int countnode(struct tree *temp) { if(temp==r) count=0; if(temp==NULL) return; else count++; countnode(temp->lptr); countnode(temp->rptr); }
int main() { struct tree *root; root=NULL; r=NULL; int i,n,a[100],item; printf("No. of elements"); scanf("%d",&n); printf("\nElements"); for(i=0;i<n;i++) scanf("%d",&a[i]); for(i=0;i<n;i++) root=insert(root,a[i],i); countnode(r); printf("%d",count); r=del(r); countnode(r); printf("\n%d",count); }
main(int argc, char **argv) { int i, j, k, l, m, n; int dist[20]; int reads; int num_vertex, num_class, num_edge; int *len_seq, num_seq, num_remain; int **num_pa; char **src_seq, **src_name; char temp[100]; ALIGN **eq_class, *align; EDGE **edge, *edge1, *edge2, *bal_edge1, *bal_edge2; PATH *path; int num_path; NODES **vertex, *begin, *node, *node_next, **start_node; LIST **list; READINTERVAL *readinterval; POSITION *position; FILE *fp, *fp1; readpar(); random1(&idum); initenv(argc, argv); printf("%d %d %d\n", sizeof(POSITION), sizeof(NODES), sizeof(LIST)); /* Input the length of the genome (required) */ len_seq = (int *) ckalloc(2 * MAX_NUM * sizeof(int)); src_name = alloc_name(MAX_NUM, 100); fp = ckopen(lenfile, "r"); num_seq = readlen(fp, len_seq, src_name); fclose(fp); src_seq = (char **) ckalloc(2 * num_seq * sizeof(char *)); l = 0; printf("Genome length: "); for(i = 0; i < num_seq; i ++) { l += len_seq[i]; printf("%d ", len_seq[i]); } printf("\n"); printf("Total length: %d\n", l); /* Make reverse complements of input sequences rev(i) --> i + num_seq */ for(i = 0; i < num_seq; i ++) { len_seq[i + num_seq] = len_seq[i]; src_seq[i] = (char *) ckalloc(len_seq[i] * sizeof(char)); src_seq[i + num_seq] = (char *) ckalloc(len_seq[i] * sizeof(char)); for(j = 0; j < len_seq[i]; j ++) { src_seq[num_seq + i][j] = rev(src_seq[i][len_seq[i] - j - 1]); } } /* Input equivalent readintervales between reads -- see the format of the equivalent readinterval files */ printf("Read equivalent readintervales...\n"); eq_class = (ALIGN **) ckalloc(2 * num_seq * sizeof(ALIGN *)); fp = ckopen(inpfile, "r"); num_class = readclass(eq_class, num_seq, fp); fclose(fp); printf("# equivalent readintervales input: %d\n", num_class); /* for(i = 0; i < 2 * num_seq; i ++) { align = eq_class[i]; while(align) { printf("See: \n"); output_align(align, src_name, src_seq, len_seq, num_seq); getchar(); align = align -> next; } } */ /* Initialize the nodes: each position in each read is assigned as a new node. An array of "list" is set up for each read */ list = (LIST **) ckalloc(2 * num_seq * sizeof(LIST *)); for(i = 0; i < 2 * num_seq; i ++) { list[i] = (LIST *) ckalloc(len_seq[i] * sizeof(LIST)); } printf("intitialize nodes...\n"); initialize(list, len_seq, num_seq); printf("done.\n"); n = countnode(list, len_seq, 2 * num_seq); printf("# of nodes before merge: %d\n", n); /* Glue together two nodes if their corresponding positions are defined as equivalent in a pairwise alignment */ printf("Merge...\n"); merge(num_seq, len_seq, eq_class, num_class, list); printf("done.\n"); for(i = 0; i < num_seq; i ++) { while(eq_class[i]) { eq_class[i] = free_align(eq_class[i]); } } free((void **) eq_class); /* Compute the width of each node */ for(i = 0; i < 2 * num_seq; i ++) { for(j = 0; j < len_seq[i]; j ++) { if(!list[i][j].node -> visit) { list[i][j].node -> num_path = countthickness(list[i][j].node); list[i][j].node -> visit = 1; } } } cleannode(list, len_seq, 2 * num_seq); n = countnode(list, len_seq, 2 * num_seq); printf("# of nodes after merge: %d\n", n); /* Add edges to the graph */ edge = (EDGE **) ckalloc(n * sizeof(EDGE *)); num_edge = graph(num_seq, len_seq, list, edge); printf("# edges: %d\n", num_edge); start_node = (NODES **) ckalloc(num_seq * sizeof(NODES *)); for(i = 0; i < num_seq; i ++) { if(len_seq[i] > 0) { start_node[i] = list[i][0].node; } else { start_node[i] = (NODES *) NULL; } } for(i = 0; i < 2 * num_seq; i ++) { free((void *) list[i]); } free((void **) list); vertex = (NODES **) ckalloc(2 * num_edge * sizeof(NODES *)); num_vertex = count_vertex(edge, num_edge, vertex); free((void **) edge); num_pa = (int **) ckalloc(MAX_BRA * sizeof(int *)); for(i = 0; i < MAX_BRA; i ++) { num_pa[i] = (int *) ckalloc(MAX_BRA * sizeof(int)); } num_edge = count_edge_simp(vertex, num_vertex, num_pa); printf("%d vertices %d edges (%d source %d sinks) remained.