+++ /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: clustal-omega.c 254 2011-06-21 13:07:50Z andreas $
- */
-
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
-
-#include <assert.h>
-
-#include "clustal-omega.h"
-#include "hhalign/general.h"
-
-/* The following comment block contains the frontpage/mainpage of the doxygen
- * documentation. Please add some more info. FIXME add more
- */
-
-/**
- *
- * @mainpage Clustal-Omega Documentation
- *
- * @section intro_sec Introduction
- *
- * For more information see http://www.clustal.org/
- *
- * @section api_section API
- *
- * @subsection example_prog_subsection An Example Program
- *
- * To use libclustalo you will have to include the clustal-omega.h header and
- * link against libclustalo. For linking against libclustalo you will have to
- * use a C++ compiler, no matter if your program was written in C or C++.
- *
- * First compile (no linking) your source (for an example see section "\ref
- * example_src_subsubsec"):
- *
- * @code
- * $ gcc -c -ansi -Wall clustalo-api-test.c
- * @endcode
- *
- * Then link against libclustalo (we recommend the use of pkg-config as
- * explained in \ref pkgconfig_subsubsec). Assuming Clustal Omega was installed
- * in system-wide default directory (e.g. /usr) just type:
- *
- * @code
- * $ g++ -ansi -Wall -o clustalo-api-test clustalo-api-test.o -lclustalo
- * @endcode
- *
- * Voila! Now you have your own alignment program which can be run with
- *
- * @code
- * $ ./clustalo-api-test <your-sequence-input>
- * @endcode
- *
- * It's best to use the same compiler that you used for compiling libclustal.
- * If libclustal was compiled with OpenMP support, you will have to use OpenMP
- * flags for you program as well.
- *
- *
- * @subsubsection pkgconfig_subsubsec Using pkg-config / Figuring out compiler flags
- *
- * Clustal Omega comes with support for <a
- * href="http://pkg-config.freedesktop.org">pkg-config</a>, which means you
- * can run
- *
- * @code
- * $ pkg-config --cflags --libs clustalo
- * @endcode
- *
- * to figure out cflags and library flags needed to compile and link against
- * libclustalo. This is especially handy if Clustal Omega was installed to a
- * non-standard directory.
- *
- * You might have to change PKG_CONFIG_PATH. For example, if you used the prefix $HOME/local/ for
- * installation then you will first need to set PKG_CONFIG_PATH:
- *
- * @code
- * $ export PKG_CONFIG_PATH=$HOME/local/lib/pkgconfig
- * $ pkg-config --cflags --libs clustalo
- * @endcode
- *
- *
- * To compile your source use:
- *
- * @code
- * $ export PKG_CONFIG_PATH=$HOME/local/lib/pkgconfig
- * $ gcc -c -ansi -Wall clustalo-api-test.c $(pkg-config --cflags clustalo)
- * $ g++ -ansi -Wall -o clustalo-api-test clustalo-api-test.o $(pkg-config --libs clustalo)
- * @endcode
- *
- *
- * @subsubsection example_src_subsubsec Example Source Code
- *
- * @include "clustalo-api-test.c"
- *
- *
- */
-
-
-
-
-/* FIXME: doc */
-/* the following are temporary flags while the code is still under construction;
- had problems internalising hhmake, so as temporary crutch
- write alignment to file and get external hmmer/hhmake via system call
- to read alignment and convert into HMM
- All this will go, once hhmake is properly internalised */
-#define INDIRECT_HMM 0 /* temp flag: (1) write aln to file, use system(hmmer/hhmake), (0) internal hhmake */
-#define USEHMMER 1 /* temp flag: use system(hmmer) to build HMM */
-#define USEHHMAKE (!USEHMMER) /* temp flag: use system(hhmake) to build HMM */
-
-
-/* shuffle order of input sequences */
-#define SHUFFLE_INPUT_SEQ_ORDER 0
-
-/* sort input sequences by length */
-#define SORT_INPUT_SEQS 0
-
-
-int iNumberOfThreads;
-
-/* broken, unused and lonely */
-static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01;
-
-
-/**
- * @brief Print Long version information to pre-allocated char.
- *
- * @note short version
- * information is equivalent to PACKAGE_VERSION
- *
- * @param[out] pcStr
- * char pointer to write to preallocated to hold iSize chars.
- * @param[in] iSize
- * size of pcStr
- */
-void
-PrintLongVersion(char *pcStr, int iSize)
-{
- snprintf(pcStr, iSize, "version %s; code-name '%s'; build date %s",
- PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__);
-}
-/* end of PrintLongVersion() */
-
-
-
-/**
- * @brief free aln opts members
- *
- */
-void
-FreeAlnOpts(opts_t *prAlnOpts) {
- if (NULL != prAlnOpts->pcGuidetreeInfile) {
- CKFREE(prAlnOpts->pcGuidetreeInfile);
- }
- if (NULL != prAlnOpts->pcGuidetreeOutfile) {
- CKFREE(prAlnOpts->pcGuidetreeOutfile);
- }
- if (NULL != prAlnOpts->pcDistmatOutfile) {
- CKFREE(prAlnOpts->pcDistmatOutfile);
- }
- if (NULL != prAlnOpts->pcDistmatInfile) {
- CKFREE(prAlnOpts->pcDistmatInfile);
- }
-}
-/* end of FreeAlnOpts() */
-
-
-
-/**
- * @brief Sets members of given user opts struct to default values
- *
- * @param[out] prOpts
- * User opt struct to initialise
- *
- */
-void
-SetDefaultAlnOpts(opts_t *prOpts) {
- prOpts->bAutoOptions = FALSE;
