R PPForest<L>::maxScore(const Algebra<R,L> &alg, size_type i, size_type j) const
{
R down, over;
if(j==0)
return 0;
if(isLeave(i))
{
over=maxScore(alg,rb(i),j-1);
return alg.replace(label(i),0,label(i),over);
}
else
{
down=maxScore(alg,i+1,noc(i));
over=maxScore(alg,rb(i),j-1);
return alg.replace(label(i),down,label(i),over);
}
}
R PPForest<L>::maxScore(const RNA_Algebra<R,L> &alg, Uint i, Uint j) const
{
R down, over;
if(j==0)
return 0;
if(isLeave(i))
{
over=maxScore(alg,rb(i),j-1);
return alg.replace(label(i),0,label(i),over);
}
else
{
down=maxScore(alg,i+1+1,noc(i)-2);
over=maxScore(alg,rb(i),j-1);
return alg.replacepair(label(i+1),label(i+1),down,label(getRightmostBrotherIndex(i+1)),label(getRightmostBrotherIndex(i+1)),over);
}
}
//------------------------------------------ Private Function Definitions ----//
bool _alignEngine
(const char * A0, long int Astart, long int & Aend,
const char * B0, long int Bstart, long int & Bend,
vector<long int> & Delta, unsigned int m_o)
// A0 is a sequence such that A [1...\0]
// B0 is a sequence such that B [1...\0]
// The alignment should use bases A [Astart...Aend] (inclusive)
// The alignment should use beses B [Bstart...Bend] (inclusive)
// of [Aend...Astart] etc. if BACKWARD_SEARCH
// Aend must never equal Astart, same goes for Bend and Bstart
// Delta is an integer vector, not necessarily empty
// m_o is the modus operandi of the function:
// FORWARD_ALIGN, FORWARD_SEARCH, BACKWARD_SEARCH
// Returns true on s.cppess (Aend & Bend reached) or false on failure
{
Diagonal * Diag; // the list of diagonals to make up edit matrix
bool TargetReached; // the target was reached
const char * A, * B; // the sequence pointers to be used by this func
long int min_score = (-1 * LONG_MAX); // minimum possible score
long int high_score = min_score; // global maximum score
long int xhigh_score = min_score; // non-optimal high score
// max score difference
long int max_diff = GOOD_SCORE [getMatrixType( )] * _break_len;
long int CDi; // conceptual diagonal index (not relating to mem)
long int Dct, Di; // diagonal counter, actual diagonal index
long int PDct, PPDct; // previous diagonal and prev prev diagonal
long int PDi, PPDi; // previous diagonal index and prev prev diag index
long int Ds, PDs, PPDs; // diagonal size, prev, prev prev diagonal size
// where 'size' = rbound - lbound + 1
long int Ll = 100; // capacity of the diagonal list
long int Dl = 2; // current conceptual diagonal length
long int lbound = 0; // current diagonal left(lower) node bound index
long int rbound = 0; // current diagonal right(upper) node bound index
long int FinishCt = 0; // diagonal containing the high_score
long int FinishCDi = 0; // conceptual index of the high_score on FinishCt
long int xFinishCt = 0; // non-optimal ...
long int xFinishCDi = 0; // non-optimal ...
long int N, M, L; // maximum matrix dimensions... N rows, M columns
long int tlb, trb;
double Dmid = .5; // diag midpoint
double Dband = _banding/2.0; // diag banding
int Iadj, Dadj, Madj; // insert, delete and match adjust values
#ifdef _DEBUG_VERBOSE
long int MaxL = 0; // biggest diagonal seen
long int TrimCt = 0; // counter of nodes trimmed
long int CalcCt = 0; // counter of nodes calculated
#endif
//-- Set up character pointers for the appropriate m_o
if ( m_o & DIRECTION_BIT ) {
A = A0 + ( Astart - 1 );
B = B0 + ( Bstart - 1 );
N = Aend - Astart + 1;
M = Bend - Bstart + 1;
} else {
A = A0 + ( Astart + 1 );
B = B0 + ( Bstart + 1 );
N = Astart - Aend + 1;
M = Bstart - Bend + 1;
}
//-- Initialize the diagonals list
Diag = (Diagonal *) Safe_malloc ( Ll * sizeof(Diagonal) );
//-- Initialize position 0,0 in the matrices
Diag[0] . lbound = lbound;
Diag[0] . rbound = rbound ++;
Diag[0] . I = (Node *) Safe_malloc ( 1 * sizeof(Node) );
Diag[0] . I[0] . S[DELETE] . value = min_score;
Diag[0] . I[0] . S[INSERT] . value = min_score;
Diag[0] . I[0] . S[MATCH] . value = 0;
Diag[0] . I[0] . max = Diag[0] . I[0] . S + MATCH;
Diag[0] . I[0] . S[DELETE] . used = NONE;
Diag[0] . I[0] . S[INSERT] . used = NONE;
