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// =============================================================== //
// //
// File : fast_aligner.cxx //
// Purpose : A fast aligner (not a multiple aligner!) //
// //
// Coded by Ralf Westram (coder@reallysoft.de) in 1998 //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// =============================================================== //
#include "fast_aligner.hxx"
#include "ClustalV.hxx"
#include "seq_search.hxx"
#include <island_hopping.h>
#include <awtc_next_neighbours.hxx>
#include <awt_sel_boxes.hxx>
#include <aw_awars.hxx>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <arbdbt.h>
#include <ad_cb.h>
#include <arb_defs.h>
#include <arb_progress.h>
#include <RangeList.h>
#include <cctype>
#include <cmath>
#include <climits>
#include <list>
// --------------------------------------------------------------------------------
#if defined(DEBUG)
// #define TRACE_CLUSTAL_DATA
// #define TRACE_ISLANDHOPPER_DATA
// #define TRACE_COMPRESSED_ALIGNMENT
// #define TRACE_RELATIVES
#endif // DEBUG
// --------------------------------------------------------------------------------
enum FA_report {
FA_NO_REPORT, // no report
FA_TEMP_REPORT, // report to temporary entries
FA_REPORT, // report to resident entries
};
enum FA_range {
FA_WHOLE_SEQUENCE, // align whole sequence
FA_AROUND_CURSOR, // align xxx positions around current cursor position
FA_SELECTED_RANGE, // align selected range
FA_SAI_MULTI_RANGE, // align versus multi range define by SAI
};
enum FA_turn {
FA_TURN_NEVER, // never try to turn sequence
FA_TURN_INTERACTIVE, // try to turn, but query user
FA_TURN_ALWAYS, // turn if score is better
};
enum FA_reference {
FA_REF_EXPLICIT, // reference sequence explicitly specified
FA_REF_CONSENSUS, // use group consensus as reference
FA_REF_RELATIVES, // search next relatives by PT server
};
enum FA_alignTarget {
FA_CURRENT, // align current species
FA_MARKED, // align all marked species
FA_SELECTED, // align selected species (= range)
};
enum FA_errorAction {
FA_NO_ACTION, // do nothing
FA_MARK_FAILED, // mark failed species (unmark rest)
FA_MARK_ALIGNED, // mark aligned species (unmark rest)
};
struct AlignParams {
FA_report report;
bool showGapsMessages; // display messages about missing gaps in master?
PosRange range; // range to be aligned
};
struct SearchRelativeParams : virtual Noncopyable {
FamilyFinder *ff;
char *pt_server_alignment; // alignment used in pt_server (may differ from 'alignment')
int maxRelatives; // max # of relatives to use
SearchRelativeParams(FamilyFinder *ff_, const char *pt_server_alignment_, int maxRelatives_)
: ff(ff_),
pt_server_alignment(strdup(pt_server_alignment_)),
maxRelatives(maxRelatives_)
{}
~SearchRelativeParams() {
free(pt_server_alignment);
delete(ff);
}
FamilyFinder *getFamilyFinder() { return ff; }
};
// --------------------------------------------------------------------------------
#define GAP_CHAR '-'
#define QUALITY_NAME "ASC_ALIGNER_CLIENT_SCORE"
#define INSERTS_NAME "AMI_ALIGNER_MASTER_INSERTS"
#define FA_AWAR_ROOT "faligner/"
#define FA_AWAR_TO_ALIGN FA_AWAR_ROOT "what"
#define FA_AWAR_REFERENCE FA_AWAR_ROOT "against"
#define FA_AWAR_REFERENCE_NAME FA_AWAR_ROOT "sagainst"
#define FA_AWAR_RANGE FA_AWAR_ROOT "range"
#define FA_AWAR_PROTECTION FA_AWAR_ROOT "protection"
#define FA_AWAR_AROUND FA_AWAR_ROOT "around"
#define FA_AWAR_MIRROR FA_AWAR_ROOT "mirror"
#define FA_AWAR_REPORT FA_AWAR_ROOT "report"
#define FA_AWAR_SHOW_GAPS_MESSAGES FA_AWAR_ROOT "show_gaps"
#define FA_AWAR_CONTINUE_ON_ERROR FA_AWAR_ROOT "continue_on_error"
#define FA_AWAR_ACTION_ON_ERROR FA_AWAR_ROOT "action_on_error"
#define FA_AWAR_USE_SECONDARY FA_AWAR_ROOT "use_secondary"
#define FA_AWAR_NEXT_RELATIVES FA_AWAR_ROOT "next_relatives"
#define FA_AWAR_RELATIVE_RANGE FA_AWAR_ROOT "relrange"
#define FA_AWAR_PT_SERVER_ALIGNMENT "tmp/" FA_AWAR_ROOT "relative_ali"
#define FA_AWAR_SAI_RANGE_NAME FA_AWAR_ROOT "sai/sainame"
#define FA_AWAR_SAI_RANGE_CHARS FA_AWAR_ROOT "sai/chars"
#define FA_AWAR_ISLAND_HOPPING_ROOT "island_hopping/"
#define FA_AWAR_USE_ISLAND_HOPPING FA_AWAR_ISLAND_HOPPING_ROOT "use"
#define FA_AWAR_ESTIMATE_BASE_FREQ FA_AWAR_ISLAND_HOPPING_ROOT "estimate_base_freq"
#define FA_AWAR_BASE_FREQ_A FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_a"
#define FA_AWAR_BASE_FREQ_C FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_c"
#define FA_AWAR_BASE_FREQ_G FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_g"
#define FA_AWAR_BASE_FREQ_T FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_t"
#define FA_AWAR_SUBST_PARA_AC FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ac"
#define FA_AWAR_SUBST_PARA_AG FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ag"
#define FA_AWAR_SUBST_PARA_AT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_at"
#define FA_AWAR_SUBST_PARA_CG FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_cg"
#define FA_AWAR_SUBST_PARA_CT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ct"
#define FA_AWAR_SUBST_PARA_GT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_gt"
#define FA_AWAR_EXPECTED_DISTANCE FA_AWAR_ISLAND_HOPPING_ROOT "expected_dist"
#define FA_AWAR_STRUCTURE_SUPPLEMENT FA_AWAR_ISLAND_HOPPING_ROOT "struct_suppl"
#define FA_AWAR_THRESHOLD FA_AWAR_ISLAND_HOPPING_ROOT "threshold"
#define FA_AWAR_GAP_A FA_AWAR_ISLAND_HOPPING_ROOT "gapa"
#define FA_AWAR_GAP_B FA_AWAR_ISLAND_HOPPING_ROOT "gapb"
#define FA_AWAR_GAP_C FA_AWAR_ISLAND_HOPPING_ROOT "gapc"
// --------------------------------------------------------------------------------
static IslandHopping *island_hopper = NULL; // NULL -> use fast aligner; else use island hopper
static GB_alignment_type global_alignmentType = GB_AT_UNKNOWN; // type of actually aligned sequence
static int currentSequenceNumber; // used for counter
static int overallSequenceNumber;
// --------------------------------------------------------------------------------
inline ARB_ERROR species_not_found(GB_CSTR species_name) {
return GBS_global_string("No species '%s' found!", species_name);
}
static ARB_ERROR reverseComplement(GBDATA *gb_species, GB_CSTR ali, int max_protection) {
GBDATA *gbd = GBT_read_sequence(gb_species, ali);
ARB_ERROR error = 0;
if (!gbd) {
error = GBS_global_string("No 'data' found for species '%s'", GBT_read_name(gb_species));
}
else {
int my_protection = GB_read_security_write(gbd);
if (my_protection<=max_protection) { // ok
char *seq = GB_read_string(gbd);
int length = GB_read_string_count(gbd);
GBDATA *gb_main = GB_get_root(gb_species);
GB_alignment_type ali_type = GBT_get_alignment_type(gb_main, ali);
char T_or_U;
error = GBT_determine_T_or_U(ali_type, &T_or_U, "reverse-complement");
if (!error) {
GBT_reverseComplementNucSequence(seq, length, T_or_U);
error = GB_write_string(gbd, seq);
}
}
else { // protection error
error = GBS_global_string("Cannot reverse-complement species '%s' because of protection level", GBT_read_name(gb_species));
}
}
return error;
}
static void build_reverse_complement(AW_window *aw, AW_CL cl_AlignDataAccess) {
const AlignDataAccess *data_access = (const AlignDataAccess *)cl_AlignDataAccess;
GBDATA *gb_main = data_access->gb_main;
GB_push_transaction(gb_main);
AW_root *root = aw->get_root();
FA_alignTarget revComplWhat = static_cast<FA_alignTarget>(root->awar(FA_AWAR_TO_ALIGN)->read_int());
char *default_alignment = GBT_get_default_alignment(gb_main);
GB_CSTR alignment = root->awar_string(AWAR_EDITOR_ALIGNMENT, default_alignment)->read_string();
ARB_ERROR error = 0;
int max_protection = root->awar(FA_AWAR_PROTECTION)->read_int();
switch (revComplWhat) {
case FA_CURRENT: { // current species
GB_CSTR species_name = root->awar(AWAR_SPECIES_NAME)->read_string();
GBDATA *gb_species = GBT_find_species(gb_main, species_name);
if (!gb_species) error = species_not_found(species_name);
if (!error) error = reverseComplement(gb_species, alignment, max_protection);
break;
}
case FA_MARKED: { // marked species
GBDATA *gb_species = GBT_first_marked_species(gb_main);
if (!gb_species) {
error = "There is no marked species";
}
while (gb_species) {
error = reverseComplement(gb_species, alignment, max_protection);
if (error) break;
gb_species = GBT_next_marked_species(gb_species);
}
break;
}
case FA_SELECTED: { // selected species (editor selection!)
Aligner_get_first_selected_species get_first_selected_species = data_access->get_first_selected_species;
Aligner_get_next_selected_species get_next_selected_species = data_access->get_next_selected_species;
int count = 0;
GBDATA *gb_species = get_first_selected_species(&count);
if (!gb_species) {
error = "There is no selected species!";
}
while (gb_species) {
error = reverseComplement(gb_species, alignment, max_protection);
if (error) break;
gb_species = get_next_selected_species();
}
break;
}
default: {
fa_assert(0);
break;
}
}
GB_end_transaction_show_error(gb_main, error, aw_message);
}
// --------------------------------------------------------------------------------
class AliChange { // describes a local alignment change
const CompactedSubSequence& Old;
const CompactedSubSequence& New;
public:
AliChange(const CompactedSubSequence& old_, const CompactedSubSequence& new_)
: Old(old_), New(new_)
{
fa_assert(Old.may_refer_to_same_part_as(New));
}
int follow(ExplicitRange& range) const {
ExplicitRange compressed(Old.compPosition(range.start()),
Old.compPosition(range.end()));
int exp_start = New.expdPosition(compressed.start());
int exp_end = New.expdPosition(compressed.end());
int gaps_before = New.no_of_gaps_before(compressed.start());
int gaps_after = New.no_of_gaps_after(compressed.end());
fa_assert(gaps_before >= 0);
fa_assert(gaps_after >= 0);
range = ExplicitRange(exp_start-gaps_before, exp_end+gaps_after);
return compressed.size(); // number of bases
}
};
class LooseBases {
typedef std::list<ExplicitRange> Ranges;
Ranges ranges;
public:
bool is_empty() const { return ranges.empty(); }
void clear() { ranges.clear(); }
void memorize(ExplicitRange range) {
ranges.push_front(range);
}
ExplicitRange recall() {
ExplicitRange range = ranges.front();
ranges.pop_front();
return range;
}
int follow_ali_change(const AliChange& change) {
// transform positions according to changed alignment (oldSequence -> newSequence)
// returns the number of bases contained in 'this'
int basecount = 0;
if (!is_empty()) {
for (Ranges::iterator r = ranges.begin(); r != ranges.end(); ++r) {
basecount += change.follow(*r);
}
}
return basecount;
}
void append(LooseBases& loose) { ranges.splice(ranges.end(), loose.ranges); }
int follow_ali_change_and_append(LooseBases& loose, const AliChange& change) {
// returns the number of loose bases (added from 'loose')
int basecount = loose.follow_ali_change(change);
append(loose);
return basecount;
}
};
static LooseBases unaligned_bases; // if fast_align cannot align (no master bases) -> stores positions here
static const char *read_name(GBDATA *gbd) {
return gbd ? GBT_read_name(gbd) : "GROUP-CONSENSUS";
}
inline int relatedBases(char base1, char base2) {
return baseMatch(base1, base2)==1;
}
inline char alignQuality(char slave, char master) {
fa_assert(slave);
fa_assert(master);
char result = '#';
if (slave==master) result = '-'; // equal
else if (slave==GAP_CHAR) result = '+'; // inserted gap
else if (master==GAP_CHAR) result = '+'; // no gap in master
else if (relatedBases(slave, master)) result = '~'; // mutation (related bases)
return result; // mutation (non-related bases)
}
// -------------------------
// Debugging stuff
#ifdef DEBUG
static char *lstr(const char *s, int len) {
static int alloc;
static char *buffer;
if (alloc<(len+1)) {
if (alloc) free(buffer);
buffer = (char*)malloc(alloc=len+100);
}
memcpy(buffer, s, len);
buffer[len] = 0;
return buffer;
}
#define BUFLEN 120
inline char compareChar(char base1, char base2) {
return base1==base2 ? '=' : (relatedBases(base1, base2) ? 'x' : 'X');
}
#if defined(TRACE_COMPRESSED_ALIGNMENT)
static void dump_n_compare_one(const char *seq1, const char *seq2, long len, long offset) {
fa_assert(len<=BUFLEN);
char compare[BUFLEN+1];
for (long l=0; l<len; l++) {
compare[l] = (is_ali_gap(seq1[l]) && is_ali_gap(seq2[l])) ? ' ' : compareChar(seq1[l], seq2[l]);
}
compare[len] = 0;
printf(" %li '%s'\n", offset, lstr(seq1, len));
printf(" %li '%s'\n", offset, lstr(seq2, len));
printf(" %li '%s'\n", offset, compare);
}
inline void dump_rest(const char *seq, long len, int idx, long offset) {
printf(" Rest von Sequenz %i:\n", idx);
while (len>BUFLEN) {
printf(" %li '%s'\n", offset, lstr(seq, BUFLEN));
seq += BUFLEN;
len -= BUFLEN;
offset += BUFLEN;
}
fa_assert(len>0);
printf(" '%s'\n", lstr(seq, len));
}
static void dump_n_compare(const char *text, const char *seq1, long len1, const char *seq2, long len2) {
long offset = 0;
printf(" Comparing %s:\n", text);
while (len1>0 && len2>0) {
long done = 0;
if (len1>=BUFLEN && len2>=BUFLEN) {
dump_n_compare_one(seq1, seq2, done=BUFLEN, offset);
}
else {
long min = len1<len2 ? len1 : len2;
dump_n_compare_one(seq1, seq2, done=min, offset);
}
seq1 += done;
seq2 += done;
len1 -= done;
len2 -= done;
offset += done;
}
if (len1>0) dump_rest(seq1, len1, 1, offset);
if (len2>0) dump_rest(seq2, len2, 2, offset);
printf(" -------------------\n");