-
- prOpts->pcDistmatInfile = NULL;
- prOpts->pcDistmatOutfile = NULL;
-
- prOpts->iClusteringType = CLUSTERING_UPGMA;
- prOpts->iPairDistType = PAIRDIST_KTUPLE;
- prOpts->bUseMbed = TRUE; /* FS, r250 -> */
- prOpts->bUseMbedForIteration = TRUE; /* FS, r250 -> */
- prOpts->pcGuidetreeOutfile = NULL;
- prOpts->pcGuidetreeInfile = NULL;
-
- prOpts->ppcHMMInput = NULL;
- prOpts->iHMMInputFiles = 0;
-
- prOpts->iNumIterations = 0;
- prOpts->bIterationsAuto = FALSE;
- prOpts->iMaxGuidetreeIterations = INT_MAX;
- prOpts->iMaxHMMIterations = INT_MAX;
- prOpts->iMacRam = 2048; /* give 2GB to MAC algorithm. FS, r240 -> r241 */
- }
-/* end of SetDefaultAlnOpts() */
-
-
-
-/**
- * @brief Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, ))
- * on Fatal logic error
- *
- * @param[in] prOpts
- * Already parsed user options
- *
- */
-void
-AlnOptsLogicCheck(opts_t *prOpts)
-{
- /* guide-tree & distmat
- *
- */
- if (prOpts->pcDistmatInfile && prOpts->pcGuidetreeInfile) {
- Log(&rLog, LOG_FATAL, "Read distances *and* guide-tree from file doesn't make sense.");
- }
-
- if (prOpts->pcDistmatOutfile && prOpts->pcGuidetreeInfile) {
- Log(&rLog, LOG_FATAL, "Won't be able to save distances to file, because I got a guide-tree as input.");
- }
-
- /* combination of options that don't make sense when not iterating
- */
- if (prOpts->iNumIterations==0 && prOpts->bIterationsAuto != TRUE) {
-
- if (prOpts->pcGuidetreeInfile && prOpts->pcGuidetreeOutfile) {
- Log(&rLog, LOG_FATAL, "Got a guide-tree as input and output which doesn't make sense when not iterating.");
- }
- /*
- if (prOpts->pcGuidetreeInfile && prOpts->bUseMbed > 0) {
- Log(&rLog, LOG_FATAL, "Got a guide-tree as input and was requested to cluster with mBed, which doesn't make sense when not iterating.");
- }
- */
- /*
- AW: bUseMbedForIteration default since at least R252
- if (prOpts->bUseMbedForIteration > 0) {
- Log(&rLog, LOG_FATAL, "No iteration requested, but mbed for iteration was set. Paranoia exit.");
- }
- */
- }
-
- if (prOpts->iMacRam < 512) {
-
- Log(&rLog, LOG_INFO, "Memory for MAC Algorithm quite low, Viterbi Algorithm may be triggered.");
-
- if (prOpts->iMacRam < 1) {
-
- Log(&rLog, LOG_WARN, "Viterbi Algorithm always turned on, increase MAC-RAM to turn on MAC.");
- }
- }
-
- return;
-}
-/* end of AlnOptsLogicCheck() */
-
-
-/**
- * @brief FIXME doc
- */
-void
-PrintAlnOpts(FILE *prFile, opts_t *prOpts)
-{
- int iAux;
-
-
- /* keep in same order as struct */
- fprintf(prFile, "option: auto-options = %d\n", prOpts->bAutoOptions);
- fprintf(prFile, "option: distmat-infile = %s\n",
- NULL != prOpts->pcDistmatInfile? prOpts->pcDistmatInfile: "(null)");
- fprintf(prFile, "option: distmat-outfile = %s\n",
- NULL != prOpts->pcDistmatOutfile? prOpts->pcDistmatOutfile: "(null)");
- fprintf(prFile, "option: clustering-type = %d\n", prOpts->iClusteringType);
- fprintf(prFile, "option: pair-dist-type = %d\n", prOpts->iPairDistType);
- fprintf(prFile, "option: use-mbed = %d\n", prOpts->bUseMbed);
- fprintf(prFile, "option: use-mbed-for-iteration = %d\n", prOpts->bUseMbedForIteration);
- fprintf(prFile, "option: guidetree-outfile = %s\n",
- NULL != prOpts->pcGuidetreeOutfile? prOpts->pcGuidetreeOutfile: "(null)");
- fprintf(prFile, "option: guidetree-infile = %s\n",
- NULL != prOpts->pcGuidetreeInfile? prOpts->pcGuidetreeInfile: "(null)");
- for (iAux=0; iAux<prOpts->iHMMInputFiles; iAux++) {
- fprintf(prFile, "option: hmm-input no %d = %s\n", iAux, prOpts->ppcHMMInput[iAux]);
- }
- fprintf(prFile, "option: hmm-input-files = %d\n", prOpts->iHMMInputFiles);
- fprintf(prFile, "option: num-iterations = %d\n", prOpts->iNumIterations);
- fprintf(prFile, "option: iterations-auto = %d\n", prOpts->bIterationsAuto);
- fprintf(prFile, "option: max-hmm-iterations = %d\n", prOpts->iMaxHMMIterations);
- fprintf(prFile, "option: max-guidetree-iterations = %d\n", prOpts->iMaxGuidetreeIterations);
-}
-/* end of PrintAlnOpts() */
-
-
-
-/**
- * @brief Returns major version of HMMER. Whichever hmmbuild version
- * is found first in your PATH will be used
- *
- * @return -1 on error, major hmmer version otherwise
- *
- */
-int
-HmmerVersion()
-{
- char zcHmmerTestCall[] = "hmmbuild -h";
- FILE *fp = NULL;
- int iMajorVersion = 0;
- char zcLine[16384];
-
- if (NULL == (fp = popen(zcHmmerTestCall, "r"))) {
- Log(&rLog, LOG_ERROR, "Couldn't exec %s", zcHmmerTestCall);
- return -1;
- }
- while (fgets(zcLine, sizeof(zcLine), fp)) {
- char *pcLocate;
- if ((pcLocate = strstr(zcLine, "HMMER "))) {
- iMajorVersion = atoi(&pcLocate[6]);
- break;
- }
- }
- pclose(fp);
-
- return iMajorVersion;
-}
-/* end of HmmerVersion() */
-
-
-
-/**
- * @brief Create a HHM file from aligned sequences
- *
- * @warning Should be eliminated in the future
- * as building routine should not create intermediate files
- *
- * @param[in] prMSeq
- * Aligned mseq_t
- * @param[in] pcHMMOut
- * HMM output file name
- *
- * @return Non-zero on error
- *
- */
-int
-AlnToHHMFile(mseq_t *prMSeq, char *pcHMMOut)
-{
