC2/seqlen - 2.0*GC1/seqlen*GC2/seqlen;
return(1+1.0*C*log(1.0-(float)P/(C*len)-(float)Q/len) + 0.5*(1.0-C)*log(1.0-2.0*Q/len));
}
inline float dist_tamura_compressed2(const estr& s1,const estr& s2,int seqlen)
{
int len=0;
int P=0; // transitions
int Q=0; // transversions
int GC1=0; // GC content seq1
int GC2=0; // GC content seq2
unsigned long *ep1=(unsigned long*)(s1._str)+(s1._strlen/8);
unsigned long *p1=(unsigned long*)s1._str;
unsigned long *p2=(unsigned long*)s2._str;
unsigned long tx,ta;
for (; p1!=ep1; ++p1,++p2){
tx=((*p1)^(*p2));
ta=((*p1)&(*p2));
P+=lt_tamura_p[ tx&0xffffu ] + lt_tamura_p[ (tx>>16)&0xffffu ] + lt_tamura_p[ (tx>>32)&0xffffu ] + lt_tamura_p[ (tx>>48)&0xffffu ];
Q+=lt_tamura_q[ tx&0xffffu ] + lt_tamura_q[ (tx>>16)&0xffffu ] + lt_tamura_q[ (tx>>32)&0xffffu ] + lt_tamura_q[ (tx>>48)&0xffffu ];
len-=lt_tamura_len[ ta&0xffffu ] + lt_tamura_len[ (ta>>16)&0xffffu ] + lt_tamura_len[ (ta>>32)&0xffffu ] + lt_tamura_len[ (ta>>48)&0xffffu ];
GC1+=lt_tamura_gc[ (*p1)&0xffffu ] + lt_tamura_gc[ ((*p1)>>16)&0xffffu ] + lt_tamura_gc[ ((*p1)>>32)&0xffffu ] + lt_tamura_gc[ ((*p1)>>48)&0xffffu ];
GC2+=lt_tamura_gc[ (*p2)&0xffffu ] + lt_tamura_gc[ ((*p2)>>16)&0xffffu ] + lt_tamura_gc[ ((*p2)>>32)&0xffffu ] + lt_tamura_gc[ ((*p2)>>48)&0xffffu ];
}
switch (seqlen%16){
case 15:
dist_tamura_inc(*p1,*p2,b4_m14,P,Q,GC1,GC2,len);
case 14:
dist_tamura_inc(*p1,*p2,b4_m13,P,Q,GC1,GC2,len);
case 13:
dist_tamura_inc(*p1,*p2,b4_m12,P,Q,GC1,GC2,len);
case 12:
dist_tamura_inc(*p1,*p2,b4_m11,P,Q,GC1,GC2,len);
case 11:
dist_tamura_inc(*p1,*p2,b4_m10,P,Q,GC1,GC2,len);
case 10:
dist_tamura_inc(*p1,*p2,b4_m9,P,Q,GC1,GC2,len);
case 9:
dist_tamura_inc(*p1,*p2,b4_m8,P,Q,GC1,GC2,len);
case 8:
dist_tamura_inc(*p1,*p2,b4_m7,P,Q,GC1,GC2,len);
case 7:
dist_tamura_inc(*p1,*p2,b4_m6,P,Q,GC1,GC2,len);
case 6:
dist_tamura_inc(*p1,*p2,b4_m5,P,Q,GC1,GC2,len);
case 5:
dist_tamura_inc(*p1,*p2,b4_m4,P,Q,GC1,GC2,len);
case 4:
dist_tamura_inc(*p1,*p2,b4_m3,P,Q,GC1,GC2,len);
case 3:
dist_tamura_inc(*p1,*p2,b4_m2,P,Q,GC1,GC2,len);
case 2:
dist_tamura_inc(*p1,*p2,b4_m1,P,Q,GC1,GC2,len);
case 1:
dist_tamura_inc(*p1,*p2,b4_m0,P,Q,GC1,GC2,len);
}
float C=GC1/seqlen + GC2/seqlen - 2.0*GC1/seqlen*GC2/seqlen;
return(1+1.0*C*log(1.0-(float)P/(C*len)-(float)Q/len) + 0.5*(1.0-C)*log(1.0-2.0*Q/len));
}
/*
void initDistMatrix();
extern int gap_matrix[16][16];
inline float dist_compressed2(const estr& s1,const estr& s2,int seqlen)
{
int len=seqlen;
int count=0;
unsigned long int *ep1=(unsigned long int*)(s1._str)+(s1._strlen/8);
unsigned long int *p1=(unsigned long int*)s1._str;
unsigned long int *p2=(unsigned long int*)s2._str;
unsigned long int tp1,tp2;
for (; p1!=ep1; ++p1,++p2){
tp1=*p1,tp2=*p2; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
