+++ /dev/null
-/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
-
-/*********************************************************************
- * Clustal Omega - Multiple sequence alignment
- *
- * Copyright (C) 2010 University College Dublin
- *
- * Clustal-Omega is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License as
- * published by the Free Software Foundation; either version 2 of the
- * License, or (at your option) any later version.
- *
- * This file is part of Clustal-Omega.
- *
- ********************************************************************/
-
-/*
- * RCS $Id: hhalignment-C.h 236 2011-04-14 11:30:04Z fabian $
- */
-
-
-/*
- * Changelog: Michael Remmert made changes to hhalign stand-alone code
- * FS implemented some of the changes on 2010-10-28 -> MR1
- *
- * Note: MR seems to have changed all [aijk]++ to ++[aijk],
- * FS did not do that on 2010-10-28
- */
-
-// hhalignment.C
-
-//////////////////////////////////////////////////////////////////////////////
-//// Class Alignment
-//////////////////////////////////////////////////////////////////////////////
-
-// hhalignment.C
-
-#ifndef MAIN
-#define MAIN
-#include <iostream> // cin, cout, cerr
-#include <fstream> // ofstream, ifstream
-#include <stdio.h> // printf
-using std::cout;
-using std::cerr;
-using std::endl;
-using std::ios;
-using std::ifstream;
-using std::ofstream;
-#include <stdlib.h> // exit
-#include <string> // strcmp, strstr
-#include <math.h> // sqrt, pow
-#include <limits.h> // INT_MIN
-#include <float.h> // FLT_MIN
-#include <time.h> // clock
-#include <ctype.h> // islower, isdigit etc
-#include "util-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
-#include "list.h" // list data structure
-#include "hash.h" // hash data structure
-#include "hhdecl-C.h"
-#include "hhutil-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
-#include "hhhmm.h"
-#endif
-
-
-enum {KEEP_NOT = 0, KEEP_CONDITIONALLY, KEEP_ALWAYS};
-
-//////////////////////////////////////////////////////////////////////////////
-// Class Alignment
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Object constructor
-//////////////////////////////////////////////////////////////////////////////
-Alignment::Alignment(int maxseq, int maxres)
-{
-
- //printf(">>>>>>>>%s:%s:%d: maxseq=%d, maxres=%d\n", __FUNCTION__, __FILE__, __LINE__, maxseq, maxres); /* (FS) */
- longname = new(char[DESCLEN]);
- sname = new(char*[maxseq+2]); /* MR1 */
- seq = new(char*[maxseq+2]); /* MR1 */
- l = new(int[maxres]);
- X = new(char*[maxseq+2]); /* MR1 */
- I = new(short unsigned int*[maxseq+2]); /* MR1 */
- keep = new(char[maxseq+2]); /* MR1 */
- display = new(char[maxseq+2]); /* MR1 */
- wg = new(float[maxseq+2]); /* MR1 */
- nseqs = new(int[maxres+2]); /* MR1 */
- N_in=L=0;
- nres=NULL; // number of residues per sequence k
- first=NULL; // first residue in sequence k
- last=NULL; // last residue in sequence k
- ksort=NULL; // sequence indices sorted by descending nres[k]
- name[0]='\0'; // no name defined yet
- longname[0]='\0'; // no name defined yet
- fam[0]='\0'; // no name defined yet
- file[0]='\0'; // no name defined yet
- readCommentLine = '0'; /* MR1 */
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// Object destructor
-//////////////////////////////////////////////////////////////////////////////
-Alignment::~Alignment()
-{
- delete[] longname; longname = NULL;
- for(int k=0; k<N_in; k++)
- {
- delete[] sname[k]; sname[k] = NULL;
- delete[] seq[k]; seq[k] = NULL;
- delete[] X[k]; X[k] = NULL;
- delete[] I[k]; I[k] = NULL;
- }
- delete[] sname; sname = NULL;
- delete[] seq; seq = NULL;
- delete[] X; X = NULL;
- delete[] I; I = NULL;
- delete[] l; l = NULL;
- delete[] keep; keep = NULL;
- delete[] display; display = NULL;
- delete[] wg; wg = NULL;
- delete[] nseqs; nseqs = NULL;
- delete[] nres; nres = NULL;
- delete[] first; first = NULL;
- delete[] last; last = NULL;
- delete[] ksort; ksort = NULL;
-}
-
-
-/**
- * @brief Reads in an alignment from file into matrix seq[k][l] as ASCII
- */
-void
-Alignment::Read(FILE* inf, char infile[], char* firstline)
-{
- int l; // Postion in alignment incl. gaps (first=1)
- int h; // Position in input line (first=0)
- int k; // Index of sequence being read currently (first=0)
- char line[LINELEN]=""; // input line
- //char cur_seq[MAXCOL]; // Sequence currently read in
- char *cur_seq=new(char[par.maxColCnt]);
- char* cur_name; // Sequence currently read in
- int linenr=0; // current line number in input file
- char skip_sequence=0;
- RemoveExtension(file,infile); //copy rootname (w/o path) of infile into file variable of class object
-
- kss_dssp=ksa_dssp=kss_pred=kss_conf=kfirst=-1;
- n_display=0;
- N_in=0;
- N_filtered=0;
- N_ss=0;
- cur_seq[0]=' '; // overwrite '\0' character at beginning to be able to do strcpy(*,cur_seq)
- l=1; k=-1;
-
- // Does firstline already contain first line of file?
- if (firstline!= NULL) strcpy(line,firstline);
-
- /////////////////////////////////////////////////////////////////////////
- // Read infile line by line
- /* FIXME: not safe to use MAXSEQ, however, don't think we ever get here (FS) */
- while(firstline || (fgetline(line,LINELEN,inf) && (k<MAXSEQ))) /* FIXME: FS introduced () around &&, precedence! MR1 */
- {
- linenr++;
- firstline=NULL;
- if (line[0]=='>') //line contains sequence name
- {
- if (k>=MAXSEQ-1)
- {
- if (v>=1 && k>=MAXSEQ)
- cerr<<endl<<"WARNING: maximum number "<<MAXSEQ<<" of sequences exceded in file "<<infile<<"\n";
- break;
- }
- cur_name=line+1; //beginning of current sequence name
- if (k>=0) //if this is at least the second name line
- {
- if (strlen(cur_seq)==0)
- {
- cerr<<endl<<"Error: sequence "<<sname[k]<<" contains no residues."<<endl;
- exit(1);
- }
-
- // Create space for residues and paste new sequence in
- seq[k]=new(char[strlen(cur_seq)+2]);
- if (!seq[k]) MemoryError("array for input sequences");
- X[k]=new(char[strlen(cur_seq)+2]);
- if (!X[k]) MemoryError("array for input sequences");
- I[k]=new(short unsigned int[strlen(cur_seq)+2]);
- if (!I[k]) MemoryError("array for input sequences");
- strcpy(seq[k],cur_seq);
- }
- skip_sequence=0;
-
- k++;
- l=1; //position in current sequence (first=1)
-
- // display[k]= 0: do not show in Q-T alignments 1: show if not filtered out later 2: show in any case (do not filter out)
- // keep[k] = 0: do not include in profile 1: include if not filtered out later 2: include in any case (do not filter out)
- /* {KEEP_NOT=0, KEEP_CONDITIONALLY=1, KEEP_ALWAYS=2} */
- if (line[1]=='@') cur_name++; //skip @-character in name
- if (!strncmp(line,">ss_dssp",8)) {
- if (kss_dssp<0) {display[k]=2; n_display++; keep[k]=KEEP_NOT; kss_dssp=k; N_ss++;} else {skip_sequence=1; k--; continue;}
- }
- else if (!strncmp(line,">sa_dssp",8)) {
- if (ksa_dssp<0) {display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; ksa_dssp=k; N_ss++;} else {skip_sequence=1; k--; continue;}
- }
- else if (!strncmp(line,">ss_pred",8)) {
- if (kss_pred<0) {display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; kss_pred=k; N_ss++;} else {skip_sequence=1; k--; continue;}
- }
- else if (!strncmp(line,">ss_conf",8)) {
- if (kss_conf<0) {display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; kss_conf=k; N_ss++;} else {skip_sequence=1; k--; continue;}
- }
- else if (!strncmp(line,">ss_",4) || !strncmp(line,">sa_",4)) {
- display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; N_ss++;
- }
- else if (!strncmp(line,">aa_",4)) { // ignore sequences beginning with ">aa_"
- skip_sequence=1; k--; continue;
- }
- //store first real seq
- else if (kfirst<0)
- {
- char word[NAMELEN];
- strwrd(word,line); // Copies first word in ptr to str
- if (strstr(word,"_consensus"))
- {display[k]=2; keep[k]=0; n_display++; kfirst=k;} /* MR1 */
- else
- {display[k]=keep[k]=KEEP_ALWAYS; n_display++; kfirst=k;}
- }
- //store all sequences
- else if (par.mark==0) {display[k]=keep[k]=KEEP_CONDITIONALLY; n_display++;}
- //store sequences up to nseqdis
- else if (line[1]=='@'&& n_display-N_ss<par.nseqdis) {display[k]=keep[k]=KEEP_ALWAYS; n_display++;}
- else {display[k]=KEEP_NOT; keep[k]=KEEP_CONDITIONALLY;}
-
- // store sequence name
- if (v>=4) printf("Reading seq %-16.16s k=%3i n_displ=%3i display[k]=%i keep[k]=%i\n",cur_name,k,n_display,display[k],keep[k]);
- sname[k] = new(char[strlen(cur_name)+1]);
- if (!sname[k]) {MemoryError("array for sequence names");}
- strcpy(sname[k],cur_name);
- } // end if(line contains sequence name)
-
- else if (line[0]=='#') // Commentary line?
- {
- // #PF01367.9 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; PDB 1taq, 1bgx (T:271-174), 1taq (271-174)
- if (name[0]) continue; // if already name defined: skip commentary line
- char *ptr1, *ptr2;
- ptr1=strscn_(line+1); // set ptr1 to first non-whitespace character after '#' -> AC number
- strncpy(longname,ptr1,DESCLEN-1); // copy whole commentary line after '# ' into longname
- longname[DESCLEN-1]='\0';
- strtr(longname,""," ");
- ptr2=strcut_(ptr1); // cut after AC number and set ptr2 to first non-whitespace character after AC number
- // strcpy(fam,ptr1); // copy AC number to fam
- // if (!strncmp(fam,"PF",2)) strcut_(fam,'.'); // if PFAM identifier contains '.' cut it off
- // strcut_(ptr2); // cut after first word ...
- strcpy(name,ptr1); // ... and copy first word into name
- readCommentLine = '1'; /* MR1 */
- }
-
- //line contains sequence residues or SS information and does not belong to a >aa_ sequence
- else if (!skip_sequence)
- {
- if (v>=4) cout<<line<<"\n"; //DEBUG
- if (k==-1 && v)
- {
- cerr<<endl<<"WARNING: No sequence name preceding following line in "<<infile<<":\n\'"<<line<<"\'\n";
- continue;
- }
-
- h=0; //counts characters in current line
-
- // Check whether all characters are correct; store into cur_seq
- if (keep[k] || (k == kfirst) ) // normal line containing residues /* MR1 */
- {
- while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
- {
- if (aa2i(line[h])>=0) // ignore white-space characters ' ', \t and \n (aa2i()==-1)
- {cur_seq[l]=line[h]; l++;}
- else if (aa2i(line[h])==-2 && v)
- cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line "<<linenr<<" of "<<infile<<"\n";
- h++;
- }
- }
- else if (k==kss_dssp) // lines with dssp secondary structure states (. - H E C S T G B)
- {
- while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
- {
- if (ss2i(line[h])>=0 && ss2i(line[h])<=7)
- {cur_seq[l]=ss2ss(line[h]); l++;}
- else if (v)
- cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line "<<linenr<<" of "<<infile<<"\n";
- h++;
- }
- }
- else if (k==ksa_dssp) // lines with dssp solvent accessibility states (. - ???)
- {
- while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
- {
- if (sa2i(line[h])>=0)
- cur_seq[l++]=line[h];
- else if (v)
- cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line "<<linenr<<" of "<<infile<<"\n";
- h++;
- }
- }
- else if (k==kss_pred) // lines with predicted secondary structure (. - H E C)
- {
- while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
- {
- if (ss2i(line[h])>=0 && ss2i(line[h])<=3)
- {cur_seq[l]=ss2ss(line[h]); l++;}
- else if (v)
- cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line "<<linenr<<" of "<<infile<<"\n";
- h++;
- }
- }
- else if (k==kss_conf) // lines with confidence values should contain only 0-9, '-', or '.'
- {
- while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
- {
- if (line[h]=='-' || line[h]=='.' || (line[h]>='0' && line[h]<='9'))
- {cur_seq[l]=line[h]; l++;}
- else if (v)
- cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<l<<" in line "<<linenr<<" of "<<infile<<"\n";
- h++;
- }
- }
- else if (display[k]) // other lines such as >sa_pred etc
- {
- while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
- {
- if (line[h]=='-' || line[h]=='.' || (line[h]>='0' && line[h]<='9') || (line[h]>='A' && line[h]<='B'))
- {cur_seq[l]=line[h]; l++;}
- else if (v)
- cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<l<<" in line "<<linenr<<" of "<<infile<<"\n";
- h++;
- }
- }
- if (v && l>=/*MAXCOL*/par.maxColCnt-1)
- {
- cerr<<endl<<"WARNING: maximum number of residues "<</*MAXCOL*/par.maxColCnt-2<<" exceded in sequence "<<sname[k]<<"\n";
- skip_sequence=1;
- }
- cur_seq[l]='\0'; //Ensure that cur_seq ends with a '\0' character
- } //end else
-
- }
- /////////////////////////////////////////////////////////////////////////
-
-
- if (k>=0) //if at least one sequence was read in
- {
- seq[k]=new(char[strlen(cur_seq)+2]);
- if (!seq[k]) MemoryError("array for input sequences");
- X[k]=new(char[strlen(cur_seq)+2]);
- if (!X[k]) MemoryError("array for input sequences");
- I[k]=new(short unsigned int[strlen(cur_seq)+2]);
- if (!I[k]) MemoryError("array for input sequences");
- strcpy(seq[k],cur_seq);
- }
- else
- {cerr<<endl<<"Error: no sequences found in file "<<infile<<"\n"; exit(1);}
-
- N_in = k+1;
-
- // Set name, longname, fam
- if (!*name) // longname, name and family were not set by '#...' line yet -> extract from first sequence
- {
- char* ptr;
- // strtr(sname[kfirst],"~"," "); // 'transpose': replaces the tilde with a blanc everywhere in sname[kfirst]
- strncpy(longname,sname[kfirst],DESCLEN-1); // longname is name of first sequence
- longname[DESCLEN-1]='\0';
- strncpy(name,sname[kfirst],NAMELEN-1); // Shortname is first word of longname...
- name[NAMELEN-1]='\0';
- ptr = strcut(name); // ...until first white-space character
- if (ptr && islower(ptr[0]) && ptr[1]=='.' && isdigit(ptr[2])) //Scop family code present as second word?
- {
- lwrstr(name); // Transform upper case to lower case
- strcut(ptr); // Non-white-space characters until next white-space character..