- char *tmp_aln = NULL;
- int retcode = OK;
-
- assert(NULL!=prMSeq);
- assert(NULL!=pcHMMOut);
-
- if (FALSE == prMSeq->aligned) {
- Log(&rLog, LOG_ERROR, "Sequences need to be aligned to create an HMM");
- return FAILURE;
- }
-
- /* Convert alignment to a2m, and call hhmake
- *
- * can't be static templates, or mktemp fails (at least on os x
- * (with a bus error))
- *
- * gcc says we should use mkstemp to avoid race conditions,
- * but that returns a file descriptor, which is of no use to
- * us
- */
- /* NOTE: the following won't work on windows: missing /tmp/ */
- tmp_aln = CkStrdup("/tmp/clustalo_tmpaln_XXXXXX");
- if (NULL == mktemp(tmp_aln)) {
- Log(&rLog, LOG_ERROR, "Could not create temporary alignment filename");
- retcode = FAILURE;
- goto cleanup_and_return;
- }
- if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_A2M)) {
- Log(&rLog, LOG_ERROR, "Could not save alignment to %s", tmp_aln);
- retcode = FAILURE;
- goto cleanup_and_return;
- }
-
- if (HHMake_Wrapper(tmp_aln, pcHMMOut)){
- Log(&rLog, LOG_ERROR, "Could not convert alignment %s into HHM", tmp_aln);
- retcode = FAILURE;
- goto cleanup_and_return;
- }
-
-
- cleanup_and_return:
-
- if (NULL != tmp_aln) {
- if (FileExists(tmp_aln)) {
- if (remove(tmp_aln)) {
- Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", tmp_aln);
- }
- }
- CKFREE(tmp_aln);
- }
-
- return retcode;
-
-} /* end of AlnToHHMFile() */
-
-
-
-/**
- * @brief Create a HMM file from aligned sequences
- *
- * @warning Should be replaced in the future by some internal HMM
- * building routine that does not call external programs
- *
- * @param[in] prMSeq
- * Aligned mseq_t
- * @param[in] pcHMMOut
- * HMM output file name
- *
- * @return Non-zero on error
- *
-
- */
-int
-AlnToHMMFile(mseq_t *prMSeq, const char *pcHMMOut)
-{
- char *tmp_aln = NULL;
- char *tmp_hmm = NULL; /* only needed for hmmer3 to hmmer2 conversion */
- char cmdbuf[16384];
- int iHmmerVersion = 0;
- int retcode = OK;
-
- assert(NULL!=prMSeq);
- assert(NULL!=pcHMMOut);
-
- if (FALSE == prMSeq->aligned) {
- Log(&rLog, LOG_ERROR, "Sequences need to be aligned to create an HMM");
- return FAILURE;
- }
-
- iHmmerVersion = HmmerVersion();
- if (2 != iHmmerVersion && 3 != iHmmerVersion) {
- Log(&rLog, LOG_ERROR, "Could not find suitable HMMER binaries");
- return FAILURE;
- }
-
- /* Convert alignment to stockholm, call hmmbuild and then
- * either hmmconvert (hmmer3) or hmmcalibrate (hmmer2)
- *
- * can't be static templates, or mktemp fails (at least on os x
- * (with a bus error))
- *
- * gcc says we should use mkstemp to avoid race conditions,
- * but that returns a file descriptor, which is of no use to
- * us
- */
- /* NOTE: the following won't work on windows: missing /tmp/ */
- tmp_aln = CkStrdup("/tmp/clustalo_tmpaln_XXXXXX");
- if (NULL == mktemp(tmp_aln)) {
- Log(&rLog, LOG_ERROR, "Could not create temporary alignment filename");
- retcode = FAILURE;
- goto cleanup_and_return;
- }
- if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_STOCKHOLM)) {
- Log(&rLog, LOG_ERROR, "Could not save alignment to %s", tmp_aln);
- retcode = FAILURE;
- goto cleanup_and_return;
- }
-
- if (2 == iHmmerVersion) {
- sprintf(cmdbuf, "hmmbuild %s %s >/dev/null && hmmcalibrate %s >/dev/null",
- pcHMMOut, tmp_aln, pcHMMOut);
- if (system(cmdbuf)) {
- Log(&rLog, LOG_ERROR, "Command '%s' failed", cmdbuf);
- retcode = FAILURE;
- goto cleanup_and_return;
- }
- } else if (3 == iHmmerVersion) {
- /* NOTE: the following won't work on windows: missing /tmp/ */
- tmp_hmm = CkStrdup("/tmp/clustalo_tmphmm2_XXXXXX");
- if (NULL == mktemp(tmp_hmm)) {
- Log(&rLog, LOG_ERROR, "Could not create temporary hmm filename");
- retcode = FAILURE;
- goto cleanup_and_return;
- }
- sprintf(cmdbuf, "hmmbuild %s %s >/dev/null && hmmconvert -2 %s > %s",
- tmp_hmm, tmp_aln, tmp_hmm, pcHMMOut);
- if (system(cmdbuf)) {
- Log(&rLog, LOG_ERROR, "Command '%s' failed", cmdbuf);
- retcode = FAILURE;
- goto cleanup_and_return;
- }
- } else {
- CKFREE(tmp_aln);
- Log(&rLog, LOG_FATAL, "Internal error: Unknown Hmmer version %d", iHmmerVersion);
- }
-
-
- cleanup_and_return:
-
- if (NULL != tmp_aln) {
- if (FileExists(tmp_aln)) {
- if (remove(tmp_aln)) {
- Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", tmp_aln);
- }
- }
- CKFREE(tmp_aln);
- }
- if (NULL != tmp_hmm) {
- if (FileExists(tmp_hmm)) {
- if (remove(tmp_hmm)) {
- Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", tmp_hmm);
- }
- }
- CKFREE(tmp_hmm);
- }
-
- return retcode;
-}
-/* end of AlnToHMMFile() */
-
-
-
-/**
- * @brief Convert a multiple sequence structure into a HMM
- *
- * @param[out] prHMM
- * Pointer to preallocted HMM which will be set here
- * @param[in] prMSeq
- * Pointer to an alignment
- *
- * @return 0 on error, non-0 otherwise
- *
- * @see AlnToHMMFile()
- *
- */
-int
-AlnToHMM(hmm_light *prHMM, mseq_t *prMSeq)
-{
- char *pcHMM; /* temp hmm file */
-
- Log(&rLog, LOG_INFO,
- "Using HMMER version %d to calculate a new HMM.",
- HmmerVersion());
- /* FIXME replace all this with internal HMM computation (HHmake) */