}
static void dump_n_compare(const char *text, const CompactedSubSequence& seq1, const CompactedSubSequence& seq2) {
dump_n_compare(text, seq1.text(), seq1.length(), seq2.text(), seq2.length());
}
#endif // TRACE_COMPRESSED_ALIGNMENT
#undef BUFLEN
inline void dumpSeq(const char *seq, long len, long pos) {
printf("'%s' ", lstr(seq, len));
printf("(Pos=%li,Len=%li)", pos, len);
}
#define dump() \
do { \
double sig = partSignificance(sequence().length(), slaveSequence.length(), bestLength); \
\
printf(" Score = %li (Significance=%f)\n" \
" Master = ", bestScore, sig); \
dumpSeq(bestMasterLeft.text(), bestLength, bestMasterLeft.leftOf()); \
printf("\n" \
" Slave = "); \
dumpSeq(bestSlaveLeft.text(), bestLength, bestSlaveLeft.leftOf()); \
printf("\n"); \
} while (0)
#endif //DEBUG
// ------------------------------------------------
// INLINE-functions used in fast_align():
inline double log3(double d) {
return log(d)/log(3.0);
}
inline double partSignificance(long seq1len, long seq2len, long partlen) {
// returns log3 of significance of the part
// usage: partSignificance(...) < log3(maxAllowedSignificance)
return log3((seq1len-partlen)*(seq2len-partlen)) - partlen;
}
inline ARB_ERROR bufferTooSmall() {
return "Cannot align - reserved buffer is to small";
}
inline long insertsToNextBase(AlignBuffer *alignBuffer, const SequencePosition& master) {
int inserts;
int nextBase;
if (master.rightOf()>0) {
nextBase = master.expdPosition();
}
else {
nextBase = master.sequence().expdPosition(master.sequence().length());
}
inserts = nextBase-alignBuffer->offset();
return inserts;
}
inline void insertBase(AlignBuffer *alignBuffer,
SequencePosition& master, SequencePosition& slave,
FastAlignReport *report)
{
char slaveBase = *slave.text();
char masterBase = *master.text();
alignBuffer->set(slaveBase, alignQuality(slaveBase, masterBase));
report->count_aligned_base(slaveBase!=masterBase);
++slave;
++master;
}
inline void insertSlaveBases(AlignBuffer *alignBuffer,
SequencePosition& slave,
int length,
FastAlignReport *report)
{
alignBuffer->copy(slave.text(), alignQuality(*slave.text(), GAP_CHAR), length);
report->count_unaligned_base(length);
slave += length;
}
inline void insertGap(AlignBuffer *alignBuffer,
SequencePosition& master,
FastAlignReport *report)
{
char masterBase = *master.text();
alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, masterBase));
report->count_aligned_base(masterBase!=GAP_CHAR);
++master;
}
static ARB_ERROR insertClustalValigned(AlignBuffer *alignBuffer,
SequencePosition& master,
SequencePosition& slave,
const char *masterAlignment, const char *slaveAlignment, long alignmentLength,
FastAlignReport *report)
{
// inserts bases of 'slave' to 'alignBuffer' according to alignment in 'masterAlignment' and 'slaveAlignment'
#define ACID '*' // contents of 'masterAlignment' and 'slaveAlignment'
#define GAP '-'
int pos;
int baseAtLeft = 0; // TRUE -> last position in alignBuffer contains a base
for (pos=0; pos<alignmentLength; pos++) {
long insert = insertsToNextBase(alignBuffer, master); // in expanded seq
if (masterAlignment[pos]==ACID) {
if (insert>0) {
if (insert>alignBuffer->free()) return bufferTooSmall();
alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), insert);
fa_assert(insertsToNextBase(alignBuffer, master)==0);
insert = 0;
}
if (!alignBuffer->free()) return bufferTooSmall();
if (slaveAlignment[pos]==ACID) {
insertBase(alignBuffer, master, slave, report);
baseAtLeft = 1;
}
else {
insertGap(alignBuffer, master, report);
baseAtLeft = 0;
}
}
else {
int slave_bases;
fa_assert(masterAlignment[pos]==GAP);
for (slave_bases=1; pos+slave_bases<alignmentLength && masterAlignment[pos+slave_bases]==GAP; slave_bases++) {
; // count gaps in master (= # of slave bases to insert)
}
if (!baseAtLeft && insert>slave_bases) {
int ins_gaps = insert-slave_bases;
fa_assert(alignBuffer->free()>=ins_gaps);
alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), ins_gaps);
insert -= ins_gaps;
}
if (insert<slave_bases) { // master has less gaps than slave bases to insert
report->memorize_insertion(master.expdPosition(), slave_bases-insert);
}
else if (insert>slave_bases) { // master has more gaps than slave bases to insert
fa_assert(baseAtLeft);
}
unaligned_bases.memorize(ExplicitRange(slave.expdPosition(), // memorize base positions without counterpart in master
slave.expdPosition(slave_bases-1)));
if (slave_bases>alignBuffer->free()) return bufferTooSmall();
insertSlaveBases(alignBuffer, slave, slave_bases, report);
pos += slave_bases-1; // -1 compensates for()-increment
baseAtLeft = 1;
}
}
return 0;
#undef GAP
#undef ACID
}
static ARB_ERROR insertAligned(AlignBuffer *alignBuffer,
SequencePosition& master, SequencePosition& slave, long partLength,
FastAlignReport *report)
{
// insert bases of 'slave' to 'alignBuffer' according to 'master'
if (partLength) {
long insert = insertsToNextBase(alignBuffer, master);
fa_assert(partLength>=0);
if (insert<0) { // insert gaps into master
long min_insert = insert;
report->memorize_insertion(master.expdPosition(), -insert);
while (insert<0 && partLength) {
if (insert<min_insert) min_insert = insert;
if (!alignBuffer->free()) {
return bufferTooSmall();
}
insertBase(alignBuffer, master, slave, report);
partLength--;
insert = insertsToNextBase(alignBuffer, master);
}
fa_assert(partLength>=0);
if (partLength==0) { // all inserted
return NULL;
}
}
fa_assert(insert>=0);
if (insert>0) { // insert gaps into slave
if (insert>alignBuffer->free()) return bufferTooSmall();
alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), insert);
fa_assert(insertsToNextBase(alignBuffer, master)==0);
}
fa_assert(partLength>=0);
while (partLength--) {
insert = insertsToNextBase(alignBuffer, master);
fa_assert(insert>=0);
if (insert>0) {
if (insert>=alignBuffer->free()) return bufferTooSmall();
alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), insert);
}
else {
if (!alignBuffer->free()) {
return bufferTooSmall();
}
}
insertBase(alignBuffer, master, slave, report);
}
}
return NULL;
}
static ARB_ERROR cannot_fast_align(const CompactedSubSequence& master, long moffset, long mlength,
const CompactedSubSequence& slaveSequence, long soffset, long slength,
int max_seq_length,
AlignBuffer *alignBuffer,
FastAlignReport *report)
{
const char *mtext = master.text(moffset);
const char *stext = slaveSequence.text(soffset);
ARB_ERROR error = 0;
if (slength) {
if (mlength) { // if slave- and master-sequences contain bases, we call the slow aligner
#ifdef TRACE_CLUSTAL_DATA
printf("ClustalV-Align:\n");
printf(" mseq = '%s'\n", lstr(mtext, mlength));
printf(" sseq = '%s'\n", lstr(stext, slength));
#endif // TRACE_CLUSTAL_DATA
int is_dna = -1;
switch (global_alignmentType) {
case GB_AT_RNA:
case GB_AT_DNA: is_dna = 1; break;
case GB_AT_AA: is_dna = 0; break;
default: error = "Unknown alignment type - aligner aborted"; break;
}
const char *maligned, *saligned;
int len;
if (!error) {
int score; // unused
error = ClustalV_align(is_dna,
1,
mtext, mlength, stext, slength,
master.gapsBefore(moffset),
max_seq_length,
maligned, saligned, len, score);
}
if (!error) {
#ifdef TRACE_CLUSTAL_DATA
printf("ClustalV returns:\n");
printf(" maligned = '%s'\n", lstr(maligned, len));
printf(" saligned = '%s'\n", lstr(saligned, len));
#endif // TRACE_CLUSTAL_DATA
SequencePosition masterPos(master, moffset);
SequencePosition slavePos(slaveSequence, soffset);
error = insertClustalValigned(alignBuffer, masterPos, slavePos, maligned, saligned, len, report);
#if (defined(DEBUG) && 0)
SequencePosition master2(master->sequence(), moffset);
SequencePosition slave2(slaveSequence, soffset);
char *cmp = new char[len];
for (int l=0; l<len; l++) {
int gaps = 0;
if (maligned[l]=='*') {
maligned[l] = *master2.text();
++master2;
}
else {
gaps++;
}
if (saligned[l]=='*') {
saligned[l] = *slave2.text();
++slave2;
}
else {
gaps++;
}
cmp[l] = gaps || maligned[l]==saligned[l] ? '=' : 'X';
}
printf(" master = '%s'\n", lstr(maligned, len));
printf(" slave = '%s'\n", lstr(saligned, len));
printf(" '%s'\n", lstr(cmp, len));
delete [] cmp;
#endif
}
}
else { // master is empty here, so we just copy in the slave bases
if (slength<=alignBuffer->free()) {
unaligned_bases.memorize(ExplicitRange(slaveSequence.expdPosition(soffset),
slaveSequence.expdPosition(soffset+slength-1)));
alignBuffer->copy(slaveSequence.text(soffset), '?', slength); // '?' means not aligned (just inserted)
// corrected by at alignBuffer->correctUnalignedPositions()
report->count_unaligned_base(slength);
}
else {
error = bufferTooSmall();
}
}
}
return error;
}
// ------------------------------------
// #define's for fast_align()
#define TEST_BETTER_SCORE() \
do { \
if (score>bestScore) { \
bestScore = score; \
bestLength = masterRight.text() - masterLeft.text(); \
bestMasterLeft = masterLeft; \
bestSlaveLeft = slaveLeft; \
} \
} while (0)
#define CAN_SCORE_LEFT() (masterLeft.leftOf() && slaveLeft.leftOf())
#define CAN_SCORE_RIGHT() (masterRight.rightOf() && slaveRight.rightOf())
#define SCORE_LEFT() \
do { \
score += *(--masterLeft).text()==*(--slaveLeft).text() ? match : mismatch; \
TEST_BETTER_SCORE(); \
} while (0)
#define SCORE_RIGHT() \
do { \
score += *(++masterRight).text()==*(++slaveRight).text() ? match : mismatch; \
TEST_BETTER_SCORE(); \
} while (0)
ARB_ERROR FastSearchSequence::fast_align(const CompactedSubSequence& slaveSequence,
AlignBuffer *alignBuffer,
int max_seq_length,
int match, int mismatch,
FastAlignReport *report) const
{
// aligns 'slaveSequence' to 'this'
//
// returns
// == NULL -> all ok -> 'alignBuffer' contains aligned sequence
// != NULL -> failure -> no results
ARB_ERROR error = NULL;
int aligned = 0;
// set the following #if to zero to test ClustalV-Aligner (not fast_aligner)
#if 1
static double lowSignificance;
static int lowSignificanceInitialized;
if (!lowSignificanceInitialized) {
lowSignificance = log3(0.01);
lowSignificanceInitialized = 1;
}
SequencePosition slave(slaveSequence);
long bestScore=0;
SequencePosition bestMasterLeft(sequence());
SequencePosition bestSlaveLeft(slaveSequence);
long bestLength=0;
while (slave.rightOf()>=3) { // with all triples of slaveSequence
FastSearchOccurrence occurrence(*this, slave.text()); // "search" first
SequencePosition rightmostSlave = slave;
while (occurrence.found()) { // with all occurrences of the triple
long score = match*3;
SequencePosition masterLeft(occurrence.sequence(), occurrence.offset());
SequencePosition masterRight(occurrence.sequence(), occurrence.offset()+3);
SequencePosition slaveLeft(slave);
SequencePosition slaveRight(slave, 3);
while (score>0) {
if (CAN_SCORE_LEFT()) {
SCORE_LEFT();
}
else {
while (score>0 && CAN_SCORE_RIGHT()) {
SCORE_RIGHT();
}
break;
}
if (CAN_SCORE_RIGHT()) {
SCORE_RIGHT();
}
else {
while (score>0 && CAN_SCORE_LEFT()) {
SCORE_LEFT();
}
break;
}
}
occurrence.gotoNext(); // "search" next
if (rightmostSlave<slaveRight) {
rightmostSlave = slaveRight;
rightmostSlave -= 3;
}
}
if (rightmostSlave>slave) slave = rightmostSlave;
else ++slave;
}
if (bestLength) {
double sig = partSignificance(sequence().length(), slaveSequence.length(), bestLength);
if (sig<lowSignificance) {
long masterLeftOf = bestMasterLeft.leftOf();
long masterRightStart = masterLeftOf+bestLength;
long masterRightOf = bestMasterLeft.rightOf()-bestLength;
long slaveLeftOf = bestSlaveLeft.leftOf();
long slaveRightStart = slaveLeftOf+bestLength;
long slaveRightOf = bestSlaveLeft.rightOf()-bestLength;
#define MIN_ALIGNMENT_RANGE 4
if (!error) {
if (masterLeftOf >= MIN_ALIGNMENT_RANGE && slaveLeftOf >= MIN_ALIGNMENT_RANGE) {
CompactedSubSequence leftCompactedMaster(sequence(), 0, masterLeftOf);
FastSearchSequence leftMaster(leftCompactedMaster);
error = leftMaster.fast_align(CompactedSubSequence(slaveSequence, 0, slaveLeftOf),
alignBuffer, max_seq_length, match, mismatch, report);
}
else if (slaveLeftOf>0) {
error = cannot_fast_align(sequence(), 0, masterLeftOf,
slaveSequence, 0, slaveLeftOf,
max_seq_length, alignBuffer, report);
}
aligned = 1;
}
// align part of slave sequence according to master sequence:
if (!error) {
#if (defined(DEBUG) && 0)
long offset = alignBuffer->offset();
long used;
#endif
error = insertAligned(alignBuffer, bestMasterLeft, bestSlaveLeft, bestLength, report);
#if (defined(DEBUG) && 0)
used = alignBuffer->offset()-offset;
printf("aligned '%s' (len=%li, address=%li)\n", lstr(alignBuffer->text()+offset, used), used, long(alignBuffer));
#endif
aligned = 1;
}
if (!error) {
if (masterRightOf >= MIN_ALIGNMENT_RANGE && slaveRightOf >= MIN_ALIGNMENT_RANGE) {
CompactedSubSequence rightCompactedMaster(sequence(), masterRightStart, masterRightOf);
FastSearchSequence rightMaster(rightCompactedMaster);
error = rightMaster.fast_align(CompactedSubSequence(slaveSequence, slaveRightStart, slaveRightOf),
alignBuffer,
max_seq_length, match, mismatch, report);
}
else if (slaveRightOf>0) {
error = cannot_fast_align(sequence(), masterRightStart, masterRightOf,
slaveSequence, slaveRightStart, slaveRightOf,
max_seq_length, alignBuffer, report);
}
aligned = 1;
}
}
}
#endif
if (!aligned && !error) {
error = cannot_fast_align(sequence(), 0, sequence().length(),
slaveSequence, 0, slaveSequence.length(),
max_seq_length, alignBuffer, report);
}
return error;
