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staden-lg/src/staden/dbsysnew.f

2964 lines
93 KiB
Fortran
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C 8-4-92 removed minimum block length changing option in dbauto
C 29.05.91 IMPLEMENTED REMOVE GEL READING
C 21-8-91 Added routines to find internal overlaps
C 2-9-91 Fixed bug in copytg
C 8-11-91 fixed bugs in "find internal joins"
C 24-02-92 fixed some bugs courtesy of Kozlowski's AIX port
C 23-Jun-92 COPYCC - params to READCC and WRITCC in wrong order
C
C SUBROUTINE TO ENTER NEW GEL SEQUENCES INTO DATA BASE.
C IT READS IN AN ARCHIVE VERSION AND WRITES OUT A WORKING VERSION.
C IT ALSO SETS UP ANY RELATIONSHIPS WITH OTHER DATA IN THE DATABASE
C BOTH BY POSITION IN A CONTIG AND POINTERS TO LEFT AND RIGHT
C NEIGHBOURS.
SUBROUTINE AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+GEL,NAMARC,X,ITYPE,ISENSE,SEQC2,ITOTPC,
+IDIM,IDC,NCONTC,LINCON,IFAIL,IDBSIZ,KBOUT,IDEVR,IDEVW,IDEVN,
+IDEVT,IDEVC,IDEVG,MAXGEL)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),X,Y
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL),NAMARC*(*)
CHARACTER SEQC2(IDC)
CHARACTER NAMARK*10
C WRITE(*,*)'X,ITYPE,ISENSE,IDIM,IDC'
C WRITE(*,*)X,ITYPE,ISENSE,IDIM,IDC
C SET FAIL FLAG
IFAIL=0
C WRITE(KBOUT,1000)
C1000 FORMAT(' TRYING TO ENTER NEW GEL READING INTO DATABASE')
C IS THERE SPACE?
IF((IDBSIZ-(NGELS+NCONTS)).GT.2)GO TO 5
C FULL
WRITE(KBOUT,1999)IDBSIZ
1999 FORMAT(' Database full, current size=',I6,' Extend with copy')
IFAIL=7
RETURN
5 CONTINUE
C NEED TO CHECK TO SEE IF GEL ALREADY IN DB
C LOOK THRU ARC FILE
DO 10 J=1,NGELS
C READ(IDEVN,REC=J)NAMARK
CALL READN(IDEVN,J,NAMARK)
IF(NAMARK.NE.NAMARC(1:10))GO TO 10
C FOUND
WRITE(KBOUT,1013)J
1013 FORMAT(' New gel already in database with number',I6,
+' Entry aborted')
IFAIL=6
RETURN
10 CONTINUE
C INCREMENT NUMBER OF GELS
NGELS=NGELS+1
C SET LENGTH THIS GEL
LNGTHG(NGELS)=IDIM*ISENSE
C WRITE NAME OF ARCHIVE TO LIST OF ARCHIVES
C NAMPRO,ARC
C WRITE(IDEVN,REC=NGELS)NAMARC(1:10)
NAMARK=NAMARC(1:10)
CALL WRITEN(IDEVN,NGELS,NAMARK)
WRITE(KBOUT,1003)NGELS
1003 FORMAT(' This gel reading has been given the number ',I6)
C WRITE GEL TO WORKING VERSION
CALL WRITEW(IDEVW,NGELS,GEL,MAXGEL)
IF(IDEVT.GT.0) CALL ENTRD(IDEVG,IDEVT,IDEVC,NAMARC,NGELS,IOK)
C CREATE TAGS FOR THIS NASTY
CALL TAGGEL(NGELS,LNGTHG(NGELS),GEL)
C SET UP RELATIONSHIPS
C DOES THIS GEL OVERLAP?
IF(ITYPE.NE.0)GO TO 100
C
C DOES NOT OVERLAP SO IT STARTS A CONTIG OF ITS OWN
C SET LEFT AND RIGHT POINTERS TO ZERO,RELPG TO 1
LNBR(NGELS)=0
RNBR(NGELS)=0
RELPG(NGELS)=1
C WRITE NEW GEL LINE
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
C WRITE(IDEVR,REC=NGELS)RELPG(NGELS),LNGTHG(NGELS),LNBR(NGELS),
C 1RNBR(NGELS)
C
C SET CONTIG POINTERS AND GENERAL VALUES
C INCREMENT NUMBER OF CONTIGS
NCONTS=NCONTS+1
C POINTER TO THIS CONTIG
N=IDBSIZ-NCONTS
C POINTER TO LEFT GEL THIS CONTIG
LNBR(N)=NGELS
C POINTER TO RIGHT GEL THIS CONTIG
RNBR(N)=NGELS
C LENGTH OF CONTIG
RELPG(N)=IDIM
C WRITE CONTIG DESCRIPTOR
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
C WRITE(IDEVR,REC=N)RELPG(N),LNGTHG(N),LNBR(N),RNBR(N)
C WRITE DB DESCRIPTOR
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
C WRITE(IDEVR,REC=IDBSIZ)NGELS,NCONTS
RETURN
C
100 CONTINUE
C
C
C DOES OVERLAP
150 CONTINUE
C
C LEFT END OR RIGHT OVERLAP?
IF(ITYPE.EQ.1)GO TO 400
C RIGHT END OR INTERNAL OVERLAP
C
160 CONTINUE
C NEED TO SEARCH THRU THIS CONTIG TO FIND LEFT AND RIGHT
C NEIGHBOURS FOR THIS NEW GEL
C LINE NUMBER OF LEFT END OF CONTIG
N=NCONTC
C LOOK THRU UNTIL CURRENT IS >= THEN IT MUST BE THE PREVIOUS ONE
200 CONTINUE
IF(RELPG(N).GT.X)GO TO 250
C IS THIS THE LAST GEL IN CONTIG?
