+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-
-#define EF_THREEWAY 1.0
-#define MAXBW 1.0
-#define MINBW 0.01
-
-#define MINLEN 0.001
-
-#if DEBUG
-Node *stopol_g;
-#endif
-
-
-void checkMinusLength( int nseq, double **len )
-{
- int i, j;
- for( i=0; i<nseq-1; i++ ) for( j=0; j<2; j++ )
- if( len[i][j] < MINLEN ) len[i][j] = MINLEN;
-}
-
-void negativeMember2( int *mem, int *query, int locnseq )
-{
- int *ptr;
- char *tmp;
- int i;
- int n;
-
- tmp = AllocateCharVec( locnseq );
-
- for( i=0; i<locnseq; i++ ) tmp[i] = 0;
- while( (n=*query++) != -1 ) tmp[n] = 1;
-
- ptr = mem;
- for( i=0; i<locnseq; i++ )
- {
- if( !tmp[i] )
- {
- *ptr++ = i;
- }
- }
- *ptr = -1;
- free( tmp );
-}
-
-int *negativeMember( int *query, int locnseq )
-{
- int *bk, *value = NULL;
- char *tmp;
- int i;
- int n;
-
- tmp = AllocateCharVec( locnseq );
- bk = value = AllocateIntVec( locnseq );
- if( !value ) ErrorExit( "Cannot allocate value" );
-
- for( i=0; i<locnseq; i++ ) tmp[i] = 0;
- while( (n=*query++) != -1 ) tmp[n] = 1;
-
- for( i=0; i<locnseq; i++ )
- {
- if( !tmp[i] )
- {
- fprintf( stderr, "%3d ", i );
- *value++ = i;
- }
- }
- fprintf( stderr, "\n" );
- *value = -1;
- free( tmp );
- return( bk );
-}
-
-int IntExistsInVec( int query, int *vector )
-{
- while( *vector != -1 )
- if( query == *vector++ ) return( 1 );
- return( 0 );
-}
-
-NodeInCub searchParent( int top, int ***topol, int Start, int End )
-{
- int i, j;
- NodeInCub value;
- for( i=Start; i<End; i++ )
- {
- for( j=0; j<2; j++ )
- {
- if( IntExistsInVec( top, topol[i][j] ) )
- {
- value.step = i;
- value.LorR = j;
- return( value );
- }
- }
- }
- fprintf( stderr, "ERROR!!!\n" );
- ErrorExit( "Error in searchParent" );
- value.step=0; // by D.Mathog, katoh
- value.LorR=0; // by D.Mathog, katoh
- return( value );
-}
-
-void stopolInit( int n, Node *stopol )
-{
- int i, j;
- for( i=0; i<n; i++ )
- {
- for( j=0; j<3; j++ )
- {
- stopol[i].length[j] = 0.0;
- stopol[i].children[j] = NULL;
- stopol[i].tmpChildren[j] = -1;
- stopol[i].top[j] = -1;
- stopol[i].members[j] = NULL;
- stopol[i].weightptr[j] = NULL;
- }
- }
-#if 0
- while( --numintvec >= 0 )
- {
- free( tmpintvec[numintvec] );
- }
- free( tmpintvec );
- numintvec = 0;
-#endif
-}
-
-void treeCnv( Node *stopol, int locnseq, int ***topol, double **len, double **bw )
-{
- int i;
- NodeInCub parent;
- int *count;
- int ccount;
- int rep;
- int tmpint;
- static int **tmpintvec = NULL;
- static int numintvec = 0;
-
- count = AllocateIntVec( 2 * locnseq ); /* oome */
- if( !count ) ErrorExit( "Cannot allocate count.\n" );
-
- checkMinusLength( locnseq, len ); /* uwagaki */