}
#undef dump
#undef TEST_BETTER_SCORE
#undef CAN_SCORE_LEFT
#undef CAN_SCORE_RIGHT
#undef SCORE_LEFT
#undef SCORE_RIGHT
inline long calcSequenceChecksum(const char *data, long length) {
return GB_checksum(data, length, 1, GAP_CHARS);
}
#if defined(WARN_TODO)
#warning firstColumn + lastColumn -> PosRange
#endif
static CompactedSubSequence *readCompactedSequence(GBDATA *gb_species,
const char *ali,
ARB_ERROR *errorPtr,
char **dataPtr, // if dataPtr != NULL it will be set to the WHOLE uncompacted sequence
long *seqChksum, // may be NULL (of part of sequence)
PosRange range) // if !range.is_whole() -> return only part of the sequence
{
ARB_ERROR error = 0;
GBDATA *gbd;
CompactedSubSequence *seq = 0;
gbd = GBT_read_sequence(gb_species, ali); // get sequence
if (gbd) {
long length = GB_read_string_count(gbd);
char *data = GB_read_string(gbd);
long partLength;
char *partData;
if (dataPtr) { // make a copy of the whole uncompacted sequence (returned to caller)
*dataPtr = data;
}
int firstColumn = range.start();
if (range.is_part()) { // take only part of sequence
int lastColumn = range.end();
fa_assert(firstColumn>=0);
fa_assert(firstColumn<=lastColumn);
// include all surrounding gaps (@@@ this might cause problems with partial alignment)
while (firstColumn>0 && is_ali_gap(data[firstColumn-1])) {
firstColumn--;
}
if (lastColumn!=-1) {
while (lastColumn<(length-1) && is_ali_gap(data[lastColumn+1])) lastColumn++;
fa_assert(lastColumn<length);
}
partData = data+firstColumn;
int slen = length-firstColumn;
fa_assert(slen>=0);
fa_assert((size_t)slen==strlen(partData));
if (lastColumn==-1) { // take all till end of sequence
partLength = slen;
}
else {
partLength = lastColumn-firstColumn+1;
if (partLength>slen) partLength = slen; // cut rest, if we have any
}
}
else {
partLength = length;
partData = data;
}
if (!error) {
if (seqChksum) {
*seqChksum = calcSequenceChecksum(partData, partLength);
}
seq = new CompactedSubSequence(partData, partLength, GBT_read_name(gb_species), firstColumn);
}
if (!dataPtr) { // free sequence only if user has not requested to get it
free(data);
}
}
else {
error = GBS_global_string("No 'data' found for species '%s'", GBT_read_name(gb_species));
if (dataPtr) *dataPtr = NULL; // (user must not care to free data if we fail)
}
fa_assert(errorPtr);
*errorPtr = error;
return seq;
}
static ARB_ERROR writeStringToAlignment(GBDATA *gb_species, GB_CSTR alignment, GB_CSTR data_name, GB_CSTR str, bool temporary) {
GBDATA *gb_ali = GB_search(gb_species, alignment, GB_DB);
ARB_ERROR error = NULL;
GBDATA *gb_name = GB_search(gb_ali, data_name, GB_STRING);
if (gb_name) {
fa_assert(GB_check_father(gb_name, gb_ali));
error = GB_write_string(gb_name, str);
if (temporary && !error) error = GB_set_temporary(gb_name);
}
else {
error = GBS_global_string("Cannot create entry '%s' for '%s'", data_name, GBT_read_name(gb_species));
}
return error;
}
// --------------------------------------------------------------------------------
static ARB_ERROR alignCompactedTo(CompactedSubSequence *toAlignSequence,
const FastSearchSequence *alignTo,
int max_seq_length,
GB_CSTR alignment,
long toAlignChksum,
GBDATA *gb_toAlign,
GBDATA *gb_alignTo, // may be NULL
const AlignParams& ali_params)
{
// if only part of the sequence should be aligned, then this functions already gets only the part
// (i.o.w.: toAlignSequence, alignTo and toAlignChksum refer to the partial sequence)
AlignBuffer alignBuffer(max_seq_length);
if (ali_params.range.start()>0) {
alignBuffer.set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), ali_params.range.start());
}
const char *master_name = read_name(gb_alignTo);
FastAlignReport report(master_name, ali_params.showGapsMessages);
{
static GBDATA *last_gb_toAlign = 0;
if (gb_toAlign!=last_gb_toAlign) {
last_gb_toAlign = gb_toAlign;
currentSequenceNumber++;
}
}
#ifdef TRACE_COMPRESSED_ALIGNMENT
printf("alignCompactedTo(): master='%s' ", master_name);
printf("slave='%s'\n", toAlignSequence->name());
#endif // TRACE_COMPRESSED_ALIGNMENT
ARB_ERROR error = GB_pop_transaction(gb_toAlign);
if (!error) {
if (island_hopper) {
error = island_hopper->do_align();
if (!error) {
fa_assert(island_hopper->was_aligned());
#ifdef TRACE_ISLANDHOPPER_DATA
printf("Island-Hopper returns:\n");
printf("maligned = '%s'\n", lstr(island_hopper->get_result_ref(), island_hopper->get_result_length()));
printf("saligned = '%s'\n", lstr(island_hopper->get_result(), island_hopper->get_result_length()));
#endif // TRACE_ISLANDHOPPER_DATA
SequencePosition masterPos(alignTo->sequence(), 0);
SequencePosition slavePos(*toAlignSequence, 0);
error = insertClustalValigned(&alignBuffer, masterPos, slavePos, island_hopper->get_result_ref(), island_hopper->get_result(), island_hopper->get_result_length(), &report);
}
}
else {
error = alignTo->fast_align(*toAlignSequence, &alignBuffer, max_seq_length, 2, -10, &report); // <- here we align
}
}
if (!error) {
alignBuffer.correctUnalignedPositions();
if (alignBuffer.free()) {
alignBuffer.set('-', alignQuality(GAP_CHAR, GAP_CHAR), alignBuffer.free()); // rest of alignBuffer is set to '-'
}
alignBuffer.restoreDots(*toAlignSequence);
}
#ifdef TRACE_COMPRESSED_ALIGNMENT
if (!error) {
CompactedSubSequence alignedSlave(alignBuffer.text(), alignBuffer.length(), toAlignSequence->name());
dump_n_compare("reference vs. aligned:", alignTo->sequence(), alignedSlave);
}
#endif // TRACE_COMPRESSED_ALIGNMENT
{
GB_ERROR err = GB_push_transaction(gb_toAlign);
if (!error) error = err;
}
if (!error) {
if (calcSequenceChecksum(alignBuffer.text(), alignBuffer.length())!=toAlignChksum) { // sequence-chksum changed
error = "Internal aligner error (sequence checksum changed) -- aborted";
#ifdef TRACE_COMPRESSED_ALIGNMENT
CompactedSubSequence alignedSlave(alignBuffer.text(), alignBuffer.length(), toAlignSequence->name());
dump_n_compare("Old Slave vs. new Slave", *toAlignSequence, alignedSlave);
#endif // TRACE_COMPRESSED_ALIGNMENT
}
else {
GB_push_my_security(gb_toAlign);
{
GBDATA *gbd = GBT_add_data(gb_toAlign, alignment, "data", GB_STRING);
if (!gbd) {
error = "Can't find/create sequence data";
}
else {
if (ali_params.range.is_part()) { // we aligned just a part of the sequence
char *buffer = GB_read_string(gbd); // so we read old sequence data
long len = GB_read_string_count(gbd);
if (!buffer) error = GB_await_error();
else {
int lenToCopy = ali_params.range.size();
long wholeChksum = calcSequenceChecksum(buffer, len);
memcpy(buffer+ali_params.range.start(), alignBuffer.text()+ali_params.range.start(), lenToCopy); // copy in the aligned part
// @@@ genau um 1 position zu niedrig
if (calcSequenceChecksum(buffer, len) != wholeChksum) {
error = "Internal aligner error (sequence checksum changed) -- aborted";
# ifdef TRACE_COMPRESSED_ALIGNMENT
char *buffer_org = GB_read_string(gbd);
dump_n_compare("Old seq vs. new seq (slave)", buffer_org, len, buffer, len);
free(buffer_org);
# endif // TRACE_COMPRESSED_ALIGNMENT
}
else {
GB_write_string(gbd, "");
error = GB_write_string(gbd, buffer);
}
}
free(buffer);
}
else {
alignBuffer.setDotsAtEOSequence();
error = GBT_write_sequence(gbd, alignment, max_seq_length, alignBuffer.text()); // aligned all -> write all
}
}
}
GB_pop_my_security(gb_toAlign);
if (!error && ali_params.report != FA_NO_REPORT) {
// create temp-entry for slave containing alignment quality:
error = writeStringToAlignment(gb_toAlign, alignment, QUALITY_NAME, alignBuffer.quality(), ali_params.report==FA_TEMP_REPORT);
if (!error) {
// create temp-entry for master containing insert dots:
int buflen = max_seq_length*2;
char *buffer = (char*)malloc(buflen+1);
char *afterLast = buffer;
if (!buffer) {
error = "out of memory";
}
else {
memset(buffer, '-', buflen);
buffer[buflen] = 0;
const FastAlignInsertion *inserts = report.insertion();
while (inserts) {
memset(buffer+inserts->offset(), '>', inserts->gaps());
afterLast = buffer+inserts->offset()+inserts->gaps();
inserts = inserts->next();
}
*afterLast = 0;
if (gb_alignTo) {
error = writeStringToAlignment(gb_alignTo, alignment, INSERTS_NAME, buffer, ali_params.report==FA_TEMP_REPORT);
}
}
}
}
}
}
return error;
}
ARB_ERROR FastAligner_delete_temp_entries(GBDATA *gb_species, const char *alignment) {
fa_assert(gb_species);
fa_assert(alignment);
GBDATA *gb_ali = GB_search(gb_species, alignment, GB_FIND);
ARB_ERROR error = NULL;
if (gb_ali) {
GBDATA *gb_name = GB_search(gb_ali, QUALITY_NAME, GB_FIND);
if (gb_name) {
error = GB_delete(gb_name);
#if defined(DEBUG)
printf("deleted '%s' of '%s' (gb_name=%p)\n", QUALITY_NAME, GBT_read_name(gb_species), gb_name);
#endif
}
if (!error) {
gb_name = GB_search(gb_ali, INSERTS_NAME, GB_FIND);
if (gb_name) {
error = GB_delete(gb_name);
#if defined(DEBUG)
printf("deleted '%s' of '%s' (gb_name=%p)\n", INSERTS_NAME, GBT_read_name(gb_species), gb_name);
#endif
}
}
}
return error;
}
static ARB_ERROR align_error(ARB_ERROR olderr, GBDATA *gb_toAlign, GBDATA *gb_alignTo) {
// used by alignTo() and alignToNextRelative() to transform errors coming from subroutines
// can be used by higher functions
const char *name_toAlign = read_name(gb_toAlign);
const char *name_alignTo = read_name(gb_alignTo);
fa_assert(olderr);
return GBS_global_string("Error while aligning '%s' to '%s':\n%s",
name_toAlign, name_alignTo, olderr.deliver());
}
static ARB_ERROR alignTo(GBDATA *gb_toAlign,
GB_CSTR alignment,
const FastSearchSequence *alignTo,
GBDATA *gb_alignTo, // may be NULL
int max_seq_length,
const AlignParams& ali_params)
{
ARB_ERROR error = NULL;
long chksum;
CompactedSubSequence *toAlignSequence = readCompactedSequence(gb_toAlign, alignment, &error, NULL, &chksum, ali_params.range);
if (island_hopper) {
GBDATA *gb_seq = GBT_read_sequence(gb_toAlign, alignment); // get sequence
if (gb_seq) {
long length = GB_read_string_count(gb_seq);
const char *data = GB_read_char_pntr(gb_seq);
island_hopper->set_toAlign_sequence(data);
island_hopper->set_alignment_length(length);
}
}
if (!error) {
error = alignCompactedTo(toAlignSequence, alignTo, max_seq_length, alignment, chksum, gb_toAlign, gb_alignTo, ali_params);
if (error) error = align_error(error, gb_toAlign, gb_alignTo);
delete toAlignSequence;
}
return error;
}
static ARB_ERROR alignToGroupConsensus(GBDATA *gb_toAlign,
GB_CSTR alignment,
Aligner_get_consensus_func get_consensus,
int max_seq_length,
const AlignParams& ali_params)
{
ARB_ERROR error = 0;
char *consensus = get_consensus(read_name(gb_toAlign), ali_params.range);
size_t cons_len = strlen(consensus);
fa_assert(cons_len);
for (size_t i = 0; i<cons_len; ++i) { // translate consensus to be accepted by aligner
switch (consensus[i]) {
case '=': consensus[i] = '-'; break;
default: break;
}
}
CompactedSubSequence compacted(consensus, cons_len, "group consensus", ali_params.range.start());
{
FastSearchSequence fast(compacted);
error = alignTo(gb_toAlign, alignment, &fast, NULL, max_seq_length, ali_params);
}
free(consensus);
return error;
}
static void appendNameAndUsedBasePositions(char **toString, GBDATA *gb_species, int usedBasePositions) {
// if usedBasePositions == -1 -> unknown;
char *currInfo;
if (usedBasePositions<0) {
currInfo = strdup(GBT_read_name(gb_species));
}
else {
fa_assert(usedBasePositions>0); // otherwise it should NOT be announced here!
currInfo = GBS_global_string_copy("%s:%i", GBT_read_name(gb_species), usedBasePositions);
}
char *newString = 0;
if (*toString) {
newString = GBS_global_string_copy("%s, %s", *toString, currInfo);
}
else {
newString = currInfo;
currInfo = 0; // don't free
}
freeset(*toString, newString);
free(currInfo);
}
inline int min(int i, int j) { return i<j ? i : j; }
static ARB_ERROR alignToNextRelative(SearchRelativeParams& relSearch,
int max_seq_length,
FA_turn turnAllowed,
GB_CSTR alignment,
GBDATA *gb_toAlign,
const AlignParams& ali_params)
{
CompactedSubSequence *toAlignSequence = NULL;
bool use_different_pt_server_alignment = 0 != strcmp(relSearch.pt_server_alignment, alignment);
ARB_ERROR error;
long chksum;
int relativesToTest = relSearch.maxRelatives*2; // get more relatives from pt-server (needed when use_different_pt_server_alignment == true)
char **nearestRelative = new char*[relativesToTest+1];
int next_relatives;
int i;
GBDATA *gb_main = GB_get_root(gb_toAlign);
if (use_different_pt_server_alignment) {
turnAllowed = FA_TURN_NEVER; // makes no sense if we're using a different alignment for the pt_server
}
for (next_relatives=0; next_relatives<relativesToTest; next_relatives++) {
nearestRelative[next_relatives] = 0;
}
next_relatives = 0;
bool restart = true;
while (restart) {
restart = false;
char *findRelsBySeq = 0;
if (use_different_pt_server_alignment) {
toAlignSequence = readCompactedSequence(gb_toAlign, alignment, &error, 0, &chksum, ali_params.range);
GBDATA *gbd = GBT_read_sequence(gb_toAlign, relSearch.pt_server_alignment); // use a different alignment for next relative search
if (!gbd) {
error = GBS_global_string("Species '%s' has no data in alignment '%s'", GBT_read_name(gb_toAlign), relSearch.pt_server_alignment);
}
else {
findRelsBySeq = GB_read_string(gbd);
}
}
else {
toAlignSequence = readCompactedSequence(gb_toAlign, alignment, &error, &findRelsBySeq, &chksum, ali_params.range);
}
if (error) {
delete toAlignSequence;
return error; // @@@ leaks ?