- strcpy(fam,ptr); // ...are the SCOP familiy code
- }
- else if (name[0]=='P' && name[1]=='F' && isdigit(name[2]) && isdigit(name[3]) ) //Pfam code
- {
- strcpy(fam,name); // set family name = Pfam code
- }
- }
-
-
-
- delete[] cur_seq; cur_seq = NULL;
-
- // Checking for warning messages
- if (v==0) return;
- if (v>=2) cout<<"Read "<<infile<<" with "<<N_in<<" sequences\n";
- if (v>=3) cout<<"Query sequence for alignment has number "<<kfirst<<" (0 is first)\n";
- return;
-}
-
-/*
- * At this point GetSeqsFromHMM() slots in, however,
- * only needed in hhbliys.C, so will skip it for moment, MR1
- */
-
-
-/////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Convert ASCII in seq[k][l] to int (0-20) in X[k][i],
- * throw out all insert states, record their number in I[k][i]
- * and store sequences to be displayed in seq[k] */
-/////////////////////////////////////////////////////////////////////////////
-void
-Alignment::Compress(const char infile[])
-{
- int i; // Index for match state (first=1)
- int l; // Postion in alignment incl. gaps (first=1)
- int k; // Index for sequences (first=0)
- int a; // amino acid index
- char c;
- int unequal_lengths=0; /* k: seq k doesn't have same number
- of match states as seq 0 => WARNING */
- /* points to next character in seq[k] to be written */
- /*static short unsigned int h[MAXSEQ];*/
- /*short*/ unsigned int *h = NULL; /* short may lead to overflow for long alignments, FS, r235 -> r236 */
-
- h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */
- float *percent_gaps = NULL; /* FS, 2010-Nov */
- char *match_state = NULL; /* FS, 2010-Nov */
-
-
- // Initialize
- for (k=0;k<N_in; k++)
- {I[k][0]=0;}
-
- if (v>=3)
- {
- if (par.M==1)
- cout<<"Using match state assignment by capital letters (a2m format)\n";
- else if (par.M==2) cout<<"Using percentage-rule match state assignment\n";
- else if (par.M==3) cout<<"Using residues of first sequence as match states\n";
- }
-
- // Create matrices X and I with amino acids represented by integer numbers
- switch(par.M)
- {
-
- /////////////////////////////////////////////////////////////////////////
- /* a2m/a3m format: match states capital case,
- inserts lower case, delete states '-', inserted gaps '.'
- The confidence values for ss prediction are interpreted as follows:
- 0-9:match states(!) '-' :match state '.':insert */
- case 1:
- default:
-
- // Warn if alignment is ment to be -M first or -M NN instead of A2M/A3M
- if (v>=2 && strchr(seq[kfirst],'-') ) // Seed/query sequence contains a gap ...
- {
- for (k=1; k<N_in; k++)
- if (strpbrk(seq[k],"abcdefghiklmnpqrstuvwxyz.")) break;
- if (k==N_in) // ... but alignment contains no lower case residue
- printf("WARNING: input alignment %s looks like aligned FASTA instead of A2M/A3M format. Consider using '-M first' or '-M 50'\n",infile);
- }
-
- // Remove '.' characters from seq[k]
- for(k=0; k<N_in; k++)
- {
- char* ptrS=seq[k]; // pointer to source: character in seq[k]
- char* ptrD=seq[k]; // pointer to destination: seq[k]
- while(1) // omit '.' symbols
- {
- if (*ptrS!='.') {*ptrD=*ptrS; ptrD++;} //leave out '.' symbols
- if (!*ptrS) break;
- ptrS++;
- }
- }
- L=/*MAXRES*/par.maxResLen-2; // needed because L=imin(L,i)
- for (k=0; k<N_in; k++)
- {
- i=1; l=1; // start at i=1, not i=0!
- if (keep[k]) //skip >ss_dssp, >ss_pred, >ss_conf, >aa_... sequences
- {
- while((c=seq[k][l++])) // assign residue to c at same time
- {
- if (c>='a' && c<='z') I[k][i-1]++;//insert state = lower case character
- else if (c!='.') //match state = upper case character
- {
- X[k][i]=aa2i(c);
- I[k][i]=0;
- i++;
- }
- }
- }
- else if (k==kss_dssp || k==kss_pred) // does alignment contain sequence of secondary structure states?
- {
- while((c=seq[k][l++])) // assign residue to c at same time
- if (c!='.' && !(c>='a' && c<='z')) X[k][i++]=ss2i(c); //match state = upper case character
- }
- else if (k==ksa_dssp) // does alignment contain sequence of prediction confidence values?
- {
- while((c=seq[k][l++])) // assign residue to c at same time
- if (c!='.' && !(c>='a' && c<='z')) X[k][i++]=sa2i(c); //match state = upper case character
- }
- else if (k==kss_conf) // does alignment contain sequence of prediction confidence values?
- {
- while((c=seq[k][l++])) // assign residue to c at same time
- if (c!='.') X[k][i++]=cf2i(c); //match state = 0-9 or '-'
- }
- else if (k==kfirst) // does alignment contain sequence of prediction confidence values?
- {
- while((c=seq[k][l++])) // assign residue to c at same time
- if (c!='.')
- {
- X[k][i]=aa2i(c);
- I[k][i]=0;
- ++i;
- }
- }
- else continue;
- i--;
- if (L!=i && L!=/*MAXRES*/par.maxResLen-2 && !unequal_lengths) unequal_lengths=k; //sequences have different lengths
- L=imin(L,i);
- }
- if (unequal_lengths) break;
-
- //Replace GAP with ENDGAP for all end gaps /* MR1 */
- for (k=0; k<N_in; ++k)
- {
- if (!keep[k]) continue;
- for (i=1; i<=L && X[k][i]==GAP; i++) X[k][i]=ENDGAP; /* MR1: NOTE i++ <- ++i */
- for (i=L; i>=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; /* MR1 */
- }
-
- for (i=1; i<=L; i++) this->l[i]=i; //assign column indices to match states
- if (L<=0)
- {
- cout<<"\nError: Alignment in "<<infile<<" contains no match states. Consider using -M first or -M <int> option"<<endl;
- exit(1);
- }
-
- if (L==/*MAXRES*/par.maxResLen-2 && v>=2)
- {
- printf("WARNING: Number of match columns too large. Only first %i match columns will be kept!\n",L);
- break;
- }
- if (v>=2) cout<<"Alignment in "<<infile<<" contains "<<L<<" match states\n";
- break;
-
- /////////////////////////////////////////////////////////////////////////
- // gap-rule assignment of match states
- case 2:
- int nl[NAA+2]; //nl[a] = number of seq's with amino acid a at position l
- /* Note: allocating statically is fine most of the time
- but when the sequences/profiles get really long
- we might run out of memory, so must really do it dynamically.
- had to move declaration of float *percent_gaps out of switch()
- */
- //float percent_gaps[MAXCOL]; //percentage of gaps in column k (with weighted sequences)
- percent_gaps = new(float[par.maxColCnt]);
-
- //determine number of columns L in alignment
- L=strlen(seq[kfirst])-1;
-
- // Conversion to integer representation, checking for unequal lengths and initialization
- if (nres==NULL) nres=new(int[N_in]);
- for (k=0; k<N_in; k++)
- {
- if (!keep[k]) continue;
- int nr=0;
- wg[k]=0; nres[k]=0;
- for (l=1; l<=L; l++)
- {
- X[k][l]=aa2i(seq[k][l]);
- if (X[k][l]<NAA) nr++;
- }
- nres[k]=nr;
- if (seq[k][L+1]!='\0' && !unequal_lengths) unequal_lengths=k;
- }
- if (unequal_lengths) break;
-
- // Quick and dirty calculation of the weight per sequence wg[k]
- for (l=1; l<=L; l++) // for all positions l in alignment
- {
- int naa=0; //number of different amino acids
- for (a=0; a<20; a++) nl[a]=0;
- for (k=0; k<N_in; k++) if (keep[k]) nl[ (int)X[k][l]]++;
- for (a=0; a<20; a++) if(nl[a]) naa++;
- if (!naa) naa=1; //naa=0 when column consists of only gaps and Xs (=ANY)
- for (k=0; k<N_in; k++)
- if (keep[k] && (X[k][l]<20) )
- {
- //wg[k]+=1.0/float(nl[ (int)X[k][l]]*naa*nres[k]+30.0); /* original version */
- wg[k] += 1.0/float(nl[ (int)X[k][l]]*naa*(nres[k]+30.0)); /* MR1 */
- // wg[k] += 1.0/float(nl[ (int)X[k][l]]*(nres[k]+30.0)); /* MR1 commented out */
- // wg[k] += (naa-1.0)/float(nl[ (int)X[k][l]]*(nres[k]+30.0)); /* MR1 commented out */
- }
- } /* 1=l<=L*/
-
- //Replace GAP with ENDGAP for all end gaps
- for (k=0; k<N_in; ++k)
- {
- if (!keep[k]) continue;
- for (i=1; i<=L && X[k][i]==GAP; i++) X[k][i]=ENDGAP; /* MR1: NOTE i++ <- ++i */
- for (i=L; i>=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; /* MR1 */
- }
-
- // Add up percentage of gaps
- for (l=1; l<=L; l++)
- {
- float res=0;
- float gap=0;
- for (k=0; k< N_in; k++){
- if (keep[k]){
- if ( X[k][l]<GAP) res+=wg[k]; /* MR1, AA or ANY, changed from <ANY */
- else if ( X[k][l] != ENDGAP) gap+=wg[k]; /* MR1, else: GAP. ENDGAPs are ignored for counting percentage */
- }
- }
- percent_gaps[l]=100.*gap/(res+gap);
- if (v>=4) cout<<"percent gaps["<<l<<"]="<<percent_gaps[l]<<" first seq:"<<seq[0][l]<<"\n";
- }
-
- /* Insert states 'bloat' the HMM,
- throwing them out 'slims' down the HMM.
- A slimmer HMM takes less time to construct.
- However, the marriage of Clustal and Hhalign
- is particularly sensitive to residues
- at the very end of the profile; these I call
- 'telomeres'. Telomeres must not be shed when
- throwing out insert states, for the telomeres
- we set the match threshold to 100%.
- */
-#define MGAP_LOGIC 0
-#define TELOMERE_LOGIC 1
-#define TELOMERE_DYNAMIC 0
-
-#define ALWAYS_ACCEPT 101.0 /* do NOT change this parameter, must be >=100,
- make slightly bigger than 100% -- to be sure to be sure */
-#define DEFAULT_MGAPS 100.0 /* Soeding's default is 50, omega default prior to telomere logic was 100
- FIXME: this used to be par.Mgaps,
- in a later version re-introduce par.Mgaps to keep this value flexible */
-#define TELOMER_LENGTH 10 /* this parameter must be > 0 (unless DEFAULT_MGAPS=100),
- if it is too big (L/2) then telomere logic has no effect,
- don't think it should be changed (much) */
-#define TELOMER_FRACTION 0.10
- //#define HMM_MIN_LENGTH 0.923
-#define HMM_MIN_LENGTH 0.950
-#define FORTRAN_OFFSET 1
- double dDefaultMgaps;
- dDefaultMgaps = DEFAULT_MGAPS;
-
-#if TELOMERE_LOGIC /* turn telomere logic on (1) or off (0) */
- int iTelomereLength;
-
-#if TELOMERE_DYNAMIC /* keep telomere length 'dynamic' */
- iTelomereLength = TELOMER_LENGTH > (int)(L*TELOMER_FRACTION) ? TELOMER_LENGTH : (int)(L*TELOMER_FRACTION);
-#else
- iTelomereLength = TELOMER_LENGTH;
-#endif /* this was dynamic telomere */
-#endif /* this was telomere logic */
-
- /* if HMMs get too small (much smaller than profile length L)
- then one is liable to get a back-tracking error.
- So we should ensure that the DEFAULT_MGAPS parameter does NOT
- shrink the HMM too much.
- take percentage-gap vector, sort it, and fix dDefaultMgaps,
- such that at least (HMM_MIN_LENGTH)*(L) are left
- */
-#if MGAP_LOGIC /* try to adapt Mgaps to size of final HMM */
- {
- float *pfPercentGaps = NULL;
- if (NULL == (pfPercentGaps = (float *)malloc((L+1)*sizeof(float)))){
- printf("%s:%s:%d: could not malloc %d float for sorted percent-gaps\n",
- __FUNCTION__, __FILE__, __LINE__, L+1);
- dDefaultMgaps = DEFAULT_MGAPS;
- }
- else {
- for (l = 0; l < L; l++) {
- pfPercentGaps[l] = percent_gaps[l+FORTRAN_OFFSET];
- }
- qsort(pfPercentGaps, L, sizeof(float), CompFltAsc);
-
- dDefaultMgaps = pfPercentGaps[(int)(HMM_MIN_LENGTH*L)];
- if (dDefaultMgaps < DEFAULT_MGAPS){
- //printf("Mgaps = %f <- %f\n", DEFAULT_MGAPS, dDefaultMgaps);
- dDefaultMgaps = DEFAULT_MGAPS;
- }
- else {
- //printf("Mgaps = %f\n", dDefaultMgaps);
- }
-
- free(pfPercentGaps); pfPercentGaps = NULL;
- }
- }
-#endif /* tried to adapt Mgaps to size of final HMM */
-
- // Throw out insert states and keep only match states
- i=0;
- for (k=0; k<N_in; k++) {h[k]=1; seq[k][0]='-';}
- for (l=1; l<=L; l++)
- {
-#if TELOMERE_LOGIC
- float fMgaps = ALWAYS_ACCEPT;
- if ( (l < iTelomereLength) || (L-l < iTelomereLength) ){
- /* residue is in telomere, always retain this position */
- fMgaps = ALWAYS_ACCEPT;
- }
- else if (0){
- /* FIXME: would like to put a transition phase in here,
- where the Mgap value gradually goes down from 100 to DEFAULT_MGAPS,
- however, may not be necessary and will make code more clunky */
- }
- else {
- /* position is in centre of sequence,
- retain position if less than DEFAULT_MGAPS% gaps at this position,
- for example, if DEFAULT_MGAPS=30 throw out if more than 30% gap.
- conversely, if DEFAULT_MGAPS=100 throw out if more than 100% gaps,
- which can never happen, so always retain */
- fMgaps = dDefaultMgaps;
- }
- if (percent_gaps[l] <= fMgaps)
-#else /* this was telomere logic */
- if (percent_gaps[l]<=float(par.Mgaps))
-#endif /* this was Soeding default */
- {
- if (i>=/*MAXRES*/par.maxResLen-2) {
- if (v>=1)
- printf("WARNING: Number of match columns too large. Only first %i match columns will be kept!\n",i);
- break;
- }
- i++;
- this->l[i]=l;
- for (k=0; k<N_in; k++)
- {
- if (keep[k])
- {
- seq[k][h[k]++]=MatchChr(seq[k][l]);
- X[k][i]=X[k][l];
- I[k][i]=0;
- }
- else if (k==kss_dssp || k==kss_pred)
- {
- seq[k][h[k]++]=MatchChr(seq[k][l]);
- X[k][i]=ss2i(seq[k][l]);
- }
- else if (k==ksa_dssp)
- {
- seq[k][h[k]++]=MatchChr(seq[k][l]);
- X[k][i]=sa2i(seq[k][l]);
- }
- else if (k==kss_conf)
- {
- seq[k][h[k]++]=seq[k][l];
- X[k][i]=cf2i(seq[k][l]);
- }
- }
- }
- else
- {
- for (k=0; k<N_in; k++)
- if (keep[k] && X[k][l]<GAP)
- {
- I[k][i]++;
- seq[k][h[k]++]=InsertChr(seq[k][l]);
- }
- }
- }
- for (k=0; k<N_in; k++) seq[k][h[k]]='\0';
-
- //printf("%d\t%d\t%d\tN/L/M\n", N_in, L, i); /* -------- FIXME */
-
- if (v>=2) cout<<"Alignment in "<<infile<<" contains "<<L<<" columns and "<<i<<" match states\n";
- L = i; //Number of match states
-
- delete[] percent_gaps; percent_gaps = NULL;
- break;
-
-
- ////////////////////////////////////////////////////////////////////////
- // Using residues of first sequence as match states
- case 3:
- /* Note: allocating statically is fine most of the time
- but when the sequences/profiles get really long
- we might run out of memory, so must really do it dynamically.