Diag[0] . I[0] . S[MATCH] . used = START;
L = N < M ? N : M;
//-- **START** of diagonal processing loop
//-- Calculate the rest of the diagonals until goal reached or score worsens
for ( Dct = 1; Dct <= N + M &&
(Dct - FinishCt) <= _break_len &&
lbound <= rbound; Dct++ ) {
//-- If diagonals capacity exceeded, realloc
if ( Dct >= Ll ) {
Ll *= 2;
Diag = (Diagonal *) Safe_realloc
( Diag, sizeof(Diagonal) * Ll );
}
Diag[Dct] . lbound = lbound;
Diag[Dct] . rbound = rbound;
//-- malloc space for the edit char and score nodes
Ds = rbound - lbound + 1;
Diag[Dct] . I = (Node *) Safe_malloc
( Ds * sizeof(Node) );
#ifdef _DEBUG_VERBOSE
//-- Keep count of trimmed and calculated nodes
CalcCt += Ds;
TrimCt += Dl - Ds;
if ( Ds > MaxL )
MaxL = Ds;
#endif
//-- Set diagonal index adjustment values
if ( Dct <= N ) {
Iadj = 0;
Madj = -1;
} else {
Iadj = 1;
Madj = Dct == N + 1 ? 0 : 1;
}
Dadj = Iadj - 1;
//-- Set parent diagonal values
PDct = Dct - 1;
PDs = Diag[PDct] . rbound - Diag[PDct] . lbound + 1;
PDi = lbound + Dadj;
PDi = PDi - Diag[PDct] . lbound;
//-- Set grandparent diagonal values
PPDct = Dct - 2;
if ( PPDct >= 0 ) {
PPDs = Diag[PPDct] . rbound - Diag[PPDct] . lbound + 1;
PPDi = lbound + Madj;
PPDi = PPDi - Diag[PPDct] . lbound;
} else
PPDi = PPDs = 0;
//-- If forced alignment, don't keep track of global max
if ( m_o & FORCED_BIT )
high_score = min_score;
//-- **START** of internal node scoring loop
//-- Calculate scores for every node (within bounds) for diagonal Dct
for ( CDi = lbound; CDi <= rbound; CDi ++ ) {
//-- Set the index (in memory) of current node and clear score
Di = CDi - Diag[Dct] . lbound;
//-- Calculate DELETE score
if ( PDi >= 0 && PDi < PDs )
scoreEdit
(Diag[Dct] . I[Di] . S[DELETE],
Diag[PDct] . I[PDi] . S[DELETE] . used == NONE ?
Diag[PDct] . I[PDi] . S[DELETE] . value :
Diag[PDct] . I[PDi] . S[DELETE] . value +
CONT_GAP_SCORE [_matrix_type],
Diag[PDct] . I[PDi] . S[INSERT] . used == NONE ?
Diag[PDct] . I[PDi] . S[INSERT] . value :
Diag[PDct] . I[PDi] . S[INSERT] . value +
OPEN_GAP_SCORE [_matrix_type],
Diag[PDct] . I[PDi] . S[MATCH] . used == NONE ?
Diag[PDct] . I[PDi] . S[MATCH] . value :
Diag[PDct] . I[PDi] . S[MATCH] . value +
OPEN_GAP_SCORE [_matrix_type]);
else {
Diag[Dct] . I[Di] . S[DELETE] . value = min_score;
Diag[Dct] . I[Di] . S[DELETE] . used = NONE;
}
PDi ++;
//-- Calculate INSERT score
if ( PDi >= 0 && PDi < PDs )
scoreEdit
(Diag[Dct] . I[Di] . S[INSERT],
Diag[PDct] . I[PDi] . S[DELETE] . used == NONE ?
Diag[PDct] . I[PDi] . S[DELETE] . value :
Diag[PDct] . I[PDi] . S[DELETE] . value +
OPEN_GAP_SCORE [_matrix_type],
Diag[PDct] . I[PDi] . S[INSERT] . used == NONE ?
Diag[PDct] . I[PDi] . S[INSERT] . value :
Diag[PDct] . I[PDi] . S[INSERT] . value +
CONT_GAP_SCORE [_matrix_type],
Diag[PDct] . I[PDi] . S[MATCH] . used == NONE ?
Diag[PDct] . I[PDi] . S[MATCH] . value :
Diag[PDct] . I[PDi] . S[MATCH] . value +
OPEN_GAP_SCORE [_matrix_type]);
else {
Diag[Dct] . I[Di] . S[INSERT] . value = min_score;
Diag[Dct] . I[Di] . S[INSERT] . used = NONE;
}
//-- Calculate MATCH/MIS-MATCH score
if ( PPDi >= 0 && PPDi < PPDs ) {
scoreEdit
(Diag[Dct] . I[Di] . S[MATCH],
Diag[PPDct] . I[PPDi] . S[DELETE] . value,
Diag[PPDct] . I[PPDi] . S[INSERT] . value,
Diag[PPDct] . I[PPDi] . S[MATCH] . value);
Diag[Dct] . I[Di] . S[MATCH] . value +=
scoreMatch (Diag[Dct], Dct, CDi, A, B, N, m_o);
} else {
Diag[Dct] . I[Di] . S[MATCH] . value = min_score;
Diag[Dct] . I[Di] . S[MATCH] . used = NONE;
}
PPDi ++;
Diag[Dct] . I[Di] . max = maxScore (Diag[Dct] . I[Di] . S);
//-- Reset high_score if new global max was found
if ( Diag[Dct] . I[Di] . max->value >= high_score ) {
high_score = Diag[Dct] . I[Di] . max->value;
FinishCt = Dct;
FinishCDi = CDi;
}
}
//-- **END** of internal node scoring loop
//-- Calculate max non-optimal score
if ( m_o & SEQEND_BIT && Dct >= L ) {
if ( L == N ) {
if ( lbound == 0 ) {
if ( Diag[Dct] . I[0] . max->value >= xhigh_score ) {
xhigh_score = Diag[Dct] . I[0] . max->value;
xFinishCt = Dct;
xFinishCDi = 0;
}
}
} else { // L == M
if ( rbound == M ) {
if ( Diag[Dct] . I[M-Diag[Dct].lbound] .