}
while (next_relatives) {
next_relatives--;
freenull(nearestRelative[next_relatives]);
}
{
// find relatives
FamilyFinder *familyFinder = relSearch.getFamilyFinder();
const PosRange& range = familyFinder->get_TargetRange();
if (range.is_part()) {
range.copy_corresponding_part(findRelsBySeq, findRelsBySeq, strlen(findRelsBySeq));
turnAllowed = FA_TURN_NEVER; // makes no sense if we're using partial relative search
}
error = familyFinder->searchFamily(findRelsBySeq, FF_FORWARD, relativesToTest+1, 0); // @@@ make min_score configurable
// @@@ case where no relative found (due to min score) handle how ? abort ? warn ?
double bestScore = 0;
if (!error) {
#if defined(DEBUG)
double lastScore = -1;
#if defined(TRACE_RELATIVES)
fprintf(stderr, "List of relatives used for '%s':\n", GBT_read_name(gb_toAlign));
#endif // TRACE_RELATIVES
#endif // DEBUG
for (const FamilyList *fl = familyFinder->getFamilyList(); fl; fl=fl->next) {
if (strcmp(toAlignSequence->name(), fl->name)!=0) {
if (GBT_find_species(gb_main, fl->name)) { // @@@
double thisScore = familyFinder->uses_rel_matches() ? fl->rel_matches : fl->matches;
#if defined(DEBUG)
// check whether family list is sorted correctly
fa_assert(lastScore < 0 || lastScore >= thisScore);
lastScore = thisScore;
#if defined(TRACE_RELATIVES)
fprintf(stderr, "- %s (%5.2f)\n", fl->name, thisScore);
#endif // TRACE_RELATIVES
#endif // DEBUG
if (thisScore>=bestScore) bestScore = thisScore;
if (next_relatives<(relativesToTest+1)) {
nearestRelative[next_relatives] = strdup(fl->name);
next_relatives++;
}
}
}
}
}
if (!error && turnAllowed != FA_TURN_NEVER) { // test if mirrored sequence has better relatives
char *mirroredSequence = strdup(findRelsBySeq);
long length = strlen(mirroredSequence);
double bestMirroredScore = 0;
char T_or_U;
error = GBT_determine_T_or_U(global_alignmentType, &T_or_U, "reverse-complement");
if (!error) {
GBT_reverseComplementNucSequence(mirroredSequence, length, T_or_U);
error = familyFinder->searchFamily(mirroredSequence, FF_FORWARD, relativesToTest+1, 0); // @@@ make min_score configurable
}
if (!error) {
#if defined(DEBUG)
double lastScore = -1;
#if defined(TRACE_RELATIVES)
fprintf(stderr, "List of relatives used for '%s' (turned seq):\n", GBT_read_name(gb_toAlign));
#endif // TRACE_RELATIVES
#endif // DEBUG
for (const FamilyList *fl = familyFinder->getFamilyList(); fl; fl = fl->next) {
double thisScore = familyFinder->uses_rel_matches() ? fl->rel_matches : fl->matches;
#if defined(DEBUG)
// check whether family list is sorted correctly
fa_assert(lastScore < 0 || lastScore >= thisScore);
lastScore = thisScore;
#if defined(TRACE_RELATIVES)
fprintf(stderr, "- %s (%5.2f)\n", fl->name, thisScore);
#endif // TRACE_RELATIVES
#endif // DEBUG
if (thisScore >= bestMirroredScore) {
if (strcmp(toAlignSequence->name(), fl->name)!=0) {
if (GBT_find_species(gb_main, fl->name)) bestMirroredScore = thisScore; // @@@
}
}
}
}
int turnIt = 0;
if (bestMirroredScore>bestScore) {
if (turnAllowed==FA_TURN_INTERACTIVE) {
const char *message;
if (familyFinder->uses_rel_matches()) {
message = GBS_global_string("'%s' seems to be the other way round (score: %.1f%%, score if turned: %.1f%%)",
toAlignSequence->name(), bestScore*100, bestMirroredScore*100);
}
else {
message = GBS_global_string("'%s' seems to be the other way round (score: %li, score if turned: %li)",
toAlignSequence->name(), long(bestScore+.5), long(bestMirroredScore+.5));
}
turnIt = aw_question("fastali_turn_sequence", message, "Turn sequence,Leave sequence alone")==0;
}
else {
fa_assert(turnAllowed == FA_TURN_ALWAYS);
turnIt = 1;
#if defined(TRACE_RELATIVES)
fprintf(stderr, "Using turned sequence!\n");
#endif // TRACE_RELATIVES
}
}
if (turnIt) { // write mirrored sequence
GBDATA *gbd = GBT_read_sequence(gb_toAlign, alignment);
GB_push_my_security(gbd);
error = GB_write_string(gbd, mirroredSequence);
GB_pop_my_security(gbd);
if (!error) {
delete toAlignSequence;
restart = true; // continue while loop
}
}
free(mirroredSequence);
}
}
free(findRelsBySeq);
}
if (!error) {
if (!next_relatives) {
char warning[200];
sprintf(warning, "No relative found for '%s'", toAlignSequence->name());
aw_message(warning);
}
else {
// assuming relatives are sorted! (nearest to farthest)
// get data pointers
typedef GBDATA *GBDATAP;
GBDATAP *gb_reference = new GBDATAP[relSearch.maxRelatives];
{
for (i=0; i<relSearch.maxRelatives && i<next_relatives; i++) {
GBDATA *gb_species = GBT_find_species(gb_main, nearestRelative[i]);
if (!gb_species) { // pt-server seems not up to date!
error = species_not_found(nearestRelative[i]);
break;
}
GBDATA *gb_sequence = GBT_read_sequence(gb_species, alignment);
if (gb_sequence) { // if relative has sequence data in the current alignment ..
gb_reference[i] = gb_species;
}
else { // remove this relative
free(nearestRelative[i]);
for (int j = i+1; j<next_relatives; ++j) {
nearestRelative[j-1] = nearestRelative[j];
}
next_relatives--;
nearestRelative[next_relatives] = 0;
i--; // redo same index
}
}
// delete superfluous relatives
for (; i<next_relatives; ++i) freenull(nearestRelative[i]);
if (next_relatives>relSearch.maxRelatives) {
next_relatives = relSearch.maxRelatives;
}
}
// align
if (!error) {
CompactedSubSequence *alignToSequence = readCompactedSequence(gb_reference[0], alignment, &error, NULL, NULL, ali_params.range);
fa_assert(alignToSequence != 0);
if (island_hopper) {
GBDATA *gb_ref = GBT_read_sequence(gb_reference[0], alignment); // get reference sequence
GBDATA *gb_align = GBT_read_sequence(gb_toAlign, alignment); // get sequence to align
if (gb_ref && gb_align) {
long length_ref = GB_read_string_count(gb_ref);
const char *data;
data = GB_read_char_pntr(gb_ref);
island_hopper->set_ref_sequence(data);
data = GB_read_char_pntr(gb_align);
island_hopper->set_toAlign_sequence(data);
island_hopper->set_alignment_length(length_ref);
}
}
{
FastSearchSequence referenceFastSeq(*alignToSequence);
error = alignCompactedTo(toAlignSequence, &referenceFastSeq,
max_seq_length, alignment, chksum,
gb_toAlign, gb_reference[0], ali_params);
}
if (error) {
error = align_error(error, gb_toAlign, gb_reference[0]);
}
else {
char *used_relatives = 0;
if (unaligned_bases.is_empty()) {
appendNameAndUsedBasePositions(&used_relatives, gb_reference[0], -1);
}
else {
if (island_hopper) {
appendNameAndUsedBasePositions(&used_relatives, gb_reference[0], -1);
if (next_relatives>1) error = "Island hopping uses only one relative";
}
else {
LooseBases loose;
LooseBases loose_for_next_relative;
int unaligned_positions;
{
CompactedSubSequence *alignedSequence = readCompactedSequence(gb_toAlign, alignment, &error, 0, 0, ali_params.range);
unaligned_positions = loose.follow_ali_change_and_append(unaligned_bases, AliChange(*toAlignSequence, *alignedSequence));
// now loose holds the unaligned (and recalculated) parts from last relative
delete alignedSequence;
}
if (!error) {
int toalign_positions = toAlignSequence->length();
if (unaligned_positions<toalign_positions) {
appendNameAndUsedBasePositions(&used_relatives, gb_reference[0], toalign_positions-unaligned_positions);
}
}
for (i=1; i<next_relatives && !error; i++) {
loose.append(loose_for_next_relative);
int unaligned_positions_for_next = 0;
while (!loose.is_empty() && !error) {
ExplicitRange partRange(intersection(loose.recall(), ali_params.range));
CompactedSubSequence *alignToPart = readCompactedSequence(gb_reference[i], alignment, &error, 0, 0, partRange);
if (!error) {
long part_chksum;
CompactedSubSequence *toAlignPart = readCompactedSequence(gb_toAlign, alignment, &error, 0, &part_chksum, partRange);
fa_assert(contradicted(error, toAlignPart));
if (!error) {
AlignParams loose_ali_params = { ali_params.report, ali_params.showGapsMessages, partRange };
FastSearchSequence referenceFastSeq(*alignToPart);
error = alignCompactedTo(toAlignPart, &referenceFastSeq,
max_seq_length, alignment, part_chksum,
gb_toAlign, gb_reference[i], loose_ali_params);
if (!error) {
CompactedSubSequence *alignedPart = readCompactedSequence(gb_toAlign, alignment, &error, 0, 0, partRange);
if (!error) {
unaligned_positions_for_next += loose_for_next_relative.follow_ali_change_and_append(unaligned_bases, AliChange(*toAlignPart, *alignedPart));
}
delete alignedPart;
}
}
delete toAlignPart;
}
delete alignToPart;
}
if (!error) {
fa_assert(unaligned_positions_for_next <= unaligned_positions); // means: number of unaligned positions has increased by use of relative
if (unaligned_positions_for_next<unaligned_positions) {
appendNameAndUsedBasePositions(&used_relatives, gb_reference[i], unaligned_positions-unaligned_positions_for_next);
unaligned_positions = unaligned_positions_for_next;
}
}
}
}
}
if (!error) { // write used relatives to db-field
error = GBT_write_string(gb_toAlign, "used_rels", used_relatives);
}
free(used_relatives);
}
delete alignToSequence;
}
delete [] gb_reference;
}
}
delete toAlignSequence;
for (i=0; i<next_relatives; i++) freenull(nearestRelative[i]);
delete [] nearestRelative;
return error;
}
// ------------------------
// AlignmentReference
class AlignmentReference : virtual Noncopyable {
GB_CSTR alignment;
int max_seq_length;
const AlignParams& ali_params;
public:
AlignmentReference(GB_CSTR alignment_,
int max_seq_length_,
const AlignParams& ali_params_)
: alignment(alignment_),
max_seq_length(max_seq_length_),
ali_params(ali_params_)
{}
virtual ~AlignmentReference() {}
virtual ARB_ERROR align_to(GBDATA *gb_toalign) const = 0;
GB_CSTR get_alignment() const { return alignment; }
int get_max_seq_length() const { return max_seq_length; }
const AlignParams& get_ali_params() const { return ali_params; }
};
#if defined(WARN_TODO)
#warning make alignTo a member of ExplicitReference (or of AlignmentReference)
#warning let alignToGroupConsensus and alignToNextRelative use ExplicitReference
#endif
class ExplicitReference: public AlignmentReference { // derived from a Noncopyable
const FastSearchSequence *targetSequence;
GBDATA *gb_alignTo;
public:
ExplicitReference(GB_CSTR alignment_,
const FastSearchSequence *targetSequence_,
GBDATA *gb_alignTo_,
int max_seq_length_,
const AlignParams& ali_params_)
: AlignmentReference(alignment_, max_seq_length_, ali_params_),
targetSequence(targetSequence_),
gb_alignTo(gb_alignTo_)
{}
ARB_ERROR align_to(GBDATA *gb_toalign) const OVERRIDE {
return alignTo(gb_toalign, get_alignment(), targetSequence, gb_alignTo, get_max_seq_length(), get_ali_params());
}
};
#if defined(WARN_TODO)
#warning make alignToGroupConsensus a member of ConsensusReference
#endif
class ConsensusReference: public AlignmentReference {
Aligner_get_consensus_func get_consensus;
public:
ConsensusReference(GB_CSTR alignment_,
Aligner_get_consensus_func get_consensus_,
int max_seq_length_,
const AlignParams& ali_params_)
: AlignmentReference(alignment_, max_seq_length_, ali_params_),
get_consensus(get_consensus_)
{}
ARB_ERROR align_to(GBDATA *gb_toalign) const OVERRIDE {
return alignToGroupConsensus(gb_toalign, get_alignment(), get_consensus, get_max_seq_length(), get_ali_params());
}
};
#if defined(WARN_TODO)
#warning make alignToNextRelative a member of SearchRelativesReference
#endif
class SearchRelativesReference: public AlignmentReference {
SearchRelativeParams& relSearch;
FA_turn turnAllowed;
public:
SearchRelativesReference(SearchRelativeParams& relSearch_,
int max_seq_length_,
FA_turn turnAllowed_,
GB_CSTR alignment_,
const AlignParams& ali_params_)
: AlignmentReference(alignment_, max_seq_length_, ali_params_),
relSearch(relSearch_),
turnAllowed(turnAllowed_)
{}
ARB_ERROR align_to(GBDATA *gb_toalign) const OVERRIDE {
return alignToNextRelative(relSearch, get_max_seq_length(), turnAllowed, get_alignment(), gb_toalign, get_ali_params());
}
};
// ----------------
// Aligner
class Aligner : virtual Noncopyable {
GBDATA *gb_main;
// define alignment target(s):
FA_alignTarget alignWhat;
GB_CSTR alignment; // name of alignment to use (==NULL -> use default)
GB_CSTR toalign; // name of species to align (used if alignWhat == FA_CURRENT)
Aligner_get_first_selected_species get_first_selected_species; // used if alignWhat == FA_SELECTED
Aligner_get_next_selected_species get_next_selected_species; // --- "" ---
// define reference sequence(s):
GB_CSTR reference; // name of reference species
Aligner_get_consensus_func get_consensus; // function to get consensus seq
SearchRelativeParams& relSearch; // params to search for relatives
// general params:
FA_turn turnAllowed;
const AlignParams& ali_params;
int maxProtection; // protection level
// -------------------- new members
int wasNotAllowedToAlign; // number of failures caused by wrong protection
int err_count; // count errors
bool continue_on_error; /* true -> run single alignments in separate transactions.