- had to move declaration of float *percent_gaps out of switch()
- */
- //char match_state[MAXCOL]; //1: column assigned to match state 0: insert state
- match_state = new(char[par.maxColCnt]);
-
- // Determine number of columns L in alignment
- L=strlen(seq[0]+1);
- if (v>=3) printf("Length of first seq = %i\n",L);
- // Check for sequences with unequal lengths
- for (k=1; k<N_in; k++)
- if (int(strlen(seq[k]+1))!=L) {unequal_lengths=k; break;}
- if (unequal_lengths) break;
-
- // Determine match states: seq kfirst has residue at pos l -> match state
- for (l=1; l<=L; l++)
- if (isalpha(seq[kfirst][l])) match_state[l]=1; else match_state[l]=0;
- // Throw out insert states and keep only match states
- for (k=0; k<N_in; k++) {h[k]=1; seq[k][0]='-';}
- i=0;
- for (l=1; l<=L; l++)
- {
- if (match_state[l]) // does sequence 0 have residue at position l?
- {
- if (i>=/*MAXRES*/par.maxResLen-2) {
- if (v>=1)
- printf("WARNING: Number of match columns too large. Only first %i match columns will be kept!\n",i);
- break;
- }
- i++;
- this->l[i]=l;
- for (k=0; k<N_in; k++)
- {
- if (keep[k])
- {
- seq[k][h[k]++]=MatchChr(seq[k][l]);
- X[k][i]=aa2i(seq[k][l]);
- I[k][i]=0;
- }
- else if (k==kss_dssp || k==kss_pred)
- {
- seq[k][h[k]++]=MatchChr(seq[k][l]);
- X[k][i]=ss2i(seq[k][l]);
- }
- else if (k==ksa_dssp)
- {
- seq[k][h[k]++]=MatchChr(seq[k][l]);
- X[k][i]=sa2i(seq[k][l]);
- }
- else if (k==kss_conf)
- {
- seq[k][h[k]++]=seq[k][l];
- X[k][i]=cf2i(seq[k][l]);
- }
- }
- }
- else
- {
- for (k=0; k<N_in; k++)
- if (keep[k] && aa2i(seq[k][l])<GAP)
- {
- I[k][i]++;
- seq[k][h[k]++]=InsertChr(seq[k][l]);
- }
- }
- }
- for (k=0; k<N_in; k++) seq[k][h[k]]='\0';
-
- //Replace GAP with ENDGAP for all end gaps /* MR1 */
- for (k=0; k<N_in; ++k)
- {
- if (!keep[k]) continue;
- for (i=1; i<=L && X[k][i]==GAP; i++) X[k][i]=ENDGAP; /* MR1, note i++ <- ++i */
- for (i=L; i>=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; /* MR1 */
- }
-
- if (v>=2) cout<<"Alignment in "<<infile<<" contains "<<L<<" columns and "<<i<<" match states\n";
- L = i; //Number of match states
-
- delete[] match_state; match_state = NULL;
- break;
-
- } //end switch()
- ///////////////////////////////////////////////////////////////////////////
-
-
- // Error
- if (unequal_lengths)
- {
- strcut(sname[unequal_lengths]);
- cerr<<endl<<"Error: sequences in "<<infile<<" do not all have the same number of columns, \ne.g. first sequence and sequence "<<sname[unequal_lengths]<<".\n";
- if(par.M==1) cerr<<".\nCheck input format for '-M a2m' option and consider using '-M first' or '-M 50'\n";
- exit(1);
- }
-
- // Avert user about -cons option?
- if (v>=2 && !par.cons)
- {
- for (i=1; i<=L; i++)
- if (X[kfirst][i]==GAP)
- {
- printf("NOTE: Use the '-cons' option to calculate a consensus sequence as first sequence of the alignment.\n");
- break;
- }
- }
- /* MR1
- //Replace GAP with ENDGAP for all end gaps
- for (k=0; k<N_in; k++)
- {
- if (!keep[k]) continue;
- for (i=1; i<=L && X[k][i]==GAP; i++) X[k][i]=ENDGAP;
- for (i=L; i>=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP;
- }*/
-
- // DEBUG
- if (v>=4)
- for (k=0; k<N_in; k++)
- {
- if (!display[k]) continue;
- cout<<">"<<sname[k]<<"\n";
- if (k==kss_dssp || k==kss_pred) {for (i=1; i<=L; i++) cout<<char(i2ss(X[k][i]));}
- else if (k==kss_conf) {for (i=1; i<=L; i++) cout<<char(i2cf(X[k][i]));}
- else if (k==ksa_dssp) {for (i=1; i<=L; i++) cout<<char(i2sa(X[k][i]));}
- else
- {
- for (i=1; i<=L; i++) cout<<char(i2aa(X[k][i]));
- cout<<"\n";
- for (i=1; i<=L; i++)
- if (I[k][i]==0) cout<<"-"; else if (I[k][i]>9) cout<<"X"; else cout<<I[k][i];
- }
- cout<<"\n";
- }
-
- delete[](h); h = NULL;
-}
-
-
-/**
- * @brief Remove sequences with seq. identity larger than seqid percent
- *(remove the shorter of two) or coverage<cov_thr
- *
- * FIXME: originally max_seqid is a variable that is the cutoff
- * above which sequences are thrown out. We want to throw out sequences
- * when building the HMM but not for display, there we want to keep all.
- * This should be really easy, but there is some hidden stuff going on
- * in this function, so I did a minimal-invasive change and just stuck
- * (effectively) a hard-wired 100 instead of the variable.
- * At a later stage we should get rid of this function alltogether
- * as it does gobble up some time (and is quadratic in noof sequences, I think)
- * FS, 2010-10-04
- */
-////////////////////////////////////////////////////////////////////////////
-/*
- */
-inline int
-Alignment::FilterForDisplay(int max_seqid, int coverage, int qid, float qsc, int N)
-{
-
- /* FIXME
- * by just returning n_display and not doing anything
- * I think we display everything and not do any work for it
- */
- return n_display; /* FS, 2010-10-04*/
-
-
- if (par.mark) return n_display;
- char *dummy = new(char[N_in+1]);
- int vtmp=v, seqid;
- v=0;
- n_display=0;
- if (kss_dssp>=0) display[kss_dssp]=KEEP_NOT;
- if (ksa_dssp>=0) display[ksa_dssp]=KEEP_NOT;
- if (kss_pred>=0) display[kss_pred]=KEEP_NOT;
- if (kss_conf>=0) display[kss_conf]=KEEP_NOT;
- for (seqid=imin(10,max_seqid); n_display<N && seqid<=max_seqid; seqid++)
- {
- for (int k=0; k<N_in; k++) dummy[k]=display[k];
- n_display = Filter2(dummy,coverage,qid,qsc,20,seqid,0);
- // printf("Seqid=%3i n_display=%4i\n",seqid,n_display);
- }
- if (n_display>N)
- {
- for (int k=0; k<N_in; k++) dummy[k]=display[k];
- n_display = Filter2(dummy,coverage,qid,qsc,20,--(--seqid),0);
- }
- v=vtmp;
- for (int k=0; k<N_in; k++) display[k]=dummy[k];
- if (kss_dssp>=0) {display[kss_dssp]=KEEP_CONDITIONALLY; n_display++;}
- if (ksa_dssp>=0) {display[ksa_dssp]=KEEP_CONDITIONALLY; n_display++;}
- if (kss_pred>=0) {display[kss_pred]=KEEP_CONDITIONALLY; n_display++;}
- if (kss_conf>=0) {display[kss_conf]=KEEP_CONDITIONALLY; n_display++;}
- delete[] dummy; dummy = NULL;
- return n_display;
-}
-
-/////////////////////////////////////////////////////////////////////////////////////
-// Remove sequences with seq. identity larger than seqid percent (remove the shorter of two) or coverage<cov_thr
-/////////////////////////////////////////////////////////////////////////////////////
-inline int Alignment::Filter(int max_seqid, int coverage, int qid, float qsc, int N)
-{
- return Filter2(keep,coverage,qid,qsc,20,max_seqid,N);
-}
-
-/////////////////////////////////////////////////////////////////////////////
-/*
- * @brief Select set of representative sequences in the multiple sequence alignment
- *
- * Filter criteria:
- * Remove sequences with coverage of query less than "coverage" percent
- * Remove sequences with sequence identity to query of less than "qid" percent
- * If Ndiff==0, remove sequences with seq. identity larger than seqid2(=max_seqid) percent
- * If Ndiff>0, remove sequences with minimum-sequence-identity filter of between seqid1
- * and seqid2 (%), where the minimum seqid threshold is determined such that,
- * in all column blocks of at least WMIN=25 residues, at least Ndiff sequences are left.
- * This ensures that in multi-domain proteins sequences covering one domain are not
- * removed completely because sequences covering other domains are more diverse.
- *
- * Allways the shorter of two compared sequences is removed (=> sort sequences by length first).
- * Please note: sequence identity of sequence x with y when filtering x is calculated as
- * number of residues in sequence x that are identical to an aligned residue in y / number of residues in x
- * Example: two sequences x and y are 100% identical in their overlapping region but one overlaps by 10% of its
- * length on the left and the other by 20% on the right. Then x has 10% seq.id with y and y has 20% seq.id. with x.
- */
-//////////////////////////////////////////////////////////////////////////////
-int
-Alignment::Filter2(char keep[], int coverage, int qid, float qsc, int seqid1, int seqid2, int Ndiff)
-{
- // In the beginnning, keep[k] is 1 for all regular amino acid sequences and 0 for all others (ss_conf, ss_pred,...)
- // In the end, keep[k] will be 1 for all regular representative sequences kept in the alignment, 0 for all others
- char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid
- char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0;
- int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering /* MR1, used to be called idmax*/
- int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL]
- int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid)
- int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i
- const int WFIL=25; // see previous line
-
- int diffNmax=Ndiff; // current maximum difference of Nmax[i] and Ndiff /* MR1 */
- int diffNmax_prev=0; // previous maximum difference of Nmax[i] and Ndiff /* MR1 */
-
- int seqid; // current maximum value for the position-dependent maximum-sequence-identity thresholds in idmax[]
- int seqid_step=0; // previous increment of seqid /* MR1 */
-
- float diff_min_frac; // minimum fraction of differing positions between sequence j and k needed to accept sequence k
- float qdiff_max_frac=0.9999-0.01*qid; // maximum allowable number of residues different from query sequence
- int diff; // number of differing positions between sequences j and k (counted so far)
- int diff_suff; // number of differing positions between sequences j and k that would be sufficient
- int qdiff_max; // maximum number of residues required to be different from query
- int cov_kj; // upper limit of number of positions where both sequence k and j have a residue
- int first_kj; // first non-gap position in sequence j AND k
- int last_kj; // last non-gap position in sequence j AND k
- int kk, jj; // indices for sequence from 1 to N_in
- int k, j; // kk=ksort[k], jj=ksort[j]
- int i; // counts residues
- int n; // number of sequences accepted so far
-
-
- // Initialize in[k]
- for (n=k=0; k<N_in; k++) if (keep[k]==KEEP_ALWAYS) {in[k]=2/*KEEP_ALWAYS??*/; n++;} else in[k]=0;
-
- // Determine first[k], last[k]?
- if (first==NULL)
- {
- first=new(int[N_in]);// first non-gap position in sequence k
- last =new(int[N_in]);// last non-gap position in sequence k
- for (k=0; k<N_in; k++) // do this for ALL sequences, not only those with in[k]==1 (since in[k] may be display[k])
- {
- for (i=1; i<=L; i++) if (X[k][i]<NAA) break;
- first[k]=i;
- for (i=L; i>=1; i--) if (X[k][i]<NAA) break;
- last[k]=i;
- }
- }
-
- // Determine number of residues nres[k]?
- if ( (nres==NULL) || (sizeof(nres)<N_in*sizeof(int)) )
- {
- nres=new(int[N_in]);
- for (k=0; k<N_in; k++) // do this for ALL sequences, not only those with in[k]==1 (since in[k] may be display[k])
- {
- int nr=0;
- for (i=first[k]; i<=last[k]; i++)
- if (X[k][i]<NAA) nr++;
- nres[k]=nr;
- // printf("%20.20s nres=%3i first=%3i last=%3i\n",sname[k],nr,first[k],last[k]);
- }
- }
-
- // Sort sequences according to length; afterwards, nres[ksort[kk]] is sorted by size
- if (ksort==NULL)
- {
- ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences
- for (k=0; k<N_in; k++) ksort[k]=k;
- QSortInt(nres,ksort,kfirst+1,N_in-1,-1); //Sort sequences after kfirst (query) in descending order
- }
- for (kk=0; kk<N_in; kk++) inkk[kk]=in[ksort[kk]];
-
- // Initialize N[i], idmax[i], idprev[i]
- for (i=1; i<first[kfirst]; i++) N[i]=0;
- for (i=first[kfirst]; i<=last[kfirst]; i++) N[i]=1;
- for (i=last[kfirst]+1; i<=L; i++) N[i]=0;
- //for (i=1; i<=L; i++) {idmax[i]=seqid1; idmaxwin[i]=-1;}
- for (i=1; i<=L; ++i) {Nmax[i]=0; idmaxwin[i]=-1;} /* MR1 */
- for (k=0; k<N_in; k++) seqid_prev[k]=-1;
- if (Ndiff<=0 || Ndiff>=N_in) {seqid1=seqid2; Ndiff=N_in; diffNmax=Ndiff;}
-
- // Check coverage and sim-to-query criteria for each sequence k
- for (k=0; k<N_in; k++)
- {
- if (keep[k]==KEEP_NOT || keep[k]==KEEP_ALWAYS) continue; // seq k not regular sequence OR is marked sequence
- if (100*nres[k]<coverage*L) {keep[k]=KEEP_NOT; continue;} // coverage too low? => reject once and for all
-
- float qsc_sum=0.0;
-
- // Check if score-per-column with query is at least qsc
- if (qsc>-10)
- {
- float qsc_min = qsc*nres[k]; // minimum total score of seq k with query
-
- int gapq=0, gapk=0; // number of consecutive gaps in query or k'th sequence at position i
- for (int i=first[k]; i<=last[k]; i++)
- {
- if (X[k][i]<20)
- {
- gapk=0;
- if (X[kfirst][i]<20)
- {
- gapq=0;
- qsc_sum += S[(int)X[kfirst][i]][(int)X[k][i]];
- }
- else if (gapq++) qsc_sum-=PLTY_GAPEXTD; else qsc_sum-=PLTY_GAPOPEN;
- }
- else if (X[kfirst][i]<20)
- {
- gapq=0;
- if (gapk++) qsc_sum-=PLTY_GAPEXTD; else qsc_sum-=PLTY_GAPOPEN;
- }
- }
- // printf("k=%3i qsc=%6.2f\n",k,qsc_sum);
- if (qsc_sum<qsc_min) {keep[k]=KEEP_NOT; continue;} // too different from query? => reject once and for all
- }
-
- //Check if sequence similarity with query at least qid?