tp1>>=4,tp2>>=4; count+=gap_matrix[b4_m0&tp1][b4_m0&tp2];
}
switch (seqlen%16){
case 15:
dist_inc(*p1,*p2,b4_m14,count);
case 14:
dist_inc(*p1,*p2,b4_m13,count);
case 13:
dist_inc(*p1,*p2,b4_m12,count);
case 12:
dist_inc(*p1,*p2,b4_m11,count);
case 11:
dist_inc(*p1,*p2,b4_m10,count);
case 10:
dist_inc(*p1,*p2,b4_m9,count);
case 9:
dist_inc(*p1,*p2,b4_m8,count);
case 8:
dist_inc(*p1,*p2,b4_m7,count);
case 7:
dist_inc(*p1,*p2,b4_m6,count);
case 6:
dist_inc(*p1,*p2,b4_m5,count);
case 5:
dist_inc(*p1,*p2,b4_m4,count);
case 4:
dist_inc(*p1,*p2,b4_m3,count);
case 3:
dist_inc(*p1,*p2,b4_m2,count);
case 2:
dist_inc(*p1,*p2,b4_m1,count);
case 1:
dist_inc(*p1,*p2,b4_m0,count);
}
return((float)count/(float)seqlen);
}
*/
/*
inline float dist_compressed(const estr& s1,const estr& s2,int seqlen)
{
int len=seqlen;
int count=0;
long int *ep1=(long int*)(s1._str)+(s1._strlen/8);
long int *p1=(long int*)s1._str;
long int *p2=(long int*)s2._str;
for (; p1!=ep1; ++p1,++p2){
dist_inc(*p1,*p2,b4_m0,count);
dist_inc(*p1,*p2,b4_m1,count);
dist_inc(*p1,*p2,b4_m2,count);
dist_inc(*p1,*p2,b4_m3,count);
dist_inc(*p1,*p2,b4_m4,count);
dist_inc(*p1,*p2,b4_m5,count);
dist_inc(*p1,*p2,b4_m6,count);
dist_inc(*p1,*p2,b4_m7,count);
dist_inc(*p1,*p2,b4_m8,count);
dist_inc(*p1,*p2,b4_m9,count);
dist_inc(*p1,*p2,b4_m10,count);
dist_inc(*p1,*p2,b4_m11,count);
dist_inc(*p1,*p2,b4_m12,count);
dist_inc(*p1,*p2,b4_m13,count);
dist_inc(*p1,*p2,b4_m14,count);
dist_inc(*p1,*p2,b4_m15,count);
}
switch (seqlen%16){
case 15:
dist_inc(*p1,*p2,b4_m14,count);
case 14:
dist_inc(*p1,*p2,b4_m13,count);
case 13:
dist_inc(*p1,*p2,b4_m12,count);
case 12:
dist_inc(*p1,*p2,b4_m11,count);
case 11:
dist_inc(*p1,*p2,b4_m10,count);
case 10:
dist_inc(*p1,*p2,b4_m9,count);
case 9:
dist_inc(*p1,*p2,b4_m8,count);
case 8:
dist_inc(*p1,*p2,b4_m7,count);
case 7:
dist_inc(*p1,*p2,b4_m6,count);
case 6:
dist_inc(*p1,*p2,b4_m5,count);
case 5:
dist_inc(*p1,*p2,b4_m4,count);
case 4:
dist_inc(*p1,*p2,b4_m3,count);
case 3:
dist_inc(*p1,*p2,b4_m2,count);
case 2:
dist_inc(*p1,*p2,b4_m1,count);
case 1:
dist_inc(*p1,*p2,b4_m0,count);
}
return((float)count/(float)seqlen);
}
*/
inline float dist_compressed2(const estr& s1,const estr& s2,int seqlen)
{
int len=seqlen;
int count=0;
unsigned long *ep1=(unsigned long*)(s1._str)+(s1._strlen/8)-1;
unsigned long *p1=(unsigned long*)s1._str;
unsigned long *p2=(unsigned long*)s2._str;
unsigned long t;
for (; p1!=ep1; ++p1,++p2){
t=((*p1) ^ (*p2));
count+=lt_gap_count[ t&0xfffful ] + lt_gap_count[ (t>>16)&0xfffful ] + lt_gap_count[ (t>>32)&0xfffful ] + lt_gap_count[ (t>>48)&0xfffful ];
}
t=((*p1) ^ (*p2));
count+=lt_gap_count[ t&0xfffful ] + lt_gap_count[ (t>>16)&0xfffful ] + lt_gap_count[ (t>>32)&0xfffful ] + lt_gap_count[ (t>>48)&0xfffful ] - (16-seqlen%16);