IF(RNBR(N).EQ.0)GO TO 350
C NO SO LOOK AT NEXT
N=RNBR(N)
GO TO 200
250 CONTINUE
C GEL LIES BETWEEN N AND LNBR(N)
C NEED TO EDIT DB HERE
IF(ITOTPC.GT.0)CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
1NGELS,NCONTS,
2GEL,LINCON,X,SEQC2,ITOTPC,IDC,IDBSIZ,KBOUT,IDEVR,IDEVW,
+MAXGEL)
C
C
C SET POINTERS IN NEW GEL
LNBR(NGELS)=LNBR(N)
RNBR(NGELS)=N
RELPG(NGELS)=X
C WRITE NEW GEL LINE
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
C WRITE(IDEVR,REC=NGELS)RELPG(NGELS),LNGTHG(NGELS),LNBR(NGELS),
C 1RNBR(NGELS)
C SET POINTERS IN LEFT AND RIGHT NEIGHBOURS
K=LNBR(N)
RNBR(K)=NGELS
C RNBR(LNBR(N))=NGELS
C WRITE LEFT AND RIGHT NEIGHBOURS
CALL WRITER(IDEVR,K,RELPG(K),LNGTHG(K),
+LNBR(K),RNBR(K))
C WRITE(IDEVR,REC=K)RELPG(K),LNGTHG(K),LNBR(K),RNBR(K)
LNBR(N)=NGELS
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
C WRITE(IDEVR,REC=N)RELPG(N),LNGTHG(N),LNBR(N),RNBR(N)
C WRITE NGELS NCONTS
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
C WRITE(IDEVR,REC=IDBSIZ)NGELS,NCONTS
C HAVE WE INCREASED LENGTH OF CONTIG?
C ITS LINE NUMBER IS LINCON
C NEED TO UPDATE IDIM IN CASE OF EDITS
IDIM=ABS(LNGTHG(NGELS))
Y=X+IDIM-1
IF(Y.LE.RELPG(LINCON))RETURN
RELPG(LINCON)=Y
C WRITE NEW CONTIG LINE
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
C WRITE(IDEVR,REC=LINCON)RELPG(LINCON),LNGTHG(LINCON),LNBR(LINCON),
C 1RNBR(LINCON)
RETURN
350 CONTINUE
C MUST BE A RIGHT END OVERLAP
C NEED TO EDIT DB HERE
IF(ITOTPC.GT.0)CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
1NGELS,NCONTS,
2GEL,LINCON,X,SEQC2,ITOTPC,IDC,IDBSIZ,KBOUT,IDEVR,IDEVW,
+MAXGEL)
C
C
C SET POINTERS FOR NEW GEL
LNBR(NGELS)=N
RNBR(NGELS)=0
RELPG(NGELS)=X
C WRITE NEW GEL LINE
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
C WRITE(IDEVR,REC=NGELS)
C 1RELPG(NGELS),LNGTHG(NGELS),LNBR(NGELS),RNBR(NGELS)
C OLD RIGHT END
RNBR(N)=NGELS
C WRITE NEW RIGHT LINE
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
C WRITE(IDEVR,REC=N)RELPG(N),LNGTHG(N),LNBR(N),RNBR(N)
C
C RESET RIGHT NAME IN CONTIG
C ITS LINE NUMBER IS LINCON
RNBR(LINCON)=NGELS
C HAVE WE INCREASED LENGTH OF CONTIG?
C NEED TO UPDATE LENGTH OF GEL IN CASE OF EDITS
IDIM=ABS(LNGTHG(NGELS))
Y=X+IDIM-1
RELPG(LINCON)=MAX(RELPG(LINCON),Y)
C WRITE HERE
C WRITE CONTIG DESCRIPTOR
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
C WRITE(IDEVR,REC=LINCON)RELPG(LINCON),LNGTHG(LINCON),LNBR(LINCON)
C 1,RNBR(LINCON)
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
C WRITE(IDEVR,REC=IDBSIZ)NGELS,NCONTS
RETURN
C
400 CONTINUE
C
C ADDING TO LEFT END
410 CONTINUE
C NEED TO EDIT DB HERE
IF(ITOTPC.GT.0)CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
1NGELS,NCONTS,
2GEL,LINCON,1,SEQC2,ITOTPC,IDC,IDBSIZ,KBOUT,IDEVR,IDEVW,
+MAXGEL)
C
420 CONTINUE
C SET POINTERS IN NEW GEL
RELPG(NGELS)=1
RNBR(NGELS)=NCONTC
LNBR(NGELS)=0
C WRITE NEW GEL LINE
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
C WRITE(IDEVR,REC=NGELS)RELPG(NGELS),LNGTHG(NGELS),LNBR(NGELS),
C 1RNBR(NGELS)
C SET POINTERS IN OLD LEFT END
LNBR(NCONTC)=NGELS
RELPG(NCONTC)=X
C WRITE NEW LEFT END
CALL WRITER(IDEVR,NCONTC,RELPG(NCONTC),LNGTHG(NCONTC),
+LNBR(NCONTC),RNBR(NCONTC))
C WRITE(IDEVR,REC=NCONTC)RELPG(NCONTC),LNGTHG(NCONTC),LNBR(NCONTC)
C 1,RNBR(NCONTC)
C NEW LENGTH OF CONTIG
RELPG(LINCON)=RELPG(LINCON)+X-1
C MAY HAVE JUST ADDED A GEL LONGER THAN CONTIG
IDIM=ABS(LNGTHG(NGELS))
Y=IDIM
IF(Y.GT.RELPG(LINCON))RELPG(LINCON)=Y
C NEW NAME OF LEFT END OF CONTIG
LNBR(LINCON)=NGELS
C WRITE CONTIG DESCRIPTOR
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
C WRITE(IDEVR,REC=LINCON)RELPG(LINCON),LNGTHG(LINCON),LNBR(LINCON)
C 1,RNBR(LINCON)
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
C WRITE(IDEVR,REC=IDBSIZ)NGELS,NCONTS
C NOW GO THRU AND CHANGE ALL RELATIVE POSITIONS
N=NCONTC
440 CONTINUE
IF(RNBR(N).EQ.0)RETURN
N=RNBR(N)
RELPG(N)=RELPG(N)+X-1
C WRITE NEW LINE
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
C WRITE(IDEVR,REC=N)RELPG(N),LNGTHG(N),LNBR(N),RNBR(N)
GO TO 440
END
C SUBROUTINE COPYRD(IDEVRD,IDEV,NGELS,NEWSIZ,IOK)
C CHARACTER MTYPE*4,NAMFIL*12