-
- stopolInit( locnseq * 2, stopol );
- for( i=0; i<locnseq * 2; i++ ) count[i] = 0;
-
- for( i=locnseq; i<locnseq*2; i++ )
- {
- rep = i - locnseq;
- parent = searchParent( rep, topol, 0, locnseq-1 );
-#if DEBUG
- fprintf( stderr, "Parent of node No.%d ( Seq No.%d ) = %d - %d\n", i, i-locnseq, parent.step, parent.LorR );
-#endif
-
- ccount = count[parent.step];
- stopol[parent.step].length[ccount] = len[parent.step][parent.LorR];
- stopol[parent.step].weightptr[ccount] = &(bw[parent.step][parent.LorR]);
- stopol[parent.step].children[ccount] = &stopol[i];
- stopol[parent.step].tmpChildren[ccount] = i;
- stopol[parent.step].members[ccount] = topol[parent.step][parent.LorR];
- count[parent.step]++;
-
- ccount = count[i];
- stopol[i].length[ccount] = len[parent.step][parent.LorR];
- stopol[i].weightptr[ccount] = &(bw[parent.step][parent.LorR]);
- stopol[i].children[ccount] = &stopol[parent.step];
- stopol[i].tmpChildren[ccount] = parent.step;
- stopol[i].members[ccount] = topol[parent.step][parent.LorR];
- count[i]++;
- }
- for( i=0; i<locnseq-2; i++ )
- {
- rep = MIN( topol[i][0][0], topol[i][1][0] );
- parent = searchParent( rep, topol, i+1, locnseq-1 );
- ccount = count[parent.step];
- stopol[parent.step].length[ccount] = len[parent.step][parent.LorR];
- stopol[parent.step].weightptr[ccount] = &(bw[parent.step][parent.LorR]);
- stopol[parent.step].children[ccount] = &stopol[i];
- stopol[parent.step].tmpChildren[ccount] = i;
- stopol[parent.step].members[ccount] = topol[parent.step][parent.LorR];
- count[parent.step]++;
-
- ccount = count[i];
- stopol[i].length[ccount] = len[parent.step][parent.LorR];
- stopol[i].weightptr[ccount] = &(bw[parent.step][parent.LorR]);
- stopol[i].children[ccount] = &stopol[parent.step];
- stopol[i].tmpChildren[ccount] = parent.step;
-#if 0
- stopol[i].members[ccount] = negativeMember( topol[parent.step][parent.LorR], locnseq );
-#else
-// fprintf( stderr, "allocating numintvec = %d\n", numintvec );
- tmpintvec = (int **)realloc( (void *)tmpintvec, (numintvec+1) * sizeof( int * ) );
- tmpintvec[numintvec] = (int *)calloc( locnseq, sizeof( int ) );
- negativeMember2( tmpintvec[numintvec], topol[parent.step][parent.LorR], locnseq );
- stopol[i].members[ccount] = tmpintvec[numintvec];
- numintvec++;
-#endif
- count[i]++;
-#if DEBUG
- fprintf( stderr, "Parent of node No.%d = %d - %d\n", i, parent.step, parent.LorR );
-#endif
- }
-/*
- Unrooted tree.
- locnseq-2 no children no nakade,
- locnseq-3 wo sashiteinai mono wo sagashite,
- locnseq-3 no children ni kuwae,
- locnseq-2 wo sashiteita node no chilren wo
- locnseq-3 ni kaeru.