* If one target fails, continue with rest.
* false -> run all in one transaction
* One fails -> all fail!
*/
FA_errorAction error_action;
typedef std::list<GBDATA*> GBDATAlist;
GBDATAlist species_to_mark; // species that will be marked after aligning
ARB_ERROR alignToReference(GBDATA *gb_toalign, const AlignmentReference& ref);
ARB_ERROR alignTargetsToReference(const AlignmentReference& ref, GBDATA *gb_species_data);
ARB_ERROR alignToExplicitReference(GBDATA *gb_species_data, int max_seq_length);
ARB_ERROR alignToConsensus(GBDATA *gb_species_data, int max_seq_length);
ARB_ERROR alignToRelatives(GBDATA *gb_species_data, int max_seq_length);
void triggerAction(GBDATA *gb_species, bool has_been_aligned) {
bool mark = false;
switch (error_action) {
case FA_MARK_FAILED: mark = !has_been_aligned; break;
case FA_MARK_ALIGNED: mark = has_been_aligned; break;
case FA_NO_ACTION: mark = false; break;
}
if (mark) species_to_mark.push_back(gb_species);
}
public:
#if defined(WARN_TODO)
#warning pass AlignmentReference from caller (replacing reference parameters)
#endif
Aligner(GBDATA *gb_main_,
// define alignment target(s):
FA_alignTarget alignWhat_,
GB_CSTR alignment_, // name of alignment to use (==NULL -> use default)
GB_CSTR toalign_, // name of species to align (used if alignWhat == FA_CURRENT)
Aligner_get_first_selected_species get_first_selected_species_, // used if alignWhat == FA_SELECTED
Aligner_get_next_selected_species get_next_selected_species_, // --- "" ---
// define reference sequence(s):
GB_CSTR reference_, // name of reference species
Aligner_get_consensus_func get_consensus_, // function to get consensus seq
SearchRelativeParams& relSearch_, // params to search for relatives
// general params:
FA_turn turnAllowed_,
const AlignParams& ali_params_,
int maxProtection_, // protection level
bool continue_on_error_,
FA_errorAction error_action_)
: gb_main(gb_main_),
alignWhat(alignWhat_),
alignment(alignment_),
toalign(toalign_),
get_first_selected_species(get_first_selected_species_),
get_next_selected_species(get_next_selected_species_),
reference(reference_),
get_consensus(get_consensus_),
relSearch(relSearch_),
turnAllowed(turnAllowed_),
ali_params(ali_params_),
maxProtection(maxProtection_),
wasNotAllowedToAlign(0),
err_count(0),
continue_on_error(continue_on_error_),
error_action(continue_on_error ? error_action_ : FA_NO_ACTION)
{}
ARB_ERROR run();
};
ARB_ERROR Aligner::alignToReference(GBDATA *gb_toalign, const AlignmentReference& ref) {
int myProtection = GB_read_security_write(GBT_read_sequence(gb_toalign, alignment));
ARB_ERROR error;
if (myProtection<=maxProtection) {
// Depending on 'continue_on_error' we either
// * stop aligning if an error occurs or
// * run the alignment of each species in its own transaction, ignore but report errors and
// optionally mark aligned or failed species.
if (continue_on_error) {
fa_assert(GB_get_transaction_level(gb_main) == 1);
error = GB_end_transaction(gb_main, error); // end global transaction
}
if (!error) {
error = GB_push_transaction(gb_main);
if (!error) error = ref.align_to(gb_toalign);
error = GB_end_transaction(gb_main, error);
if (error) err_count++;
triggerAction(gb_toalign, !error);
}
if (continue_on_error) {
if (error) {
GB_warning(error.deliver());
error = NULL;
}
error = GB_begin_transaction(gb_main); // re-open global transaction
}
}
else {
wasNotAllowedToAlign++;
triggerAction(gb_toalign, false);
}
return error;
}
ARB_ERROR Aligner::alignTargetsToReference(const AlignmentReference& ref, GBDATA *gb_species_data) {
ARB_ERROR error;
fa_assert(GB_get_transaction_level(gb_main) == 1);
switch (alignWhat) {
case FA_CURRENT: { // align one sequence
fa_assert(toalign);
GBDATA *gb_toalign = GBT_find_species_rel_species_data(gb_species_data, toalign);
if (!gb_toalign) {
error = species_not_found(toalign);
}
else {
currentSequenceNumber = overallSequenceNumber = 1;
error = alignToReference(gb_toalign, ref);
}
break;
}
case FA_MARKED: { // align all marked sequences
int count = GBT_count_marked_species(gb_main);
GBDATA *gb_species = GBT_first_marked_species_rel_species_data(gb_species_data);
arb_progress progress("Aligning marked species", count);
progress.auto_subtitles("Species");
currentSequenceNumber = 1;
overallSequenceNumber = count;
while (gb_species && !error) {
error = alignToReference(gb_species, ref);
progress.inc_and_check_user_abort(error);
gb_species = GBT_next_marked_species(gb_species);
}
break;
}
case FA_SELECTED: { // align all selected species
int count;
GBDATA *gb_species = get_first_selected_species(&count);
currentSequenceNumber = 1;
overallSequenceNumber = count;
if (!gb_species) {
aw_message("There is no selected species!");
}
else {
arb_progress progress("Aligning selected species", count);
progress.auto_subtitles("Species");
while (gb_species && !error) {
error = alignToReference(gb_species, ref);
progress.inc_and_check_user_abort(error);
gb_species = get_next_selected_species();
}
}
break;
}
}
fa_assert(GB_get_transaction_level(gb_main) == 1);
return error;
}
ARB_ERROR Aligner::alignToExplicitReference(GBDATA *gb_species_data, int max_seq_length) {
ARB_ERROR error;
GBDATA *gb_reference = GBT_find_species_rel_species_data(gb_species_data, reference);
if (!gb_reference) {
error = species_not_found(reference);
}
else {
long referenceChksum;
CompactedSubSequence *referenceSeq = readCompactedSequence(gb_reference, alignment, &error, NULL, &referenceChksum, ali_params.range);
if (island_hopper) {
#if defined(WARN_TODO)
#warning setting island_hopper reference has to be done in called function (seems that it is NOT done for alignToConsensus and alignToRelatives). First get tests in place!
#endif
GBDATA *gb_seq = GBT_read_sequence(gb_reference, alignment); // get sequence
if (gb_seq) {
long length = GB_read_string_count(gb_seq);
const char *data = GB_read_char_pntr(gb_seq);
island_hopper->set_ref_sequence(data);
island_hopper->set_alignment_length(length);
}
}
if (!error) {
#if defined(WARN_TODO)
#warning do not pass FastSearchSequence to ExplicitReference, instead pass sequence and length (ExplicitReference shall create it itself)
#endif
FastSearchSequence referenceFastSeq(*referenceSeq);
ExplicitReference target(alignment, &referenceFastSeq, gb_reference, max_seq_length, ali_params);
error = alignTargetsToReference(target, gb_species_data);
}
delete referenceSeq;
}
return error;
}
ARB_ERROR Aligner::alignToConsensus(GBDATA *gb_species_data, int max_seq_length) {
return alignTargetsToReference(ConsensusReference(alignment, get_consensus, max_seq_length, ali_params),
gb_species_data);
}
ARB_ERROR Aligner::alignToRelatives(GBDATA *gb_species_data, int max_seq_length) {
return alignTargetsToReference(SearchRelativesReference(relSearch, max_seq_length, turnAllowed, alignment, ali_params),
gb_species_data);
}
ARB_ERROR Aligner::run() {
// (reference == NULL && get_consensus==NULL -> use next relative for (each) sequence)
fa_assert(GB_get_transaction_level(gb_main) == 0); // no open transaction allowed here!
ARB_ERROR error = GB_push_transaction(gb_main);
bool search_by_pt_server = reference==NULL && get_consensus==NULL;
err_count = 0;
wasNotAllowedToAlign = 0; // incremented for every sequence which has higher protection level (and was not aligned)
species_to_mark.clear();
fa_assert(reference==NULL || get_consensus==NULL); // can't do both modes
if (turnAllowed != FA_TURN_NEVER) {
if ((ali_params.range.is_part()) || !search_by_pt_server) {
// if not selected 'Range/Whole sequence' or not selected 'Reference/Auto search..'
turnAllowed = FA_TURN_NEVER; // then disable mirroring for the current call
}
}
if (!error && !alignment) {
alignment = (GB_CSTR)GBT_get_default_alignment(gb_main); // get default alignment
if (!alignment) error = "No default alignment";
}
if (!error && alignment) {
global_alignmentType = GBT_get_alignment_type(gb_main, alignment);
if (search_by_pt_server) {
GB_alignment_type pt_server_alignmentType = GBT_get_alignment_type(gb_main, relSearch.pt_server_alignment);
if (pt_server_alignmentType != GB_AT_RNA &&
pt_server_alignmentType != GB_AT_DNA) {
error = "pt_servers only support RNA/DNA sequences.\n"
"In the aligner window you may specify a RNA/DNA alignment \n"
"and use a pt_server build on that alignment.";
}
}
}
if (!error) {
GBDATA *gb_species_data = GBT_get_species_data(gb_main);
int max_seq_length = GBT_get_alignment_len(gb_main, alignment);
if (reference) error = alignToExplicitReference(gb_species_data, max_seq_length);
else if (get_consensus) error = alignToConsensus(gb_species_data, max_seq_length);
else error = alignToRelatives(gb_species_data, max_seq_length);
}
ClustalV_exit();
unaligned_bases.clear();
error = GB_end_transaction(gb_main, error); // close global transaction
if (wasNotAllowedToAlign>0) {
const char *mess = GBS_global_string("%i species were not aligned (because of protection level)", wasNotAllowedToAlign);
aw_message(mess);
}
if (err_count) {
aw_message_if(error);
error = GBS_global_string("Aligner produced %i error%c", err_count, err_count==1 ? '\0' : 's');
}
if (error_action != FA_NO_ACTION) {
fa_assert(continue_on_error);
GB_transaction ta(gb_main);
GBT_mark_all(gb_main, 0);
for (GBDATAlist::iterator sp = species_to_mark.begin(); sp != species_to_mark.end(); ++sp) {
GB_write_flag(*sp, 1);
}
const char *whatsMarked = (error_action == FA_MARK_ALIGNED) ? "aligned" : "failed";
size_t markCount = species_to_mark.size();
if (markCount>0) {
const char *msg = GBS_global_string("%zu %s species %s been marked",
markCount,
whatsMarked,
(markCount == 1) ? "has" : "have");
aw_message(msg);
}
}
return error;
}
void FastAligner_start(AW_window *aw, AW_CL cl_AlignDataAccess) {
AW_root *root = aw->get_root();
char *reference = NULL; // align against next relatives
char *toalign = NULL; // align marked species
ARB_ERROR error = NULL;
const AlignDataAccess *data_access = (const AlignDataAccess *)cl_AlignDataAccess;
int get_consensus = 0;
int pt_server_id = -1;
Aligner_get_first_selected_species get_first_selected_species = 0;
Aligner_get_next_selected_species get_next_selected_species = 0;
fa_assert(island_hopper == 0);
if (root->awar(FA_AWAR_USE_ISLAND_HOPPING)->read_int()) {
island_hopper = new IslandHopping;
if (root->awar(FA_AWAR_USE_SECONDARY)->read_int()) {
if (data_access->helix_string) island_hopper->set_helix(data_access->helix_string);
else error = "Warning: No HELIX found. Can't use secondary structure";
}
if (!error) {
island_hopper->set_parameters(root->awar(FA_AWAR_ESTIMATE_BASE_FREQ)->read_int(),
root->awar(FA_AWAR_BASE_FREQ_T)->read_float(),
root->awar(FA_AWAR_BASE_FREQ_C)->read_float(),
root->awar(FA_AWAR_BASE_FREQ_A)->read_float(),
root->awar(FA_AWAR_BASE_FREQ_C)->read_float(),
root->awar(FA_AWAR_SUBST_PARA_CT)->read_float(),
root->awar(FA_AWAR_SUBST_PARA_AT)->read_float(),
root->awar(FA_AWAR_SUBST_PARA_GT)->read_float(),
root->awar(FA_AWAR_SUBST_PARA_AC)->read_float(),
root->awar(FA_AWAR_SUBST_PARA_CG)->read_float(),
root->awar(FA_AWAR_SUBST_PARA_AG)->read_float(),
root->awar(FA_AWAR_EXPECTED_DISTANCE)->read_float(),
root->awar(FA_AWAR_STRUCTURE_SUPPLEMENT)->read_float(),
root->awar(FA_AWAR_GAP_A)->read_float(),
root->awar(FA_AWAR_GAP_B)->read_float(),
root->awar(FA_AWAR_GAP_C)->read_float(),
root->awar(FA_AWAR_THRESHOLD)->read_float()
);
}
}
FA_alignTarget alignWhat = static_cast<FA_alignTarget>(root->awar(FA_AWAR_TO_ALIGN)->read_int());
if (!error) {
switch (alignWhat) {
case FA_CURRENT: { // align current species
toalign = root->awar(AWAR_SPECIES_NAME)->read_string();
break;
}
case FA_MARKED: { // align marked species
break;
}
case FA_SELECTED: { // align selected species
get_first_selected_species = data_access->get_first_selected_species;
get_next_selected_species = data_access->get_next_selected_species;
break;
}
default: {
fa_assert(0);
break;
}
}
switch (static_cast<FA_reference>(root->awar(FA_AWAR_REFERENCE)->read_int())) {
case FA_REF_EXPLICIT: // align against specified species
reference = root->awar(FA_AWAR_REFERENCE_NAME)->read_string();
break;
case FA_REF_CONSENSUS: // align against group consensus
if (data_access->get_group_consensus) {
get_consensus = 1;
}
else {
error = "Can't get group consensus here.";
}
break;
case FA_REF_RELATIVES: // align against species searched via pt_server
pt_server_id = root->awar(AWAR_PT_SERVER)->read_int();
if (pt_server_id<0) {
error = "No pt_server selected";
}
break;
default: fa_assert(0);
break;
}
}
RangeList ranges;
bool autoRestrictRange4nextRelSearch = true;
if (!error) {
switch (static_cast<FA_range>(root->awar(FA_AWAR_RANGE)->read_int())) {
case FA_WHOLE_SEQUENCE:
autoRestrictRange4nextRelSearch = false;
ranges.add(PosRange::whole());
break;
case FA_AROUND_CURSOR: {
int curpos = root->awar(AWAR_CURSOR_POSITION_LOCAL)->read_int();
int size = root->awar(FA_AWAR_AROUND)->read_int();
ranges.add(PosRange(curpos-size, curpos+size));
break;
}
case FA_SELECTED_RANGE: {
PosRange range;
if (!data_access->get_selected_range(range)) {
error = "There is no selected species!";
}
else {
ranges.add(range);
}
break;
}
case FA_SAI_MULTI_RANGE: {
GB_transaction ta(data_access->gb_main);
char *sai_name = root->awar(FA_AWAR_SAI_RANGE_NAME)->read_string();
char *aliuse = GBT_get_default_alignment(data_access->gb_main);
GBDATA *gb_sai = GBT_expect_SAI(data_access->gb_main, sai_name);
if (!gb_sai) error = GB_await_error();
else {
GBDATA *gb_data = GBT_read_sequence(gb_sai, aliuse);
if (!gb_data) {
error = GB_have_error()
? GB_await_error()
: GBS_global_string("SAI '%s' has no data in alignment '%s'", sai_name, aliuse);
}
else {
char *sai_data = GB_read_string(gb_data);
char *set_bits = root->awar(FA_AWAR_SAI_RANGE_CHARS)->read_string();
ranges = build_RangeList_from_string(sai_data, set_bits, false);
free(set_bits);
free(sai_data);
}
}
free(aliuse);
free(sai_name);
break;
}
}
}
if (!error) {
for (RangeList::iterator r = ranges.begin(); r != ranges.end() && !error; ++r) {
PosRange range = *r;
GBDATA *gb_main = data_access->gb_main;
char *editor_alignment = 0;
{
GB_transaction ta(gb_main);
char *default_alignment = GBT_get_default_alignment(gb_main);
editor_alignment = root->awar_string(AWAR_EDITOR_ALIGNMENT, default_alignment)->read_string();
free(default_alignment);
}
char *pt_server_alignment = root->awar(FA_AWAR_PT_SERVER_ALIGNMENT)->read_string();
PosRange relRange = PosRange::whole(); // unrestricted!
