fix: add include
This commit is contained in:
parent
525c9eb122
commit
b2951105ae
2 changed files with 2449 additions and 2789 deletions
446
HGL_SRC/Alloc.c
446
HGL_SRC/Alloc.c
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@ -1,133 +1,122 @@
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#include <stdio.h>
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#include "global_defs.h"
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#include <ctype.h>
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#include <malloc.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include "global_defs.h"
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/*
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* Alloc.c
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* Memory functions for Harvard Genome Laboratory.
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* Last revised 6/3/91
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*
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* Print error message, and die
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*/
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void ErrorOut(code,string)
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int code;
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* Alloc.c
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* Memory functions for Harvard Genome Laboratory.
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* Last revised 6/3/91
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*
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* Print error message, and die
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*/
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void ErrorOut(code, string) int code;
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char *string;
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{
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if (code == 0)
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{
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fprintf(stderr,"Error:%s\n",string);
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exit(1);
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}
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return;
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}
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/*
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* Calloc count*size bytes with memory aligned to size.
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* Return pointer to new block.
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*/
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char *Calloc(count,size)
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int count,size;
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/*unsigned count,size;*/
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{
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char *temp;
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temp = calloc(count,(unsigned)size);
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if(count*size == 0)
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fprintf(stderr,"Allocate ZERO blocks?\n");
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ErrorOut(temp,"Cannot allocate memory");
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return(temp);
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}
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/*
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* Reallocate memory at block, expand to size.
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* Return pointer to (possibly) new block.
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*/
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char *Realloc(block,size)
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char *block;
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unsigned size;
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{
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char *temp;
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temp=realloc(block,size);
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ErrorOut(temp,"Cannot change memory size");
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return(temp);
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}
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/*
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* Free block Allocated by Calloc.
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* Return error code from free().
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*/
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void Cfree(block)
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char* block;
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{
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extern void Warning();
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if(block != NULL)
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{
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#ifdef SUN4
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if(free(block) == 0)
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Warning("Error in Cfree...");
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#endif
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}
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/* else
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Warning("Error in Cfree, NULL block");
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*/
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return;
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}
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/*
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* Print Warning message to stderr.
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*/
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void Warning(s)
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char *s;
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{
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fprintf(stderr,"Warning:%s\n",s);
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if (code == 0) {
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fprintf(stderr, "Error:%s\n", string);
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exit(1);
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}
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return;
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}
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/*
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* Get array element from a sequence structure. The index
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* is relative to the alignment.
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*/
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char GetElem(seq,indx)
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Sequence *seq; /*Sequence to search*/
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int indx; /*Index relative to the global offset*/
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* Calloc count*size bytes with memory aligned to size.
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* Return pointer to new block.
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*/
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char *Calloc(count, size)
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int count, size;
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/*unsigned count,size;*/
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{
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if((indx<seq->offset) || (indx >= seq->offset + seq->seqlen))
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return('-');
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else
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return((char)(seq->c_elem[indx-seq->offset]));
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char *temp;
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temp = calloc(count, (unsigned)size);
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if (count * size == 0) fprintf(stderr, "Allocate ZERO blocks?\n");
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ErrorOut(temp, "Cannot allocate memory");
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return (temp);
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}
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/*
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* Replace the array element at seq[indx] with elem. The index
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* is relative to the alignment.
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*/
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void ReplaceElem(seq,indx,elem)
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Sequence *seq; /*Sequence */
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int indx; /*Position to overwrite (replace) */
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unsigned char elem; /*Character to replace with */
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* Reallocate memory at block, expand to size.
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* Return pointer to (possibly) new block.
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*/
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char *Realloc(block, size)
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char *block;
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unsigned size;
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{
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int j;
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char *temp;
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temp = realloc(block, size);
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ErrorOut(temp, "Cannot change memory size");
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return (temp);
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}
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/*
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* Free block Allocated by Calloc.
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* Return error code from free().
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*/
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void Cfree(block) char *block;
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{
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extern void Warning();
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if (block != NULL) {
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#ifdef SUN4
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if (free(block) == 0) Warning("Error in Cfree...");
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#endif
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}
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/* else
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Warning("Error in Cfree, NULL block");
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*/
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return;
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}
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/*
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* Print Warning message to stderr.
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*/
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void Warning(s) char *s;
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{
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fprintf(stderr, "Warning:%s\n", s);
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return;
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}
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/*
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* Get array element from a sequence structure. The index
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* is relative to the alignment.