-
- /**
- * @warning the following probably won't work on windows: missing
- * /tmp/. Should be ok on Cygwin though
- */
- pcHMM = CkStrdup("/tmp/clustalo-hmm-iter_XXXXXX");
- if (NULL == mktemp(pcHMM)) {
- Log(&rLog, LOG_ERROR, "Could not create temporary hmm filename");
- CKFREE(pcHMM);
- return FAILURE;
- }
-
- /* Create a HMM representing the current alignment
- */
-#if USEHMMER
- if (AlnToHMMFile(prMSeq, pcHMM)) {
- Log(&rLog, LOG_ERROR, "AlnToHMMFile() on %s failed.", pcHMM);
- CKFREE(pcHMM);
- return FAILURE;
- }
-#elif USEHHMAKE
- if (AlnToHHMFile(prMSeq, pcHMM)) {
- Log(&rLog, LOG_ERROR, "AlnToHHMFile() on %s failed.", pcHMM);
- CKFREE(pcHMM);
- return FAILURE;
- }
- /* Log(&rLog, LOG_FATAL, "Method to create HHM (HMM using hhmake) not installed yet"); */
-#else
- Log(&rLog, LOG_FATAL, "Unknown method to create temporary HMM");
-#endif
-
- /* Read HMM information
- */
- if (OK != readHMMWrapper(prHMM, pcHMM)){
- Log(&rLog, LOG_ERROR, "Processing of HMM file %s failed", pcHMM);
- CKFREE(pcHMM);
- return FAILURE;
- }
-
- if (remove(pcHMM)) {
- Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", pcHMM);
- }
- CKFREE(pcHMM);
-
- return OK;
-}
-/* end of AlnToHMM() */
-
-
-
-/**
- * @brief FIXME
- *
- */
-void
-InitClustalOmega(int iNumThreadsRequested)
-{
-
-#ifdef HAVE_OPENMP
- iNumberOfThreads = iNumThreadsRequested;
- omp_set_num_threads(iNumberOfThreads);
-#else
- if (iNumThreadsRequested>1) {
- Log(&rLog, LOG_FATAL, "Cannot change number of threads to %d. %s was build without OpenMP support.",
- iNumThreadsRequested, PACKAGE_NAME);
- }
- iNumberOfThreads = 1; /* need to set this, even if build without support */
-#endif
-
- Log(&rLog, LOG_INFO, "Using %d threads",
- iNumberOfThreads);
-
-}
-/* end of InitClustalOmega() */
-
-
-
-/**
- * @brief Defines an alignment order, which adds sequences
- * sequentially, i.e. one at a time starting with seq 1 & 2
- *
- * @param[out] piOrderLR_p
- * order in which nodes/profiles are to be merged/aligned
- * @param[in] iNumSeq
- * Number of sequences
- *
- * @see TraverseTree()
- *
- */
-void
-SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq)
-{
- unsigned int uNodes = iNumSeq*2-1;
- unsigned int uNodeCounter = 0;
- unsigned int uSeqCounter = 0;
-
- Log(&rLog, LOG_FATAL, "FIXME: Untested...");
-
- (*piOrderLR_p) = (int *)CKCALLOC(DIFF_NODE * uNodes, sizeof(int));
- /* loop over merge nodes, which have per definition even indices
- * and set up children which have odd indices
- */
- uSeqCounter = 0;
- for (uNodeCounter=iNumSeq; uNodeCounter<uNodes; uNodeCounter+=1) {
- unsigned int uLeftChildNodeIndex = uNodeCounter-1;
- unsigned int uRightChildNodeIndex = uNodeCounter-iNumSeq+1;
- unsigned int uParentNodeIndex = uNodeCounter+1;
-
- /* merge node setup */
- (*piOrderLR_p)[DIFF_NODE*uNodeCounter+LEFT_NODE] = uLeftChildNodeIndex;
- (*piOrderLR_p)[DIFF_NODE*uNodeCounter+RGHT_NODE] = uRightChildNodeIndex;
- (*piOrderLR_p)[DIFF_NODE*uNodeCounter+PRNT_NODE] = uParentNodeIndex;
- /* only setup left child if at first merge node, all other left childs
- * should be merge nodes that are already set up. also correct
- * left node number here.
- */
- if (uNodeCounter==iNumSeq) {
- (*piOrderLR_p)[DIFF_NODE*uNodeCounter+LEFT_NODE] = 0;
-
- (*piOrderLR_p)[0+LEFT_NODE] = 0;
- (*piOrderLR_p)[0+RGHT_NODE] = 0;
- (*piOrderLR_p)[0+PRNT_NODE] = uNodeCounter;
- uSeqCounter++;
-
- Log(&rLog, LOG_FORCED_DEBUG, "Set up first leaf with node counter %d: left=%d right=%d parent=%d",
- 0,
- (*piOrderLR_p)[DIFF_NODE*uLeftChildNodeIndex+LEFT_NODE],
- (*piOrderLR_p)[DIFF_NODE*uLeftChildNodeIndex+RGHT_NODE],
- (*piOrderLR_p)[DIFF_NODE*uLeftChildNodeIndex+PRNT_NODE]);
- }
- Log(&rLog, LOG_FORCED_DEBUG, "Set up merge node with node counter %d: left=%d right=%d parent=%d",
- uNodeCounter, (*piOrderLR_p)[DIFF_NODE*uNodeCounter+LEFT_NODE],
- (*piOrderLR_p)[DIFF_NODE*uNodeCounter+RGHT_NODE],
- (*piOrderLR_p)[DIFF_NODE*uNodeCounter+PRNT_NODE]);
-
- /* right child */
- (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+LEFT_NODE] = uSeqCounter;
- (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+RGHT_NODE] = uSeqCounter;
- (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+PRNT_NODE] = uNodeCounter;
- uSeqCounter++;
-
- Log(&rLog, LOG_FORCED_DEBUG, "Set up leaf with node counter %d: left=%d right=%d parent=%d",
- uRightChildNodeIndex, (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+LEFT_NODE],
- (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+RGHT_NODE],
- (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+PRNT_NODE]);
- }
-}
-/* end of SequentialAlignmentOrder() */
-
-
-
-/**
- * @brief Defines the alignment order by calculating a guide tree. In
- * a first-step pairwise distances will be calculated (or read from a
- * file). In a second step those distances will be clustered and a
- * guide-tree created. Steps 1 and 2 will be skipped if a guide-tree
- * file was given, in which case the guide-tree will be just read from
- * the file.