\n", num_vertex, num_edge, num_pa[0][1], num_pa[1][0]); /* Assign the complementary edges of each edge */ for(i = 0; i < num_vertex; i ++) { for(j = 0; j < vertex[i] -> num_nextedge; j ++) { edge1 = vertex[i] -> nextedge[j]; edge1 -> bal_edge = find_bal_edge(edge1, len_seq, num_seq, i); } } /* Remove bulges in the graph */ printf("Shave...\n"); num_vertex = shave_graph(vertex, num_vertex); printf("done.\n"); /* Remove cycles shorter than some threshold in the graph */ /* printf("Shaving graph...\n"); num_vertex = rem_cycle(vertex, num_vertex); printf("done.\n%d vertices remained.\n", num_vertex); */ /* remove short edges */ /* printf("Remove shortedges...\n"); num_vertex = rem_short_edge(vertex, num_vertex, len_seq); printf("done.\n%d vertices remained.\n", num_vertex); fflush(stdout); */ num_edge = count_edge_simp(vertex, num_vertex, num_pa); printf("%d vertices %d edges (%d source %d sinks) remained.\n", num_vertex, num_edge, num_pa[0][1], num_pa[1][0]); fflush(stdout); /* Allocate the spaces for paths */ printf("Allocating paths...\n"); for(i = 0; i < num_vertex; i ++) { vertex[i] -> num_path = 0; } /* Build sequence paths */ printf("Define paths...\n"); m = 0; for(i = 0; i < num_vertex; i ++) { for(j = 0; j < vertex[i] -> num_nextedge; j ++) { m += vertex[i] -> nextedge[j] -> multip; } } path = (PATH *) ckalloc(2 * num_seq * sizeof(PATH)); for(i = 0; i < 2 * num_seq; i ++) { path[i].edge = (EDGE **) ckalloc(m * sizeof(EDGE *)); } num_path = readpath(start_node, path, num_seq); free((void **) start_node); num_edge = count_edge_simp(vertex, num_vertex, num_pa); m = l = 0; for(i = 0; i < num_vertex; i ++) { for(j = 0; j < vertex[i] -> num_nextedge; j ++) { l += vertex[i] -> nextedge[j] -> length; if(vertex[i] -> nextedge[j] -> length > m) { m = vertex[i] -> nextedge[j] -> length; } } } printf("%d vertics %d edges (%d source %d sinks) remained: total length %d (maximal %d).\n", num_vertex, num_edge, num_pa[0][1], num_pa[1][0], l, m); fflush(stdout); /* Make consensus of edges */ initial_edge(vertex, num_vertex, src_seq, num_seq); printf("edge initialed\n"); /* Output sequence path */ n = 0; for(i = 0; i < num_vertex; i ++) { vertex[i] -> visit = i; for(j = 0; j < vertex[i] -> num_nextedge; j ++) { vertex[i] -> nextedge[j] -> start_cover = n; n ++; } } for(m = 0; m < num_seq; m ++) { printf("len_path %d\n", path[m].len_path); printf("Sequence%d: ", m + 1); for(i = 0; i < path[m].len_path; i ++) { printf("%d -- %d(%d,%d) --> ", path[m].edge[i] -> begin -> visit, path[m].edge[i] -> start_cover, path[m].edge[i] -> multip, path[m].edge[i] -> length); if(i % 5 == 4) { printf("\n"); } } if(path[m].len_path > 0) { printf("%d\n", path[m].edge[i - 1] -> end -> visit); } else { printf("\n"); } fflush(stdout); } /* Output graph & contigs */ sprintf(temp, "%s.edge", seqfile); fp = ckopen(temp, "w"); sprintf(temp, "%s.graph", seqfile); fp1 = ckopen(temp, "w"); write_graph(vertex, num_vertex, fp, fp1); fclose(fp); fclose(fp1); /* Output read intervals in each edge */ sprintf(temp, "%s.intv", seqfile); fp = ckopen(temp, "w"); write_interval(vertex, num_vertex, fp); fclose(fp); /* Output graphviz format graph */ sprintf(temp, "%s", outfile); fp = ckopen(temp, "w"); output_graph(vertex, num_vertex, fp); fclose(fp); for(i = 0; i < MAX_BRA; i ++) { free((void *) num_pa[i]); } free((void **) num_pa); for(i = 0; i < 2 * num_seq; i ++) { if(path[i].len_path > 0) { free((void **) path[i].edge); } } free((void *) path); free_graph(vertex, num_vertex); for(i = 0; i < 2 * num_seq; i ++) { free((void *) src_seq[i]); } free((void **) src_seq); free_name(src_name, MAX_NUM); free((void *) len_seq); }
