Mercurial > repos > dawe > srf2fastq
view srf2fastq/io_lib-1.12.2/io_lib/read_alloc.c @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
---|---|
date | Tue, 07 Jun 2011 17:48:05 -0400 |
parents | |
children |
line wrap: on
line source
/* * Copyright (c) Medical Research Council 1994. All rights reserved. * * Permission to use, copy, modify and distribute this software and its * documentation for any purpose is hereby granted without fee, provided that * this copyright and notice appears in all copies. * * This file was written by James Bonfield, Simon Dear, Rodger Staden, * as part of the Staden Package at the MRC Laboratory of Molecular * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. * * MRC disclaims all warranties with regard to this software. */ /* * File: read_alloc.c * Purpose: Performs the allocation/freeing of Read structures * Last update: 01/09/94 */ /* The Read data type is designed so that it can hold a varying degree of information about sequences, yet have a single set of calls to access the data. There are plenty of assumptions around that both the number of bases and the number of points will fit into an int_2, a short. */ /* ---- Includes ---- */ #include <stdlib.h> #include <stdio.h> #include <string.h> #include <assert.h> #include "io_lib/misc.h" #include "io_lib/Read.h" /* * Allocate a new sequence, with the given sizes. * Returns: * "Read *" for success * "NULLRead" for failure */ Read *read_allocate(int num_points, int num_bases) { Read *seq = NULLRead; int sections = read_sections(0); /* Allocate the body of the sequence */ if ((seq = (Read *)xmalloc(sizeof(Read))) == NULL) return(NULLRead); seq->NPoints = num_points; seq->NBases = num_bases; /* * Initialise the body, all pointers are set to NULL so we can * happily call `read_deallocate()`. */ seq->leftCutoff = 0; seq->rightCutoff = 0; seq->maxTraceVal = 0; seq->baseline = 0; seq->traceC = NULL; seq->traceA = NULL; seq->traceG = NULL; seq->traceT = NULL; seq->base = NULL; seq->basePos = NULL; seq->info = NULL; seq->format = TT_ANY; seq->trace_name = NULL; seq->prob_A = NULL; seq->prob_C = NULL; seq->prob_G = NULL; seq->prob_T = NULL; seq->orig_trace_format = TT_ANY; seq->orig_trace = NULL; seq->orig_trace_free = NULL; seq->ident = NULL; /* Allocate space for the bases - 1 extra for the ->base field so * that we can treat it as a NULL terminated string. */ if (sections & READ_BASES && (((seq->base = (char *)xcalloc(num_bases+1,1)) == NULL) || ((seq->basePos = (uint_2 *)xcalloc(num_bases+1,2)) == NULL) || ((seq->prob_A = (char *)xcalloc(num_bases+1,1)) == NULL) || ((seq->prob_C = (char *)xcalloc(num_bases+1,1)) == NULL) || ((seq->prob_G = (char *)xcalloc(num_bases+1,1)) == NULL) || ((seq->prob_T = (char *)xcalloc(num_bases+1,1)) == NULL)) ) { read_deallocate(seq); return NULLRead; } if (sections & READ_SAMPLES && (((seq->traceC =(TRACE *)xcalloc(num_points+1, 2)) == NULL)|| ((seq->traceA =(TRACE *)xcalloc(num_points+1, 2)) == NULL)|| ((seq->traceG =(TRACE *)xcalloc(num_points+1, 2)) == NULL)|| ((seq->traceT =(TRACE *)xcalloc(num_points+1, 2)) == NULL)) ) { read_deallocate(seq); return NULLRead; } seq->nflows = 0; seq->flow_order = NULL; seq->flow = NULL; seq->flow_raw = NULL; seq->private_data = NULL; seq->private_size = 0; return seq; } /* * Free memory allocated to a sequence by read_allocate(). */ void read_deallocate(Read *read) { if (read == NULLRead) return; if (read->traceC != NULL) xfree(read->traceC); if (read->traceA != NULL) xfree(read->traceA); if (read->traceG != NULL) xfree(read->traceG); if (read->traceT != NULL) xfree(read->traceT); if (read->base != NULL) xfree(read->base); if (read->basePos != NULL) xfree(read->basePos); if (read->info != NULL) xfree(read->info); if (read->prob_A != NULL) xfree(read->prob_A); if (read->prob_C != NULL) xfree(read->prob_C); if (read->prob_G != NULL) xfree(read->prob_G); if (read->prob_T != NULL) xfree(read->prob_T); if (read->trace_name != NULL) xfree(read->trace_name); if (read->orig_trace != NULL) { if (read->orig_trace_free) read->orig_trace_free(read->orig_trace); else xfree(read->orig_trace); } if (read->ident != NULL) xfree(read->ident); if (read->flow_order) xfree(read->flow_order); if (read->flow) xfree(read->flow); if (read->flow_raw) xfree(read->flow_raw); if (read->private_data) xfree(read->private_data); xfree(read); } /* * Duplicates the read structure and optionally gives it a new filename. * The following fields are not duplicated: * * int orig_trace_format; * void (*orig_trace_free)(void *ptr); * void *orig_trace; * char *ident; * * Returns: * "Read *" for success * "NULLRead" for failure */ Read* read_dup( Read* src, const char* new_name ) { int n; Read* dst; assert(src); /* Allocate storage and initialise */ dst = read_allocate( src->NPoints, src->NBases ); if( dst == NULLRead ) return 0; dst->info = 0; dst->trace_name = 0; /* Copy over possibly new name */ if( new_name ) n = strlen(new_name); else if( src->trace_name ) n = strlen(src->trace_name); else n = 0; if( n > 0 ) { dst->trace_name = (char*) xmalloc(n+1); if( !dst->trace_name ) goto error; if(new_name) strcpy( dst->trace_name, new_name ); else strcpy( dst->trace_name, src->trace_name ); } /* Copy over info */ if( src->info ) { dst->info = strdup(src->info); } /* Copy single fields */ dst->format = src->format; dst->maxTraceVal = src->maxTraceVal; dst->leftCutoff = src->leftCutoff; dst->rightCutoff = src->rightCutoff; dst->baseline = src->baseline; /* Copy NPoints fields if they exist */ if( src->traceA ) { for( n=0; n<src->NPoints; n++ ) { dst->traceA[n] = src->traceA[n]; dst->traceC[n] = src->traceC[n]; dst->traceG[n] = src->traceG[n]; dst->traceT[n] = src->traceT[n]; } } /* Copy NBases fields if they exist */ if( src->base && src->base[0] ) { for( n=0; n<src->NBases; n++ ) { dst->base[n] = src->base[n]; dst->basePos[n] = src->basePos[n]; if( src->prob_A ) { dst->prob_A[n] = src->prob_A[n]; dst->prob_C[n] = src->prob_C[n]; dst->prob_G[n] = src->prob_G[n]; dst->prob_T[n] = src->prob_T[n]; } } } /* Success */ return dst; error: /* Failure */ read_deallocate(dst); return NULLRead; }