- if (qdiff_max_frac<0.999)
- {
- qdiff_max=int(qdiff_max_frac*nres[k]+0.9999);
- // printf("k=%-4i nres=%-4i qdiff_max=%-4i first=%-4i last=%-4i",k,nres[k],qdiff_max,first[k],last[k]);
- diff=0;
- for (int i=first[k]; i<=last[k]; i++)
- // enough different residues to reject based on minimum qid with query? => break
- if (X[k][i]<20 && X[k][i]!=X[kfirst][i] && ++diff>=qdiff_max) break;
- // printf(" diff=%4i\n",diff);
- if (diff>=qdiff_max) {keep[k]=KEEP_NOT; continue;} // too different from query? => reject once and for all
- }
- // printf(" qsc=%6.2f qid=%6.2f \n",qsc_sum/nres[k],100.0*(1.0-(float)(diff)/nres[k]));
- }
-
- if (seqid1>seqid2)
- {
- for (n=k=0; k<N_in; k++) if (keep[k]>KEEP_NOT) n++;
- return n;
- }
-
- // Successively increment idmax[i] at positons where N[i]<Ndiff
- //for (seqid=seqid1; seqid<=seqid2; seqid+=1+(seqid>=50)) /* MR1 */
- seqid=seqid1;
- while (seqid<=seqid2)
- {
- /*
- // Update idmax[i]
- for (i=1; i<=L; i++) if (N[i]<Ndiff) idmax[i]=seqid;
-
- // Update idmaxwin[i] as minimum of idmax[i-WFIL,i+WFIL]. If idmaxwin[] has not changed then stop
- char stop=1;
- for (i=1; i<=L; i++)
- {
- int idmax_min=seqid2;
- for (j=imax(1,imin(L-2*WFIL+1,i-WFIL)); j<=imin(L,imax(2*WFIL,i+WFIL)); j++)
- if (idmax[j]<idmax_min) idmax_min=idmax[j];
- if (idmax_min>idmaxwin[i]) stop=0; // idmaxwin[i] has changed => do not stop
- idmaxwin[i]=idmax_min;
- }
- */
- char stop=1;
- // Update Nmax[i]
- diffNmax_prev = diffNmax;
- diffNmax = 0;
- for (i=1; i<=L; ++i)
- {
- int max=0;
- for (j=imax(1,imin(L-2*WFIL+1,i-WFIL)); j<=imin(L,imax(2*WFIL,i+WFIL)); ++j)
- if (N[j]>max) max=N[j];
- if (Nmax[i]<max) Nmax[i]=max;
- if (Nmax[i]<Ndiff)
- {
- stop=0;
- idmaxwin[i]=seqid;
- if (diffNmax<Ndiff-Nmax[i]) diffNmax=Ndiff-Nmax[i];
- }
-
- }
-
- //printf("seqid=%3i diffNmax_prev= %-4i diffNmax= %-4i n=%-5i N_in-N_ss=%-5i\n",seqid,diffNmax_prev,diffNmax,n,N_in-N_ss);
-
- if (stop) break;
-
- // // DEBUG
- // printf("idmax ");
- // for (i=1; i<=L; i++) printf("%2i ",idmax[i]);
- // printf("\n");
- // printf("idmaxwin ");
- // for (i=1; i<=L; i++) printf("%2i ",idmaxwin[i]);
- // printf("\n");
- // printf("N[i] ");
- // for (i=1; i<=L; i++) printf("%2i ",N[i]);
- // printf("\n");
-
- // Loop over all candidate sequences kk (-> k)
- for (kk=0; kk<N_in; kk++)
- {
- if (inkk[kk]) continue; // seq k already accepted
- k=ksort[kk];
- if (!keep[k]) continue; // seq k is not regular aa sequence or already suppressed by coverage or qid criterion
- if (keep[k]==KEEP_ALWAYS) {inkk[kk]=2; continue;} // accept all marked sequences (no n++, since this has been done already)
-
- // Calculate max-seq-id threshold seqidk for sequence k (as maximum over idmaxwin[i])
- if (seqid>=100) {in[k]=inkk[kk]=1; n++; continue;}
- float seqidk=seqid1;
- for (i=first[k]; i<=last[k]; i++)
- if (idmaxwin[i]>seqidk) seqidk=idmaxwin[i];
- if (seqid==seqid_prev[k]) continue; // sequence has already been rejected at this seqid threshold => reject this time
- seqid_prev[k]=seqid;
- diff_min_frac =0.9999-0.01*seqidk; // min fraction of differing positions between sequence j and k needed to accept sequence k
-
- // Loop over already accepted sequences
- for (jj=0; jj<kk; jj++)
- {
- if (!inkk[jj]) continue;
- j=ksort[jj];
- first_kj=imax(first[k],first[j]);
- last_kj =imin(last[k],last[j]);
- cov_kj = last_kj-first_kj+1;
- diff_suff=int(diff_min_frac*imin(nres[k],cov_kj)+0.999); // nres[j]>nres[k] anyway because of sorting /* MR1 0.999 */
- diff=0;
- for (int i=first_kj; i<=last_kj; i++)
- {
- // enough different residues to accept? => break
- if (X[k][i]>=NAA || X[j][i]>=NAA)
- cov_kj--;
- else
- if (X[k][i]!=X[j][i] && ++diff>=diff_suff) break; // accept (k,j)
- }
- // // DEBUG
- // printf("%20.20s with %20.20s: diff=%i diff_min_frac*cov_kj=%f diff_suff=%i nres=%i cov_kj=%i\n",sname[k],sname[j],diff,diff_min_frac*cov_kj,diff_suff,nres[k],cov_kj);
- // printf("%s\n%s\n\n",seq[k],seq[j]);
-
- //if (float(diff)<fmin(diff_min_frac*cov_kj,diff_suff)) break; //similarity > acceptace threshold? Reject! /* MR1 */
- if (diff<diff_suff && float(diff)<=diff_min_frac*cov_kj) break; //dissimilarity < acceptace threshold? Reject! /* MR1 */
-
-
- }
- if (jj>=kk) // did loop reach end? => accept k. Otherwise reject k (the shorter of the two)
- {
- in[k]=inkk[kk]=1;
- n++;
- for (i=first[k]; i<=last[k]; i++) N[i]++; // update number of sequences at position i
- // printf("%i %20.20s accepted\n",k,sname[k]);
- }
- // else
- // {
- // printf("%20.20s rejected: too similar with seq %20.20s diff=%i diff_min_frac*cov_kj=%f diff_suff=%i nres=%i cov_kj=%i\n",sname[k],sname[j],diff,diff_min_frac*cov_kj,diff_suff,nres[k],cov_kj);
- // printf("%s\n%s\n\n",seq[k],seq[j]);
- // }
-
- } // End Loop over all candidate sequences kk
-
- // // DEBUG
- // printf("\n");
- // printf("seqid_prev[k]= \n");
- // for (k=0; k<N_in; k++) printf("%2i ",seqid_prev[k]);
- // printf("\n");
-
- // Increment seqid /* MR1 */
- seqid_step = imax(1,imin(5,diffNmax/(diffNmax_prev-diffNmax+1)*seqid_step/2));
- seqid += seqid_step;
-
- } // End Loop over seqid
-
- if (v>=2)
- {
- printf("%i out of %i sequences passed filter (",n,N_in-N_ss);
- if (par.coverage)
- printf("%i%% min coverage, ",coverage);
- if (qid)
- printf("%i%% min sequence identity to query, ",qid);
- if (qsc>-10)
- printf("%.2f bits min score per column to query, ",qsc);
- if (Ndiff<N_in && Ndiff>0)
- printf("up to %i%% position-dependent max pairwise sequence identity)\n",seqid);
- else
- printf("%i%% max pairwise sequence identity)\n",seqid1);
- }
-
- for (k=0; k<N_in; k++) keep[k]=in[k];
- delete[] in; in = NULL;
- delete[] inkk; inkk = NULL;
- //delete[] idmax; idmax = NULL;
- delete[] Nmax; /* MR1 */
- delete[] idmaxwin; idmaxwin = NULL;
- delete[] seqid_prev; seqid_prev = NULL;
- delete[] N; N = NULL;
-#if 0
- printf("%s:%s:%d: sequences accepted = %d/%d\n", __FUNCTION__, __FILE__, __LINE__, n, N_in-N_ss);
-#endif
- return n;
-}
-
-
-
-/* MR1: the Alignment::HomologyFilter is no longer needed in hhalign-stand-alone */
-/////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Filter for min score per column coresc with core query profile,
- * defined by coverage_core and qsc_core
- */
-/////////////////////////////////////////////////////////////////////////////
-int
-Alignment::HomologyFilter(int coverage_core, float qsc_core, float coresc)
-{
- const int seqid_core=90; //maximum sequence identity in core alignment
- const int qid_core=0;
- const int Ndiff_core=0;
- int n;
- HMM qcore;
- char* coreseq=new(char[N_in]); // coreseq[k]=1 if sequence belongs to core of alignment (i.e. it is very similar to query)
- for (int k=0; k<N_in; k++) coreseq[k]=keep[k]; // Copy keep[] into coreseq[]
-
- // Remove sequences with seq. identity larger than seqid percent (remove the shorter of two)
- int v1=v; v=1;
- n = Filter2(coreseq,coverage_core,qid_core,qsc_core,seqid_core,seqid_core,Ndiff_core);
- v=v1;
- if (v>=2)
- {
- printf("%i out of %i core alignment sequences passed filter (",n,N_in-N_ss);
- if (par.coverage_core)
- printf("%i%% min coverage, ",coverage_core);
- if (qid_core)
- printf("%i%% min sequence identity to query, ",qid_core);
- if (qsc_core>-10)
- printf("%.2f bits min score per column to query, ",qsc_core);
- printf("%i%% max pairwise sequence identity)\n",seqid_core);
- }
-
- // Calculate bare AA frequencies and transition probabilities -> qcore.f[i][a], qcore.tr[i][a]
- FrequenciesAndTransitions(qcore,coreseq);
-
- // Add transition pseudocounts to query -> q.p[i][a] (gapd=1.0, gape=0.333, gapf=gapg=1.0, gaph=gapi=1.0, gapb=1.0
- qcore.AddTransitionPseudocounts(1.0,0.333,1.0,1.0,1.0,1.0,1.0);
-
- // Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
- qcore.PreparePseudocounts();
-
- // Add amino acid pseudocounts to query: qcore.p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
- qcore.AddAminoAcidPseudocounts(2,1.5,2.0,1.0); // pcm=2, pca=1.0, pcb=2.5, pcc=1.0
-
- // Filter out all sequences below min score per column with qcore
- n=FilterWithCoreHMM(keep, coresc, qcore);
-
- if (v>=2) cout<<n<<" out of "<<N_in-N_ss<<" sequences filtered by minimum score-per-column threshold of "<<qsc_core<<"\n";
- delete[] coreseq; coreseq = NULL;
- return n;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Filter out all sequences below a minimum score per column with profile qcore
- */
-int
-Alignment::FilterWithCoreHMM(char in[], float coresc, HMM& qcore)
-{
- int k; // count sequences in alignment
- int i; // column in query alignment
- int a; // amino acid (0..19)
- int n=1; // number of sequences that passed filter
- float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore
- char gap; // 1: previous state in seq k was a gap 0: previous state in seq k was an amino acid
- float score; // score of sequence k aligned with qcore
-
- for (i=1; i<=L; i++) logodds[i]=new(float[21]);
-
- // Determine first[k], last[k]?
- if (first==NULL)
- {
- first=new(int[N_in]);// first non-gap position in sequence k
- last =new(int[N_in]);// last non-gap position in sequence k
- for (k=0; k<N_in; k++) // do this for ALL sequences, not only those with in[k]==1 (since in[k] may be display[k])
- {
- for (i=1; i<=L; i++) if (X[k][i]<NAA) break;
- first[k]=i;
- for (i=L; i>=1; i--) if (X[k][i]<NAA) break;
- last[k]=i;
- }
- }
-
- // Determine number of residues nres[k]?
- if (nres==NULL)
- {
- nres=new(int[N_in]);
- for (k=0; k<N_in; k++) // do this for ALL sequences, not only those with in[k]==1 (since in[k] may be display[k])
- {
- int nr=0;
- for (i=first[k]; i<=last[k]; i++)
- if (X[k][i]<NAA) nr++;
- nres[k]=nr;
- // printf("%20.20s nres=%3i first=%3i last=%3i\n",sname[k],nr,f,l);
- }
- }
-
- // Precalculate the log-odds for qcore
- for (i=1; i<=L; i++)
- {
- for (a=0; a<NAA; a++)
- logodds[i][a]=fast_log2(qcore.p[i][a]/pb[a]);
- logodds[i][ANY]=-0.5; // half a bit penalty for X
-
- // printf(" A R N D C Q E G H I L K M F P S T W Y V\n");
- // printf("%6i ",i);
- // for (a=0; a<20; ++a) fprintf(stdout,"%5.1f ",100*qcore.f[i][a]);
- // printf("\n");
- // printf(" ");
- // for (a=0; a<20; ++a) fprintf(stdout,"%5.1f ",100*qcore.g[i][a]);
- // printf("\n");
- // printf(" ");
- // for (a=0; a<20; ++a) fprintf(stdout,"%5.1f ",100*qcore.p[i][a]);
- // printf("\n");
- // printf(" ");
- // for (a=0; a<20; ++a) fprintf(stdout,"%5.1f ",100*pb[a]);
- // printf("\n");
- // printf(" ");
- // for (a=0; a<20; ++a) fprintf(stdout,"%5.2f ",fast_log2(qcore.p[i][a]/pb[a]));
- // printf("\n");
- }
-
- // Main loop: test all sequences k
- for (k=kfirst+1; k<N_in; k++)
- {
- if (!in[k]) continue; // if in[k]==0 sequence k will be suppressed directly
-
- float score_M=0.0;
- float score_prev=0.0;
-
- // Calculate score of sequence k with core HMM
- score=0; gap=0;
- for (i=first[k]; i<=last[k]; i++)
- {
- score_M=0.0;
- if (X[k][i]<=ANY) // current state is Match
- {
- score_M=logodds[i][ (int)X[k][i]];
- score+=logodds[i][ (int)X[k][i]];
- if (gap) score+=qcore.tr[i][D2M]; else score+=qcore.tr[i][M2M];
- gap=0;
- }
- else if (X[k][i]==GAP) // current state is Delete (ignore ENDGAPs)
- {
- if (gap) score+=qcore.tr[i][D2D]; else score+=qcore.tr[i][M2D];
- gap=1;
- }
- if (I[k][i]) score+=qcore.tr[i][M2I]+(I[k][i]-1)*qcore.tr[i][I2I]+qcore.tr[i][I2M];
- // if (k==2) printf("i=%3i %c:%c score_M=%6.2f score=%6.2f score_sum=%6.2f \n",i,i2aa(X[kfirst][i]),i2aa(X[k][i]),score_M,score-score_prev,score);
- score_prev=score;
- }
-
- printf("k=%3i score=%6.2f\n",k,score);
- if (score<nres[k]*coresc) in[k]=0; else n++;// reject sequence k?