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*/
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char GetElem(seq, indx)
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Sequence *seq; /*Sequence to search*/
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int indx; /*Index relative to the global offset*/
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{
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if ((indx < seq->offset) || (indx >= seq->offset + seq->seqlen))
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return ('-');
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else
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return ((char)(seq->c_elem[indx - seq->offset]));
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}
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/*
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* Replace the array element at seq[indx] with elem. The index
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* is relative to the alignment.
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*/
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void ReplaceElem(seq, indx, elem) Sequence *seq; /*Sequence */
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int indx; /*Position to overwrite (replace) */
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unsigned char elem; /*Character to replace with */
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{
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int j;
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extern char *Calloc();
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int width;
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/*
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* If no c_elem has been allocated yet...
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*/
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/* if(index("abcdefghijklmnopqrstuvwxyz-0123456789",elem)==0)
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fprintf(stderr,"Warning (ReplaceElem) elem = %c\n",elem);
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*/
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width = seq->offset-indx;
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if(seq->seqlen == 0 && elem != '-')
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{
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if(seq->seqmaxlen == 0 || seq->c_elem == NULL)
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{
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seq->c_elem = Calloc(4,sizeof(char));
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/*
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* If no c_elem has been allocated yet...
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*/
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/* if(index("abcdefghijklmnopqrstuvwxyz-0123456789",elem)==0)
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fprintf(stderr,"Warning (ReplaceElem) elem =
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%c\n",elem);
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*/
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width = seq->offset - indx;
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if (seq->seqlen == 0 && elem != '-') {
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if (seq->seqmaxlen == 0 || seq->c_elem == NULL) {
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seq->c_elem = Calloc(4, sizeof(char));
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seq->offset = indx;
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seq->seqmaxlen = 4;
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}
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@ -135,118 +124,109 @@ unsigned char elem; /*Character to replace with */
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seq->c_elem[0] = elem;
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seq->offset = indx;
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}
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/*
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* If inserting before the c_elem (< offset)
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*/
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else if((indx<seq->offset) && (elem!='-'))
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{
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/*
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* If inserting before the c_elem (< offset)
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*/
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else if ((indx < seq->offset) && (elem != '-')) {
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seq->seqmaxlen += width;
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seq->c_elem = Realloc(seq->c_elem,seq->seqmaxlen*sizeof(char));
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for(j=seq->seqmaxlen-1;j>=width;j--)
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seq->c_elem[j] = seq->c_elem[j-width];
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for(j=0;j<width;j++)
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seq->c_elem[j] = '-';
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seq->c_elem =
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Realloc(seq->c_elem, seq->seqmaxlen * sizeof(char));
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for (j = seq->seqmaxlen - 1; j >= width; j--)
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seq->c_elem[j] = seq->c_elem[j - width];
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for (j = 0; j < width; j++) seq->c_elem[j] = '-';
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seq->c_elem[0] = elem;
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seq->seqlen += width;
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seq->offset = indx;
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}
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/*
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* if inserting after c_elem (indx > offset + seqlen)
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*/
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else if((indx>=seq->offset+seq->seqlen) && (elem!='-'))
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{
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if(indx-seq->offset >= seq->seqmaxlen)
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{
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seq->seqmaxlen = indx-seq->offset+256;
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seq->c_elem = Realloc(seq->c_elem,seq->seqmaxlen*
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sizeof(char));
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/*
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* if inserting after c_elem (indx > offset + seqlen)
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*/
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else if ((indx >= seq->offset + seq->seqlen) && (elem != '-')) {
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if (indx - seq->offset >= seq->seqmaxlen) {
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seq->seqmaxlen = indx - seq->offset + 256;
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seq->c_elem =
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Realloc(seq->c_elem, seq->seqmaxlen * sizeof(char));
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}
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for(j=seq->seqlen;j<seq->seqmaxlen;j++)