-*/
-#if DEBUG
- fprintf( stderr, "BEFORE MODIFY\n" );
- for( i=0; i<locnseq*2; i++ )
- {
- for( j=0; j<3; j++ )
- {
- fprintf( stderr, "stopol[%d].tmpChildren[%d] = %d, children[%d] = %d \n", i, j, stopol[i].tmpChildren[j], j, stopol[i].children[j] - stopol );
- }
- }
-#endif
-
- if ( stopol[locnseq-2].children[0] == &stopol[locnseq-3] ) i = 1;
- else if( stopol[locnseq-2].children[1] == &stopol[locnseq-3] ) i = 0;
- else ErrorExit( "?\n" );
-
- stopol[locnseq-3].length[2] = len[locnseq-2][0] + len[locnseq-2][1];
- stopol[locnseq-3].weightptr[2] = &bw[locnseq-2][0];
- stopol[locnseq-3].children[2] = stopol[locnseq-2].children[i];
- stopol[locnseq-3].tmpChildren[2] = stopol[locnseq-2].tmpChildren[i];
-
- tmpint = (int)( stopol[locnseq-2].children[i] - stopol );
-
- stopol[tmpint].children[2] = &stopol[locnseq-3];
- stopol[tmpint].length[2] = len[locnseq-2][0] + len[locnseq-2][1];
- stopol[tmpint].weightptr[2] = &bw[locnseq-2][0];
- stopol[tmpint].tmpChildren[2] = locnseq-3;
-
-
-#if DEBUG
- for( i=0; i<locnseq*2; i++ )
- {
- for( j=0; j<3; j++ )
- {
- fprintf( stderr, "stopol[%d].tmpChildren[%d] = %d, children[%d] = %d \n", i, j, stopol[i].tmpChildren[j], j, stopol[i].children[j] - stopol );
- }
- }
-
- for( i=0; i<locnseq*2; i++ )
- {
- fprintf( stderr, "-- stopol[%d]\n", i );
- for( j=0; j<3; j++ )
- {
- if( !stopol[i].members[j] )
- {
- fprintf( stderr, "LEAF\n" );
- break;
- }
- fprintf( stderr, " group %d are \n", j );
- for( k=0; (n=stopol[i].members[j][k]) != -1; k++ )
- {
- fprintf( stderr, "%#5d", n );
- }
- fprintf( stderr, "\n" );
- }
- fprintf( stderr, "\n" );
- }
-#endif
-
-#if DEBUG
- stopol_g = stopol;
-#endif
- free( count );
-}
-
-int isLeaf( Node node )
-{
- if( node.children[1] ) return( 0 );
- else return( 1 );
-}
-
-double syntheticLength( Node *ob, Node *oppositeNode )
-{
- int i, count;
- int dir_ch[3];
- int dir_pa = -10; // by katoh
- double value, tmpvalue0, tmpvalue1;
- int nanflag = 0;
-
-#if DEBUG
- fprintf( stderr, "In syntheticLength\n" );
- fprintf( stderr, "ob - stopol_g = %d\n", ob - stopol_g );
- fprintf( stderr, "op - stopol_g = %d\n", oppositeNode - stopol_g );
-#endif
-
- if( isLeaf( *ob ) )
- {
-#if DEBUG
- fprintf( stderr, "LEAF\n\n" );
-#endif
- return( ob->length[0] );
- }
-
- for( i=0, count=0; i<3; i++ )
- {
-#if DEBUG
- fprintf( stderr, "ob->tmpChildren[%d] = %d\n", i, ob->tmpChildren[i] );
-#endif
- if( oppositeNode != ob->children[i] ) dir_ch[count++] = i;
- else dir_pa = i;
- }
-#if DEBUG
- fprintf( stderr, "\n" );
-#endif
- if( count != 2 )
- {
-#if DEBUG
- fprintf( stderr, "Node No.%d has no child like No.%d \n", ob-stopol_g, oppositeNode-stopol_g );
-#endif
- ErrorExit( "Invalid call\n" );
- }
-
- tmpvalue0 = syntheticLength( ob->children[dir_ch[0]], ob );
- tmpvalue1 = syntheticLength( ob->children[dir_ch[1]], ob );
-
-#if DEBUG
- fprintf( stderr, "tmpvalue0 = %f\n", tmpvalue0 );
- fprintf( stderr, "tmpvalue1 = %f\n", tmpvalue1 );