C DO 10 I = 1,NGELS
C CALL READRD(IDEVRD,I,LENR,LCUT,LENW,MTYPE,NAMFIL)
C CALL WRITRD(IDEV,I,LENR,LCUT,LENW,MTYPE,NAMFIL)
C 10 CONTINUE
C CALL WRITRD(IDEV,NEWSIZ,LENR,LCUT,LENW,MTYPE,NAMFIL)
C IOK = 0
C END
SUBROUTINE COPYTG(IDEVT,IDEV,IOK,IDBSIZ,NEWSIZ,NGELS)
C Read tag details
IDIFF = NEWSIZ - IDBSIZ
CALL READTG(IDEVT,IDBSIZ,ICNT,LLEN,LCOM,LTYPE,NEXT)
IF (NEXT.NE.0) NEXT = NEXT + IDIFF
CALL WRITTG(IDEV,NEWSIZ,ICNT+IDIFF,LLEN,LCOM,LTYPE,NEXT)
C Copy headers for each gels
DO 10 I = 1,NGELS
CALL READTG(IDEVT,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
IF (NEXT.NE.0) NEXT = NEXT + IDIFF
CALL WRITTG(IDEV,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
10 CONTINUE
C Copy rest of tags
DO 20 I = IDBSIZ+1, ICNT
CALL READTG(IDEVT,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
IF (NEXT.NE.0) NEXT = NEXT + IDIFF
CALL WRITTG(IDEV,I+IDIFF,LPOS,LLEN,LCOM,LTYPE,NEXT)
20 CONTINUE
IOK = 0
END
SUBROUTINE COPYCC(IDEVC,IDEV,IOK)
C COMMENT_LENGTH
CHARACTER NOTE*40
CALL READCC(IDEVC,1,ICNT,NEXT,NOTE)
CALL WRITCC(IDEV,1,ICNT,NEXT,NOTE)
DO 10 I = 2,ICNT
CALL READCC(IDEVC,I,ICNT,NEXT,NOTE)
CALL WRITCC(IDEV,I,ICNT,NEXT,NOTE)
10 CONTINUE
IOK = 0
END
SUBROUTINE DBAUTO(RELPG,LNGTHG,LNBR,RNBR,MAXDB,IDBSIZ,
+NGELS,NCONTS,MAXGEL,
+TEMP3,WORDP,WORDN,LPOWRC,POSNS,GELN,
+SEQ1,MAXSEQ,SEQ2,SEQ3,SEQ4,SEQ5,SEQC2,SEQG2,MATCH,
+MAXGLM,MAXGL2,CHRSIZ,ECHRSZ,LENGTH,
+SAV1,SAV2,SAV3,MAXSAV,CENDS,NENDS,MAXCON,CONST,
+KBIN,KBOUT,IDEV1,IDEV2,IDEV3,IDEV4,IDEV7,IDEV8,IDEV,IDEVT,IDEVC,
+IHELPS,IHELPE,HELPF,IDEVH,NAMARC,NAMPRO,FILE,
+PERCD,IOPEN,IDM,SEQG3,SEQC3,IOK)
INTEGER CHRSIZ,ECHRSZ
INTEGER RELPG(MAXDB),PL(2),PR(2),RMOST
INTEGER LNGTHG(MAXDB),LNBR(MAXDB),RNBR(MAXDB)
INTEGER JOINT(2),ITOTPC(2),ITOTPG(2),IDIM22(2),IDOUT(2)
INTEGER LINCON(2),LLINO(2),ITYPE(2),IFAIL(2)
INTEGER ILEFTS(2),ILC(2),IPOSC(2),IPOSG(2),ISENSE(2)
INTEGER LREG,RREG,X,ANS,ANSJOK
INTEGER TEMP3(ECHRSZ,MAXGL2),CONST(LENGTH)
INTEGER POSNS(MAXSEQ),WORDP(LPOWRC),WORDN(LPOWRC),GELN(MAXGLM)
INTEGER CENDS(MAXCON),NENDS(MAXCON)
CHARACTER SEQ3(MAXGLM),SEQC2(MAXGLM,2),SEQG2(MAXGLM,2)
CHARACTER SEQ1(MAXSEQ),SEQ2(MAXGLM),MATCH(MAXGLM),SEQ4(MAXGLM)
INTEGER SAV1(MAXSAV),SAV2(MAXSAV),SAV3(MAXSAV)
CHARACTER NAMARC*(*),NAMPRO*(*),FILE*(*)
CHARACTER GET,SEQ5(MAXGLM),HELPF*(*),SEQG3(MAXGLM),SEQC3(MAXGLM)
PARAMETER (MAXPRM = 32)
CHARACTER PROMPT(3)*(MAXPRM)
SAVE GET
DATA GET/'>'/
WRITE(KBOUT,*)' Automatic sequence assembler'
IFAIL(1) = 0
IEMPTY=0
IF(NGELS.LT.1)IEMPTY=1
CALL DBCHEK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+TEMP3,IERR,KBOUT)
IF(IERR.GT.1) RETURN
CALL YESNO(IOKENT,'Permit entry',
+IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(IOKENT.LT.0) RETURN
CALL YESNO(INF,'Use file of file names',
+IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(INF.LT.0) RETURN
IF(INF.EQ.0) THEN
FILE = ' '
CALL OPENF1(IDEV7,FILE,0,IOK,KBIN,KBOUT,
+ 'File of gel reading names',
+ IHELPS,IHELPE,HELPF,IDEVH)
IF(IOK.NE.0) RETURN
END IF
IF(IOKENT.EQ.0) THEN
FILE = ' '
CALL OPENF1(IDEV8,FILE,1,IOK,KBIN,KBOUT,
+ 'File for names of failures',
+ IHELPS,IHELPE,HELPF,IDEVH)
IF(IOK.NE.0) RETURN
END IF
PROMPT(1) = 'Perform normal shotgun assembly'
PROMPT(2) = 'Put all sequences in one contig'
PROMPT(3) = 'Put all sequences in new contigs'
IOPT = 1
CALL RADION('Select entry mode',PROMPT,3,IOPT,
+IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(IOPT.LT.1) RETURN
IF(IOPT.EQ.1) THEN
C parameters for normal assembly
ANSJOK = 0
CALL YESNO(ANSJOK,'Permit joins',
+IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(ANSJOK.LT.0) RETURN
MN = LENGTH*2
MX = MAXGLM + 1
MINMAT = MAX(15,MN)
CALL GETINT(MN,MX,MINMAT,
+'Minimum initial match',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MINMAT = IVAL
MINSLI = 3
MN = 0
MX = 25
MAXPG = 8
CALL GETINT(MN,MX,MAXPG,
+'Maximum pads per gel',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MAXPG = IVAL
MN = 0
MX = 25
MAXPC = 8
CALL GETINT(MN,MX,MAXPC,
+'Maximum pads per gel in contig',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MAXPC = IVAL
IF(IOKENT.EQ.0) THEN
RMN = 0.