return((float)count/(float)seqlen);
}
inline float dist_compressed(const estr& s1,const estr& s2,int seqlen)
{
int len=seqlen;
int count=0;
long int *ep1=(long int*)(s1._str)+(s1._strlen/8)-1;
long int *p1=(long int*)s1._str;
long int *p2=(long int*)s2._str;
long int tp1,tp2;
for (; p1!=ep1; ++p1,++p2){
tp1=*p1,tp2=*p2; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
tp1>>=4,tp2>>=4; dist_inc(tp1,tp2,b4_m0,count);
}
switch (seqlen%16){
case 15:
dist_inc(*p1,*p2,b4_m14,count);
case 14:
dist_inc(*p1,*p2,b4_m13,count);
case 13:
dist_inc(*p1,*p2,b4_m12,count);
case 12:
dist_inc(*p1,*p2,b4_m11,count);
case 11:
dist_inc(*p1,*p2,b4_m10,count);
case 10:
dist_inc(*p1,*p2,b4_m9,count);
case 9:
dist_inc(*p1,*p2,b4_m8,count);
case 8:
dist_inc(*p1,*p2,b4_m7,count);
case 7:
dist_inc(*p1,*p2,b4_m6,count);
case 6:
dist_inc(*p1,*p2,b4_m5,count);
case 5:
dist_inc(*p1,*p2,b4_m4,count);
case 4:
dist_inc(*p1,*p2,b4_m3,count);
case 3:
dist_inc(*p1,*p2,b4_m2,count);
case 2:
dist_inc(*p1,*p2,b4_m1,count);
case 1:
dist_inc(*p1,*p2,b4_m0,count);
}
return((float)count/(float)seqlen);
}
inline void dist_nogap_inc(const estr& s1,const estr& s2,int i,int& count,int& len){
int bp=i >> 4; // i/16
int bm=(i%16)*4;
unsigned long int mask=(b4_m0 << bm);
if ((*(((unsigned long int*)s1._str)+bp)&mask)==mask && (*(((unsigned long int*)s2._str)+bp)&mask)==mask)
--len;
else if ((*(((unsigned long int*)s1._str)+bp)&mask)==(*(((unsigned long int*)s2._str)+bp)&mask))
++count;
}
inline void dist_nogap_dec(const estr& s1,const estr& s2,int i,int& count,int& len){
int bp=i >> 4; // i/16
int bm=(i%16)*4;
unsigned long int mask=(b4_m0 << bm);
if ((*(((unsigned long int*)s1._str)+bp)&mask)==mask && (*(((unsigned long int*)s2._str)+bp)&mask)==mask)
++len;
else if ((*(((unsigned long int*)s1._str)+bp)&mask)==(*(((unsigned long int*)s2._str)+bp)&mask))
--count;
}
inline float dist_nogap_compressed_window(const estr& s1,const estr& s2,int seqlen,int winlen)
{
int len=winlen;
int count=0;
int i,j;
for (i=0; i<seqlen && i<winlen; ++i)
dist_nogap_inc(s1,s2,i,count,len);
float tmpdiff=float(count)/len;
float maxdiff=tmpdiff;
for (j=0; i<seqlen; ++i,++j){
dist_nogap_inc(s1,s2,i,count,len);
dist_nogap_dec(s1,s2,j,count,len);
tmpdiff=float(count)/len;
if (tmpdiff<maxdiff) maxdiff=tmpdiff;
}
return(maxdiff);
}
inline float dist_nogap_compressed2(const estr& s1,const estr& s2,int seqlen)
{
int len=0;
int count=0;
unsigned long *ep1=(unsigned long*)(s1._str)+(s1._strlen/8);
unsigned long *p1=(unsigned long*)s1._str;
unsigned long *p2=(unsigned long*)s2._str;
unsigned long tx,ta;
for (; p1!=ep1; ++p1,++p2){
tx=((*p1) ^ (*p2));
ta=((*p1) & (*p2));
count+=lt_nogap_count[ tx&0xffffu ] + lt_nogap_count[ (tx>>16)&0xffffu ] + lt_nogap_count[ (tx>>32)&0xffffu ] + lt_nogap_count[ (tx>>48)&0xffffu ];