-#endif
- if( tmpvalue0 ) tmpvalue0 = 1.0 / tmpvalue0;
- else nanflag = 1;
- if( tmpvalue1 ) tmpvalue1 = 1.0 / tmpvalue1;
- else nanflag = 1;
-
- if( nanflag ) value = 0.0;
- else
- {
- value = tmpvalue0 + tmpvalue1;
- value = 1.0 / value;
- }
- value += ob->length[dir_pa];
-#if DEBUG
- fprintf( stderr, "value = %f\n", value );
-#endif
-
- return( value );
-}
-
-double calcW( Node *ob, Node *op )
-{
- int i, count;
- int dir_ch[3];
- int dir_pa = -10; // by katoh
- double a, b, c, f, s;
- double value;
-
- if( isLeaf( *ob ) )
- return( 1.0 );
-
- for( i=0, count=0; i<3; i++ )
- {
- if( op != ob->children[i] ) dir_ch[count++] = i;
- else dir_pa = i;
- }
- if( count != 2 ) ErrorExit( "Invalid call of calcW\n" );
-
-#if DEBUG
- fprintf( stderr, "In calcW\n" );
- fprintf( stderr, "ob = %d\n", ob - stopol_g );
- fprintf( stderr, "op = %d\n", op - stopol_g );
- fprintf( stderr, "ob->children[c1] = %d\n", ob->children[dir_ch[0]] - stopol_g );
- fprintf( stderr, "ob->children[c2] = %d\n", ob->children[dir_ch[1]] - stopol_g );
- fprintf( stderr, "ob->children[pa] = %d\n", ob->children[dir_pa] - stopol_g );
- fprintf( stderr, "\n" );
-#endif
-
- a = syntheticLength( ob->children[dir_ch[0]], ob );
- b = syntheticLength( ob->children[dir_ch[1]], ob );
- c = syntheticLength( ob->children[dir_pa], ob );
-
-#if DEBUG
- fprintf( stderr, "a = %f\n", a );
- fprintf( stderr, "b = %f\n", b );
- fprintf( stderr, "c = %f\n", c );
-#endif
-
- if( !c ) return( MAXBW );
- if ( !a || !b ) return( MINBW ); /* ? */
-
- f = EF_THREEWAY;
- s = ( b*c + c*a + a*b );
-
- value = a*b*(c+a)*(c+b) / ( c*(a+b) * f * s );
-
- value = sqrt( value );
-
- return( value );
-}
-
-void calcBranchWeight( double **bw, int locnseq, Node *stopol, int ***topol, double **len )
-{
- NodeInCub parent;
- int i;
- int rep;
- Node *topNode, *btmNode;
- double topW, btmW;
-
- for( i=locnseq; i<locnseq*2; i++ )
- {
- rep = i - locnseq;
- parent = searchParent( rep, topol, 0, locnseq-1 );
- if( parent.step == locnseq - 2 ) continue;
-
- topNode = stopol+parent.step; btmNode = stopol+i;
-#if DEBUG
- fprintf( stderr, "In calcBranchWeight, topNode=%d, btmNode=%d\n", topNode-stopol_g, btmNode-stopol_g );
-#endif
- topW = calcW( topNode, btmNode );
- btmW = calcW( btmNode, topNode );
- bw[parent.step][parent.LorR] = topW * btmW;
- }
- for( i=0; i<locnseq-3; i++ )
- {
- rep = MIN( topol[i][0][0], topol[i][1][0] );
- parent = searchParent( rep, topol, i+1, locnseq-1 );
- if( parent.step == locnseq - 2 ) continue;
- topNode = stopol+parent.step;
- btmNode = stopol+i;
-#if DEBUG
- fprintf( stderr, "In calcBranchWeight, topNode=%d, btmNode=%d\n", topNode-stopol_g, btmNode-stopol_g );
-#endif
- topW = calcW( topNode, btmNode );
- btmW = calcW( btmNode, topNode );
- bw[parent.step][parent.LorR] = topW * btmW;
- }
-
- topNode = stopol[locnseq-3].children[2];
- btmNode = stopol + i;
- topW = calcW( topNode, btmNode );