RMX = 15.
PERMAX = 8.
CALL GETRL(RMN,RMX,PERMAX,
+ 'Maximum percent mismatch after alignment',
+ VAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
PERMAX = VAL
END IF
IDIM1=0
MAXOVR=MAXGEL-3*MAX(MAXPC,MAXPG)
ANS=0
IF(IEMPTY.EQ.0)
+CALL ACONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM1,ANS,KDUMM,KDUMM,KDUMM,TEMP3,
+ECHRSZ,MAXGL2,KBOUT,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
END IF
JGEL = 0
JNGEL = 0
JNJOIN = 0
IMATC = 0
IF(IFAIL(1).NE.0)GO TO 900
C
C
1 CONTINUE
C
C
IDIM2=MAXGEL
IF(INF.EQ.1) THEN
3 CONTINUE
MN = 0
CALL GTSTR('Gel reading name',' ',NAMARC,MN,KBOUT,KBIN,INFLAG)
IF(INFLAG.EQ.3) RETURN
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 3
END IF
ELSE
READ(IDEV7,1002,END=900)NAMARC
END IF
1002 FORMAT( A)
DO 77 MM=1,80
MATCH(MM)=GET
77 CONTINUE
WRITE(IDEV,1077)(MATCH(KK),KK=1,79)
1077 FORMAT(' ',79A1)
JGEL = JGEL + 1
WRITE(IDEV,*)'Processing',JGEL,' in batch'
1007 FORMAT(' Gel reading name=',A)
WRITE(IDEV,1007)NAMARC
CALL OPENRS(IDEV4,NAMARC,IOK,LRECL,2)
IF(IOK.NE.0)THEN
IF(INF.EQ.1) RETURN
WRITE(IDEV,*)' Error opening gel reading file'
GO TO 1
END IF
CALL ARRFIM(IDEV4,SEQ2,IDIM2,KBOUT)
CLOSE(UNIT=IDEV4)
WRITE(IDEV,1800)IDIM2
1800 FORMAT(' Gel reading length=',I6)
IF(IOPT.NE.1) THEN
CALL DBAUTP(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+ IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,MAXDB,IDEV,
+ IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL,IMATC,IEMPTY,IOPT)
IF(IFAIL(1).NE.0) GO TO 800
JNGEL = JNGEL + 1
GO TO 1
END IF
IF(IDIM2.LT.MINMAT)THEN
WRITE(IDEV,*)
+' Reading shorter than minimum match, so not processed'
GO TO 1
END IF
CALL SQCOPY(SEQ2,SEQ3,IDIM2)
IFCOMP=0
IMATC=0
IF(IEMPTY.EQ.0)
+CALL AUTOCN(SEQ1,IDIM1,SEQ2,IDIM2,ILEFTS,ILC,IPOSC,
+IPOSG,ISENSE,LLINO,IMATC,IFCOMP,MINMAT,POSNS,WORDP,WORDN,
+CONST,LENGTH,LPOWRC,IDEV,MATCH,MAXGEL,MAXGLM,SEQ5,GELN,
+SAV1,SAV2,SAV3,MAXSAV,CENDS,NENDS,MAXCON,
+SEQG2,SEQC2,SEQ4,IDOUT,IDIM22,ITOTPG,ITOTPC,JOINT,IFAIL,
+ITYPE,MAXPC,MAXPG,PERMAX,MINSLI,SEQG3,SEQC3,KFAIL)
IF(IOKENT.NE.0) GO TO 1
C THIS RETURNS THE FOLLOWING:
C ILEFTS POSITION IN CONSENSUS OF LEFT END OF MATCHING CONTIGS
C ILC LENGTHS OF MATCHING CONTIGS
C IPOSC POSITION OF MATCH RELATIVE TO CONTIG
C IPOSG POSITION OF MATCH RELATIVE TO NEW GEL
C ISENSE SENSE OF NEW GEL
C LLINO LEFT GEL NUMBER IN MATCHING CONTIGS
C IMATC THE NUMBER OF MATCHING CONTIGS (>2 IS ERROR!)
