116 lines
3.0 KiB
C
116 lines
3.0 KiB
C
#ifndef _seqIOEdit_h
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#define _seqIOEdit_h
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/*
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Title: seqIOEdit
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File: seqIOEdit.h
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Purpose: IO of edited sequences
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Last update: Tue Jan 15 1991
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Change log :-
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15.01.91 SD
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Removed parts required for complementation and put them in opp.h
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*/
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/* ---- Imports ---- */
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#include "seq.h" /* IMPORT: Seq */
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#include <stdio.h> /* IMPORT: fopen, fclose, fseek, ftell, fgetc */
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#include <ctype.h> /* IMPORT: isprint */
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#include <X11/Intrinsic.h> /* IMPORT: Boolean */
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/* ---- Private ---- */
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/* ---- Exports ---- */
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extern Boolean writeEdSeq(Seq seq, char *fn);
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/*
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Write the clipped, edited part of the sequence `seq'
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into file `fn'. The result indicates success.
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(*==fn in the following description)
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addition by lfw, 10/24/90,
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1. writes *.out as text file without printing bases
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before left and right cutoff, and without
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printing base numbers (in this program)
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2. write *.1 as text if seq.1 does not exist
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write *.2 as text if seq.1 does exist
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write *.3 as text if seq.2 does exist
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...
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write *.n as text if seq.(n-1) does exist
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( in writeEdSeq in seqIOEdit.c )
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*/
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extern Boolean readEdSeq(Seq seq, String fn, int dotnum);
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/*reads in the most recent fn.seq.n file. This
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file should be of the form:
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basePos;edBasePos;edBase
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returns True if it read in the sequence from
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an editted file, and False if there was no
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editted file or if there was a problem
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dotnum == -1 if the user did not specify a
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version number of the sequence to read in,
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m if they want version m read in. */
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extern Boolean processEdSeqFile(Seq seq, String fn);
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/* processes a char vector containing the Editted
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sequence in the following format:
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NedBases*NorigBases*leftCutoff*rightCutoff*negative
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components of edits array in the form (position,
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negative number)*non NULL componenets edBase array*
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non NULL components edBasePos array*
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each division ends in an H. The end of the
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edits array is signaled by a -1 -1 entry. Within
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each division entries are separated by spaces
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sticks the information it finds into the seq array
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returns false if there was a problem with the file format */
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extern Boolean isDotSeq(char *fn);
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/* checks to see if the filename already has the .seq
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suffix or not */
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extern int isDotNum(char *fn);
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/* checks if there is a .1 or .2 or .m on the inputfilename.
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If there is, then returns that num. If not returns -1.
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*/
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extern void stripDotNum(char *fn);
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/* if there is a .num (indicating that the user has input
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an edited version of the sequence they wish to have
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read in) on the end of fn, strip it off */
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extern int findLeftCutoff(Seq seq, char *enzString);
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/* if the sequence has not previously been edited, this
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subroutine is used for auto-clipping */
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extern int findRightCutoff(Seq seq);
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/* if the sequence has not previously been edited, this
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subroutine is used for auto-clipping */
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#endif /*_seqIOEdit_h*/
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