- *
- * @param[out] piOrderLR_p
- * order in which nodes/profiles are to be merged/aligned
- * @param[out] pdSeqWeights_p
- * Sequence weights
- * @param[out] pdSeqWeights_p
- * Sequence weights
- * @param[in] prMSeq
- * The sequences from which the alignment order is to be calculated
- * @param[in] iPairDistType
- * Method of pairwise distance comparison
- * @param[in] pcDistmatInfile
- * If not NULL distances will be read from this file instead of being
- * calculated
- * @param[in] pcDistmatOutfile
- * If not NULL computed pairwise distances will be written to this file
- * @param[in] iClusteringType
- * Clustering method to be used to cluster the pairwise distances
- * @param[in] pcGuidetreeInfile
- * If not NULL guidetree will be read from this file. Skips pairwise
- * distance and guidetree computation
- * @param[in] pcGuidetreeOutfile
- * If not NULL computed guidetree will be written to this file
- * @param[in] bUseMbed
- * If TRUE, fast mBed guidetree computation will be employed
- *
- * @return Non-zero on error
- *
- */
-int
-AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq,
- int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile,
- int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile,
- bool bUseMbed)
-{
- /* pairwise distance matrix (tmat in 1.83) */
- symmatrix_t *distmat = NULL;
- /* guide tree */
- tree_t *prTree = NULL;
- int i = 0;
-
-
- /* Shortcut for only two sequences: Do not compute k-tuple
- * distances. Use the same logic as in TraverseTree() to setup
- * piOrderLR_p. Changes there will have to be reflected here as
- * well. */
- if (2==prMSeq->nseqs) {
- Log(&rLog, LOG_VERBOSE,
- "Have only two sequences: No need to compute pairwise score and compute a tree.");
-
- (*piOrderLR_p) = (int*) CKMALLOC(DIFF_NODE * 3 * sizeof(int));
- (*piOrderLR_p)[DIFF_NODE*0+LEFT_NODE] = 0;
- (*piOrderLR_p)[DIFF_NODE*0+RGHT_NODE] = 0;
- (*piOrderLR_p)[DIFF_NODE*0+PRNT_NODE] = 0;
-
- (*piOrderLR_p)[DIFF_NODE*1+LEFT_NODE] = 1;
- (*piOrderLR_p)[DIFF_NODE*1+RGHT_NODE] = 1;
- (*piOrderLR_p)[DIFF_NODE*1+PRNT_NODE] = 1;
-
- /* root */
- (*piOrderLR_p)[DIFF_NODE*2+LEFT_NODE] = 0;
- (*piOrderLR_p)[DIFF_NODE*2+RGHT_NODE] = 1;
- (*piOrderLR_p)[DIFF_NODE*2+PRNT_NODE] = 2;
-
- /* Same logic as CalcClustalWeights(). Changes there will
- have to be reflected here as well. */
-#if USE_WEIGHTS
- (*pdWeights_p) = (double *) CKMALLOC(uNodeCount * sizeof(double));
- (*pdWeights_p)[0] = 0.5;
- (*pdWeights_p)[1] = 0.5;
-#endif
-
- return OK;
- }
-
-
- /* compute distance & guide tree, alternatively read distances or
- * guide tree from file
- *
- */
- if (NULL != pcGuidetreeInfile) {
- Log(&rLog, LOG_INFO, "Reading guide-tree from %s", pcGuidetreeInfile);
- if (GuideTreeFromFile(&prTree, prMSeq, pcGuidetreeInfile)) {
- Log(&rLog, LOG_ERROR, "Reading of guide tree %s failed.", pcGuidetreeInfile);
- return FAILURE;
- }
-
- } else {
-
- if (bUseMbed) {
- if (Mbed(&prTree, prMSeq, iPairDistType, pcGuidetreeOutfile)) {
- Log(&rLog, LOG_ERROR, "mbed execution failed.");
- return FAILURE;
- }
- Log(&rLog, LOG_INFO, "Guide-tree computation (mBed) done.");
- if (NULL != pcDistmatOutfile) {
- Log(&rLog, LOG_INFO,
- "Ignoring request to write distance matrix (am in mBed mode)");
- }
- } else {
-
- if (PairDistances(&distmat, prMSeq, iPairDistType,
- 0, prMSeq->nseqs, 0, prMSeq->nseqs,
- pcDistmatInfile, pcDistmatOutfile)) {
- Log(&rLog, LOG_ERROR, "Couldn't compute pair distances");
- return FAILURE;
- }
-
- /* clustering of distances to get guide tree
- */
- if (CLUSTERING_UPGMA == iClusteringType) {
- char **labels;
- labels = (char**) CKMALLOC(prMSeq->nseqs * sizeof(char*));
- for (i=0; i<prMSeq->nseqs; i++) {
- labels[i] = prMSeq->sqinfo[i].name;
- }
-
- GuideTreeUpgma(&prTree, labels, distmat, pcGuidetreeOutfile);
- Log(&rLog, LOG_INFO, "Guide-tree computation done.");
-
- CKFREE(labels);
- } else {
- Log(&rLog, LOG_FATAL, "INTERNAL ERROR %s",
- "clustering method should have been checked before");
- }
- }
- }
-
-#if USE_WEIGHTS
- /* derive sequence weights from tree
- *
- */
- Log(&rLog, LOG_INFO, "Calculating sequence weights");
- CalcClustalWeights(pdSeqWeights_p, prTree);
- for (i = 0; i < GetLeafCount(prTree); i++) {
- Log(&rLog, LOG_VERBOSE,
- "Weight for seq no %d: %s = %f",
- i, prMSeq->sqinfo[i].name, (*pdSeqWeights_p)[i]);
- }
-#else
- Log(&rLog, LOG_DEBUG, "Not using weights");
-#endif
-
-
- /* define traversing order of tree
- *
- */
- TraverseTree(piOrderLR_p, prTree, prMSeq);
- if (rLog.iLogLevelEnabled <= LOG_DEBUG) {
- /* FIXME: debug only, FS */
- uint uNodeIndex;
- FILE *fp = LogGetFP(&rLog, LOG_INFO);
- Log(&rLog, LOG_DEBUG, "left/right order after tree traversal");
- for (uNodeIndex = 0; uNodeIndex < GetNodeCount(prTree); uNodeIndex++) {
- fprintf(fp, "%3d:\t%2d/%2d -> %d\n", i,
- (*piOrderLR_p)[DIFF_NODE*uNodeIndex+LEFT_NODE],
- (*piOrderLR_p)[DIFF_NODE*uNodeIndex+RGHT_NODE],
- (*piOrderLR_p)[DIFF_NODE*uNodeIndex+PRNT_NODE]);
- }
- }
-
- FreeMuscleTree(prTree);
- FreeSymMatrix(&distmat);
-
-#if 0
- Log(&rLog, LOG_FATAL, "DEBUG EXIT before leaving %s", __FUNCTION__);
-#endif
- return OK;
-}
-/* end of AlignmentOrder() */
-
-
-
-/**
- * @brief Set some options automatically based on number of sequences. Might
- * overwrite some user-set options.