if (autoRestrictRange4nextRelSearch) {
AW_awar *awar_relrange = root->awar(FA_AWAR_RELATIVE_RANGE);
const char *relrange = awar_relrange->read_char_pntr();
if (relrange[0]) {
int region_plus = atoi(relrange);
fa_assert(range.is_part());
relRange = PosRange(range.start()-region_plus, range.end()+region_plus); // restricted
awar_relrange->write_as_string(GBS_global_string("%i", region_plus)); // set awar to detected value (avoid misbehavior when it contains ' ' or similar)
}
}
if (island_hopper) {
island_hopper->set_range(range);
range = PosRange::whole();
}
SearchRelativeParams relSearch(new PT_FamilyFinder(gb_main,
pt_server_id,
root->awar(AWAR_NN_OLIGO_LEN)->read_int(),
root->awar(AWAR_NN_MISMATCHES)->read_int(),
root->awar(AWAR_NN_FAST_MODE)->read_int(),
root->awar(AWAR_NN_REL_MATCHES)->read_int(),
RSS_BOTH_MIN), // old scaling as b4 [8520] @@@ make configurable
pt_server_alignment,
root->awar(FA_AWAR_NEXT_RELATIVES)->read_int());
relSearch.getFamilyFinder()->restrict_2_region(relRange);
struct AlignParams ali_params = {
static_cast<FA_report>(root->awar(FA_AWAR_REPORT)->read_int()),
bool(root->awar(FA_AWAR_SHOW_GAPS_MESSAGES)->read_int()),
range
};
{
arb_progress progress("FastAligner");
progress.allow_title_reuse();
int cont_on_error = root->awar(FA_AWAR_CONTINUE_ON_ERROR)->read_int();
Aligner aligner(gb_main,
alignWhat,
editor_alignment,
toalign,
get_first_selected_species,
get_next_selected_species,
reference,
get_consensus ? data_access->get_group_consensus : NULL,
relSearch,
static_cast<FA_turn>(root->awar(FA_AWAR_MIRROR)->read_int()),
ali_params,
root->awar(FA_AWAR_PROTECTION)->read_int(),
cont_on_error,
(FA_errorAction)root->awar(FA_AWAR_ACTION_ON_ERROR)->read_int());
error = aligner.run();
if (error && cont_on_error) {
aw_message_if(error);
error = NULL;
}
}
free(pt_server_alignment);
free(editor_alignment);
}
}
if (island_hopper) {
delete island_hopper;
island_hopper = 0;
}
if (toalign) free(toalign);
aw_message_if(error);
if (data_access->do_refresh) data_access->refresh_display();
}
void FastAligner_create_variables(AW_root *root, AW_default db1) {
root->awar_string(FA_AWAR_REFERENCE_NAME, "", db1);
root->awar_int(FA_AWAR_TO_ALIGN, FA_CURRENT, db1);
root->awar_int(FA_AWAR_REFERENCE, FA_REF_EXPLICIT, db1);
root->awar_int(FA_AWAR_RANGE, FA_WHOLE_SEQUENCE, db1);
AW_awar *ali_protect = root->awar_int(FA_AWAR_PROTECTION, 0, db1);
if (ARB_in_novice_mode(root)) {
ali_protect->write_int(0); // reset protection for noobs
}
root->awar_int(FA_AWAR_AROUND, 25, db1);
root->awar_int(FA_AWAR_MIRROR, FA_TURN_INTERACTIVE, db1);
root->awar_int(FA_AWAR_REPORT, FA_NO_REPORT, db1);
root->awar_int(FA_AWAR_SHOW_GAPS_MESSAGES, 1, db1);
root->awar_int(FA_AWAR_CONTINUE_ON_ERROR, 1, db1);
root->awar_int(FA_AWAR_ACTION_ON_ERROR, FA_NO_ACTION, db1);
root->awar_int(FA_AWAR_USE_SECONDARY, 0, db1);
root->awar_int(AWAR_PT_SERVER, 0, db1);
root->awar_int(FA_AWAR_NEXT_RELATIVES, 1, db1)->set_minmax(1, 100);
root->awar_string(FA_AWAR_RELATIVE_RANGE, "", db1);
root->awar_string(FA_AWAR_PT_SERVER_ALIGNMENT, root->awar(AWAR_DEFAULT_ALIGNMENT)->read_char_pntr(), db1);
root->awar_string(FA_AWAR_SAI_RANGE_NAME, "", db1);
root->awar_string(FA_AWAR_SAI_RANGE_CHARS, "x1", db1);
// island hopping:
root->awar_int(FA_AWAR_USE_ISLAND_HOPPING, 0, db1);
root->awar_int(FA_AWAR_ESTIMATE_BASE_FREQ, 1, db1);
root->awar_float(FA_AWAR_BASE_FREQ_A, 0.25, db1);
root->awar_float(FA_AWAR_BASE_FREQ_C, 0.25, db1);
root->awar_float(FA_AWAR_BASE_FREQ_G, 0.25, db1);
root->awar_float(FA_AWAR_BASE_FREQ_T, 0.25, db1);
root->awar_float(FA_AWAR_SUBST_PARA_AC, 1.0, db1);
root->awar_float(FA_AWAR_SUBST_PARA_AG, 4.0, db1);
root->awar_float(FA_AWAR_SUBST_PARA_AT, 1.0, db1);
root->awar_float(FA_AWAR_SUBST_PARA_CG, 1.0, db1);
root->awar_float(FA_AWAR_SUBST_PARA_CT, 4.0, db1);
root->awar_float(FA_AWAR_SUBST_PARA_GT, 1.0, db1);
root->awar_float(FA_AWAR_EXPECTED_DISTANCE, 0.3, db1);
root->awar_float(FA_AWAR_STRUCTURE_SUPPLEMENT, 0.5, db1);
root->awar_float(FA_AWAR_THRESHOLD, 0.005, db1);
root->awar_float(FA_AWAR_GAP_A, 8.0, db1);
root->awar_float(FA_AWAR_GAP_B, 4.0, db1);
root->awar_float(FA_AWAR_GAP_C, 7.0, db1);
AWTC_create_common_next_neighbour_vars(root);
}
void FastAligner_set_align_current(AW_root *root, AW_default db1) {
root->awar_int(FA_AWAR_TO_ALIGN, FA_CURRENT, db1);
}
void FastAligner_set_reference_species(AW_window * /* aww */, AW_CL cl_AW_root) {
// sets the aligner reference species to current species
AW_root *root = (AW_root*)cl_AW_root;
char *specName = root->awar(AWAR_SPECIES_NAME)->read_string();
root->awar(FA_AWAR_REFERENCE_NAME)->write_string(specName);
free(specName);
}
static AW_window *create_island_hopping_window(AW_root *root, AW_CL) {
AW_window_simple *aws = new AW_window_simple;
aws->init(root, "ISLAND_HOPPING_PARA", "Parameters for Island Hopping");
aws->load_xfig("faligner/islandhopping.fig");
aws->at("close");
aws->callback ((AW_CB0)AW_POPDOWN);
aws->create_button("CLOSE", "CLOSE", "O");
aws->at("help");
aws->callback(makeHelpCallback("islandhopping.hlp"));
aws->create_button("HELP", "HELP");
aws->at("use_secondary");
aws->label("Use secondary structure (only for re-align)");
aws->create_toggle(FA_AWAR_USE_SECONDARY);
aws->at("freq");
aws->create_toggle_field(FA_AWAR_ESTIMATE_BASE_FREQ, "Base freq.", "B");
aws->insert_default_toggle("Estimate", "E", 1);
aws->insert_toggle("Define here: ", "D", 0);
aws->update_toggle_field();
aws->at("freq_a"); aws->label("A:"); aws->create_input_field(FA_AWAR_BASE_FREQ_A, 4);
aws->at("freq_c"); aws->label("C:"); aws->create_input_field(FA_AWAR_BASE_FREQ_C, 4);
aws->at("freq_g"); aws->label("G:"); aws->create_input_field(FA_AWAR_BASE_FREQ_G, 4);
aws->at("freq_t"); aws->label("T:"); aws->create_input_field(FA_AWAR_BASE_FREQ_T, 4);
int xpos[4], ypos[4];
{
aws->button_length(1);
int dummy;
aws->at("h_a"); aws->get_at_position(&xpos[0], &dummy); aws->create_button(NULL, "A");
aws->at("h_c"); aws->get_at_position(&xpos[1], &dummy); aws->create_button(NULL, "C");
aws->at("h_g"); aws->get_at_position(&xpos[2], &dummy); aws->create_button(NULL, "G");
aws->at("h_t"); aws->get_at_position(&xpos[3], &dummy); aws->create_button(NULL, "T");
aws->at("v_a"); aws->get_at_position(&dummy, &ypos[0]); aws->create_button(NULL, "A");
aws->at("v_c"); aws->get_at_position(&dummy, &ypos[1]); aws->create_button(NULL, "C");
aws->at("v_g"); aws->get_at_position(&dummy, &ypos[2]); aws->create_button(NULL, "G");
aws->at("v_t"); aws->get_at_position(&dummy, &ypos[3]); aws->create_button(NULL, "T");
}
aws->at("subst"); aws->create_button(NULL, "Substitution rate parameters:");
#define XOFF -25
#define YOFF 0
aws->at(xpos[1]+XOFF, ypos[0]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_AC, 4);
aws->at(xpos[2]+XOFF, ypos[0]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_AG, 4);
aws->at(xpos[3]+XOFF, ypos[0]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_AT, 4);
aws->at(xpos[2]+XOFF, ypos[1]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_CG, 4);
aws->at(xpos[3]+XOFF, ypos[1]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_CT, 4);
aws->at(xpos[3]+XOFF, ypos[2]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_GT, 4);
#undef XOFF
#undef YOFF
aws->label_length(22);
aws->at("dist");
aws->label("Expected distance");
aws->create_input_field(FA_AWAR_EXPECTED_DISTANCE, 5);
aws->at("supp");
aws->label("Structure supplement");
aws->create_input_field(FA_AWAR_STRUCTURE_SUPPLEMENT, 5);
aws->at("thres");
aws->label("Threshold");
aws->create_input_field(FA_AWAR_THRESHOLD, 5);
aws->label_length(10);
aws->at("gapA");
aws->label("Gap A");
aws->create_input_field(FA_AWAR_GAP_A, 5);
aws->at("gapB");
aws->label("Gap B");
aws->create_input_field(FA_AWAR_GAP_B, 5);
aws->at("gapC");
aws->label("Gap C");
aws->create_input_field(FA_AWAR_GAP_C, 5);
return (AW_window *)aws;
}
static AW_window *create_family_settings_window(AW_root *root) {
static AW_window_simple *aws = 0;
if (!aws) {
aws = new AW_window_simple;
aws->init(root, "FAMILY_PARAMS", "Family search parameters");
aws->load_xfig("faligner/family_settings.fig");
aws->at("close");
aws->callback ((AW_CB0)AW_POPDOWN);
aws->create_button("CLOSE", "CLOSE", "O");
aws->at("help");
aws->callback(makeHelpCallback("next_neighbours_common.hlp"));
aws->create_button("HELP", "HELP");
AWTC_create_common_next_neighbour_fields(aws);
}
return aws;
}
AW_window *FastAligner_create_window(AW_root *root, const AlignDataAccess *data_access) {
AW_window_simple *aws = new AW_window_simple;
aws->init(root, "INTEGRATED_ALIGNERS", INTEGRATED_ALIGNERS_TITLE);
aws->load_xfig("faligner/faligner.fig");
aws->label_length(10);
aws->button_length(10);
aws->at("close");
aws->callback ((AW_CB0)AW_POPDOWN);
aws->create_button("CLOSE", "CLOSE", "O");
aws->at("help");
aws->callback(makeHelpCallback("faligner.hlp"));
aws->create_button("HELP", "HELP");
aws->at("aligner");
aws->create_toggle_field(FA_AWAR_USE_ISLAND_HOPPING, "Aligner", "A");
aws->insert_default_toggle("Fast aligner", "F", 0);
aws->sens_mask(AWM_EXP);
aws->insert_toggle ("Island Hopping", "I", 1);
aws->sens_mask(AWM_ALL);
aws->update_toggle_field();
aws->button_length(12);
aws->at("island_para");
aws->callback(AW_POPUP, (AW_CL)create_island_hopping_window, 0);
aws->sens_mask(AWM_EXP);
aws->create_button("island_para", "Parameters", "");
aws->sens_mask(AWM_ALL);
aws->button_length(10);
aws->at("rev_compl");
aws->callback(build_reverse_complement, (AW_CL)data_access);
aws->create_button("reverse_complement", "Turn now!", "");
aws->at("what");
aws->create_toggle_field(FA_AWAR_TO_ALIGN, "Align what?", "A");
aws->insert_toggle ("Current Species:", "A", FA_CURRENT);
aws->insert_default_toggle("Marked Species", "M", FA_MARKED);
aws->insert_toggle ("Selected Species", "S", FA_SELECTED);
aws->update_toggle_field();
aws->at("swhat");
aws->create_input_field(AWAR_SPECIES_NAME, 2);
aws->at("against");
aws->create_toggle_field(FA_AWAR_REFERENCE, "Reference", "");
aws->insert_toggle ("Species by name:", "S", FA_REF_EXPLICIT);
aws->insert_toggle ("Group consensus", "K", FA_REF_CONSENSUS);
aws->insert_default_toggle("Auto search by pt_server:", "A", FA_REF_RELATIVES);
aws->update_toggle_field();
aws->at("sagainst");
aws->create_input_field(FA_AWAR_REFERENCE_NAME, 2);
aws->at("copy");
aws->callback(FastAligner_set_reference_species, (AW_CL)root);
aws->create_button("Copy", "Copy", "");
aws->label_length(0);
aws->at("pt_server");
awt_create_selection_list_on_pt_servers(aws, AWAR_PT_SERVER, true);
aws->at("relrange");
aws->label("Data from range only, plus");
aws->create_input_field(FA_AWAR_RELATIVE_RANGE, 3);
aws->at("use_ali");
aws->label("Alignment");
aws->create_input_field(FA_AWAR_PT_SERVER_ALIGNMENT, 12);
aws->at("relatives");
aws->label("Number of relatives to use");
aws->create_input_field(FA_AWAR_NEXT_RELATIVES, 3);
aws->at("relSett");
aws->callback(AW_POPUP, (AW_CL)create_family_settings_window, (AW_CL)root);