- btmW = calcW( btmNode, topNode );
- bw[locnseq-2][0] = topW * btmW;
- bw[locnseq-2][1] = 1.0;
-}
-
-void branchWeightToPairWeight( int locnseq, int ***topol, double **pw, double **bw )
-{
- int i, j, k, n0, n1;
-#if 0
- double wFromLeaf[locnseq];
-#else
- static double *wFromLeaf = NULL;
- if( wFromLeaf == NULL )
- wFromLeaf = AllocateDoubleVec( locnseq );
-#endif
-
-#if DEBUG
- for( i=0; i<locnseq-1; i++ ) for( j=0; j<2; j++ )
- fprintf( stderr, "pw[%d][%d] = %f\n", i, j, bw[i][j] );
-#endif
-
- for( i=0; i<locnseq; i++ ) wFromLeaf[i] = 1.0;
- for( i=0; i<locnseq; i++ ) for( j=0; j<locnseq; j++ )
- pw[i][j] = 0.0;
- for( i=0; i<locnseq-1; i++ )
- {
- for( j=0; (n0=topol[i][0][j])!=-1; j++ )
- for( k=0; (n1=topol[i][1][k])!=-1; k++ )
- pw[MIN( n0, n1 )][MAX( n0, n1 )]
- = wFromLeaf[n0] * wFromLeaf[n1] * bw[i][0] * bw[i][1];
- for( j=0; (n0=topol[i][0][j])!=-1; j++ )
- wFromLeaf[n0] *= bw[i][0];
- for( j=0; (n1=topol[i][1][j])!=-1; j++ )
- wFromLeaf[n1] *= bw[i][1];
- }
-}
-
-void weightFromABranch_rec( double *result, Node *ob, Node *op )
-{
- int i, n, count;
- int dir_ch[3], dir_pa;
-
-#if DEBUG
- fprintf( stderr, "In weightFromABranch_rec, ob = %d\n", ob - stopol_g );
-#endif
- if( isLeaf( *ob ) ) return;
- for( i=0, count=0; i<3; i++ )
- {
- if( ob->children[i] != op ) dir_ch[count++] = i;
- else dir_pa = i;
- }
- if( count != 2 )
- {
-#if DEBUG
- fprintf( stderr, "Node No.%d has no child like No.%d \n", ob-stopol_g, op-stopol_g );
-#endif
- ErrorExit( "Incorrect call of weightFromABranch_rec" );
- }
- for( i=0; (n=ob->members[dir_ch[0]][i])!=-1; i++ )
- result[n] *= *ob->weightptr[dir_ch[0]];
- weightFromABranch_rec( result, ob->children[dir_ch[0]], ob );
-
- for( i=0; (n=ob->members[dir_ch[1]][i])!=-1; i++ )
- result[n] *= *ob->weightptr[dir_ch[1]];
- weightFromABranch_rec( result, ob->children[dir_ch[1]], ob );
-}
-
-void weightFromABranch( int nseq, double *result, Node *stopol, int ***topol, int step, int LorR )
-{
- Node *topNode, *btmNode;
- int i;
-
- if( step == nseq - 2 )
- {
- topNode = stopol[nseq-2].children[0];
- btmNode = stopol + nseq-3;
-#if DEBUG
- fprintf( stderr, "Now step == nseq-3, topNode = %d, btmNode = %d\n", topNode - stopol_g, btmNode-stopol_g );
-#endif
- }
-
- else
- {
- for( i=0; i<3; i++ )
- {
- if( stopol[step].members[i][0] == topol[step][LorR][0] )
- break;
- }
- if( i== 3 ) ErrorExit( "Incorrect call of weightFromABranch." );
- btmNode = stopol[step].children[i];
- topNode = stopol+step;
- }
-
- for( i=0; i<nseq; i++ ) result[i] = 1.0;
- weightFromABranch_rec( result, btmNode, topNode );
- weightFromABranch_rec( result, topNode, btmNode );
-#if 0
- for( i=0; i<nseq; i++ )
- fprintf( stdout, "w[%d] = %f\n", i, result[i] );
-#endif
-// fprintf( stderr, "new weight!\n" );
-// for( i=0; i<nseq; i++ )
-// result[i] *= result[i];
-
-
-}
-void assignstrweight_rec( double *strweight, Node *ob, Node *op, char *kozoari, double *seqweight )