- }
- for (i=1; i<=L; i++){
- delete[] logodds[i]; logodds[i] = NULL;
- }
- delete[] logodds; logodds = NULL;
- return n;
-}
-
-
-/* MR1 */
-#if 0
-/////////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Filter alignment to given diversity/Neff
- */
-bool
-Alignment::FilterNeff()
-{
- int v1=v;
- v=v1-1;
- const float TOLX=0.001;
- const float TOLY=0.02;
- char dummy[N_in+1];
- for (int k=0; k<N_in; ++k) dummy[k]=keep[k];
- float x=0.0,y=0.0;
- float x0=-1.0;
- float x1=+2.0;
- float y0=filter_by_qsc(x0,dummy);
- float y1=filter_by_qsc(x1,dummy);
- int i=2;
- while (y0-par.Neff>0 && par.Neff-y1>0)
- {
- x = x0 + (par.Neff-y0)*(x1-x0)/(y1-y0); // linear interpolation between (x0,y0) and (x1,y1)
- y = filter_by_qsc(x,dummy);
- if (v>=2) printf(" %3i x0=%6.3f -> %6.3f x=%6.3f -> %6.3f x1=%6.3f -> %6.3f \n",++i,x0,y0,x,y,x1,y1);
- if (y>par.Neff) {x0=x; y0=y;} else {x1=x; y1=y;}
- if (fabs(par.Neff-y)<TOLY || x1-x0<TOLX) break;
- }
- v=v1;
-
- if (y0>=par.Neff && y1<=par.Neff)
- {
- // Write filtered alignment WITH insert states (lower case) to alignment file
- if (v>=2) printf("Found Neff=%6.3f at filter threshold qsc=%6.3f\n",y,x);
- return true;
- }
- else if (v>=1)
- printf("Diversity of unfiltered alignment %.2f is below target diversity %.2f. No alignment written\n",y0,par.Neff);
-
- return false;
-}
-
-float Alignment::filter_by_qsc(float qsc, char* dummy)
-{
- HMM q;
- for (int k=0; k<N_in; ++k) keep[k]=dummy[k];
- Filter2(keep,par.coverage,0,qsc,par.max_seqid+1,par.max_seqid,0);
- FrequenciesAndTransitions(q);
- // printf("qsc=%4.1f N_filtered=%-3i Neff=%6.3f\n",qsc,n,q.Neff_HMM);
- return q.Neff_HMM;
-}
-#endif
-
-/////////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Calculate AA frequencies q.p[i][a] and transition probabilities q.tr[i][a] from alignment
- */
-void
-Alignment::FrequenciesAndTransitions(HMM& q, char* in)
-{
- int k; // index of sequence
- int i; // position in alignment
- int a; // amino acid (0..19)
- int ni[NAA+3]; // number of times amino acid a occurs at position i
- int naa; // number of different amino acids
-
- if (v>=3)
- cout<<"Calculating position-dependent weights on subalignments\n";
-
- if (in==NULL) in=keep; // what's this good for?
-
- if (N_filtered>1)
- {
- for (k=0; k<N_in; k++) wg[k]=0.0; // initialized wg[k]
- // Calculate global weights
- for (i=1; i<=L; i++) // for all positions i in alignment
- {
- for (a=0; a<20; a++) ni[a]=0;
- for (k=0; k<N_in; k++) if (in[k]) ni[ (int)X[k][i]]++;
- naa=0; for (a=0; a<20; a++) if(ni[a]) naa++;
- if (!naa) naa=1; //naa=0 when column consists of only gaps and Xs (=ANY)
- for (k=0; k<N_in; k++)
- if (in[k] && X[k][i]<20)
- wg[k] += 1.0/float(ni[ (int)X[k][i]]*naa*(nres[k]+30));
- // ensure that each residue of a short sequence contributes as much as a residue of a long sequence:
- // contribution is proportional to one over sequence length nres[k] plus 30.
- }
- NormalizeTo1(wg,N_in);
-
-
- // Do pos-specific sequence weighting and calculate amino acid frequencies and transitions
- for (k=0; k<N_in; k++) X[k][0]=ENDGAP; // make sure that sequences ENTER subalignment j for j=1
- for (k=0; k<N_in; k++) X[k][L+1]=ENDGAP; // does it have an influence?
-
-#ifdef HAVE_OPENMP
- if(par.wg != 1)
- {
- #pragma omp parallel sections
- {
- #pragma omp section
- Amino_acid_frequencies_and_transitions_from_M_state(q,in); // use subalignments of seqs with residue in i
- #pragma omp section
- Transitions_from_I_state(q,in); // use subalignments of seqs with insert in i
- #pragma omp section
- Transitions_from_D_state(q,in); // use subalignments of seqs with delete in i. Must be last of these three calls if par.wg==1!
- }
- }
- else
- {
- #pragma omp parallel sections
- {
- #pragma omp section
- Amino_acid_frequencies_and_transitions_from_M_state(q,in); // use subalignments of seqs with residue in i
- #pragma omp section
- Transitions_from_I_state(q,in); // use subalignments of seqs with insert in i
- }
- Transitions_from_D_state(q,in); // use subalignments of seqs with delete in i. Must be last of these three calls if par.wg==1!
- }
-#else
- Amino_acid_frequencies_and_transitions_from_M_state(q,in);
- Transitions_from_I_state(q,in);
- Transitions_from_D_state(q,in);
-#endif
- }
- else // N_filtered==1
- {
- X[kfirst][0]=X[kfirst][L+1]=ANY; // (to avoid anallowed access within loop)
- q.Neff_HMM=1.0f;
- for (i=0; i<=L+1; i++) // for all positions i in alignment
- {
- q.Neff_M[i]=1.0f;
- q.Neff_I[i]=q.Neff_D[i]=0.0f;
- for (a=0; a<20; a++) q.f[i][a]=0.0;
- /* this is the crucial change that makes terminal-X work */
- //q.f[i][ (int)(X[kfirst][i]) ] = 1.0; /* MR1 */
- if (X[kfirst][i] < ANY) /* MR1 */
- q.f[i][(unsigned int) X[kfirst][i] ] = 1.0;
- else
- for (a=0; a<20; ++a) q.f[i][a]=pb[a];
- q.tr[i][M2M]=0;
- q.tr[i][M2I]=-100000.0;
- q.tr[i][M2D]=-100000.0;
- q.tr[i][I2M]=-100000.0;
- q.tr[i][I2I]=-100000.0;
- q.tr[i][D2M]=-100000.0;
- q.tr[i][D2D]=-100000.0;
- }
- q.tr[0][I2M]=0;
- q.tr[L][I2M]=0;
- q.tr[0][D2M]=0;
- q.Neff_M[0]=q.Neff_I[0]=q.Neff_D[0]=99.999; // Neff_av[0] is used for calculation of transition pseudocounts for the start state
- }
-
- if (v>=3)
- {
- printf("\nMatches:\n");
- printf("col Neff nseqs\n");
- for (i=1; i<=imin(L,100); i++)
- printf("%3i %5.2f %3i\n",i,q.Neff_M[i],nseqs[i]);
-
- printf("\nInserts:\n");
- printf("col Neff nseqs\n");
- for (i=1; i<=imin(L,100); i++)
- printf("%3i %5.2f %3i\n",i,q.Neff_I[i],nseqs[i]);
-
- printf("\nDeletes:\n");
- printf("col Neff nseqs\n");
- for (i=1; i<=imin(L,100); i++)
- printf("%3i %5.2f %3i\n",i,q.Neff_D[i],nseqs[i]);
- }
-
- // Copy column information into HMM q
- q.L=L;
- q.N_in=N_in;
- q.N_filtered=N_filtered;
- for (i=1; i<=L; i++) q.l[i]=l[i];
-
- // Set names in HMM q
- if (strlen(q.name)==0) strcpy(q.name,name);
- if (strlen(q.longname)==0) strcpy(q.longname,longname);
- if (strlen(q.fam)==0) strcpy(q.fam,fam);
- ScopID(q.cl,q.fold,q.sfam,q.fam); // derive superfamily, fold and class code from family name
- strcpy(q.file,file); // Store basename of alignment file name in q.file
-
- // Copy sequences to be displayed into HMM
- q.nss_dssp=q.nsa_dssp=q.nss_pred=q.nss_conf=q.nfirst=-1;
- int n=0;
- if (kss_dssp>=0) q.nss_dssp=n++; // copy dssp sequence?
- if (ksa_dssp>=0) q.nsa_dssp=n++; // copy dssp sequence?
- if (kss_pred>=0) q.nss_pred=n++; // copy psipred sequence?
- if (kss_conf>=0) q.nss_conf=n++; // copy confidence value sequence?
-
- // Calculate consensus sequence?
- if (par.showcons || par.cons)
- {
- float maxw;
- int maxa;
- if (par.showcons)
- {
- // Reserve space for consensus/conservation sequence as Q-T alignment mark-up
- q.ncons=n++;
- q.sname[q.ncons]=new(char[10]);
- if (!q.sname[q.ncons]) {MemoryError("array of names for displayed sequences");}
- strcpy(q.sname[q.ncons],"Consensus");
- q.seq[q.ncons]=new(char[L+2]);
- if (!q.seq[q.ncons]) {MemoryError("array of names for displayed sequences");}
- }
- if (par.cons)
- {
- // Reserve space for consensus sequence as first sequence in alignment
- q.nfirst=n++; kfirst=-1;
- q.sname[q.nfirst]=new(char[strlen(name)+11]);
- if (!q.sname[q.nfirst]) {MemoryError("array of names for displayed sequences");}
- strcpy(q.sname[q.nfirst],name);
- strcat(q.sname[q.nfirst],"_consensus");
- q.seq[q.nfirst]=new(char[L+2]);
- if (!q.seq[q.nfirst]) {MemoryError("array of names for displayed sequences");}
- }
- // Calculate consensus amino acids using similarity matrix
- for (i=1; i<=L; i++)
- {
- maxw=0.0; maxa=0;
- for (a=0; a<20; a++)
- if (q.f[i][a]-pb[a]>maxw) {maxw = q.f[i][a]-pb[a]; maxa = a;}
-
- if (par.showcons)
- {
- maxw =0.0;
- for (int b=0; b<20; b++) maxw += q.f[i][b]*Sim[maxa][b]*Sim[maxa][b];
- maxw *= q.Neff_M[i]/(q.Neff_HMM+1); // columns with many gaps don't get consensus symbol
- if (maxw>0.6) q.seq[q.ncons][i] = uprchr(i2aa(maxa));
- else if (maxw>0.4) q.seq[q.ncons][i] = lwrchr(i2aa(maxa));
- else q.seq[q.ncons][i] = 'x';
- }
- if (par.cons) q.seq[q.nfirst][i] = uprchr(i2aa(maxa));
- }
- if (par.showcons)
- {
- q.seq[q.ncons][0]='-';
- q.seq[q.ncons][L+1]='\0';
- }
- if (par.cons)
- {
- q.seq[q.nfirst][0]='-';
- q.seq[q.nfirst][L+1]='\0';
- }
- }
-
- // Copy sequences to be displayed from alignment to HMM
- for (k=0; k<N_in; k++)
- {
- int nn;
- if (display[k])
- {
- if (0 && (n>=MAXSEQDIS)) {
- /* FIXME: the test was if(n>=MAXSEQDIS),
- this test was necessary because alignment memory was static,
- now it should be dynamic, and should always have the right size,
- there are at least number-of-sequences plus a 'bit' more
- however, I do not know what that 'bit' is likely to be (in the future).
- at the moment it is 1 for the consnseus and 1 for structure,
- but this might change (FS)
- */
- if (par.mark) cerr<<"WARNING: maximum number "<<MAXSEQDIS<<" of sequences for display of alignment exceeded\n";
- break;
- }
- if (k==kss_dssp) nn=q.nss_dssp; // copy dssp sequence to nss_dssp
- else if (k==ksa_dssp) nn=q.nsa_dssp;
- else if (k==kss_pred) nn=q.nss_pred;
- else if (k==kss_conf) nn=q.nss_conf;
- else if (k==kfirst) nn=q.nfirst=n++;
- else nn=n++;
- // strcut(sname[k]," "); // delete rest of name line beginning with two spaces " " // Why this?? Problem for pdb seqs without chain
- q.sname[nn]=new(char[strlen(sname[k])+1]);
- if (!q.sname[nn]) {MemoryError("array of names for displayed sequences");}
- strcpy(q.sname[nn],sname[k]);
- q.seq[nn]=new(char[strlen(seq[k])+1]);
- if (!q.seq[nn]) {MemoryError("array of names for displayed sequences");}
- strcpy(q.seq[nn],seq[k]);
- }
- }
- q.n_display=n; // how many sequences to be displayed in alignments?
-
- // Copy secondary structure information into HMM
- if (kss_dssp>=0)
- for (i=1; i<=L; i++) q.ss_dssp[i]=X[kss_dssp][i];
- if (ksa_dssp>=0)
- for (i=1; i<=L; i++) q.sa_dssp[i]=X[ksa_dssp][i];
- if (kss_pred>=0)
- {
- for (i=1; i<=L; i++) q.ss_pred[i]=X[kss_pred][i];
- if (kss_conf>=0)
- for (i=1; i<=L; i++) q.ss_conf[i]=X[kss_conf][i];
- else
- for (i=1; i<=L; i++) q.ss_conf[i]=5;
- }
-
- q.lamda=0.0;
- q.mu=0.0;
-
- // Debug: print occurence of amino acids for each position i
- if (v>=2) printf("Effective number of sequences exp(entropy) = %-4.1f\n",q.Neff_HMM); //PRINT
- if (v>=3)
- {
- cout<<"\nMatr: ";
- for (a=0; a<20; a++) printf("%4.1f ",100*pb[a]);
- cout<<"\nAmino acid frequencies without pseudocounts:\n";
- cout<<" A R N D C Q E G H I L K M F P S T W Y V\n";
- for (i=1; i<=L; i++)
- {
- printf("%3i: ",i);
- for (a=0; a<20; a++) printf("%4.0f ",100*q.f[i][a]);
- cout<<endl;
- }
- cout<<"\n";
-
- printf("\nListing transition probabilities without pseudocounts:\n");
- printf(" i M->M M->I M->D I->M I->I D->M D->D Neff_M Neff_I Neff_D\n");
- for (i=0; i<=L; i++)
- {
- printf("%4i %6.3f %6.3f %6.3f ",i,pow(2.0,q.tr[i][M2M]),pow(2.0,q.tr[i][M2I]),pow(2.0,q.tr[i][M2D]));
- printf("%6.3f %6.3f ",pow(2.0,q.tr[i][I2M]),pow(2.0,q.tr[i][I2I]));
- printf("%6.3f %6.3f ",pow(2.0,q.tr[i][D2M]),pow(2.0,q.tr[i][D2D]));
- printf("%6.3f %6.3f %6.3f\n",q.Neff_M[i],q.Neff_I[i],q.Neff_D[i]);
- }
- }
- q.trans_lin=0;
- q.has_pseudocounts=false; /* MR1 */
-
- return;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////////////
-/*
- * FIXME: one of the most time consuming routines (according to gprof on r112)
- */
-/**
- * @brief Calculate freqs q.f[i][a] and transitions q.tr[i][a] (a=MM,MI,MD) with pos-specific subalignments
- * Pos-specific weights are calculated like in "GetPositionSpecificWeights()"
- */
-void
-Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM& q, char* in)
-{
- // Calculate position-dependent weights wi[k] for each i.
- // For calculation of weights in column i use sub-alignment
- // over sequences which have a *residue* in column i (no gap, no end gap)
- // and over columns where none of these sequences has an end gap.
- // This is done by updating the arrays n[j][a] at each step i-1->i while letting i run from 1 to L.
- // n[j][a] = number of occurences of amino acid a at column j of the subalignment,
- // => only columns with n[j][ENDGAP]=0 are contained in the subalignment!
- // If no sequences enter or leave the subalignment at the step i-1 -> i (i.e. change=0)
- // then the old values wi[k], Neff[i-1], and ncol are used for the new position i.
- // Index a can be an amino acid (0-19), ANY=20, GAP=21, or ENDGAP=22
-
- int k; // index of sequence
- int i,j; // position in alignment
- int a; // amino acid (0..19)
- int naa; // number of different amino acids
- int** n; // n[j][a] = number of seq's with some residue at column i AND a at position j
- //float wi[MAXSEQ]; // weight of sequence k in column i, calculated from subalignment i
- float *wi=NULL; // weight of sequence k in column i, calculated from subalignment i
- //float Neff[MAXRES]; // diversity of subalignment i
- float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
- int nseqi=0; // number of sequences in subalignment i
- int ncol=0; // number of columns j that contribute to Neff[i]
- char change; // has the set of sequences in subalignment changed? 0:no 1:yes
- float fj[NAA+3]; // to calculate entropy
- float sum;
-
- wi = new(float[N_in+2]);
-
- // Global weights?