int main( int argc, char *argv[] ) { static int nlen[M]; static char **name, **seq; static char **oseq; static double **pscore; static double *eff; static double **node0, **node1; static double *gapc; static double *avgap; double tmpavgap; int i, j, m, goffset; static int ***topol; static double **len; FILE *prep; char c; int corestart, coreend; int alloclen; int winsize; char *pt, *ot; double gapmin; arguments( argc, argv ); getnumlen( stdin ); rewind( stdin ); if( njob < 2 ) { fprintf( stderr, "At least 2 sequences should be input!\n" "Only %d sequence found.\n", njob ); exit( 1 ); } seq = AllocateCharMtx( njob, nlenmax*9+1 ); name = AllocateCharMtx( njob, B+1 ); oseq = AllocateCharMtx( njob, nlenmax*9+1 ); alloclen = nlenmax*9; topol = AllocateIntCub( njob, 2, njob ); len = AllocateDoubleMtx( njob, 2 ); pscore = AllocateDoubleMtx( njob, njob ); eff = AllocateDoubleVec( njob ); node0 = AllocateDoubleMtx( njob, njob ); node1 = AllocateDoubleMtx( njob, njob ); gapc = AllocateDoubleVec( alloclen ); avgap = AllocateDoubleVec( alloclen ); #if 0 Read( name, nlen, seq ); #else readData_pointer( stdin, name, nlen, seq ); #endif constants( njob, seq ); #if 0 fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset ); #endif initSignalSM(); initFiles(); WriteOptions( trap_g ); c = seqcheck( seq ); if( c ) { fprintf( stderr, "Illeagal character %c\n", c ); exit( 1 ); } writePre( njob, name, nlen, seq, 0 ); if( tbutree == 0 ) { for( i=1; i<njob; i++ ) { if( nlen[i] != nlen[0] ) { fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" ); exit( 1 ); } } for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ ) { /* pscore[i][j] = (double)score_calc1( seq[i], seq[j] ); */ pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] ); } } else { fprintf( stderr, "Loading 'hat2' ... " ); prep = fopen( "hat2", "r" ); if( prep == NULL ) ErrorExit( "Make hat2." ); readhat2_pointer( prep, njob, name, pscore ); fclose( prep ); fprintf( stderr, "done.\n" ); #if 0 prep = fopen( "hat2_check", "w" ); WriteHat2( prep, njob, name, pscore ); fclose( prep ); #endif } fprintf( stderr, "Constructing dendrogram ... " ); if( treemethod == 'x' ) supg( njob, pscore, topol, len ); else if( treemethod == 's' ) spg( njob, pscore, topol, len ); else if( treemethod == 'p' ) upg2( njob, pscore, topol, len ); else ErrorExit( "Incorrect tree\n" ); fprintf( stderr, "done.\n" ); countnode( njob, topol, node0 ); if( tbrweight ) { weight = 3; #if 0 utree = 0; counteff( njob, topol, len, eff ); utree = 1; #else counteff_simple( njob, topol, len, eff ); #endif } else { for( i=0; i<njob; i++ ) eff[i] = 1.0; } for( i=0; i<nlenmax; i++ ) { gapc[i] = 0.0; for( j=0; j<njob; j++ ) { if( seq[j][i] == '-' ) gapc[i] += eff[j]; } } gapmin = 1.0; winsize = fftWinSize; goffset = winsize/2; tmpavgap = 0.0; corestart = coreend = -1; for( i=0; i<winsize; i++ ) { tmpavgap += gapc[i]; } for( i=winsize; i<nlenmax; i++ ) { m = i - goffset; avgap[m] = tmpavgap / winsize; // fprintf( stdout, "%d %f %f\n", m, avgap[m], gapc[i] ); if( avgap[m] < corethr ) { if( corestart == -1 ) corestart = i - winsize; // fprintf( stdout, "ok, gapmin = %f, corestart = %d, coreend = %d\n", gapmin, corestart, coreend ); if( avgap[m] < gapmin ) { gapmin = avgap[m]; } coreend = i; } tmpavgap -= gapc[i-winsize]; tmpavgap += gapc[i]; } if( corestart == -1 || coreend == -1 ) { corestart = 0; coreend = nlenmax-1; } for( i=0; i<njob; i++ ) { pt = oseq[i]; m = winsize; while( m-- ) *pt++ = '-'; for( j=corestart; j<=coreend; j++ ) *pt++ = seq[i][j]; m = winsize; while( m-- ) *pt++ = '-'; *pt = 0; ot = oseq[i]+winsize-1; pt = seq[i]+corestart-1; if( coreext ) m = winsize; else m = 0; while( m && --pt > seq[i] ) if( *pt != '-' ) { *ot-- = *pt; m--; } ot = oseq[i]+winsize+coreend-corestart+1; pt = seq[i]+coreend; if( coreext ) m = winsize; else m = 0; while( m && *(++pt) ) { if( *pt != '-' ) { *ot++ = *pt; m--; } } fprintf( stdout, ">%s\n", name[i] ); fprintf( stdout, "%s\n", oseq[i] ); } exit( 1 ); SHOWVERSION; return( 0 ); }