- *
- * @param[out] prOpts
- * Pointer to alignment options structure
- * @param[in] iNumSeq
- * Number of sequences to align
- */
-void
-SetAutoOptions(opts_t *prOpts, int iNumSeq) {
-
- Log(&rLog, LOG_INFO,
- "Setting options automatically based on input sequence characteristics (might overwrite some of your options).");
-
- /* AW: new version of mbed is always good (uses subclusters) */
- if (FALSE == prOpts->bUseMbed) {
- Log(&rLog, LOG_INFO, "Auto settings: Enabling mBed.");
- prOpts->bUseMbed = TRUE;
- }
-
- if (iNumSeq >= 1000) {
- if (0 != prOpts->iNumIterations) {
- Log(&rLog, LOG_INFO, "Auto settings: Disabling iterations.");
- prOpts->iNumIterations = 0;
- }
-
- } else if (iNumSeq < 1000) {
- if (1 != prOpts->iNumIterations) {
- Log(&rLog, LOG_INFO, "Auto settings: Setting iteration to 1.");
- prOpts->iNumIterations = 1;
- }
- }
-}
-/* end of */
-
-
-
-/**
- * @brief The main alignment function which wraps everything else.
- *
- * @param[out] prMSeq
- * *the* multiple sequences structure
- * @param[in] prMSeqProfile
- * optional profile to align against
- * @param[in] prOpts
- * alignmemnt options to use
- *
- * @return 0 on success, -1 on failure
- *
- */
-int
-Align(mseq_t *prMSeq,
- mseq_t *prMSeqProfile,
- opts_t *prOpts,
- hhalign_para rHhalignPara) {
-
- /* HMM
- */
- /* structs with pseudocounts etc; one for each HMM infile, i.e.
- * index range: 0..iHMMInputFiles */
- hmm_light *prHMMs = NULL;
-
- /* MSA order in which nodes/profiles are to be merged/aligned
- (order of nodes in guide tree (left/right)*/
- int *piOrderLR = NULL;
-
- /* weights per sequence */
- double *pdSeqWeights = NULL;
-
- /* Iteration
- */
- int iIterationCounter = 0;
- double dAlnScore;
- /* last dAlnScore for iteration */
- double dLastAlnScore = -666.666;
-
- int i, j; /* aux */
-
- assert(NULL != prMSeq);
- if (NULL != prMSeqProfile) {
- assert(TRUE == prMSeqProfile->aligned);
- }
-
-
- /* automatic setting of options
- *
- */
- if (prOpts->bAutoOptions) {
- SetAutoOptions(prOpts, prMSeq->nseqs);
- }
-
-
-#if SHUFFLE_INPUT_SEQ_ORDER
- /*
- * shuffle input: only useful for testing/debugging
- */
- Log(&rLog, LOG_WARN, "Shuffling input sequences! (Will also change output order)");
- ShuffleMSeq(prMSeq);
-#endif
-
-
-#if SORT_INPUT_SEQS
- /*
- * sort input:
- *
- * would ensure we *always* (unless we get into the mbed k-means stage)
- * get the same answer. usually you don't, because most pairwise alignment
- * scores are in theory not symmetric, therefore sequence ordering might
- * have an effect on the guide-tree. Sorting by length should get rid of
- * this (and takes no time even for 100k seqs). Benchmark results on
- * Balibase show almost no difference after sorting.
- */
- Log(&rLog, LOG_WARN, "Sorting input seq by length! This will also change the output order");
- SortMSeqByLength(prMSeq, 'd');
-
-#endif
-
-
- /* Read backgrounds HMMs and store in prHMMs
- *
- */
- if (0 < prOpts->iHMMInputFiles) {
- int iHMMInfileIndex;
-
- /**
- * @warning old structure used to be initialised like this:
- * hmm_light rHMM = {0};
- */
- prHMMs = (hmm_light *) CKMALLOC(prOpts->iHMMInputFiles * sizeof(hmm_light));
-
- for (iHMMInfileIndex=0; iHMMInfileIndex<prOpts->iHMMInputFiles; iHMMInfileIndex++) {
- char *pcHMMInput = prOpts->ppcHMMInput[iHMMInfileIndex];
- if (OK != readHMMWrapper(&prHMMs[iHMMInfileIndex], pcHMMInput)){
- Log(&rLog, LOG_ERROR, "Processing of HMM file %s failed", pcHMMInput);
- return -1;
- }
-
-#if 0
- Log(&rLog, LOG_FORCED_DEBUG, "HMM length is %d", prHMMs[iHMMInfileIndex].L);
- Log(&rLog, LOG_FORCED_DEBUG, "n-display is %d", prHMMs[iHMMInfileIndex].n_display);
- for (i = 0; NULL != prHMMs[prOpts->iHMMInputFiles].seq[i]; i++){
- printf("seq[%d]: %s\n", i, prHMMs[iHMMInfileIndex].seq[i]);
- }
- Log(&rLog, LOG_FORCED_DEBUG, "Neff_HMM is %f", prHMMs[iHMMInfileIndex].Neff_HMM);
-#endif
- if (rLog.iLogLevelEnabled <= LOG_DEBUG){
- Log(&rLog, LOG_DEBUG, "print frequencies");
- for (i = 0; i < prHMMs[iHMMInfileIndex].L; i++){
-#define PRINT_TAIL 5
- if ( (PRINT_TAIL+1 == i) && (prHMMs[iHMMInfileIndex].L-PRINT_TAIL != i) ){
- printf("....\n");
- }
- if ( (i > PRINT_TAIL) && (i < prHMMs[iHMMInfileIndex].L-PRINT_TAIL) ){
- continue;
- }
- printf("%3d:", i);
- for (j = 0; j < 20; j++){
- printf("\t%1.3f", prHMMs[iHMMInfileIndex].f[i][j]);
- }
- printf("\n");
- }
- } /* debug print block */
-
- CKFREE(prOpts->ppcHMMInput[iHMMInfileIndex]);
- } /* for each background HMM file */
- CKFREE(prOpts->ppcHMMInput);
- } /* there were background HMM files */
-
-
-
- /* If the input ("non-profile") sequences are aligned, then turn
- * the alignment into a HMM and add to the list of background HMMs
- *
- */
- if (TRUE == prMSeq->aligned) {
- /* FIXME: gcc warns about missing initialiser here (-Wall -Wextra -pedantic) */
- hmm_light rHMMLocal = {0};
-
- Log(&rLog, LOG_INFO,
- "Input sequences are aligned. Will turn alignment into HMM and add it to the user provided background HMMs.");
- if (OK !=
-#if INDIRECT_HMM
- AlnToHMM(&rHMMLocal, prMSeq)
-#else
- AlnToHMM2(&rHMMLocal, prMSeq->seq, prMSeq->nseqs)
-#endif
- ) {
- Log(&rLog, LOG_ERROR, "Couldn't convert aligned input sequences to HMM. Will try to continue");
- } else {
- prHMMs = (hmm_light *) CKREALLOC(prHMMs, ((prOpts->iHMMInputFiles+1) * sizeof(hmm_light)));
- memcpy(&(prHMMs[prOpts->iHMMInputFiles]), &rHMMLocal, sizeof(hmm_light));
- prOpts->iHMMInputFiles++;
- }
- }
-
-
- /* If we have a profile turn it into a HMM and add to
- * the list of background HMMs.