max->value >= xhigh_score ) {
xhigh_score = Diag[Dct] . I[M-Diag[Dct].lbound] .
max->value;
xFinishCt = Dct;
xFinishCDi = M;
}
}
}
}
//-- If in extender modus operandi, free soon to be greatgrandparent diag
if ( m_o & SEARCH_BIT && Dct > 1 )
free ( Diag[PPDct] . I );
//-- Trim hopeless diagonal nodes
for ( Di = 0; Di < Ds; Di ++ ) {
if ( high_score - Diag[Dct] . I[Di] . max->value > max_diff )
lbound ++;
else
break;
}
for ( Di = Ds - 1; Di >= 0; Di -- ) {
if ( high_score - Diag[Dct] . I[Di] . max->value > max_diff )
rbound --;
else
break;
}
//-- Grow new diagonal and reset boundaries
if ( Dct < N && Dct < M ) {
Dl ++;
rbound ++;
Dmid = (Dct+1)/2.0;
} else if ( Dct >= N && Dct >= M ) {
Dl --;
lbound --;
Dmid = N - (Dct+1)/2.0;
} else if ( Dct >= N ) {
lbound --;
Dmid = N - (Dct+1)/2.0;
} else {
rbound ++;
Dmid = (Dct+1)/2.0;
}
//-- Trim at hard band
if ( Dband > 0 ) {
tlb = (long int)ceil(Dmid - Dband);
if ( lbound < tlb )
lbound = tlb;
trb = (long int)floor(Dmid + Dband);
if ( rbound > trb )
rbound = trb;
}
if ( lbound < 0 )
lbound = 0;
if ( rbound >= Dl )
rbound = Dl - 1;
}
//-- **END** of diagonal processing loop
Dct --;
//-- Check if the target was reached
// If OPTIMAL, backtrack to last high_score to maximize alignment score
TargetReached = false;
if ( Dct == N + M ) {
if ( ~m_o & OPTIMAL_BIT || m_o & SEQEND_BIT ) {
TargetReached = true;
FinishCt = N + M;
FinishCDi = 0;
} else if ( FinishCt == Dct )
TargetReached = true;
} else if ( m_o & SEQEND_BIT && xFinishCt != 0 ) {
//-- non-optimal, extend alignment to end of shortest seq if possible
FinishCt = xFinishCt;
FinishCDi = xFinishCDi;
}
//-- Set A/Bend to finish positions
long int Aadj = FinishCt <= N ? FinishCt - FinishCDi - 1 : N - FinishCDi - 1;
long int Badj = FinishCt <= N ? FinishCDi - 1 : FinishCt - N + FinishCDi - 1;
if ( ~m_o & DIRECTION_BIT ) {
Aadj *= -1;
Badj *= -1;
}
Aend = Astart + Aadj;
Bend = Bstart + Badj;
#ifdef _DEBUG_VERBOSE
assert (FinishCt > 1);
//-- Ouput calculation statistics
if ( TargetReached )
fprintf(stderr,"Finish score = %ld : %ld,%ld\n",
Diag[FinishCt] . I[0] . max->value, N, M);
else
fprintf(stderr,"High score = %ld : %ld,%ld\n", high_score,
labs(Aadj) + 1, labs(Badj) + 1);
fprintf(stderr, "%ld nodes calculated, %ld nodes trimmed\n", CalcCt, TrimCt);
if ( m_o & DIRECTION_BIT )
fprintf(stderr, "%ld bytes used\n",
(long int)sizeof(Diagonal) * Dct + (long int)sizeof(Node) * CalcCt);
else
fprintf(stderr, "%ld bytes used\n",
((long int)sizeof(Diagonal) + (long int)sizeof(Node) * MaxL) * 2);
#endif
//-- If in forward alignment m_o, create the Delta information
if ( ~m_o & SEARCH_BIT )
generateDelta (Diag, FinishCt, FinishCDi, N, Delta);
//-- Free the scoring and edit spaces remaining
for ( Di = m_o & SEARCH_BIT ? Dct - 1 : 0; Di <= Dct; Di ++ )
free ( Diag[Di] . I );
free ( Diag );
return TargetReached;
}