-{
- int i, n, count, lastkozo;
- int dir_ch[3], dir_pa;
- double sumweight;
-
-#if DEBUG
- fprintf( stderr, "In weightFromABranch_rec, ob = %d\n", ob - stopol_g );
-#endif
- if( isLeaf( *ob ) )
- {
-// fprintf( stderr, "Leaf!\n" );
- return;
- }
- for( i=0, count=0; i<3; i++ )
- {
- if( ob->children[i] != op ) dir_ch[count++] = i;
- else dir_pa = i;
- }
- if( count != 2 )
- {
-#if DEBUG
- fprintf( stderr, "Node No.%d has no child like No.%d \n", ob-stopol_g, op-stopol_g );
-#endif
- ErrorExit( "Incorrect call of weightFromABranch_rec" );
- }
-
-
-// fprintf( stderr, "\n" );
- sumweight = 0.0;
- count = 0;
- lastkozo = -1;
- for( i=0; (n=ob->members[dir_ch[0]][i])!=-1; i++ )
- {
-// fprintf( stderr, "member1! n=%d\n", n );
- sumweight += seqweight[n];
- if( kozoari[n] )
- {
- count++;
- lastkozo = n;
- }
- }
- for( i=0; (n=ob->members[dir_ch[1]][i])!=-1; i++ )
- {
-// fprintf( stderr, "member2! n=%d\n", n );
- sumweight += seqweight[n];
- if( kozoari[n] )
- {
- count++;
- lastkozo = n;
- }
- }
-
-// fprintf( stderr, "count = %d\n", count );
-
- if( count == 1 )
- strweight[lastkozo] = sumweight;
- else if( count > 1 )
- {
- assignstrweight_rec( strweight, ob->children[dir_ch[0]], ob, kozoari, seqweight );
- assignstrweight_rec( strweight, ob->children[dir_ch[1]], ob, kozoari, seqweight );
- }
-}
-
-void assignstrweight( int nseq, double *strweight, Node *stopol, int ***topol, int step, int LorR, char *kozoari, double *seqweight )
-{
- Node *topNode, *btmNode;
- int i;
-
- if( step == nseq - 2 )
- {
- topNode = stopol[nseq-2].children[0];
- btmNode = stopol + nseq-3;
-#if DEBUG
- fprintf( stderr, "Now step == nseq-3, topNode = %d, btmNode = %d\n", topNode - stopol_g, btmNode-stopol_g );
-#endif
- }
-
- else
- {
- for( i=0; i<3; i++ )
- {
- if( stopol[step].members[i][0] == topol[step][LorR][0] )
- break;
- }
- if( i== 3 ) ErrorExit( "Incorrect call of weightFromABranch." );
- btmNode = stopol[step].children[i];
- topNode = stopol+step;
- }
-
- for( i=0; i<nseq; i++ ) strweight[i] = 0.0;
- for( i=0; i<nseq; i++ ) if( kozoari[i] ) strweight[i] = seqweight[i];
-// fprintf( stderr, "calling _rec (1)\n" );
- assignstrweight_rec( strweight, btmNode, topNode, kozoari, seqweight );
-// fprintf( stderr, "calling _rec (2)\n" );
- assignstrweight_rec( strweight, topNode, btmNode, kozoari, seqweight );
-
-#if 1 // nazeka kokowo tobasuto seido ga sagaru ?????
- fprintf( stderr, "STEP %d\n", step );
- for( i=0; topol[step][0][i]>-1; i++ )
- fprintf( stderr, "%3d ", topol[step][0][i] );
- fprintf( stderr, "\n" );
- for( i=0; topol[step][1][i]>-1; i++ )
- fprintf( stderr, "%3d ", topol[step][1][i] );
- fprintf( stderr, "\n" );
- for( i=0; i<nseq; i++ )
- fprintf( stderr, "seqweight[%d] = %f\n", i, seqweight[i] );
- for( i=0; i<nseq; i++ )
- fprintf( stderr, "strweight[%d] = %f\n", i, strweight[i] );
- fprintf( stderr, "\n" );
-#endif
-}
git://source.jalview.org / jabaws.git / blobdiff