len+=lt_nogap_len[ ta&0xffffu ] + lt_nogap_len[ (ta>>16)&0xffffu ] + lt_nogap_len[ (ta>>32)&0xffffu ] + lt_nogap_len[ (ta>>48)&0xffffu ];
}
tx=((*p1) ^ (*p2));
ta=((*p1) & (*p2));
count+=lt_nogap_count[ tx&0xffffu ] + lt_nogap_count[ (tx>>16)&0xffffu ] + lt_nogap_count[ (tx>>32)&0xffffu ] + lt_nogap_count[ (tx>>48)&0xffffu ] - (16-seqlen%16);
len+=lt_nogap_len[ ta&0xffffu ] + lt_nogap_len[ (ta>>16)&0xffffu ] + lt_nogap_len[ (ta>>32)&0xffffu ] + lt_nogap_len[ (ta>>48)&0xffffu ];
return((float)(count-len)/(float)(seqlen-len));
}
inline float dist_nogap_compressed(const estr& s1,const estr& s2,int seqlen)
{
int len=seqlen;
int count=0;
long int *ep1=(long int*)(s1._str)+(s1._strlen/8);
long int *p1=(long int*)s1._str;
long int *p2=(long int*)s2._str;
for (; p1!=ep1; ++p1,++p2){
dist_nogap_inc2(*p1,*p2,b4_m0,count,len);
dist_nogap_inc2(*p1,*p2,b4_m1,count,len);
dist_nogap_inc2(*p1,*p2,b4_m2,count,len);
dist_nogap_inc2(*p1,*p2,b4_m3,count,len);
dist_nogap_inc2(*p1,*p2,b4_m4,count,len);
dist_nogap_inc2(*p1,*p2,b4_m5,count,len);
dist_nogap_inc2(*p1,*p2,b4_m6,count,len);
dist_nogap_inc2(*p1,*p2,b4_m7,count,len);
dist_nogap_inc2(*p1,*p2,b4_m8,count,len);
dist_nogap_inc2(*p1,*p2,b4_m9,count,len);
dist_nogap_inc2(*p1,*p2,b4_m10,count,len);
dist_nogap_inc2(*p1,*p2,b4_m11,count,len);
dist_nogap_inc2(*p1,*p2,b4_m12,count,len);
dist_nogap_inc2(*p1,*p2,b4_m13,count,len);
dist_nogap_inc2(*p1,*p2,b4_m14,count,len);
dist_nogap_inc2(*p1,*p2,b4_m15,count,len);
}
switch (seqlen%16){
case 15:
dist_nogap_inc2(*p1,*p2,b4_m14,count,len);
case 14:
dist_nogap_inc2(*p1,*p2,b4_m13,count,len);
case 13:
dist_nogap_inc2(*p1,*p2,b4_m12,count,len);
case 12:
dist_nogap_inc2(*p1,*p2,b4_m11,count,len);
case 11:
dist_nogap_inc2(*p1,*p2,b4_m10,count,len);
case 10:
dist_nogap_inc2(*p1,*p2,b4_m9,count,len);
case 9:
dist_nogap_inc2(*p1,*p2,b4_m8,count,len);
case 8:
dist_nogap_inc2(*p1,*p2,b4_m7,count,len);
case 7:
dist_nogap_inc2(*p1,*p2,b4_m6,count,len);
case 6:
dist_nogap_inc2(*p1,*p2,b4_m5,count,len);
case 5:
dist_nogap_inc2(*p1,*p2,b4_m4,count,len);
case 4:
dist_nogap_inc2(*p1,*p2,b4_m3,count,len);
case 3:
dist_nogap_inc2(*p1,*p2,b4_m2,count,len);
case 2:
dist_nogap_inc2(*p1,*p2,b4_m1,count,len);
case 1:
dist_nogap_inc2(*p1,*p2,b4_m0,count,len);
}
return((float)count/(float)len);
}
inline float dist_nogapsingle_compressed(const estr& s1,const estr& s2,int seqlen) // count a continuous gap as a single mismatch, gap-gap does not count
{
int gapmiss=0;
int len=seqlen;
int count=0;
long int *ep1=(long int*)(s1._str)+MIN(s1._strlen/8,seqlen/16);
long int *p1=(long int*)(s1._str);
long int *p2=(long int*)(s2._str);
for (; p1<ep1; ++p1,++p2){