- *
- */
- if (NULL != prMSeqProfile) {
- /* FIXME: gcc warns about missing initialiser here (-Wall -Wextra -pedantic) */
- hmm_light rHMMLocal = {0};
- Log(&rLog, LOG_INFO,
- "Turning profile1 into HMM and will use it during progressive alignment.");
- if (OK !=
-#if INDIRECT_HMM
- AlnToHMM(&rHMMLocal, prMSeqProfile)
-#else
- AlnToHMM2(&rHMMLocal, prMSeqProfile->seq, prMSeqProfile->nseqs)
-#endif
- ) {
- Log(&rLog, LOG_ERROR, "Couldn't convert profile1 to HMM. Will try to continue");
- } else {
- prHMMs = (hmm_light *) CKREALLOC(prHMMs, ((prOpts->iHMMInputFiles+1) * sizeof(hmm_light)));
- memcpy(&(prHMMs[prOpts->iHMMInputFiles]), &rHMMLocal, sizeof(hmm_light));
- prOpts->iHMMInputFiles++;
- }
- }
-
-
- /* Now do a first alignment of the input sequences (prMSeq) adding
- * all collected background HMMs
- *
- */
- /* Determine progressive alignment order
- */
- if (TRUE == prMSeq->aligned) {
- Log(&rLog, LOG_INFO, "%s %s",
- "Input sequences are aligned.",
- "Will use Kimura distances of aligned sequences.");
- prOpts->iPairDistType = PAIRDIST_SQUIDID_KIMURA;
- }
-
-#if 0
- Log(&rLog, LOG_WARN, "Using a sequential alignment order.");
- SequentialAlignmentOrder(&piOrderLR, prMSeq->nseqs);
-#else
- if (OK != AlignmentOrder(&piOrderLR, &pdSeqWeights, prMSeq,
- prOpts->iPairDistType,
- prOpts->pcDistmatInfile, prOpts->pcDistmatOutfile,
- prOpts->iClusteringType,
- prOpts->pcGuidetreeInfile, prOpts->pcGuidetreeOutfile,
- prOpts->bUseMbed)) {
- Log(&rLog, LOG_ERROR, "AlignmentOrder() failed. Cannot continue");
- return -1;
- }
-#endif
-
- /* Progressive alignment of input sequences. Order defined by
- * branching of guide tree (piOrderLR). Use optional
- * background HMM information (prHMMs[0..prOpts->iHMMInputFiles-1])
- *
- */
- dAlnScore = HHalignWrapper(prMSeq, piOrderLR, pdSeqWeights,
- 2*prMSeq->nseqs -1/* nodes */,
- prHMMs, prOpts->iHMMInputFiles, -1, rHhalignPara);
- dLastAlnScore = dAlnScore;
- Log(&rLog, LOG_VERBOSE,
- "Alignment score for first alignment = %f", dAlnScore);
-
-
-
-
- /* ------------------------------------------------------------
- *
- * prMSeq is aligned now. Now start iterations if requested and save the
- * alignment at the very end.