C IFCOMP ERROR FLAG FOR COMPARISON (COMPARISON ARRAYS OVERFLOWED)
IF(IFCOMP.NE.0)GO TO 800
CALL SQCOPY(SEQ3,SEQ2,IDIM2)
IF(IMATC.GT.0)GO TO 200
C
C NO OVERLAP NEW CONTIG
C
C ITYPE 0 = NO OVERLAP
C ISENSE 1 = SAME SENSE AS ARCHIVE
IF(IFAIL(1).NE.0) GO TO 800
ITYPE(1)=0
ISENSE(1)=1
IDOUT(1)=MAXGEL
WRITE(IDEV,1015)
1015 FORMAT(' New gel reading does not overlap: start a new contig')
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQ2,NAMARC,X,ITYPE,ISENSE,SEQC2(1,1),ITOTPC(1),
+IDIM2,IDOUT(1),LLINO,LINCON,IFAIL,IDBSIZ,IDEV,
+IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL)
IF(IFAIL(1).NE.0)GO TO 800
IEMPTY=0
IDIM1=IDIM1+1
IF((IDIM1+19+IDIM2).GT.MAXSEQ)THEN
WRITE(IDEV,1021)MAXSEQ
1021 FORMAT(' Database maximum consensus length (',I6,') exceeded')
GO TO 900
END IF
CALL ADDTIT(SEQ1(IDIM1),NAMPRO,NGELS,IDIM1)
CALL MSTLKL(SEQ2,IDIM2)
CALL SQCOPY(SEQ2,SEQ1(IDIM1),IDIM2)
IDIM1=IDIM1+IDIM2-1
JNGEL = JNGEL + 1
GO TO 1
C
C
C
200 CONTINUE
C
C
C OVERLAP SO TRY TO ALIGN THE SEQUENCES
C
C
DO 100 I=1,IMATC
N=IDBSIZ-NCONTS
DO 99 J=N,IDBSIZ-1
IF(LNBR(J).NE.LLINO(I))GO TO 99
LINCON(I)=J
GO TO 100
99 CONTINUE
WRITE(IDEV,10077)LLINO(I)
10077 FORMAT(' Contig line for contig',I6,' not found!')
GO TO 800
100 CONTINUE
C
IF((IMATC.EQ.2).AND.(ANSJOK.EQ.0))GO TO 400
C
C
C SINGLE OVERLAP
C
C
C
WRITE(IDEV,1014)LLINO(1)
1014 FORMAT(' New gel reading overlaps contig',I6)
IF(ITOTPG(1).GT.0) CALL CCTA(SEQG2(1,1),IDIM22(1))
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQG2(1,1),NAMARC,JOINT(1),ITYPE(1),ISENSE(1),
+SEQC2(1,1),
+ITOTPC(1),IDIM22(1),IDOUT(1),LLINO(1),LINCON(1),
+IFAIL(1),IDBSIZ,IDEV,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL)
IF(IFAIL(1).NE.0)GO TO 800
CALL DELCON(SEQ1,ILEFTS(1),ILC(1),IDIM1)
LREG=1
RREG=RELPG(LINCON(1))
IGELC=LNBR(LINCON(1))
ANS=1
CALL ACONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM1,ANS,IGELC,LREG,RREG,TEMP3,
+ECHRSZ,MAXGL2,IDEV,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
IF(IFAIL(1).NE.0)GO TO 900
JNGEL = JNGEL + 1
IF(KFAIL.NE.0) GO TO 800
GO TO 1
C
C
C DOUBLE OVERLAP
C
C
400 CONTINUE
WRITE(IDEV,1013)LLINO
1013 FORMAT(' Overlap between contigs',I6,' and',I6)
IF(ANSJOK.NE.0)GO TO 800
IF(LLINO(1).EQ.LLINO(2))THEN
WRITE(IDEV,*)' Trying to form loop in contig',LLINO(1)
WRITE(IDEV,*)' Gel not entered'
GO TO 800
END IF
CALL AJOIN3(RELPG,IDBSIZ,LINCON,ITYPE,ISENSE,JOINT,
+IDIM22,KLASS,IOVER,IDEV,PL,PR)
IF(IOVER.GT.MAXOVR)THEN
WRITE(IDEV,*)' Overlap too large: entry only'
IFAIL(2)=1
GO TO 600
END IF
C WHICH CONTIG IS LEFTMOST?
LMOST=1
RMOST=2
IF(PL(1).GT.PL(2))THEN
LMOST=2
RMOST=1
END IF
C SAVE LENGTH OF RMOST CONTIG FOR DELETION STEP LATER
ILCR=ILC(RMOST)
IF(ITOTPG(LMOST).GT.0) CALL CCTA(SEQG2(1,LMOST),IDIM22(LMOST))
WRITE(IDEV,1012)LLINO(LMOST)
1012 FORMAT(' Entering the new gel reading into contig',I6)
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQG2(1,LMOST),NAMARC,JOINT(LMOST),ITYPE(LMOST),
+ISENSE(LMOST),SEQC2(1,LMOST),ITOTPC(LMOST),
+IDIM22(LMOST),IDOUT(LMOST),LLINO(LMOST),LINCON(LMOST),
+IFAIL(LMOST),IDBSIZ,IDEV,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,
+MAXGEL)
IF(IFAIL(LMOST).NE.0)GO TO 800
JNGEL = JNGEL + 1
IF(ITYPE(LMOST).EQ.1)LLINO(LMOST)=NGELS
IF(ILEFTS(LMOST).LT.ILEFTS(RMOST))THEN
ILEFTS(RMOST)=ILEFTS(RMOST)-ILC(LMOST)-20
END IF
CALL DELCON(SEQ1,ILEFTS(LMOST),ILC(LMOST),IDIM1)
LREG=1
RREG=RELPG(LINCON(LMOST))
IGELC=LNBR(LINCON(LMOST))
ANS=1
CALL ACONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM1,ANS,IGELC,LREG,RREG,TEMP3,
+ECHRSZ,MAXGL2,IDEV,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
IF(IFAIL(1).NE.0)GO TO 900