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for (j = seq->seqlen; j < seq->seqmaxlen; j++)
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seq->c_elem[j] = '-';
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seq->c_elem[indx-seq->offset] = elem;
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seq->seqlen = indx-seq->offset+1;
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}
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else
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{
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if(indx-(seq->offset)>=0 && indx-(seq->offset)<seq->seqlen)
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seq->c_elem[indx-(seq->offset)] = elem;
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else if(elem!='-')
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fprintf(stderr,"%c better be a -\n",elem);
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seq->c_elem[indx - seq->offset] = elem;
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seq->seqlen = indx - seq->offset + 1;
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}
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return;
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else {
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if (indx - (seq->offset) >= 0 &&
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indx - (seq->offset) < seq->seqlen)
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seq->c_elem[indx - (seq->offset)] = elem;
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else if (elem != '-')
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fprintf(stderr, "%c better be a -\n", elem);
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}
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return;
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}
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/*
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* InsertElem is a modification of InsertElems, and should be
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* optimized. s.s.5/6/91
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*/
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int InsertElem(a,b,ch)
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Sequence *a; /* Sequence */
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int b; /*Position to insert BEFORE*/
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char ch; /*element to insert */
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* InsertElem is a modification of InsertElems, and should be
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* optimized. s.s.5/6/91
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*/
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int InsertElem(a, b, ch)
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Sequence *a; /* Sequence */
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int b; /*Position to insert BEFORE*/
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char ch; /*element to insert */
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{
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char c[2];
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c[0]=ch;
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c[1] = '\0';
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return (InsertElems(a,b,c));
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char c[2];
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c[0] = ch;
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c[1] = '\0';
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return (InsertElems(a, b, c));
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}
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/*
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* Make a copy of Sequence one, place in Sequence two
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*/
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void SeqCopy(one,two)
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Sequence *one,*two;
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* Make a copy of Sequence one, place in Sequence two
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*/
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void SeqCopy(one, two) Sequence *one, *two;
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{
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int j;
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*two = *one;
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if(two->seqmaxlen)
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two->c_elem = Calloc(one->seqmaxlen,sizeof(char));
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if(two->commentsmaxlen)
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two->comments = Calloc(one->commentsmaxlen,sizeof(char));
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for(j=0;j<one->seqlen;j++)
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two->c_elem[j] = one->c_elem[j];
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for(j=0;j<one->commentslen;j++)
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if (two->seqmaxlen) two->c_elem = Calloc(one->seqmaxlen, sizeof(char));
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if (two->commentsmaxlen)
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two->comments = Calloc(one->commentsmaxlen, sizeof(char));
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for (j = 0; j < one->seqlen; j++) two->c_elem[j] = one->c_elem[j];
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for (j = 0; j < one->commentslen; j++)
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two->comments[j] = one->comments[j];
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return;
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}
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/*
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* Normalize seq (remove leading indels in the c_elem;
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*/
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void SeqNormal(seq)
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Sequence *seq;
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* Normalize seq (remove leading indels in the c_elem;
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*/
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void SeqNormal(seq) Sequence *seq;
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{
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int len,j,shift_width,trailer;
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int len, j, shift_width, trailer;
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char *c_elem;
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len = seq->seqlen;
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c_elem = seq->c_elem;
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if(len == 0) return;
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if (len == 0) return;
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for(shift_width=0; (shift_width<len) && (c_elem[shift_width] == '-');
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shift_width++);
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for (shift_width = 0;
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(shift_width < len) && (c_elem[shift_width] == '-'); shift_width++)
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;
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for(j=0;j<len-shift_width;j++)
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c_elem[j] = c_elem[j+shift_width];