dist_nogapsingle_inc(*p1,*p2,b4_m0,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m1,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m2,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m3,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m4,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m5,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m6,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m7,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m8,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m9,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m10,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m11,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m12,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m13,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m14,count,len,gapmiss);
dist_nogapsingle_inc(*p1,*p2,b4_m15,count,len,gapmiss);
}
switch (seqlen%16){
case 15:
dist_nogapsingle_inc(*p1,*p2,b4_m14,count,len,gapmiss);
case 14:
dist_nogapsingle_inc(*p1,*p2,b4_m13,count,len,gapmiss);
case 13:
dist_nogapsingle_inc(*p1,*p2,b4_m12,count,len,gapmiss);
case 12:
dist_nogapsingle_inc(*p1,*p2,b4_m11,count,len,gapmiss);
case 11:
dist_nogapsingle_inc(*p1,*p2,b4_m10,count,len,gapmiss);
case 10:
dist_nogapsingle_inc(*p1,*p2,b4_m9,count,len,gapmiss);
case 9:
dist_nogapsingle_inc(*p1,*p2,b4_m8,count,len,gapmiss);
case 8:
dist_nogapsingle_inc(*p1,*p2,b4_m7,count,len,gapmiss);
case 7:
dist_nogapsingle_inc(*p1,*p2,b4_m6,count,len,gapmiss);
case 6:
dist_nogapsingle_inc(*p1,*p2,b4_m5,count,len,gapmiss);
case 5:
dist_nogapsingle_inc(*p1,*p2,b4_m4,count,len,gapmiss);
case 4:
dist_nogapsingle_inc(*p1,*p2,b4_m3,count,len,gapmiss);
case 3:
dist_nogapsingle_inc(*p1,*p2,b4_m2,count,len,gapmiss);
case 2:
dist_nogapsingle_inc(*p1,*p2,b4_m1,count,len,gapmiss);
case 1:
dist_nogapsingle_inc(*p1,*p2,b4_m0,count,len,gapmiss);
}
return((float)count/(float)len);
}
inline void dist_nogap_inc_dash(long int a1,long int a2,long int mask,long int dash,int& count,int& len){
if ((a1&mask)==(a2&mask)){
if ((a1&mask)!=mask)
++count;
else
--len;
}
}
//inline void dist_nogap_inc_dash(long int a1,long int a2,long int mask,long int dash,int& count,int& len){
// if (!((a1&mask)==dash || (a2&mask)==dash)){
// if ((a1&mask)==(a2&mask)) ++count;
// ++len;
// }
//}
inline float dist_nogap(const estr& s1,const estr& s2)
{
int count=0;
int len=s1._strlen;
long int *ep1=((long int*)s1._str)+(s1._strlen/8);
long int *p1=(long int*)s1._str;
long int *p2=(long int*)s2._str;
for (; p1!=ep1; ++p1,++p2){
dist_nogap_inc_dash(*p1,*p2,b8_m0,b8_d0,count,len);
dist_nogap_inc_dash(*p1,*p2,b8_m1,b8_d1,count,len);
dist_nogap_inc_dash(*p1,*p2,b8_m2,b8_d2,count,len);
dist_nogap_inc_dash(*p1,*p2,b8_m3,b8_d3,count,len);
dist_nogap_inc_dash(*p1,*p2,b8_m4,b8_d4,count,len);