ILC(LMOST)=RREG
ILEFTS(LMOST)=IDIM1-RREG+1
DO 500 I=1,2
IF(ISENSE(I).EQ.-1)THEN
CALL CMPLMT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON(I),
+ LLINO(I),SEQ2,IDBSIZ,IDEV,IDEV1,IDEV2,MAXGEL)
CALL SQREV(SEQ1(ILEFTS(I)),ILC(I))
CALL SQCOM(SEQ1(ILEFTS(I)),ILC(I))
KT=IDIM1
CALL ADDTIT(SEQ1((ILEFTS(I)-20)),NAMPRO,LNBR(LINCON(I)),KT)
END IF
500 CONTINUE
C NEED TO KNOW POSITION OF OVERLAP RELATIVE TO CONTIG, TO CONSENSUS
C WHICH BITS TO SEND TO ALIGNMENT ROUTINES
C SET UP FOR ALINE (NOTE RMOST IS EQUIVALENT TO THE GEL READING AND
C SO IS SLID ALONG THE LMOST CONTIG. THE SECTION SENT TO ALINE MUST
C BE OF LENGTH < MAXGEL-2*MAX(MAXPC,MAXPG)
C IT MUST START AT POSITION 1 IN THE RMOST CONTIG AND EXTEND
IPOSC(LMOST)=PL(RMOST)+RELPG(NGELS)-1
ILCT = RELPG(LINCON(LMOST)) - RELPG(NGELS) - PL(RMOST) + 2
ILC(RMOST)=MIN(ILCT,ILC(RMOST))
IPOSC(RMOST)=1
IDOUT(LMOST)=MAXGEL
IDOUT(RMOST)=MAXGEL
IDSAV=MAXSAV
C ON INPUT TO ALINE ILC(RMOST) CONTAINS THE OVERLAP LENGTH
C ON OUTPUT IT CONTAINS THE LENGTH OF THE ALIGNED SECTION (IE INCLUDING
C PADS)
WRITE(IDEV,1009)
1009 FORMAT(' Trying to align the two contigs')
CALL ALINE(SEQ1(ILEFTS(LMOST)),SEQ1(ILEFTS(RMOST)),
+SEQC2(1,RMOST),SEQC2(1,LMOST),SAV1,SAV2,SAV3,IDSAV,
+ILC(LMOST),ILC(RMOST),IDOUT(LMOST),IPOSC(LMOST),IPOSC(RMOST),
+MINSLI,JOINT(LMOST),ITOTPC(LMOST),ITOTPC(RMOST),IFAIL(1),
+ITYPE(1),MAXPC,MAXPC,PERMAX,IDEV,SEQ4,MAXGEL,Z)
C SEQC2(1,LMOST) NOW CONTAINS THE ALIGNED SECTION OF THE LMOST CONTIG
C SEQC2(1,RMOST) NOW CONTAINS THE ALIGNED SECTION OF THE RMOST CONTIG
C ILC(RMOST) IS NOW THE LENGTH OF ALIGNED SECTION OF THE RMOST CONTIG
C IDOUT(LMOST) IS NOW THE LENGTH OF ALIGNED SECTION OF THE LMOST CONTIG
C JOINT(LMOST) IS THE POSITION OF THE JOIN RLETIVE TO THE LMOST CONTIG
C ITYPE IS TYPE OF OVERLAP (-1 = RIGHT END OR INTERNAL, 1 = LEFT END)
C NB SHOULD ALWAYS BE -1
C IF THIS HAS BEEN DONE OK WE CAN EDIT THE TWO CONTIGS THEN JOIN
IF(IFAIL(1).NE.0)THEN
WRITE(IDEV,*)' Failed to align the two overlapping contigs'
GO TO 800
END IF
IF(ITOTPC(LMOST).GT.0)THEN
WRITE(IDEV,1017)LLINO(LMOST)
1017 FORMAT(' Editing contig',I6)
CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
+ NGELS,NCONTS,SEQ3,LINCON(LMOST),JOINT(LMOST),SEQC2(1,LMOST),
+ ITOTPC(LMOST),IDOUT(LMOST),IDBSIZ,IDEV,IDEV1,IDEV2,
+ MAXGEL)
END IF
JOINT(RMOST)=1
IDOUT(RMOST)=ILC(RMOST)
IF(ITOTPC(RMOST).GT.0)THEN
WRITE(IDEV,1017)LLINO(RMOST)
CALL ABEDIN(RELPG,LNGTHG,LNBR,RNBR,
+ NGELS,NCONTS,SEQ3,LINCON(RMOST),JOINT(RMOST),SEQC2(1,RMOST),
+ ITOTPC(RMOST),IDOUT(RMOST),IDBSIZ,IDEV,IDEV1,IDEV2,
+ MAXGEL)
END IF
ILC(RMOST)=ILCR
LTL=LNBR(LINCON(LMOST))
LTR=LNBR(LINCON(RMOST))
WRITE(IDEV,1018)LNBR(LINCON(LMOST)),LNBR(LINCON(RMOST))
1018 FORMAT(' Completing the join between contigs',I6,' and',I6)
CALL AJOIN2(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+JOINT(LMOST),LTL,LTR,LINCON(LMOST),LINCON(RMOST),IDEV1)
LLINO(1)=LTL
IF(ILEFTS(LMOST).GT.ILEFTS(RMOST))THEN
CALL DELCON(SEQ1,ILEFTS(LMOST),ILC(LMOST),IDIM1)
CALL DELCON(SEQ1,ILEFTS(RMOST),ILC(RMOST),IDIM1)
END IF
IF(ILEFTS(RMOST).GE.ILEFTS(LMOST))THEN
CALL DELCON(SEQ1,ILEFTS(RMOST),ILC(RMOST),IDIM1)
CALL DELCON(SEQ1,ILEFTS(LMOST),ILC(LMOST),IDIM1)
END IF
LREG=1
RREG=JOINT(LMOST)
IGELC=LLINO(1)
ANS=1
CALL ACONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM1,ANS,IGELC,LREG,RREG,TEMP3,
+ECHRSZ,MAXGL2,IDEV,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
IF(IFAIL(1).NE.0)GO TO 900
C CALL FMTDB(SEQ1,IDIM1,1,IDIM1,60,IDEV)
JNJOIN = JNJOIN + 1
IF(KFAIL.NE.0) GO TO 800
GO TO 1
C
C
C JOINS THAT FAIL INITIAL ALIGNMENT CRITERIA
C
C
600 CONTINUE