- if (par.wg==1)
- for (k=0; k<N_in; k++) wi[k]=wg[k];
-
- // Initialization
- q.Neff_HMM=0.0f;
- Neff[0]=0.0; // if the first column has no residues (i.e. change==0), Neff[i]=Neff[i-1]=Neff[0]
- n = new(int*[L+2]);
- for (j=1; j<=L; j++) n[j]=new(int[NAA+3]);
- for (j=1; j<=L; j++)
- for (a=0; a<NAA+3; a++) n[j][a]=0;
-
-
- //////////////////////////////////////////////////////////////////////////////////////////////
- // Main loop through alignment columns
- for (i=1; i<=L; i++) // Calculate wi[k] at position i as well as Neff[i]
- {
-
- if (par.wg==0)
- {
-
- change=0;
- // Check all sequences k and update n[j][a] and ri[j] if necessary
- for (k=0; k<N_in; k++)
- {
- if (!in[k]) continue;
- if (X[k][i-1]>=ANY && X[k][i]<ANY)
- { // ... if sequence k was NOT included in i-1 and has to be included for column i
- change=1;
- nseqi++;
- for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]++;
- }
- else if (X[k][i-1]<ANY && X[k][i]>=ANY)
- { // ... if sequence k WAS included in i-1 and has to be thrown out for column i
- change=1;
- nseqi--;
- for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]--;
- }
- } //end for (k)
- nseqs[i]=nseqi;
-
- // If subalignment changed: update weights wi[k] and Neff[i]
- if (change)
- {
- // Initialize weights and numbers of residues for subalignment i
- ncol=0;
- for (k=0; k<N_in; k++) wi[k]=1E-8; // for pathological alignments all wi[k] can get 0; /* MR1 */
-
- // sum wi[k] over all columns j and sequences k of subalignment
- for (j=1; j<=L; j++)
- {
- // do at least a fraction MAXENDGAPFRAC of sequences in subalignment contain an end gap in j?
- if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
- naa=0; for (a=0; a<20; a++) if(n[j][a]) naa++;
- if (naa==0) continue;
- ncol++;
- for (k=0; k<N_in; k++)
- {
- if (in[k] && X[k][i]<ANY && X[k][j]<ANY)
- {
- // if (!n[j][ (int)X[k][j]]) {fprintf(stderr,"Error: Mi=%i: n[%i][X[%i]]=0! (X[%i]=%i)\n",i,j,k,k,X[k][j]);}
- wi[k]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
- }
- }
- }
-
- // Check whether number of columns in subalignment is sufficient
- if (ncol<NCOLMIN)
- // Take global weights
- for (k=0; k<N_in; k++)
- if(in[k] && X[k][i]<ANY) wi[k]=wg[k]; else wi[k]=0.0;
-
- // Calculate Neff[i]
- Neff[i]=0.0;
- for (j=1; j<=L; j++)
- {
- // do at least a fraction MAXENDGAPFRA of sequences in subalignment contain an end gap in j?
- if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
- for (a=0; a<20; a++) fj[a]=0;
- for (k=0; k<N_in; k++)
- if (in[k] && X[k][i]<ANY && X[k][j]<ANY)
- fj[ (int)X[k][j] ]+=wi[k];
- NormalizeTo1(fj,NAA);
- for (a=0; a<20; a++)
- if (fj[a]>1E-10) Neff[i]-=fj[a]*fast_log2(fj[a]);
- }
- if (ncol>0) Neff[i]=pow(2.0,Neff[i]/ncol); else Neff[i]=1.0;
-
- }
-
- else //no update was necessary; copy values for i-1
- {
- Neff[i]=Neff[i-1];
- }
- }
-
-
- // Calculate amino acid frequencies q.f[i][a] from weights wi[k]
- for (a=0; a<20; a++) q.f[i][a]=0;
- for (k=0; k<N_in; k++) if (in[k]) q.f[i][ (int)X[k][i] ]+=wi[k];
- NormalizeTo1(q.f[i],NAA,pb);
-
- // Calculate transition probabilities from M state
- q.tr[i][M2M]=q.tr[i][M2D]=q.tr[i][M2I]=0.0;
- for (k=0; k<N_in; k++) //for all sequences
- {
- if (!in[k]) continue;
- //if input alignment is local ignore transitions from and to end gaps
- if (X[k][i]<ANY) //current state is M
- {
- if (I[k][i]) //next state is I
- q.tr[i][M2I]+=wi[k];
- else if (X[k][i+1]<=ANY) //next state is M
- q.tr[i][M2M]+=wi[k];
- else if (X[k][i+1]==GAP) //next state is D
- q.tr[i][M2D]+=wi[k];
- }
- } // end for(k)
- // Normalize and take log
- sum = q.tr[i][M2M]+q.tr[i][M2I]+q.tr[i][M2D]+FLT_MIN;
- q.tr[i][M2M]=log2(q.tr[i][M2M]/sum);
- q.tr[i][M2I]=log2(q.tr[i][M2I]/sum);
- q.tr[i][M2D]=log2(q.tr[i][M2D]/sum);
-
- // for (k=0; k<N_in; k++) if (in[k]) w[k][i]=wi[k];
- }
- // DD TODO:fill in all the missing Neff values
-
-
- // end loop through alignment columns i
- //////////////////////////////////////////////////////////////////////////////////////////////
-
- delete[](wi); wi=NULL;
- // delete n[][]
- for (j=1; j<=L; j++){
- delete[](n[j]); (n[j]) = NULL;
- }
- delete[](n); (n) = NULL;
-
- q.tr[0][M2M]=0;
- q.tr[0][M2I]=-100000;
- q.tr[0][M2D]=-100000;
- q.tr[L][M2M]=0;
- q.tr[L][M2I]=-100000;
- q.tr[L][M2D]=-100000;
- q.Neff_M[0]=99.999; // Neff_av[0] is used for calculation of transition pseudocounts for the start state
-
- // Set emission probabilities of zero'th (begin) state and L+1st (end) state to background probabilities
- for (a=0; a<20; a++) q.f[0][a]=q.f[L+1][a]=pb[a];
-
- // Assign Neff_M[i] and calculate average over alignment, Neff_M[0]
- if (par.wg==1)
- {
- for (i=1; i<=L; i++)
- {
- float sum=0.0f;
- for (a=0; a<20; a++)
- if (q.f[i][a]>1E-10) sum -= q.f[i][a]*fast_log2(q.f[i][a]);
- q.Neff_HMM+=pow(2.0,sum);
- }
- q.Neff_HMM/=L;
- float Nlim=fmax(10.0,q.Neff_HMM+1.0); // limiting Neff
- float scale=log2((Nlim-q.Neff_HMM)/(Nlim-1.0)); // for calculating Neff for those seqs with inserts at specific pos
- for (i=1; i<=L; i++)
- {
- float w_M=-1.0/N_filtered;
- for (k=0; k<N_in; k++)
- if (in[k] && X[k][i]<=ANY) w_M+=wg[k];
- if (w_M<0) q.Neff_M[i]=1.0;
- else q.Neff_M[i] = Nlim - (Nlim-1.0)*fpow2(scale*w_M);
- // fprintf(stderr,"M i=%3i ncol=--- Neff_M=%5.2f Nlim=%5.2f w_M=%5.3f Neff_M=%5.2f\n",i,q.Neff_HMM,Nlim,w_M,q.Neff_M[i]);
- }
- }
- else
- {
- for (i=1; i<=L; i++)
- {
- q.Neff_HMM+=Neff[i];
- q.Neff_M[i]=Neff[i];
- if (q.Neff_M[i] == 0) { q.Neff_M[i] = 1; } /* MR1 */
- }
- q.Neff_HMM/=L;
- }
-
- delete[] Neff; Neff = NULL;
-
- return;
-
-} /* this is the end of Alignment::Amino_acid_frequencies_and_transitions_from_M_state() */
-
-
-/////////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Calculate transitions q.tr[i][a] (a=DM,DD) with pos-specific subalignments
- */
-void
-Alignment::Transitions_from_I_state(HMM& q, char* in)
-{
- // Calculate position-dependent weights wi[k] for each i.
- // For calculation of weights in column i use sub-alignment
- // over sequences which have a INSERT in column i
- // and over columns where none of these sequences has an end gap.
- // This is done by calculating the arrays n[j][a] and rj[j] at each step i-1->i while letting i run from 1 to L.
- // n[j][a] = number of occurences of amino acid a at column j of the subalignment,
- // => only columns with n[j][ENDGAP]=0 are contained in the subalignment!
- // If no sequences enter or leave the subalignment at the step i-1 -> i (i.e. change=0)
- // then the old values wi[k], Neff[i-1], and ncol are used for the new position i.
- // Index a can be an amino acid (0-19), ANY=20, GAP=21, or ENDGAP=22
-
- int k; // index of sequence
- int i,j; // position in alignment
- int a; // amino acid (0..19)
- int naa; // number of different amino acids
- int** n; // n[j][a] = number of seq's with some residue at column i AND a at position j
- //float wi[MAXSEQ]; // weight of sequence k in column i, calculated from subalignment i
- float *wi = NULL; // weight of sequence k in column i, calculated from subalignment i
- //float Neff[MAXRES]; // diversity of subalignment i
- float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
- int nseqi; // number of sequences in subalignment i
- int ncol; // number of columns j that contribute to Neff[i]
- float fj[NAA+3]; // to calculate entropy
- float sum;
- float Nlim=0.0; // only for global weights
- float scale=0.0; // only for global weights
-
- wi = new(float[N_in+2]);
-
- // Global weights?
- if (par.wg==1)
- {
- for (k=0; k<N_in; k++) wi[k]=wg[k];
- Nlim=fmax(10.0,q.Neff_HMM+1.0); // limiting Neff
- scale=log2((Nlim-q.Neff_HMM)/(Nlim-1.0)); // for calculating Neff for those seqs with inserts at specific pos
- }
-
- // Initialization
- n = new(int*[L+2]);
- for (j=1; j<=L; j++) n[j]=new(int[NAA+3]);
-
- //////////////////////////////////////////////////////////////////////////////////////////////
- // Main loop through alignment columns
- for (i=1; i<=L; i++) // Calculate wi[k] at position i as well as Neff[i]
- {
- if (par.wg==0) // local weights?
- {
-
- // Calculate n[j][a] and ri[j]
- nseqi=0;
- for (k=0; k<N_in; k++)
- {
- if (in[k] && I[k][i]>0)
- {
- if (nseqi==0) // Initialize only if inserts present! Otherwise O(L*L) even for single sequences!
- {
- // Initialization of n[j][a]
- for (j=1; j<=L; j++)
- for (a=0; a<NAA+3; a++) n[j][a]=0;
- }
- nseqi++;
- for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]++;
- }
- } //end for (k)
- nseqs[i]=nseqi;
-
- // If there is no sequence in subalignment j ...
- if (nseqi==0)
- {
- ncol=0;
- Neff[i]=0.0; // effective number of sequence = 0!
- q.tr[i][I2M]=-100000;
- q.tr[i][I2I]=-100000;
- continue;
- }
-
- // update weights wi[k] and Neff[i]
- // if (1)
- {
- // Initialize weights and numbers of residues for subalignment i
- ncol=0;
- for (k=0; k<N_in; k++) wi[k]=0.0;
-
- // sum wi[k] over all columns j and sequences k of subalignment
- for (j=1; j<=L; j++)
- {
- if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
- naa=0; for (a=0; a<20; a++) if(n[j][a]) naa++;
- if (naa==0) continue;
- ncol++;
- for (k=0; k<N_in; k++)
- {
- if (in[k] && I[k][i]>0 && X[k][j]<ANY)
- {
- if (!n[j][ (int)X[k][j]]) {fprintf(stderr,"Error: Ii=%i: n[%i][X[%i]]=0! (X[%i]=%i)\n",i,j,k,k,X[k][j]);}
- wi[k]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
- }
- }
- }
-
- // Check whether number of columns in subalignment is sufficient
- if (ncol>=NCOLMIN)
- // Take global weights
- for (k=0; k<N_in; k++)
- if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0;
-
- // Calculate Neff[i]
- Neff[i]=0.0;
- for (j=1; j<=L; j++)
- {
- if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
- for (a=0; a<20; a++) fj[a]=0;
- for (k=0; k<N_in; k++)
- if (in[k] && I[k][i]>0 && X[k][j]<ANY)
- fj[ (int)X[k][j] ]+=wi[k];
- NormalizeTo1(fj,NAA);
- for (a=0; a<20; a++)
- if (fj[a]>1E-10) Neff[i]-=fj[a]*fast_log2(fj[a]);
- }
- if (ncol>0) Neff[i]=pow(2.0,Neff[i]/ncol); else Neff[i]=1.0;
-
- }
- // Calculate transition probabilities from I state
- q.tr[i][I2M]=q.tr[i][I2I]=0.0;
- for (k=0; k<N_in; k++) //for all sequences
- {
- if (in[k] && I[k][i]>0) //current state is I
- {
- q.tr[i][I2M]+=wi[k];
- q.tr[i][I2I]+=wi[k]*(I[k][i]-1);
- }
- } // end for(k)
- }
-
- else // fast global weights?
- {
- float w_I=-1.0/N_filtered;
- ncol=0;
- q.tr[i][I2M]=q.tr[i][I2I]=0.0;
- // Calculate amino acid frequencies fj[a] from weights wg[k]
- for (k=0; k<N_in; k++)
- if (in[k] && I[k][i]>0)
- {
- ncol++;
- w_I+=wg[k];
- q.tr[i][I2M]+=wi[k];
- q.tr[i][I2I]+=wi[k]*(I[k][i]-1);
- }
- if (ncol>0)
- {
- if (w_I<0) Neff[i]=1.0;
- else Neff[i] = Nlim - (Nlim-1.0)*fpow2(scale*w_I);
- // fprintf(stderr,"I i=%3i ncol=%3i Neff_M=%5.2f Nlim=%5.2f w_I=%5.3f Neff_I=%5.2f\n",i,ncol,q.Neff_HMM,Nlim,w_I,Neff[i]);
- }
- else
- {
- Neff[i]=0.0;
- q.tr[i][I2M]=-100000;
- q.tr[i][I2I]=-100000;
- continue;
- }
- }
-
- // Normalize and take log
- sum = q.tr[i][I2M]+q.tr[i][I2I];
- q.tr[i][I2M]=log2(q.tr[i][I2M]/sum);
- q.tr[i][I2I]=log2(q.tr[i][I2I]/sum);
-
- }
- // end loop through alignment columns i
- //////////////////////////////////////////////////////////////////////////////////////////////
-
- delete[](wi); wi = NULL;
- // delete n[][]
- for (j=1; j<=L; j++){
- delete[](n[j]); (n[j]) = NULL;
- }
- delete[](n); (n) = NULL;
-
- q.tr[0][I2M]=0;
- q.tr[0][I2I]=-100000;
- q.tr[L][I2M]=0;
- q.tr[L][I2I]=-100000;
- q.Neff_I[0]=99.999;
-
- // Assign Neff_I[i]
- for (i=1; i<=L; i++) // Calculate wi[k] at position i as well as Neff[i] and Neff[i]
- q.Neff_I[i]=Neff[i];
-
- delete[] Neff; Neff = NULL;
- return;
-
-} /* this is the end of Alignment::Transitions_from_I_state() */
-
-
-/////////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Calculate transitions q.tr[i][a] (a=DM,DD) with pos-specific subalignments
- */
-void
-Alignment::Transitions_from_D_state(HMM& q, char* in)
-{
- // Calculate position-dependent weights wi[k] for each i.
- // For calculation of weights in column i use sub-alignment
- // over sequences which have a DELETE in column i
- // and over columns where none of these sequences has an end gap.
- // This is done by updating the arrays n[j][a] and rj[j] at each step i-1->i while letting i run from 1 to L.
- // n[j][a] = number of occurences of index a at column j of the subalignment,
- // => only columns with n[j][ENDGAP]=0 are contained in the subalignment!