dist_nogap_inc_dash(*p1,*p2,b8_m5,b8_d5,count,len);
dist_nogap_inc_dash(*p1,*p2,b8_m6,b8_d6,count,len);
dist_nogap_inc_dash(*p1,*p2,b8_m7,b8_d7,count,len);
}
switch (s1._strlen%8){
case 7:
dist_nogap_inc_dash(*p1,*p2,b8_m6,b8_d6,count,len);
case 6:
dist_nogap_inc_dash(*p1,*p2,b8_m5,b8_d5,count,len);
case 5:
dist_nogap_inc_dash(*p1,*p2,b8_m4,b8_d4,count,len);
case 4:
dist_nogap_inc_dash(*p1,*p2,b8_m3,b8_d3,count,len);
case 3:
dist_nogap_inc_dash(*p1,*p2,b8_m2,b8_d2,count,len);
case 2:
dist_nogap_inc_dash(*p1,*p2,b8_m1,b8_d1,count,len);
case 1:
dist_nogap_inc_dash(*p1,*p2,b8_m0,b8_d0,count,len);
}
return((float)count/(float)len);
}
/*
inline float dist_nogap(const estr& s1,const estr& s2)
{
int i;
int count=0;
int len=0;
for (i=0; i<s1._strlen; ++i){
if (s1._str[i]=='-' || s2._str[i]=='-') continue;
if (s1._str[i]==s2._str[i]) ++count;
++len;
}
return((float)count/(float)len);
}
*/
inline float dist(const estr& s1,const estr& s2)
{
int i;
int count=0;
for (i=0; i<s1.len(); ++i){
if (s1._str[i]==s2._str[i]) ++count;
}
return((float)count/(float)s1.len());
}
inline float cooc_dist(int i,int j,earray<eintarray>& neigharr)
{
int k;
int cooc1,cooc2,common;
cooc1=0; cooc2=0; common=0;
if (neigharr[i].size()==0 || neigharr[j].size()==0) return(2.0);
ldieif(j>=neigharr.size(),"j larger than neigharr.size()? "+estr(j)+">"+estr(neigharr.size()));
ldieif(i>=neigharr.size(),"i larger than neigharr.size()? "+estr(i)+">"+estr(neigharr.size()));
ldieif(neigharr[i].size() != neigharr[j].size(),"size mismatch: "+estr(neigharr[i].size())+" != "+estr(neigharr[j].size()));
for (k=0; k<neigharr[i].size(); ++k){
if (neigharr[i][k]!=0){ ++cooc1; if (neigharr[j][k]!=0) ++common; }
if (neigharr[j][k]!=0){ ++cooc2; }
}
return(1.0-(float)common/(cooc1+cooc2-common));
}
inline void xy2estr(int x,int y,estr& str)
{
str.clear();
if (x<y){
serialint(x,str);
serialint(y,str);
}else{
serialint(y,str);
serialint(x,str);
}
}
/*
template <class T,class M,class K,float (*fdist)(const estr&,const estr&,int)>
int t_calc_dists_noise(emutex& mutex,T& arr,K& dists,int seqlen,int node,int tnodes,float thres)
{
ernd rng;
float noise=0.0125;
long int i,i2,j;
long int start,end;
start=(long int)(node)*(long int)(arr.size()-1)/(long int)(2*tnodes);
end=(long int)(node+1)*(long int)(arr.size()-1)/(long int)(2*tnodes);
float tmpid,tmpid2,tmpid3;
K tmpdists;
for (i=start; i<end; ++i){
for (j=i+1; j<arr.size(); ++j){
tmpid=fdist(arr[i],arr[j],seqlen)+rng.gaussian(noise);
if (tmpid>1.0) tmpid=1.0; else if (tmpid<0.0) tmpid=0.0;
if (tmpid>=thres) tmpdists.add(M(i,j,tmpid));
}
i2=arr.size()-i-2;
for (j=i2+1; j<arr.size(); ++j){
tmpid=fdist(arr[i2],arr[j],seqlen)+rng.gaussian(noise);
if (tmpid>1.0) tmpid=1.0; else if (tmpid<0.0) tmpid=0.0;