aws->create_autosize_button("Settings", "More settings", "");
// Range
aws->label_length(10);
aws->at("range");
aws->create_toggle_field(FA_AWAR_RANGE, "Range", "");
aws->insert_default_toggle("Whole sequence", "", FA_WHOLE_SEQUENCE);
aws->insert_toggle ("Positions around cursor: ", "", FA_AROUND_CURSOR);
aws->insert_toggle ("Selected range", "", FA_SELECTED_RANGE);
aws->insert_toggle ("Multi-Range by SAI", "", FA_SAI_MULTI_RANGE);
aws->update_toggle_field();
aws->at("around");
aws->create_input_field(FA_AWAR_AROUND, 2);
aws->at("sai");
awt_create_SAI_selection_button(data_access->gb_main, aws, FA_AWAR_SAI_RANGE_NAME);
aws->at("rchars");
aws->create_input_field(FA_AWAR_SAI_RANGE_CHARS, 2);
// Protection
aws->at("protection");
aws->label("Protection");
aws->create_option_menu(FA_AWAR_PROTECTION, true);
aws->insert_default_option("0", 0, 0);
aws->insert_option("1", 0, 1);
aws->insert_option("2", 0, 2);
aws->insert_option("3", 0, 3);
aws->insert_option("4", 0, 4);
aws->insert_option("5", 0, 5);
aws->insert_option("6", 0, 6);
aws->update_option_menu();
// MirrorCheck
aws->at("mirror");
aws->label("Turn check");
aws->create_option_menu(FA_AWAR_MIRROR, true);
aws->insert_option ("Never turn sequence", "", FA_TURN_NEVER);
aws->insert_default_option("User acknowledgment ", "", FA_TURN_INTERACTIVE);
aws->insert_option ("Automatically turn sequence", "", FA_TURN_ALWAYS);
aws->update_option_menu();
// Report
aws->at("insert");
aws->label("Report");
aws->create_option_menu(FA_AWAR_REPORT, true);
aws->insert_option ("No report", "", FA_NO_REPORT);
aws->sens_mask(AWM_EXP);
aws->insert_default_option("Report to temporary entries", "", FA_TEMP_REPORT);
aws->insert_option ("Report to resident entries", "", FA_REPORT);
aws->sens_mask(AWM_ALL);
aws->update_option_menu();
aws->at("gaps");
aws->create_toggle(FA_AWAR_SHOW_GAPS_MESSAGES);
aws->at("continue");
aws->create_toggle(FA_AWAR_CONTINUE_ON_ERROR);
aws->at("on_failure");
aws->label("On failure");
aws->create_option_menu(FA_AWAR_ACTION_ON_ERROR, true);
aws->insert_default_option("do nothing", "", FA_NO_ACTION);
aws->insert_option ("mark failed", "", FA_MARK_FAILED);
aws->insert_option ("mark aligned", "", FA_MARK_ALIGNED);
aws->update_option_menu();
aws->at("align");
aws->callback(FastAligner_start, (AW_CL)data_access);
aws->highlight();
aws->create_button("GO", "GO", "G");
return aws;
}
// --------------------------------------------------------------------------------
#ifdef UNIT_TESTS
#include <test_unit.h>
// ---------------------
// OligoCounter
#include <map>
#include <string>
using std::map;
using std::string;
typedef map<string, size_t> OligoCount;
class OligoCounter {
size_t oligo_len;
size_t datasize;
mutable OligoCount occurance;
static string removeGaps(const char *seq) {
size_t len = strlen(seq);
string nogaps;
nogaps.reserve(len);
for (size_t p = 0; p<len; ++p) {
char c = seq[p];
if (c != '-' && c != '.') nogaps.append(1, c);
}
return nogaps;
}
void count_oligos(const string& seq) {
occurance.clear();
size_t max_pos = seq.length()-oligo_len;
for (size_t p = 0; p <= max_pos; ++p) {
string oligo(seq, p, oligo_len);
occurance[oligo]++;
}
}
public:
OligoCounter()
: oligo_len(0),
datasize(0)
{}
OligoCounter(const char *seq, size_t oligo_len_)
: oligo_len(oligo_len_)
{
string seq_nogaps = removeGaps(seq);
datasize = seq_nogaps.length();
count_oligos(seq_nogaps);
}
OligoCounter(const OligoCounter& other)
: oligo_len(other.oligo_len),
datasize(other.datasize),
occurance(other.occurance)
{}
size_t oligo_count(const char *oligo) {
fa_assert(strlen(oligo) == oligo_len);
return occurance[oligo];
}
size_t similarity_score(const OligoCounter& other) const {
size_t score = 0;
if (oligo_len == other.oligo_len) {
for (OligoCount::const_iterator o = occurance.begin(); o != occurance.end(); ++o) {
const string& oligo = o->first;
size_t count = o->second;
score += min(count, other.occurance[oligo]);
}
}
return score;
}
size_t getDataSize() const { return datasize; }
};
void TEST_OligoCounter() {
OligoCounter oc1("CCAGGT", 3);
OligoCounter oc2("GGTCCA", 3);
OligoCounter oc2_gaps("..GGT--CCA..", 3);
OligoCounter oc3("AGGTCC", 3);
OligoCounter oc4("AGGTCCAGG", 3);
TEST_EXPECT_EQUAL(oc1.oligo_count("CCA"), 1);
TEST_EXPECT_ZERO(oc1.oligo_count("CCG"));
TEST_EXPECT_EQUAL(oc4.oligo_count("AGG"), 2);
int sc1_2 = oc1.similarity_score(oc2);
int sc2_1 = oc2.similarity_score(oc1);
TEST_EXPECT_EQUAL(sc1_2, sc2_1);
int sc1_2gaps = oc1.similarity_score(oc2_gaps);
TEST_EXPECT_EQUAL(sc1_2, sc1_2gaps);
int sc1_3 = oc1.similarity_score(oc3);
int sc2_3 = oc2.similarity_score(oc3);
int sc3_4 = oc3.similarity_score(oc4);
TEST_EXPECT_EQUAL(sc1_2, 2); // common oligos (CCA GGT)
TEST_EXPECT_EQUAL(sc1_3, 2); // common oligos (AGG GGT)
TEST_EXPECT_EQUAL(sc2_3, 3); // common oligos (GGT GTC TCC)
TEST_EXPECT_EQUAL(sc3_4, 4);
}
// -------------------------
// FakeFamilyFinder
class FakeFamilyFinder: public FamilyFinder { // derived from a Noncopyable
// used by unit tests to detect next relatives instead of asking the pt-server
GBDATA *gb_main;
string ali_name;
map<string, OligoCounter> oligos_counted; // key = species name
PosRange counted_for_range;
size_t oligo_len;
public:
FakeFamilyFinder(GBDATA *gb_main_, string ali_name_, bool rel_matches_, size_t oligo_len_)
: FamilyFinder(rel_matches_, RSS_BOTH_MIN),
gb_main(gb_main_),
ali_name(ali_name_),
counted_for_range(PosRange::whole()),
oligo_len(oligo_len_)
{}
GB_ERROR searchFamily(const char *sequence, FF_complement compl_mode, int max_results, double min_score) OVERRIDE { // @@@ use min_score
// 'sequence' has to contain full sequence or part corresponding to 'range'
TEST_EXPECT_EQUAL(compl_mode, FF_FORWARD); // not fit for other modes
delete_family_list();
OligoCounter seq_oligo_count(sequence, oligo_len);
if (range != counted_for_range) {
oligos_counted.clear(); // forget results for different range
counted_for_range = range;
}
char *buffer = 0;
int buffersize = 0;
bool partial_match = range.is_part();
GB_transaction ta(gb_main);
int results = 0;
for (GBDATA *gb_species = GBT_first_species(gb_main);
gb_species && results<max_results;
gb_species = GBT_next_species(gb_species))
{
string name = GBT_get_name(gb_species);
if (oligos_counted.find(name) == oligos_counted.end()) {
GBDATA *gb_data = GBT_read_sequence(gb_species, ali_name.c_str());
const char *spec_seq = GB_read_char_pntr(gb_data);
if (partial_match) {
int spec_seq_len = GB_read_count(gb_data);
int range_len = ExplicitRange(range, spec_seq_len).size();
if (buffersize<range_len) {
delete [] buffer;
buffersize = range_len;
buffer = new char[buffersize+1];
}
range.copy_corresponding_part(buffer, spec_seq, spec_seq_len);
oligos_counted[name] = OligoCounter(buffer, oligo_len);
}
else {
oligos_counted[name] = OligoCounter(spec_seq, oligo_len);
}
}
const OligoCounter& spec_oligo_count = oligos_counted[name];
size_t score = seq_oligo_count.similarity_score(spec_oligo_count);
FamilyList *newMember = new FamilyList;
newMember->name = strdup(name.c_str());
newMember->matches = score;
newMember->rel_matches = score/spec_oligo_count.getDataSize();
newMember->next = NULL;
family_list = newMember->insertSortedBy_matches(family_list);
results++;
}
delete [] buffer;
return NULL;
}
};
// ----------------------------
// test_alignment_data
#include <arb_unit_test.h>
static const char *test_aliname = "ali_test";
static const char *get_aligned_data_of(GBDATA *gb_main, const char *species_name) {
GB_transaction ta(gb_main);
ARB_ERROR error;
const char *data = NULL;
GBDATA *gb_species = GBT_find_species(gb_main, species_name);
if (!gb_species) error = GB_await_error();
else {
GBDATA *gb_data = GBT_read_sequence(gb_species, test_aliname);
if (!gb_data) error = GB_await_error();
else {
data = GB_read_char_pntr(gb_data);
if (!data) error = GB_await_error();
}
}
TEST_EXPECT_NULL(error.deliver());
return data;
}
static const char *get_used_rels_for(GBDATA *gb_main, const char *species_name) {
GB_transaction ta(gb_main);
const char *result = NULL;
GBDATA *gb_species = GBT_find_species(gb_main, species_name);
if (!gb_species) result = GBS_global_string("<No such species '%s'>", species_name);
else {
GBDATA *gb_used_rels = GB_search(gb_species, "used_rels", GB_FIND);
if (!gb_used_rels) result = "<No such field 'used_rels'>";
else result = GB_read_char_pntr(gb_used_rels);
}
return result;
}
static GB_ERROR forget_used_relatives(GBDATA *gb_main) {
GB_ERROR error = NULL;
GB_transaction ta(gb_main);
for (GBDATA *gb_species = GBT_first_species(gb_main);
gb_species && !error;
gb_species = GBT_next_species(gb_species))
{
GBDATA *gb_used_rels = GB_search(gb_species, "used_rels", GB_FIND);
if (gb_used_rels) {
error = GB_delete(gb_used_rels);
}
}
return error;
}
#define ALIGNED_DATA_OF(name) get_aligned_data_of(gb_main, name)
#define USED_RELS_FOR(name) get_used_rels_for(gb_main, name)
// ----------------------------------------
static GBDATA *selection_fake_gb_main = NULL;
static GBDATA *selection_fake_gb_last = NULL;
static GBDATA *fake_first_selected(int *count) {
selection_fake_gb_last = NULL;
*count = 2; // we fake two species as selected ("c1" and "c2")
return GBT_find_species(selection_fake_gb_main, "c1");
}
static GBDATA *fake_next_selected() {
if (!selection_fake_gb_last) {
selection_fake_gb_last = GBT_find_species(selection_fake_gb_main, "c2");
}
else {
selection_fake_gb_last = NULL;
}
return selection_fake_gb_last;
}
static char *fake_get_consensus(const char*, PosRange range) {
const char *data = get_aligned_data_of(selection_fake_gb_main, "s1");
if (range.is_whole()) return strdup(data);
return GB_strpartdup(data+range.start(), data+range.end());
}
static void test_install_fakes(GBDATA *gb_main) {
selection_fake_gb_main = gb_main;
}
// ----------------------------------------
static AlignParams test_ali_params = {
FA_NO_REPORT,
false, // showGapsMessages
PosRange::whole()
};
static AlignParams test_ali_params_partial = {
FA_NO_REPORT,
false, // showGapsMessages
PosRange(25, 60)
};
// ----------------------------------------
static struct arb_unit_test::test_alignment_data TestAlignmentData_TargetAndReferenceHandling[] = {
{ 0, "s1", ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........." }, // reference
{ 0, "s2", "AUCUCCUAAACCCAACCGUAGUUCGAAUUGAGGACUGUAACUC......................................................" }, // align single sequence (same data as reference)
{ 1, "m1", "UAGAGGAUUUGGGUUGGCAUCAAGCUUAACUCCUGACAUUGAG......................................................" }, // align marked sequences.. (complement of reference)
{ 1, "m2", "...UCCUAAACCAACCCGUAGUUCGAAUUGAGGACUGUAA........................................................." },
{ 1, "m3", "AUC---UAAACCAACCCGUAGUUCGAAUUGAGGACUG---CUC......................................................" },
{ 0, "c1", "AUCUCCUAAACCCAACC--------AAUUGAGGACUGUAACUC......................................................" }, // align selected sequences..