- // If no sequences enter or leave the subalignment at the step i-1 -> i (i.e. change=0)
- // then the old values wi[k], Neff[i-1], and ncol are used for the new position i.
- // Index a can be an amino acid (0-19), ANY=20, GAP=21, or ENDGAP=22
-
- int k; // index of sequence
- int i,j; // position in alignment
- int a; // amino acid (0..19)
- int naa; // number of different amino acids
- int** n; // n[j][a] = number of seq's with some residue at column i AND a at position j
- //float wi[MAXSEQ]; // weight of sequence k in column i, calculated from subalignment i
- float *wi=NULL; // weight of sequence k in column i, calculated from subalignment i
- //float Neff[MAXRES]; // diversity of subalignment i
- float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
- int nseqi=0; // number of sequences in subalignment i (for DEBUGGING)
- int ncol=0; // number of columns j that contribute to Neff[i]
- char change; // has the set of sequences in subalignment changed? 0:no 1:yes
- float fj[NAA+3]; // to calculate entropy
- float sum;
- float Nlim=0.0; // only for global weights
- float scale=0.0; // only for global weights
-
- wi = new(float[N_in+2]); /* FIXME: FS */
- // Global weights?
- if (par.wg==1)
- {
- for (k=0; k<N_in; k++) wi[k]=wg[k];
- Nlim=fmax(10.0,q.Neff_HMM+1.0); // limiting Neff
- scale=log2((Nlim-q.Neff_HMM)/(Nlim-1.0)); // for calculating Neff for those seqs with dels at specific pos
- }
-
- // Initialization
- n = new(int*[L+2]);
- for (j=1; j<=L; j++) n[j]=new(int[NAA+3]);
- for (j=1; j<=L; j++)
- for (a=0; a<NAA+3; a++) n[j][a]=0;
-
-
-
- //////////////////////////////////////////////////////////////////////////////////////////////
- // Main loop through alignment columns
- for (i=1; i<=L; i++) // Calculate wi[k] at position i as well as Neff[i]
- {
- if (par.wg==0) // if local weights
- {
- change=0;
- // Check all sequences k and update n[j][a] and ri[j] if necessary
- for (k=0; k<N_in; k++)
- {
- if (!in[k]) continue;
- if (X[k][i-1]!=GAP && X[k][i]==GAP)
- { // ... if sequence k was NOT included in i-1 and has to be included for column i
- change=1;
- nseqi++;
- for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]++;
- }
- else if (X[k][i-1]==GAP && X[k][i]!=GAP)
- { // ... if sequence k WAS included in i-1 and has to be thrown out for column i
- change=1;
- nseqi--;
- for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]--;
- }
- } //end for (k)
- nseqs[i]=nseqi;
-
- // If there is no sequence in subalignment j ...
- if (nseqi==0)
- {
- ncol=0;
- Neff[i]=0.0; // effective number of sequences = 0!
- q.tr[i][D2M]=-100000;
- q.tr[i][D2D]=-100000;
- continue;
- }
-
- // If subalignment changed: update weights wi[k] and Neff[i]
- if (change)
- {
- // Initialize weights and numbers of residues for subalignment i
- ncol=0;
- for (k=0; k<N_in; k++) wi[k]=0.0;
-
- // sum wg[k][i] over all columns j and sequences k of subalignment
- for (j=1; j<=L; j++)
- {
- if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
- naa=0; for (a=0; a<20; a++) if(n[j][a]) naa++;
- if (naa==0) continue;
- ncol++;
- for (k=0; k<N_in; k++)
- {
- if (in[k] && X[k][i]==GAP && X[k][j]<ANY)
- {
- if (!n[j][ (int)X[k][j]]) {fprintf(stderr,"Error: Di=%i: n[%i][X[%i]]=0! (X[%i]=%i)\n",i,j,k,k,X[k][j]);}
- wi[k]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
- }
- }
- }
-
- // Check whether number of columns in subalignment is sufficient
- if (ncol<NCOLMIN)
- // Take global weights
- for (k=0; k<N_in; k++)
- if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0;
-
- // Calculate Neff[i]
- Neff[i]=0.0;
- for (j=1; j<=L; j++)
- {
- if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
- for (a=0; a<20; a++) fj[a]=0;
- for (k=0; k<N_in; k++)
- if (in[k] && X[k][i]==GAP && X[k][j]<ANY)
- fj[ (int)X[k][j] ]+=wi[k];
- NormalizeTo1(fj,NAA);
- for (a=0; a<20; a++)
- if (fj[a]>1E-10) Neff[i]-=fj[a]*fast_log2(fj[a]);
- }
- if (ncol>0) Neff[i]=pow(2.0,Neff[i]/ncol); else Neff[i]=1.0;
-
- }
-
- else //no update was necessary; copy values for i-1
- {
- Neff[i]=Neff[i-1];
- }
-
- // Calculate transition probabilities from D state
- q.tr[i][D2M]=q.tr[i][D2D]=0.0;
- for (k=0; k<N_in; k++) //for all sequences
- {
- if (in[k] && X[k][i]==GAP) //current state is D
- {
- if (X[k][i+1]==GAP) //next state is D
- q.tr[i][D2D]+=wi[k];
- else if (X[k][i+1]<=ANY) //next state is M
- q.tr[i][D2M]+=wi[k];
- }
- } // end for(k)
- }
-
- else // fast global weights?
- {
- float w_D=-1.0/N_filtered;
- ncol=0;
- q.tr[i][D2M]=q.tr[i][D2D]=0.0;
- // Calculate amino acid frequencies fj[a] from weights wg[k]
- for (k=0; k<N_in; k++) //for all sequences
- if (in[k] && X[k][i]==GAP) //current state is D
- {
- ncol++;
- w_D+=wg[k];
- if (X[k][i+1]==GAP) //next state is D
- q.tr[i][D2D]+=wi[k];
- else if (X[k][i+1]<=ANY) //next state is M
- q.tr[i][D2M]+=wi[k];
- }
- if (ncol>0)
- {
- if (w_D<0) Neff[i]=1.0;
- else Neff[i] = Nlim - (Nlim-1.0)*fpow2(scale*w_D);
- // fprintf(stderr,"D i=%3i ncol=%3i Neff_M=%5.2f Nlim=%5.2f w_D=%5.3f Neff_D=%5.2f\n",i,ncol,q.Neff_HMM,Nlim,w_D,Neff[i]);
- }
- else
- {
- Neff[i]=0.0; // effective number of sequences = 0!
- q.tr[i][D2M]=-100000;
- q.tr[i][D2D]=-100000;
- continue;
- }
- }
-
- // Normalize and take log
- sum = q.tr[i][D2M]+q.tr[i][D2D];
- q.tr[i][D2M]=log2(q.tr[i][D2M]/sum);
- q.tr[i][D2D]=log2(q.tr[i][D2D]/sum);
-
- }
- // end loop through alignment columns i
- //////////////////////////////////////////////////////////////////////////////////////////////
-
- q.tr[0][D2M]=0;
- q.tr[0][D2D]=-100000;
- q.Neff_D[0]=99.999;
-
- // Assign Neff_D[i]
- for (i=1; i<=L; i++)
- q.Neff_D[i]=Neff[i];
-
- delete[](wi); wi = NULL;/* FIXME: FS */
- // delete n[][]
- for (j=1; j<=L; j++){
- delete[](n[j]); (n[j]) = NULL;
- }
- delete[](n); (n) = NULL;
-
- delete[] Neff; Neff = NULL;
- return;
-
-} /* this is the end of Alignment::Transitions_from_D_state() */
-
-
-
-/////////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Write alignment without insert states (lower case) to alignment file?
- */
-void
-Alignment::WriteWithoutInsertsToFile(char* alnfile)
-{
- if (v>=2) cout<<"Writing alignment to "<<alnfile<<"\n";
- FILE* alnf;
- if (!par.append) alnf = fopen(alnfile,"w"); else alnf = fopen(alnfile,"a");
- if (!alnf) OpenFileError(alnfile);
- // If alignment name is different from that of query: write name into commentary line
- if (strncmp(longname,sname[kfirst],DESCLEN-1)) fprintf(alnf,"#%s\n",longname);
- if (v>=2) cout<<"Writing alignment to "<<alnfile<<"\n";
- for (int k=0; k<N_in; k++)
- if (keep[k] || display[k]==KEEP_ALWAYS) // print if either in profile (keep[k]>0) or display is obligatory (display[k]==2)
- {
- fprintf(alnf,">%s\n",sname[k]);
- for (int i=1; i<=L; i++) fprintf(alnf,"%c",i2aa(X[k][i]));
- fprintf(alnf,"\n");
- }
- fclose(alnf);
-}
-
-/////////////////////////////////////////////////////////////////////////////////////
-// Write stored,filtered sequences WITH insert states (lower case) to alignment file?
-/////////////////////////////////////////////////////////////////////////////////////
-void Alignment::WriteToFile(char* alnfile, const char format[])
-{
- FILE* alnf;
- if (!par.append) alnf = fopen(alnfile,"w"); else alnf = fopen(alnfile,"a");
- if (!alnf) OpenFileError(alnfile);
- // If alignment name is different from that of query: write name into commentary line
- if (strncmp(longname,sname[kfirst],DESCLEN-1)) fprintf(alnf,"#%s\n",longname);
- if (!format || !strcmp(format,"a3m"))
- {
- if (v>=2) cout<<"Writing A3M alignment to "<<alnfile<<"\n";
- for (int k=0; k<N_in; k++)
- if (keep[k] || display[k]==KEEP_ALWAYS) // print if either in profile (keep[k]>0) or display obligatory (display[k]==2)
- fprintf(alnf,">%s\n%s\n",sname[k],seq[k]+1);
- }
- else // PSI-BLAST format
- {
- if (v>=2) cout<<"Writing PSI-BLAST-formatted alignment to "<<alnfile<<"\n";
- for (int k=kfirst; k<N_in; k++) // skip sequences before kfirst!!
- if (keep[k] || display[k]==KEEP_ALWAYS) // print if either in profile (keep[k]>0) or display obligatory (display[k]==2)
- {
- strcut(sname[k]);
- fprintf(alnf,"%-20.20s ",sname[k]);
- // for (int i=1; i<=L; i++) fprintf(alnf,"%c",i2aa(X[k][i]));
- // fprintf(alnf,"\n");
- char* ptr=seq[k];
- for (; *ptr!='\0'; ptr++)
- if (*ptr==45 || (*ptr>=65 && *ptr<=90)) fprintf(alnf,"%c",*ptr);
- fprintf(alnf,"\n");
- }
- }
-
- fclose(alnf);
-}
-
-
-
-/*
- * FIXME: this function contains a reference to MAXSEQ & MAXCOL
- * however, this may not be accessed (FS)
- */
-/////////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Read a3m slave alignment of hit from file and merge into (query) master alignment
- */
-void
-Alignment::MergeMasterSlave(Hit& hit, char ta3mfile[])
-{
- Alignment Tali;
- char* cur_seq = new(char[MAXCOL]); // Sequence currently read in
- int maxcol=MAXCOL;
- int l,ll; // position in unaligned template (T) sequence Tali.seq[l]
- int i; // counts match states in query (Q) HMM
- int j; // counts match states in T sequence Tali.seq[l]
- int h; // position in aligned T sequence cur_seq[h]
- int k; // sequence index
- char c; //
- printf("****************%s:%s:%d: did get into MergeMasterSlave\n", __FUNCTION__, __FILE__, __LINE__);
- if (v>=3) printf("Merging %s to query alignment\n",ta3mfile);
-
- // If par.append==1 do not print query alignment
- if (par.append) for (k=0; k<N_in; k++) keep[k]=display[k]=KEEP_NOT;
-
- // Read template alignment into Tali
- FILE* ta3mf=fopen(ta3mfile,"r");
- if (!ta3mf) OpenFileError(ta3mfile);
- Tali.Read(ta3mf,ta3mfile);
- fclose(ta3mf);
-
- // Filter Tali alignment
- Tali.Compress(ta3mfile);
- N_filtered = Tali.Filter(par.max_seqid,par.coverage,par.qid,par.qsc,par.Ndiff);
-
- // Record imatch[j]
- int* imatch=new(int[hit.j2+1]);
- int step = hit.nsteps;
- for (j=hit.j1; j<=hit.j2; j++)
- {
- // Advance to position of next T match state j
- while (hit.j[step]<j) step--;
- imatch[j] = hit.i[step];
-// printf("step=%-3i i=%-3i j=%-3i\n",step,imatch[j],j);
- }
-
- // Determine number of match states of Qali
- for (L=0,l=1; seq[kfirst][l]>'\0'; l++)
- if ((seq[kfirst][l]>='A' && seq[kfirst][l]<='Z') || seq[kfirst][l]=='-') L++;
-
- // For each sequence in T alignment: align to Qali
- for (k=0; k<Tali.N_in; k++)
- {
- if (!Tali.keep[k]) continue;
- if (N_in>=MAXSEQ)
- {
- fprintf(stderr,"WARNING in %s: maximum number of %i sequences exceeded while reading %s. Skipping all following sequences\n",program_name,MAXSEQ,ta3mfile);
- break;
- }
- cur_seq[0]=' '; // 0'th position not used
-
- // Add the hit.i1-1 left end gaps to aligned sequence
- for (h=1; h<hit.i1; h++) cur_seq[h]='-';
-
- // Advance to match state hit.j1 of Tali.seq[k]
- for (j=0, l=1; (c=Tali.seq[k][l])>'\0'; l++)
- if ((c>='A' && c<='Z') || c=='-') // match state at position l?