if (tmpid>=thres) tmpdists.add(M(i2,j,tmpid));
}
}
if (node==tnodes-1 && arr.size()%2==0){
i=arr.size()/2-1;
for (j=i+1; j<arr.size(); ++j){
tmpid=fdist(arr[i],arr[j],seqlen)+rng.gaussian(noise);
if (tmpid>1.0) tmpid=1.0; else if (tmpid<0.0) tmpid=0.0;
if (tmpid>=thres) tmpdists.add(M(i,j,tmpid));
}
}
mutex.lock();
dists+=tmpdists;
mutex.unlock();
return(tmpdists.size());
}
*/
template <class T,class M,class K,float (*fdist)(const eshortseq&,const eshortseq&)>
int t_calc_dists(emutex& mutex,T& arr,K& dists,int node,int tnodes,float thres)
{
long int i,i2,j;
long int start,end;
start=(long int)(node)*(long int)(arr.size()-1)/(long int)(2*tnodes);
end=(long int)(node+1)*(long int)(arr.size()-1)/(long int)(2*tnodes);
float tmpid,tmpid2,tmpid3;
K tmpdists;
for (i=start; i<end; ++i){
for (j=i+1; j<arr.size(); ++j){
tmpid=fdist(arr[i],arr[j]);
if (tmpid>=thres) tmpdists.add(M(i,j,tmpid));
}
i2=arr.size()-i-2;
for (j=i2+1; j<arr.size(); ++j){
tmpid=fdist(arr[i2],arr[j]);
if (tmpid>=thres) tmpdists.add(M(i2,j,tmpid));
}
}
if (node==tnodes-1 && arr.size()%2==0){
i=arr.size()/2-1;
for (j=i+1; j<arr.size(); ++j){
tmpid=fdist(arr[i],arr[j]);
if (tmpid>=thres) tmpdists.add(M(i,j,tmpid));
}
}
mutex.lock();
dists+=tmpdists;
mutex.unlock();
return(0);
}
template <class T,class M,float (*fdist)(const estr&,const estr&,int)>
int part_calc_dists_u(emutex& mutex,ebasicarray<INDTYPE>& uniqind,T& arr,ebasicarray<INDTYPE>& curotuid,int seqlen,long int node,long int tnodes,float thres)
{
long int i,i2,j;
long int start,end;
mutex.lock();
ebasicarray<INDTYPE> otuid(curotuid);
mutex.unlock();
start=((long int)(node)*(long int)(uniqind.size()-1l))/(long int)(2l*tnodes);
end=((long int)(node+1l)*(long int)(uniqind.size()-1l))/(long int)(2l*tnodes);
// cout << "start: " << start << " end: " << end << " uniqind.size(): " << uniqind.size() << endl;
float tmpid,tmpid2,tmpid3;
long tmpoid,nextoid;
long oid_i,oid_j;
for (i=start; i<end; ++i){
oid_i=otuid[i];
if (oid_i!=otuid[oid_i]){
for (oid_i=otuid[oid_i]; oid_i!=otuid[oid_i]; oid_i=otuid[oid_i]);
for (tmpoid=i; tmpoid!=otuid[tmpoid]; tmpoid=nextoid) { nextoid=otuid[tmpoid]; otuid[tmpoid]=oid_i; }
}
for (j=i+1; j<uniqind.size(); ++j){
oid_j=otuid[j];
if (oid_i==oid_j) continue; // skip distances for sequences already in the same otu
if (oid_j!=otuid[oid_j]){
for (oid_j=otuid[oid_j]; oid_j!=otuid[oid_j]; oid_j=otuid[oid_j]);
for (tmpoid=j; tmpoid!=otuid[tmpoid]; tmpoid=nextoid) { nextoid=otuid[tmpoid]; otuid[tmpoid]=oid_j; }
}
if (oid_i==oid_j) continue; // skip distances for sequences already in the same otu
tmpid=fdist(arr[uniqind[i]],arr[uniqind[j]],seqlen);
if (tmpid>=thres){
otuid[oid_j]=oid_i;
// cout << "merge: " << oid_i << " " << oid_j << endl;
}
}
i2=uniqind.size()-i-2l;
oid_i=otuid[i2];