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for (j = 0; j < len - shift_width; j++)
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c_elem[j] = c_elem[j + shift_width];
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seq->seqlen -= shift_width;
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seq->offset += shift_width;
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for(trailer=seq->seqlen-1;(c_elem[trailer] =='-' ||
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c_elem[trailer] == '\0') && trailer>=0;
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trailer--)
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c_elem[trailer] = '\0';
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seq->seqlen = trailer+1;
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for (trailer = seq->seqlen - 1;
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(c_elem[trailer] == '-' || c_elem[trailer] == '\0') &&
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trailer >= 0;
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trailer--)
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c_elem[trailer] = '\0';
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seq->seqlen = trailer + 1;
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return;
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}
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void SeqRev(seq,min,max)
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Sequence *seq;
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int min,max;
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void SeqRev(seq, min, max) Sequence *seq;
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int min, max;
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/*
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SeqRev will reverse a given sequence within a window from
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min to max (inclusive). The idea is to allow several sequences
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@ -260,72 +240,68 @@ int min,max;
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*/
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{
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int j;
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char temp1,temp2;
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char temp1, temp2;
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extern char GetElem();
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extern void ReplaceElem();
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for(j=0;j<= (max-min)/2;j++)
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{
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temp1 = GetElem(seq,min+j);
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temp2 = GetElem(seq,max-j);
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ReplaceElem(seq,min+j,(unsigned char)temp2);
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ReplaceElem(seq,max-j,(unsigned char)temp1);
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for (j = 0; j <= (max - min) / 2; j++) {
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temp1 = GetElem(seq, min + j);
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temp2 = GetElem(seq, max - j);
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ReplaceElem(seq, min + j, (unsigned char)temp2);
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ReplaceElem(seq, max - j, (unsigned char)temp1);
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}
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seq->direction *= -1;
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SeqNormal(seq);
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return;
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}
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}
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/* sequence complementing. */
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void SeqComp(seq)
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Sequence *seq;
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void SeqComp(seq) Sequence *seq;
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{
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int j;
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unsigned char in,out,case_bit;
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int j;
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unsigned char in, out, case_bit;
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char *c;
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static int tmatr[16] = {'-','a','c','m','g','r','s','v',
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't','w','y','h','k','d','b','n'};
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static int matr[128] = {
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0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0x00,
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0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
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0x01,0x0e,0x02,0x0d,0,0,0x04,0x0b,0,0,0x0c,0,0x03,0x0f,0,0x05,0,0x05,0x06,
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0x08,0x08,0x07,0x09,0x00,0x0a,0,0,0,0,0,0,0,0x01,0x0e,0x02,0x0d,0,0,0x04,
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0x0b,0,0,0x0c,0,0x03,0x0f,0,0x05,0,0x05,0x06,0x08,0x08,0x07,0x09,0x00,0x0a,
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0,0,0,0,0x00,0
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};
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static int tmatr[16] = {'-', 'a', 'c', 'm', 'g', 'r', 's', 'v',
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't', 'w', 'y', 'h', 'k', 'd', 'b', 'n'};
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static int matr[128] = {
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0x00, 0,
|
||||
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
|
||||
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
|
||||
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0x01,
|
||||
0x0e, 0x02, 0x0d, 0, 0, 0x04, 0x0b, 0, 0, 0x0c, 0,
|
||||
0x03, 0x0f, 0, 0x05, 0, 0x05, 0x06, 0x08, 0x08, 0x07, 0x09,
|
||||
0x00, 0x0a, 0, 0, 0, 0, 0, 0, 0, 0x01, 0x0e,
|
||||
0x02, 0x0d, 0, 0, 0x04, 0x0b, 0, 0, 0x0c, 0, 0x03,
|
||||
0x0f, 0, 0x05, 0, 0x05, 0x06, 0x08, 0x08, 0x07, 0x09, 0x00,
|
||||
0x0a, 0, 0, 0, 0, 0x00, 0};
|
||||
|
||||
c = seq->c_elem;
|
||||
for(j=0;j<seq->seqlen;j++)
|
||||
{
|
||||
/*
|
||||
* Save Case bit...
|
||||
*/
|
||||
case_bit = c[j] & 32;
|
||||
for (j = 0; j < seq->seqlen; j++) {
|
||||
/*
|
||||
* Save Case bit...
|
||||
*/
|
||||
case_bit = c[j] & 32;
|
||||
out = 0;
|
||||
in = matr[c[j]];
|
||||
if(in&1)
|
||||
out|=8;
|
||||
if(in&2)
|
||||
out|=4;
|
||||
if(in&4)
|
||||
out|=2;
|
||||
if(in&8)
|
||||
out|=1;
|
||||
if (in & 1) out |= 8;
|
||||
if (in & 2) out |= 4;
|
||||
if (in & 4) out |= 2;
|
||||
if (in & 8) out |= 1;
|
||||
|
||||
if(case_bit == 0)
|
||||
c[j] = toupper(tmatr[out]);
|
||||
if (case_bit == 0)
|
||||
c[j] = toupper(tmatr[out]);
|
||||
else
|
||||
c[j] = tmatr[out];
|
||||
c[j] = tmatr[out];
|
||||
}
|
||||
|
||||
seq->direction *= -1;
|
||||
seq->strandedness = ( seq->strandedness == 2)?1:
|
||||
( seq->strandedness == 1)?2:
|
||||
0;
|
||||
seq->strandedness = (seq->strandedness == 2) ? 1
|
||||
: (seq->strandedness == 1) ? 2
|
||||
: 0;
|
||||
return;
|
||||
|
||||
}
|
||||
|
|
|
|||
4792
HGL_SRC/HGLfuncs.c
4792
HGL_SRC/HGLfuncs.c
File diff suppressed because it is too large
Load diff
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Reference in a new issue