- if ((++j)==hit.j1) break; // yes: increment j. Reached hit,j1? yes: break
-
- if (j<hit.j1)
- {printf("Error: did not find %i match states in sequence %i of %s. Sequence:\n%s\n",hit.j1,k,Tali.name,Tali.seq[k]); exit(1);}
-
- // Write first match state to cur_seq
- int iprev=hit.i1; // index of previous query match state
- int lprev=l; // previous T match state in Tali.seq[k][l]
- cur_seq[h++] = Tali.seq[k][l]; // first column of alignment is Match-Match state
-
- // For each further match state j in alignment
- step = hit.nsteps;
- for (j=hit.j1+1; j<=hit.j2; j++)
- {
- // Advance to position of next T match state j
- i=imatch[j];
-
- // Advance to position of next T match state j
- while ((c=Tali.seq[k][++l])>'\0' && ((c>='a' && c<='z') || c=='.')) ;
-
- int di=i-iprev; // number of Match states in Q between T match state j-1 and j
- int dl=l-lprev; // 1 + number of inserted residues in T sequence between T match state j-1 and j
- if (di==1)
- {
- // One Q match state for one T match state (treated as special case for speed reasons)
- // i: i-1 i di=1
- // Q: XXXXXX.....XXXXXX
- // T: YYYYYYyyyyyYYYYYY
- // j: j-1 j
- // l: lprev l dl=6
-
- // Inserts in lower case
- for (ll=lprev+1; ll<l; ll++)
- if (Tali.seq[k][ll]!='-' && Tali.seq[k][ll]!='.') cur_seq[h++] = lwrchr(Tali.seq[k][ll]);
-
- // Template Match state -> upper case
- cur_seq[h++] = Tali.seq[k][ll];
- }
- else if (di==0)
- {
- // Gap in query: no Q match state for on T match state (special case for speed reasons)
- // i: i-1 i-1 di=0
- // Q: XXXXXX.....~~~XXX
- // T: YYYYYYyyyyyYYYYYY
- // j: j-1 j
- // l: lprev l dl=6
-
- // All T residues (including T match state) in lower case
- for (ll=lprev+1; ll<=l; ll++)
- if (Tali.seq[k][ll]!='-' && Tali.seq[k][ll]!='.') cur_seq[h++] = lwrchr(Tali.seq[k][ll]);
- }
- else if (di>=dl)
- {
- // More Match states in Q than Inserts in the T sequence
- // => half T inserts y left, half right-aligned in uc, gaps to fill up
- // Number of T insert residues to be left-aligned: (int)(dl/2)
- // i: iprev i di=7
- // Q: XXXXXXXXXXXXXXXXXX
- // T: YYYYYYYyyy-yyYYYYY
- // j: j-1 j
- // l: lprev l dl=6
-
- // Add left-bounded template residues
- for (ll=lprev+1; ll<=lprev+(int)(dl/2); ll++)
- cur_seq[h++]=uprchr(Tali.seq[k][ll]);
-
- // Add central gaps
- for (int gap=1; gap<=di-dl; gap++) cur_seq[h++]='-';
-
- // Add right-bounded residues
- for (; ll<=l; ll++)
- cur_seq[h++]=uprchr(Tali.seq[k][ll]);
- }
- else if (di<dl)
- {
- // Fewer Match states in Q than inserts in T sequence
- // => half of available space di for left- half for right-aligned T inserts, rest in lc
- // number of T inserts to be left-aligned in uc: (int)(di/2),
- // i: iprev i di=5
- // Q: XXXXXXXXX.XXXXXXX
- // T: YYYYYYYyyyyyYYYYY
- // j: j-1 j
- // l: lprev l dl=6
-
- // Add left-bounded template residues
- for (ll=lprev+1; ll<=lprev+(int)(di/2); ll++)
- cur_seq[h++]=uprchr(Tali.seq[k][ll]);
-
- // Add central inserts
- for (int ins=1; ins<=dl-di; ins++,ll++)
- if (Tali.seq[k][ll]!='-' && Tali.seq[k][ll]!='.') cur_seq[h++] = lwrchr(Tali.seq[k][ll]);
-
- // Add right-bounded residues
- for (; ll<=l; ll++)
- cur_seq[h++]=uprchr(Tali.seq[k][ll]);
- }
-// printf("i=%-3i j=%-3i l=%-3i cur_seq=%s\n",i,j,l,cur_seq);
-
- iprev=i; lprev=l;
- if (h>=maxcol-1000) // too few columns? Reserve double space
- {
- char* new_seq=new(char[2*maxcol]);
- strncpy(new_seq,cur_seq,maxcol); //////// check: maxcol-1 ????
- delete[](cur_seq); (cur_seq) = NULL;
- cur_seq=new_seq;
- maxcol*=2;
- }
- }
-
- // Add the remaining gaps '-' to the end of the template sequence
- for (i=hit.i2+1; i<=L; i++) cur_seq[h++]='-';
- cur_seq[h++]='\0';
-
- keep[N_in] = display[N_in] = KEEP_CONDITIONALLY;
- seq[N_in]=new(char[h]);
- if (!seq[N_in]) MemoryError("array for input sequences");
- strcpy(seq[N_in],cur_seq);
- X[N_in]=new(char[h]);
- if (!X[N_in]) MemoryError("array for input sequences");
- I[N_in]=new(short unsigned int[h]);
- if (!I[N_in]) MemoryError("array for input sequences");
- sname[N_in]=new(char[strlen(Tali.sname[k])+1]);
- if (!sname[N_in]) MemoryError("array for input sequences");
- strcpy(sname[N_in],Tali.sname[k]);
- N_in++;
-
-// printf("k=%-3i %s\n",k,Tali.seq[k]);
-// printf("Query %s\n",seq[kfirst]);
-// printf("k=%-3i %s\n\n",k,cur_seq);
-
- } // end for (k)
-
-// printf("N_in=%-5i HMM=%s with %i sequences\n",N_in,ta3mfile,N_filtered);
-
- delete[] cur_seq; cur_seq = NULL;
- delete[] imatch; imatch = NULL;
- delete[] ksort; ksort=NULL; // if ksort already existed it will be to short for merged alignment
- delete[] first; first=NULL; // if first already existed it will be to short for merged alignment
- delete[] last; last=NULL; // if last already existed it will be to short for merged alignment
-
-} /* this is the end of Alignment::MergeMasterSlave() */
-
-
-/////////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Add a sequence to Qali
- */
-void
-Alignment::AddSequence(char Xk[], int Ik[])
-{
- int i; // position in query and target
- if (L<=0) InternalError("L is not set in AddSequence()");
- X[N_in]=new(char[L+2]);
- for (i=0; i<=L+1; i++) X[N_in][i]=Xk[i];
- if (Ik==NULL)
- for (i=0; i<=L+1; i++) I[N_in][i]=0;
- else
- for (i=0; i<=L+1; i++) I[N_in][i]=Ik[i];
- N_in++;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief Determine matrix of position-specific weights w[k][i] for multiple alignment
- * Pos-specific weights are calculated like in "Amino_acid_frequencies_and_transitions_from_M_state()"
- */
-void
-Alignment::GetPositionSpecificWeights(float* w[])
-{
- // Calculate position-dependent weights wi[k] for each i.
- // For calculation of weights in column i use sub-alignment
- // over sequences which have a *residue* in column i (no gap, no end gap)
- // and over columns where none of these sequences has an end gap.
- // This is done by updating the arrays n[j][a] at each step i-1->i while letting i run from 1 to L.
- // n[j][a] = number of occurences of amino acid a at column j of the subalignment,
- // => only columns with n[j][ENDGAP]=0 are contained in the subalignment!
- // If no sequences enter or leave the subalignment at the step i-1 -> i (i.e. change=0)
- // then the old values w[k][i] and ncol are used for the new position i.
- // Index a can be an amino acid (0-19), ANY=20, GAP=21, or ENDGAP=22
-
- char* in=keep; // to keep the code similar to Amino_acid_frequencies_and_transitions_from_M_state()
- int k; // index of sequence
- int i,j; // position in alignment
- int a; // amino acid (0..19)
- int naa; // number of different amino acids
- int** n; // n[j][a] = number of seq's with some residue at column i AND a at position j
- int nseqi=0; // number of sequences in subalignment i
- int ncol=0; // number of columns j that contribute to Neff[i]
- char change; // has the set of sequences in subalignment changed? 0:no 1:yes
-
-
- // Global weights?
- if (par.wg==1)
- {
- for (k=0; k<N_in; k++)
- for (i=1; i<=L; i++) w[k][i]=wg[k];
- }
- else
- {
-
- // Initialization
- n = new(int*[L+2]);
- for (j=1; j<=L; j++) n[j]=new(int[NAA+3]);
- for (j=1; j<=L; j++)
- for (a=0; a<NAA+3; a++) n[j][a]=0;
-
- //////////////////////////////////////////////////////////////////////////////////////////////
- // Main loop through alignment columns
- for (i=1; i<=L; i++) // Calculate w[k][i]
- {
- change=0;
- // Check all sequences k and update n[j][a] and ri[j] if necessary
- for (k=0; k<N_in; k++)
- {
- if (!in[k]) continue;
- if (X[k][i-1]>=ANY && X[k][i]<ANY)
- { // ... if sequence k was NOT included in i-1 and has to be included for column i
- change=1;
- nseqi++;
- for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]++;
- }
- else if (X[k][i-1]<ANY && X[k][i]>=ANY)
- { // ... if sequence k WAS included in i-1 and has to be thrown out for column i
- change=1;
- nseqi--;
- for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]--;
- }
- } //end for (k)
- nseqs[i]=nseqi;
-
- // If subalignment changed: update weights w[k][i] and Neff[i]
- if (change)
- {
- // Initialize weights and numbers of residues for subalignment i
- ncol=0;
- for (k=0; k<N_in; k++) w[k][i]=0.0;
-
- // sum wi[k] over all columns j and sequences k of subalignment
- for (j=1; j<=L; j++)
- {
- // do at least a fraction MAXENDGAPFRAC of sequences in subalignment contain an end gap in j?
- if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
- naa=0; for (a=0; a<20; a++) if(n[j][a]) naa++;
- if (naa==0) continue;
- ncol++;
- for (k=0; k<N_in; k++)
- {
- if (in[k] && X[k][i]<ANY && X[k][j]<ANY)
- {
-// if (!n[j][ (int)X[k][j]]) {fprintf(stderr,"Error: Mi=%i: n[%i][X[%i]]=0! (X[%i]=%i)\n",i,j,k,k,X[k][j]);}
- w[k][i]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
- }
- }
- }
-
- // Check whether number of columns in subalignment is sufficient
- if (ncol<NCOLMIN)
- // Take global weights
- for (k=0; k<N_in; k++)
- if(in[k]) {if(X[k][i]<ANY) w[k][i]=wg[k]; else w[k][i]=0.0;}
- }
- }
- // end loop through alignment columns i
- ///////////////////////////////////////////////////////////////////////
-
- // delete n[][]
- for (j=1; j<=L; j++){
- delete[](n[j]); (n[j]) = NULL;
- }
- delete[](n); (n) = NULL;
-
- }
- return;
-}
-
-#ifdef CLUSTALO
-/* @* Transfer
- *
- * take sequence data from Clustal and transfer it into
- * hhalign accessible information (structure/class)
- *
- * Note that hhalign does not see all sequences/profiles
- * but only sequences that are elements of the 2 profiles
- * to be aligned.
- *
- * References to the required sequences are passed into hhalign
- * through auxilliary pointers that are shallow copies of the
- * sequence/profile data available to Clustal.
- *
- * Re-allocating memory for these auxilliary pointers
- * would be desaterous, as it might detach the memory
- * seen by Clustal.
- */
-void
-Alignment::Transfer(char **ppcProf, int iCnt){
-
- /* @<variables local to Transfer@> */
- int iLen; /* length of profile */
- int k; /* generic iterator */
-
- /* @<initialisation@> */
- N_in = iCnt;
- N_filtered = N_ss = 0;
- kss_dssp = ksa_dssp = kss_pred = kss_conf = -1;
- kfirst = 0;
- strcpy(longname, "unknown_long_seq_name");
- strcpy(name, "unknown_seq_name");
- strcpy(file, "unknown_file_name");
- n_display = iCnt;
-
- /* @<determine length of profile@>
- all sequences in profile should have same length,
- so only do it for 1st */
- for (iLen = 0; '\0' != ppcProf[0][iLen]; iLen++);
-
- /* @<allocate memory for sequences etc@> */
- for (k = 0; k < iCnt; k++){
-#define GOOD_MEASURE 1000 /* Temporary -- can be removed once rest in place */
- I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]);
- X[k] = new(char[iLen+2+GOOD_MEASURE]);
- seq[k] = new(char[iLen+2+GOOD_MEASURE]);
- seq[k][0] = ' ';
- seq[k][1] = '\0';
- if (NULL == ppcProf[k]){
- printf("%s:%d: Arena[%d]=NULL, cnt=%d\n", __FILE__, __LINE__, k, iCnt);
- exit(-1);
- }
- strcat(seq[k], ppcProf[k]);
- keep[k] = KEEP_CONDITIONALLY;
- display[k] = KEEP_CONDITIONALLY;
- sname[k] = new(char[GOOD_MEASURE]);
- strcpy(sname[k], "unknown_sname");
- } /* (0 <= k < iCnt) */
- /* FIXME: Soeding always makes 1st sequence permanent */
- /*keep[0] = KEEP_ALWAYS;
- display[k] = KEEP_ALWAYS;*/
-#if 1
- /* Believe that the first and last positions are
- most important in stability of this algorithm.
- Must make sure that at least 2 sequences with
- residues in these positions are kept.
- Think any sequence will do, but better to keep
- the one with the longest 'contig'
- */
- int iSeq; /* sequence iterator */
- int iHeadLen = 0, iHeadID = -1; /* length & ID of longest head contig */
- int iTailLen = 0, iTailID = -1; /* length & ID of longest head contig */
- int iCont = -1;
- char *pcFind = NULL;
-
-#if 0
- printf("%s:%s:%d: NEW PROFILE (%d seq) ================\n",
- __FUNCTION__, __FILE__, __LINE__, iCnt);
-#endif
- for (iSeq = 0; iSeq < iCnt; iSeq++){
-#if 0
- printf("%s:%s:%d: consider seq %d ------------------\n",
- __FUNCTION__, __FILE__, __LINE__, iSeq);
-#endif
- pcFind = strchr(&seq[iSeq][1], '-');
- if (NULL == pcFind){
- /* no gap at all in this sequences, spans entire profile */
- iHeadID = iTailID = iSeq;
- iHeadLen = iTailLen = iLen;
- break;
- }
- iCont = (int)(pcFind - &seq[iSeq][1]);
- if (iCont > iHeadLen){
- iHeadLen = iCont;
- iHeadID = iSeq;
- }
- pcFind = strrchr(seq[iSeq], '-');
- iCont = iLen - (int)(pcFind - seq[iSeq]);
- if (iCont > iTailLen){
- iTailLen = iCont;
- iTailID = iSeq;
- }
-
-#if 0
- printf("%s:%s:%d: seq %3d: len = %d(%d) %s\n",
- __FUNCTION__, __FILE__, __LINE__, iSeq, iCont, iLen, seq[iSeq]);
-#endif
- } /* 0 <= iSeq < iCnt */
-#if 0
- printf("%s:%s:%d: seq %d is winner with head contig of %d, seq %d tail contig of %d\n"
- , __FUNCTION__, __FILE__, __LINE__, iHeadID, iHeadLen, iTailID, iTailLen);
-#endif
- if ( (-1 == iHeadID) || (-1 == iTailID) ){
- printf("%s:%s:%d: profile has no leading and/or trailing residues (h=%d:t=%d:#=%d)\n",
- __FUNCTION__, __FILE__, __LINE__, iHeadID, iTailID, iCnt);
- }
- else{
- keep[iHeadID] = KEEP_ALWAYS;
- keep[iTailID] = KEEP_ALWAYS;
- }
-#endif
- /* @= */
- return;
-
-} /* this is the end of Transfer() */
-#endif
-
-#ifdef CLUSTALO
-/* @* Alignment::ClobberGlobal (eg: qali)
- *
- * Note: originally hhalign() was stand-alone code,
- * there are a couple of GLOBAL (!) variables,
- * which would have been destroyed on exit.
- * However, now there is no 'exit' from hhalign(),
- * and on re-entry the global variable must be clean again.
- */
-void
-Alignment::ClobberGlobal(void){
-
- /* @<essentials@>
- these are essential to re-set (as some of them are used as flags) */
- for(int k=0; k<N_in; k++)
- {
- delete[] sname[k]; sname[k] = NULL;
- delete[] seq[k]; seq[k] = NULL;
- delete[] X[k]; X[k] = NULL;
- delete[] I[k]; I[k] = NULL;
- }
- delete[] nres; nres = NULL;
- delete[] first; first = NULL;
- delete[] last; last = NULL;
- delete[] ksort; ksort = NULL;
- N_in = N_filtered = n_display = 0;
- L = 0;
- kss_dssp = ksa_dssp = kss_pred = kss_conf = kfirst = -1;
-
- /* @<re-set but keep memory@>
- do not free the memory but re-set content */
- longname[0] = '\0'; //delete[] longname; longname = NULL;
- keep[0] = '\0'; //delete[] keep; keep = NULL;
- display[0] = '\0'; //delete[] display; display = NULL;
- wg[0] = 0; //delete[] wg; wg = NULL;
- nseqs[0] = 0; //delete[] nseqs; nseqs = NULL;
- name[0]='\0';
- fam[0]='\0';
- file[0]='\0';
- //delete[] sname; sname = NULL;
- //delete[] seq; seq = NULL;
- //delete[] X; X = NULL;
- //delete[] I; I = NULL;
- //delete[] l; l = NULL;
-
- /* @= */
- return;
-}
-#endif
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