{ 0, "c2", "AUCUCCU------AACCGUAGUUCCCCGAA------ACUGUAACUC..................................................." },
{ 0, "r1", "GAGUUACAGUCCUCAAUUCGGGGAACUACGGUUGGGUUUAGGAGAU..................................................." }, // align by faked pt_server
};
void TEST_Aligner_TargetAndReferenceHandling() {
// performs some alignments to check logic of target and reference handling
GB_shell shell;
ARB_ERROR error;
GBDATA *gb_main = TEST_CREATE_DB(error, test_aliname, TestAlignmentData_TargetAndReferenceHandling, false);
TEST_EXPECT_NULL(error.deliver());
SearchRelativeParams search_relative_params(new FakeFamilyFinder(gb_main, test_aliname, false, 8),
test_aliname,
2);
test_install_fakes(gb_main);
arb_suppress_progress silence;
// bool cont_on_err = true;
bool cont_on_err = false;
TEST_EXPECT_EQUAL(GBT_count_marked_species(gb_main), 3); // we got 3 marked species
{
Aligner aligner(gb_main,
FA_CURRENT,
test_aliname,
"s2", // toalign
NULL, // get_first_selected_species
NULL, // get_next_selected_species
"s1", // reference species
NULL, // get_consensus
search_relative_params, // relative search
FA_TURN_ALWAYS,
test_ali_params,
0,
cont_on_err,
FA_NO_ACTION);
error = aligner.run();
TEST_EXPECT_NULL(error.deliver());
}
TEST_EXPECT_EQUAL(GBT_count_marked_species(gb_main), 3); // we still got 3 marked species
{
Aligner aligner(gb_main,
FA_MARKED,
test_aliname,
NULL, // toalign
NULL, // get_first_selected_species
NULL, // get_next_selected_species
"s1", // reference species
NULL, // get_consensus
search_relative_params, // relative search
FA_TURN_ALWAYS,
test_ali_params,
0,
cont_on_err,
FA_MARK_FAILED);
error = aligner.run();
TEST_EXPECT_NULL(error.deliver());
TEST_EXPECT(!cont_on_err || GBT_count_marked_species(gb_main) == 0); // FA_MARK_FAILED (none failed -> none marked)
}
{
Aligner aligner(gb_main,
FA_SELECTED,
test_aliname,
NULL, // toalign
fake_first_selected, // get_first_selected_species
fake_next_selected, // get_next_selected_species
NULL, // reference species
fake_get_consensus, // get_consensus
search_relative_params, // relative search
FA_TURN_ALWAYS,
test_ali_params,
0,
cont_on_err,
FA_MARK_ALIGNED);
error = aligner.run();
TEST_EXPECT_NULL(error.deliver());
TEST_EXPECT(!cont_on_err || GBT_count_marked_species(gb_main) == 2); // FA_MARK_ALIGNED (2 selected were aligned)
}
{
Aligner aligner(gb_main,
FA_CURRENT,
test_aliname,
"r1", // toalign
NULL, // get_first_selected_species
NULL, // get_next_selected_species
NULL, // reference species
NULL, // get_consensus
search_relative_params, // relative search
FA_TURN_ALWAYS,
test_ali_params,
0,
cont_on_err,
FA_MARK_ALIGNED);
error = aligner.run();
TEST_EXPECT_NULL(error.deliver());
TEST_EXPECT(!cont_on_err || GBT_count_marked_species(gb_main) == 1);
}
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s2"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C...........");
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m1"), ".......UAG--AGG-A------U-U-UGGGU-UG-G-C-A-U-CAA-GCU--------UAA-C-UCCUG-AC--A-UUGAG...............");
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m2"), "..............U-C------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA................");
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m3"), ".........A--U----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----CU-C...........");
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-------------------AA-U-UGAGG-AC--U-GUAA-CU-C...........");
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c2"), ".........A--UCU-C------C-U-AA---------C-C-G-UAG-UUC------------C-CCGAA-AC--U-GUAA-CU-C...........");
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("r1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUCCCC-----GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // here sequence shall be turned!
TEST_EXPECT_EQUAL(USED_RELS_FOR("r1"), "s2:43, s1:1");
// ----------------------------------------------
// now align all others vs next relative
search_relative_params.maxRelatives = 5;
TEST_EXPECT_NO_ERROR(forget_used_relatives(gb_main));
int species_count = ARRAY_ELEMS(TestAlignmentData_TargetAndReferenceHandling);
for (int sp = 0; sp<species_count; ++sp) {
const char *name = TestAlignmentData_TargetAndReferenceHandling[sp].name;
if (strcmp(name, "r1") != 0) { // skip "r1" (already done above)
Aligner aligner(gb_main,
FA_CURRENT,
test_aliname,
name, // toalign
NULL, // get_first_selected_species
NULL, // get_next_selected_species
NULL, // reference species
NULL, // get_consensus
search_relative_params, // relative search
FA_TURN_ALWAYS,
test_ali_params,
0,
cont_on_err,
FA_MARK_ALIGNED);
error = aligner.run();
TEST_EXPECT_NULL(error.deliver());
TEST_EXPECT(!cont_on_err || GBT_count_marked_species(gb_main) == 1);
}
}
TEST_EXPECT_EQUAL(USED_RELS_FOR("s1"), "s2");
TEST_EXPECT_EQUAL(USED_RELS_FOR("s2"), "s1"); // same as done manually
TEST_EXPECT_EQUAL(USED_RELS_FOR("m1"), "r1:42");
TEST_EXPECT_EQUAL(USED_RELS_FOR("m2"), "m3");
TEST_EXPECT_EQUAL(USED_RELS_FOR("m3"), "m2");
TEST_EXPECT_EQUAL(USED_RELS_FOR("c1"), "r1");
TEST_EXPECT_EQUAL(USED_RELS_FOR("c2"), "r1");
// range aligned below (see test_ali_params_partial)
// "-------------------------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX------------------------------------"
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // 1st aligning of 's1'
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s2"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above (again aligned vs 's1')
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m1"), ".........U--AGA-G------G---AUUUG-GG-U-U-G-G-CAU-CAAGCU-----UAA-C-UCCUG-AC--A-UUGAG---------------"); // changed; @@@ bug: no dots at end
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m2"), ".........U--C----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----UA-A..........."); // changed (1st align vs 's1', this align vs 'm3')
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m3"), ".........A--U----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----CU-C..........."); // same_as_above (1st align vs 's1', this align vs 'm2')
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-------------------AA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c2"), ".........A--UCU-C------C-U--------A-A-C-C-G-UAG-UUCCCC-----GA--------A-AC--U-GUAA-CU-C..........."); // changed
// --------------------------------------
// test partial relative search
search_relative_params.getFamilyFinder()->restrict_2_region(test_ali_params_partial.range);
TEST_EXPECT_NO_ERROR(forget_used_relatives(gb_main));
for (int sp = 0; sp<species_count; ++sp) {
const char *name = TestAlignmentData_TargetAndReferenceHandling[sp].name;
Aligner aligner(gb_main,
FA_CURRENT,
test_aliname,
name, // toalign
NULL, // get_first_selected_species
NULL, // get_next_selected_species
NULL, // reference species
NULL, // get_consensus
search_relative_params, // relative search
FA_TURN_NEVER,
test_ali_params_partial,
0,
cont_on_err,
FA_MARK_ALIGNED);
error = aligner.run();
TEST_EXPECT_NULL(error.deliver());
TEST_EXPECT(!cont_on_err || GBT_count_marked_species(gb_main) == 1);
}
TEST_EXPECT_EQUAL(USED_RELS_FOR("s1"), "s2");
TEST_EXPECT_EQUAL(USED_RELS_FOR("s2"), "s1");
TEST_EXPECT_EQUAL(USED_RELS_FOR("m1"), "r1"); // (not really differs)
TEST_EXPECT_EQUAL(USED_RELS_FOR("m2"), "m3");
TEST_EXPECT_EQUAL(USED_RELS_FOR("m3"), "m2");
TEST_EXPECT_EQUAL(USED_RELS_FOR("c1"), "r1");
TEST_EXPECT_EQUAL(USED_RELS_FOR("c2"), "r1");
TEST_EXPECT_EQUAL(USED_RELS_FOR("r1"), "s2:20, c2:3");
// aligned range (see test_ali_params_partial)
// "-------------------------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX------------------------------------"
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s2"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m1"), ".........U--AGA-G------G-A-UU-UG-GG-U-U-G-G-CAU-CAAGCU-----UAA-C-UCCUG-AC--A-UUGAG---------------"); // changed
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m2"), ".........U--C----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----UA-A..........."); // same_as_above
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m3"), ".........A--U----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----CU-C..........."); // same_as_above
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-------------------AA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c2"), ".........A--UCU-C------C---------UA-A-C-C-G-UAG-UUCCCC-----GA--------A-AC--U-GUAA-CU-C..........."); // changed
TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("r1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUCCCC-----GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
GB_close(gb_main);
}
// ----------------------------------------
static struct arb_unit_test::test_alignment_data TestAlignmentData_checksumError[] = {
{ 0, "MtnK1722", "...G-GGC-C-G............CCC-GG--------CAAUGGGGGCGGCCCGGCGGAC----GG--C-UCAGU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUG-CGGC-UGGAUCACCUCC....." }, // gets aligned
{ 0, "MhnFormi", "...A-CGA-U-C------------CUUCGG--------GGUCG-U-GG-C-GU-A--C------GG--C-UCAGU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUG-CGGC-UGGAUCACCUCCU...." }, // 1st relative
{ 0, "MhnT1916", "...A-CGA-A-C------------CUU-GU--------GUUCG-U-GG-C-GA-A--C------GG--C-UCAGU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUG-CGGC-UGGAUCACCUCCU...." }, // next relative
{ 0, "MthVanni", "...U-GGU-U-U------------C-------------GGCCA-U-GG-C-GG-A--C------GG--C-UCAUU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUG-CGGC-UGGAUCACCUCC....." }, // next relative
{ 0, "ThcCeler", "...G-GGG-C-G...CC-U---U--------GC--G--CGCAC-C-GG-C-GG-A--C------GG--C-UCAGU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUA-CGGC-UCGAUCACCUCCU...." }, // next relative
};
void TEST_SLOW_Aligner_checksumError() {
// @@@ SLOW cause this often gets terminated in nightly builds
// no idea why. normally it runs a few ms
// this produces an internal aligner error
GB_shell shell;
ARB_ERROR error;
GBDATA *gb_main = TEST_CREATE_DB(error, test_aliname, TestAlignmentData_checksumError, false);
SearchRelativeParams search_relative_params(new FakeFamilyFinder(gb_main, test_aliname, false, 8),
test_aliname,
10); // use up to 10 relatives
test_install_fakes(gb_main);
arb_suppress_progress silence;
bool cont_on_err = true;
if (!error) {
Aligner aligner(gb_main,
FA_CURRENT,
test_aliname,
"MtnK1722", // toalign
NULL, // get_first_selected_species
NULL, // get_next_selected_species
NULL, // reference species
NULL, // get_consensus
search_relative_params, // relative search
FA_TURN_ALWAYS,
test_ali_params,
0,
cont_on_err,
FA_MARK_ALIGNED);
error = aligner.run();
}
{
GB_ERROR err = error.deliver();
TEST_EXPECT_NULL__BROKEN(err, "Aligner produced 1 error");
}
TEST_EXPECT_EQUAL__BROKEN(USED_RELS_FOR("MtnK1722"), "???", "<No such field 'used_rels'>"); // subsequent failure
GB_close(gb_main);
}
static const char *asstr(LooseBases& ub) {
LooseBases tmp;
while (!ub.is_empty()) tmp.memorize(ub.recall());
const char *result = "";
while (!tmp.is_empty()) {
ExplicitRange r = tmp.recall();
result = GBS_global_string("%s %i/%i", result, r.start(), r.end());
ub.memorize(r);
}
return result;
}
void TEST_BASIC_UnalignedBases() {
LooseBases ub;
TEST_EXPECT(ub.is_empty());
TEST_EXPECT_EQUAL(asstr(ub), "");
// test add+remove
ub.memorize(ExplicitRange(5, 7));
TEST_REJECT(ub.is_empty());
TEST_EXPECT_EQUAL(asstr(ub), " 5/7");
TEST_EXPECT(ub.recall() == ExplicitRange(5, 7));
TEST_EXPECT(ub.is_empty());
ub.memorize(ExplicitRange(2, 4));
TEST_EXPECT_EQUAL(asstr(ub), " 2/4");
ub.memorize(ExplicitRange(4, 9));
TEST_EXPECT_EQUAL(asstr(ub), " 2/4 4/9");
ub.memorize(ExplicitRange(8, 10));
ub.memorize(ExplicitRange(11, 14));
ub.memorize(ExplicitRange(12, 17));
TEST_EXPECT_EQUAL(asstr(ub), " 2/4 4/9 8/10 11/14 12/17");
TEST_EXPECT_EQUAL(asstr(ub), " 2/4 4/9 8/10 11/14 12/17"); // check asstr has no side-effect
{
LooseBases toaddNrecalc;
CompactedSubSequence Old("ACGTACGT", 8, "name1");
CompactedSubSequence New("--A-C--G-T--A-C-G-T", 19, "name2");
// ---------------------- 0123456789012345678
toaddNrecalc.memorize(ExplicitRange(1, 7));
toaddNrecalc.memorize(ExplicitRange(3, 5));
TEST_EXPECT_EQUAL(asstr(toaddNrecalc), " 1/7 3/5");
ub.follow_ali_change_and_append(toaddNrecalc, AliChange(Old, New));
TEST_EXPECT_EQUAL(asstr(ub), " 3/18 8/15 2/4 4/9 8/10 11/14 12/17");
TEST_EXPECT(toaddNrecalc.is_empty());
LooseBases selfRecalc;
selfRecalc.follow_ali_change_and_append(ub, AliChange(New, New));
TEST_EXPECT_EQUAL__BROKEN(asstr(selfRecalc),
" 3/18 8/15 0/6 3/11 8/11 10/15 10/17", // wanted behavior?
" 3/18 8/17 0/6 3/11 8/13 10/15 10/18"); // doc wrong behavior @@@ "8/17", "8/13", "10/18" are wrong
ub.follow_ali_change_and_append(selfRecalc, AliChange(New, Old));
TEST_EXPECT_EQUAL__BROKEN(asstr(ub),
" 1/7 3/5 0/1 1/3 3/3 4/5 4/6", // wanted behavior? (from wanted behavior above)
" 1/7 3/7 0/2 1/4 3/5 4/6 4/7"); // document wrong behavior
TEST_EXPECT_EQUAL__BROKEN(asstr(ub),
" 1/7 3/6 0/1 1/3 3/4 4/5 4/7", // wanted behavior? (from wrong result above)
" 1/7 3/7 0/2 1/4 3/5 4/6 4/7"); // document wrong behavior
}
}
#endif // UNIT_TESTS
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