C COME HERE FOR JOINS THAT FAIL: WE MIGHT BE ABLE TO ENTER THE GEL
C INTO A SINGLE CONTIG
IGOOD=0
IF(IFAIL(1).EQ.0)IGOOD=1
IF(IFAIL(2).EQ.0)IGOOD=2
IF(IGOOD.EQ.0)GO TO 800
IF(ITOTPG(IGOOD).GT.0) CALL CCTA(SEQG2(1,IGOOD),IDIM22(IGOOD))
WRITE(IDEV,1012)LLINO(IGOOD)
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQG2(1,IGOOD),NAMARC,JOINT(IGOOD),ITYPE(IGOOD),
+ISENSE(IGOOD),SEQC2(1,IGOOD),ITOTPC(IGOOD),
+IDIM22(IGOOD),IDOUT(IGOOD),LLINO(IGOOD),LINCON(IGOOD),
+IFAIL(IGOOD),IDBSIZ,IDEV,IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,
+MAXGEL)
IF(IFAIL(IGOOD).NE.0)GO TO 800
JNGEL = JNGEL + 1
CALL DELCON(SEQ1,ILEFTS(IGOOD),ILC(IGOOD),IDIM1)
ANS=1
IGELC=LNBR(LINCON(IGOOD))
LREG=1
RREG=RELPG(LINCON(IGOOD))
CALL ACONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM1,ANS,IGELC,LREG,RREG,TEMP3,
+ECHRSZ,MAXGL2,IDEV,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD)
IF(IFAIL(1).NE.0)GO TO 900
WRITE(IDEV,1020)LLINO,LLINO(IGOOD)
1020 FORMAT(' Could not join contigs',I4,' and',I4,' but the gel',
+' has been entered into contig',I4,/,
+' If required do the join manually.')
C
C
C ALL FAILURES
C
C
C
800 CONTINUE
WRITE(IDEV,10888)
10888 FORMAT(' Failed gel name written to error file')
WRITE(IDEV8,1002)NAMARC
GO TO 1
900 CONTINUE
WRITE(KBOUT,*)'Batch finished'
WRITE(KBOUT,*)JGEL,' sequences processed'
WRITE(KBOUT,*)JNGEL,' sequences entered into database'
WRITE(KBOUT,*)JNJOIN,' joins made'
RETURN
END
SUBROUTINE DBAUTP(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,MAXDB,IDEV,
+IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL,IMATC,IEMPTY,IOPT)
INTEGER RELPG(MAXDB)
INTEGER LNGTHG(MAXDB),LNBR(MAXDB),RNBR(MAXDB)
CHARACTER SEQ2(MAXGEL),SEQC2(MAXGEL)
CHARACTER NAMARC*(*)
C deals with entering all readings into contig 1 (IOPT=2)
C or all readings into new contigs (IOPT=3)
IF(IOPT.EQ.2) THEN
IF(IMATC.EQ.0) THEN
ITYPE=0
ISENSE=1
IDOUT=MAXGEL
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+ IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,IDEV,
+ IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL)
IF(IFAIL.NE.0) RETURN
IEMPTY=0
IMATC = 1
ELSE
ITYPE= - 1
ISENSE=1
JOINT = 1
LLINO = 1
LINCON = IDBSIZ - 1
ITOTPC = 0
IDOUT=MAXGEL
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+ IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,IDEV,
+ IDEV1,IDEV2,IDEV3,IDEVT,IDEVT,IDEV4,MAXGEL)
IF(IFAIL.NE.0) RETURN
END IF
ELSE IF(IOPT.EQ.3) THEN
ITYPE=0
ISENSE=1
IDOUT=MAXGEL
CALL AENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ2,NAMARC,JOINT,ITYPE,ISENSE,SEQC2,ITOTPC,
+ IDIM2,IDOUT,LLINO,LINCON,IFAIL,IDBSIZ,IDEV,
+ IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,IDEV4,MAXGEL)
IF(IFAIL.NE.0) RETURN
END IF
END
SUBROUTINE DBCOPY(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,GEL,
+NAMPRO,IDEV,IDBSIZ,IERR,KBIN,KBOUT,IDEVR,IDEVW,IDEVN,
+IDEVT,IDEVC,
+IHELPS,IHELPE,FILEH,IDEVH,MAXGEL,MAXDB,IDM)
CHARACTER FILEH*(*)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ)
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER NAMPRO*(*),NAMARC*10,GEL(MAXGEL)
CHARACTER V2,V1
INTEGER IWORD,DELDB
PARAMETER (IWORD=4)
PARAMETER (MAXPRM = 21)
CHARACTER PERR(2)*(MAXPRM)
EXTERNAL DELDB
IERR=1
1 CONTINUE
L = 1
V1='1'
CALL GTSTR('Make version',V1,V2,L,KBOUT,KBIN,INFLAG)
CALL CCASE(V2,1)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 1
END IF
IF(L.LT.1) V2 = V1
MN = NGELS + NCONTS + 1
MX = MAXDB
NEWSIZ = IDBSIZ
CALL GETINT(MN,MX,NEWSIZ,
+'New database size',
+IVAL,KBIN,KBOUT,IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
CALL BUSY(KBOUT)
NEWSIZ = IVAL
C WHERE SHOULD CHARS BE CHANGED ?