- *
- * @note We discard the background HMM information at this point,
- * because it was already used. Could consider to make this choice
- * optional. FIXME
- *
- * ------------------------------------------------------------ */
-
-
- /* iteration after first alignment was computed (if not profile-profile
- * alignment)
- *
- */
- for (iIterationCounter=0;
- (iIterationCounter < prOpts->iNumIterations || prOpts->bIterationsAuto);
- iIterationCounter++) {
-
- hmm_light rHMMLocal = {0};
- /* FIXME Keep copy of old alignment in case new one sucks? */
-
-
- if (iIterationCounter >= prOpts->iMaxHMMIterations
- &&
- iIterationCounter >= prOpts->iMaxGuidetreeIterations) {
- Log(&rLog, LOG_VERBOSE, "Reached maximum number of HMM and guide-tree iterations");
- break;
- }
-
- if (! prOpts->bIterationsAuto) {
- Log(&rLog, LOG_INFO, "Iteration step %d out of %d",
- iIterationCounter+1, prOpts->iNumIterations);
- } else {
- Log(&rLog, LOG_INFO, "Iteration step %d out of <auto>",
- iIterationCounter+1);
- }
-#if 0
- if (rLog.iLogLevelEnabled <= LOG_VERBOSE) {
- char zcIntermediate[1000] = {0};
- char *pcFormat = "fasta";
- sprintf(zcIntermediate, "clustalo-aln-iter~%d~", iIterationCounter);
- if (WriteAlignment(prMSeq, zcIntermediate, MSAFILE_A2M)) {
- Log(&rLog, LOG_ERROR, "Could not save alignment to %s", zcIntermediate);
- return -1;
- }
- }
-#endif
-
-
- /* new guide-tree
- *
- */
- if (iIterationCounter < prOpts->iMaxGuidetreeIterations) {
- /* determine progressive alignment order
- *
- * few things are different now when calling AlignmentOrder:
- * - we have to ignore prOpts->pcDistmatInfile and pcGuidetreeInfile
- * as they were used before
- * - the corresponding outfiles are still valid though
- */
- /* Free stuff that has already been allocated by or further
- * downstream of AlignmentOrder()
- */
- if (NULL != piOrderLR)
- CKFREE(piOrderLR);
- if (NULL != pdSeqWeights)
- CKFREE(pdSeqWeights);
- if (AlignmentOrder(&piOrderLR, &pdSeqWeights, prMSeq,
- PAIRDIST_SQUIDID_KIMURA /* override */, NULL, prOpts->pcDistmatOutfile,
- prOpts->iClusteringType, NULL, prOpts->pcGuidetreeOutfile,
- prOpts->bUseMbedForIteration)) {
- Log(&rLog, LOG_ERROR, "AlignmentOrder() failed. Cannot continue");
- return -1;
- }
- } else {
- Log(&rLog, LOG_INFO, "Skipping guide-tree iteration at iteration step %d (reached maximum)",
- iIterationCounter);
- }
-
-
- /* new local hmm iteration
- *
- */
- if (iIterationCounter < prOpts->iMaxHMMIterations) {
- if (OK !=
-#if INDIRECT_HMM
- AlnToHMM(&rHMMLocal, prMSeq)
-#else
- AlnToHMM2(&rHMMLocal, prMSeq->seq, prMSeq->nseqs)
-#endif
- ) {
- Log(&rLog, LOG_ERROR, "Couldn't convert alignment to HMM. Will stop iterating now...");
- break;
- }
- } else {
- Log(&rLog, LOG_INFO, "Skipping HMM iteration at iteration step %d (reached maximum)",
- iIterationCounter);
- }
-
-
- /* align the sequences (again)
- */
- dAlnScore = HHalignWrapper(prMSeq, piOrderLR, pdSeqWeights,
- 2*prMSeq->nseqs -1/* nodes */, &rHMMLocal, 1, -1, rHhalignPara);
- Log(&rLog, LOG_VERBOSE,
- "Alignment score for alignmnent in hmm-iteration no %d = %f (last score = %f)",
- iIterationCounter+1, dAlnScore, dLastAlnScore);
-
-
- FreeHMMstruct(&rHMMLocal);
-
-#if 0
- /* FIXME: need a better score for automatic iteration */
- if (prOpts->bIterationsAuto) {
- /* automatic iteration: break if score improvement was not
- * big enough
- */
- double dScoreImprovement = (dAlnScore-dLastAlnScore)/dLastAlnScore;
- if (dScoreImprovement < ITERATION_SCORE_IMPROVEMENT_THRESHOLD) {
- Log(&rLog, LOG_INFO,
- "Stopping after %d guide-tree iterations. No further alignment score improvement achieved.",
- iIterationCounter+1);
- /* use previous alignment */
- FreeMSeq(&prMSeq);
- Log(&rLog, LOG_FORCED_DEBUG, "FIXME: %s", "CopyMSeq breaks things in this context");
- CopyMSeq(&prMSeq, prMSeqCopy);
- /* FIXME: prOpts->pcDistmatOutfile and pcGuidetreeOutfile
- * might have been updated, but then discarded here?
- */
- break;
- } else {
- Log(&rLog, LOG_INFO,
- "Got a %d%% better score in iteration step %d",
- (int)dScoreImprovement*100, iIterationCounter+1);
- FreeMSeq(&prMSeqCopy);
- }
- }
- dLastAlnScore = dAlnScore;
-#endif
-
- }
- /* end of iterations */
-
-
-
- /* Last step: if a profile was also provided then align now-aligned mseq
- * with this profile
- *
- * Don't use the backgrounds HMMs anymore and don't iterate.
- * (which was done before).
- *
- */
- if (NULL != prMSeqProfile) {
- if (AlignProfiles(prMSeq, prMSeqProfile, rHhalignPara)) {
- Log(&rLog, LOG_ERROR, "An error occured during the profile/profile alignment");
- return -1;
- }
- }
-
-
- if (NULL != piOrderLR) {
- CKFREE(piOrderLR);
- }
- if (NULL != pdSeqWeights) {
- CKFREE(pdSeqWeights);
- }
- if (0 < prOpts->iHMMInputFiles) {
- for (i=0; i<prOpts->iHMMInputFiles; i++) {
- FreeHMMstruct(&prHMMs[i]);
- }
- CKFREE(prHMMs);
- }
-
- return 0;
-}
-/* end of Align() */
-
-
-
-
-/**
- * @brief Align two profiles, ie two sets of prealigned sequences. Already
- * aligned columns won't be changed.
- *
- * @param[out] prMSeqProfile1
- * First profile/aligned set of sequences. Merged alignment will be found in
- * here.
- * @param[in] prMSeqProfile2
- * First profile/aligned set of sequences
- *
- * @return 0 on success, -1 on failure
- *
- */
-int
-AlignProfiles(mseq_t *prMSeqProfile1,
- mseq_t *prMSeqProfile2, hhalign_para rHhalignPara) {
-
- double dAlnScore;
-
- /* number of seqs in first half of joined profile */
- int iProfProfSeparator = prMSeqProfile1->nseqs;
-
- assert(TRUE == prMSeqProfile1->aligned);
- assert(TRUE == prMSeqProfile2->aligned);
-
- Log(&rLog, LOG_INFO, "Performing profile/profile alignment");
-
- /* Combine the available mseqs into prMSeq
- * which will be aligned afterwards.
- */
- JoinMSeqs(&prMSeqProfile1, prMSeqProfile2);
-
-
- /* set alignment flag explicitly to FALSE */
- prMSeqProfile1->aligned = FALSE;
-
- dAlnScore = HHalignWrapper(prMSeqProfile1,
- NULL, /* no order */
- NULL, /* no weights */
- 3, /* nodes: root+2profiles */
- NULL, 0 /* no bg-hmms */,
- iProfProfSeparator, rHhalignPara);
-
- Log(&rLog, LOG_VERBOSE, "Alignment score is = %f", dAlnScore);
-
- return 0;
-}
-/* end of AlignProfiles() */
-
-
git://source.jalview.org / jabaws.git / blobdiff