LLL = INDEX(NAMPRO,'.') + 1
NAMPRO(LLL:)='RL'//V2
CALL OPENRS(IDEV,NAMPRO,IOK,4,3)
IF(IOK.NE.0) THEN
C problem opening file
IF(IOK.EQ.2) THEN
CALL ERROM(KBOUT,'File already exists')
PERR(1) = 'Retype version number'
PERR(2) = 'Replace database'
IDO = 1
CALL RADION('Select action',PERR,2,IDO,
+ IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF(IDO.LT.1) RETURN
IF(IDO.EQ.1) GO TO 1
IF(IDO.EQ.2) THEN
IOK = DELDB(NAMPRO,V2,IDEV,MAXGEL)
IF(IOK.EQ.0) THEN
LLL = INDEX(NAMPRO,'.') + 1
NAMPRO(LLL:)='RL'//V2
CALL OPENRS(IDEV,NAMPRO,IOK,4,3)
IF(IOK.EQ.0) GO TO 2
ELSE
CALL ERROM(KBOUT,'File delete failed')
END IF
END IF
END IF
GO TO 100
END IF
2 CONTINUE
CALL WRITER(IDEV,NEWSIZ,NGELS,NCONTS,NGELS,NCONTS)
DO 10 I=1,NGELS
CALL WRITER(IDEV,I,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
10 CONTINUE
M=NEWSIZ-NCONTS
N=IDBSIZ-NCONTS
DO 15 I=N,IDBSIZ-1
CALL WRITER(IDEV,M,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
M=M+1
15 CONTINUE
CLOSE(UNIT=IDEV)
C DO SEQUENCES
NAMPRO(LLL:)='SQ'//V2
IREC=MAXGEL/IWORD
IF(MOD(MAXGEL,IWORD).NE.0)IREC=IREC+1
CALL OPENRS(IDEV,NAMPRO,IOK,IREC,3)
IF(IOK.NE.0)GO TO 100
C
C MAKE SURE FILE IS NEWSIZ LINES LONG!
CALL WRITEW(IDEV,NEWSIZ,GEL,MAXGEL)
DO 20 I=1,NGELS
CALL READW(IDEVW,I,GEL,MAXGEL)
CALL WRITEW(IDEV,I,GEL,MAXGEL)
20 CONTINUE
CLOSE(UNIT=IDEV)
C DO ARCHIVE NAMES
NAMPRO(LLL:)='AR'//V2
CALL OPENRS(IDEV,NAMPRO,IOK,3,3)
IF(IOK.NE.0)GO TO 100
DO 30 I=1,NGELS
CALL READN(IDEVN,I,NAMARC)
CALL WRITEN(IDEV,I,NAMARC)
30 CONTINUE
C MAKE SURE FILE IS 1000 LINES LONG
C ******** PROBLEMS HERE WRITING INTEGER TO NAMES FILE
WRITE(IDEV,REC=MAXDB)NEWSIZ,MAXGEL,IDM
CLOSE(UNIT=IDEV)
C IF(IDEVRD.GT.0) THEN
C NAMPRO(LLL:) = 'RD'//V2
C CALL OPENRS(IDEV,NAMPRO,IOK,7,3)
C IF(IOK.NE.0) GO TO 100
C CALL COPYRD(IDEVRD,IDEV,NGELS,NEWSIZ,IOK)
C IF(IOK.NE.0) GO TO 100
C END IF
C DO TAGS + COMMENTS
IF(IDEVT.GT.0.AND.IDEVC.GT.0) THEN
NAMPRO(LLL:)='TG'//V2
CALL OPENRS(IDEV,NAMPRO,IOK,5,3)
IF(IOK.NE.0)GO TO 100
CALL COPYTG(IDEVT,IDEV,IOK,IDBSIZ,NEWSIZ,NGELS)
NAMPRO(LLL:)='CC'//V2
C COMMENT_LENGTH: 11 = (40 + long)/long
CALL OPENRS(IDEV,NAMPRO,IOK,11,3)
IF(IOK.NE.0)GO TO 100
CALL COPYCC(IDEVC,IDEV,IOK)
ENDIF
IERR=0
RETURN
100 CONTINUE
WRITE(KBOUT,9999)
9999 FORMAT(' Error opening new database, copy aborted')
RETURN
END
INTEGER FUNCTION DELDB(NAMPRO,VERSN,IDEV,MAXGEL)
CHARACTER NAMPRO*(*),VERSN
INTEGER DELF
EXTERNAL DELF
C
C delete an xdap database
C
C assume relationships are 4 words, names are 3 and seqs are maxgel
C all recls in BYTES
C
DELDB = 1
LLL = INDEX(NAMPRO,'.') + 1
NAMPRO(LLL:)='RL'//VERSN
IF(DELF(NAMPRO,IDEV,16,4).NE.0) RETURN
NAMPRO(LLL:)='AR'//VERSN
IF(DELF(NAMPRO,IDEV,12,4).NE.0) RETURN
NAMPRO(LLL:)='SQ'//VERSN
IF(DELF(NAMPRO,IDEV,MAXGEL,4).NE.0) RETURN
NAMPRO(LLL:)='CC'//VERSN
C COMMENT_LENGTH: 11 = (40 + long)/long
IF(DELF(NAMPRO,IDEV,44,4).NE.0) RETURN
NAMPRO(LLL:)='TG'//VERSN
IF(DELF(NAMPRO,IDEV,20,4).NE.0) RETURN
DELDB = 0
END
SUBROUTINE DBFIX(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+GEL,GEL2,IDBSIZ,KBIN,KBOUT,IDEVR,IDEVW,IDEVN,
+IHELPS,IHELPE,IHELP1,IHELP2,FILEH,IDEVH,MAXGEL,IDEVT,IDEVC)
CHARACTER FILEH*(*)
C AUTHOR: RODGER STADEN
C 12-12-90 Added function to change raw data parameter file
C and changed menu routines accordingly
INTEGER RELPG(IDBSIZ),X
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL)
CHARACTER NAME*10,NEWNAM*10
INTEGER L,M,N
CHARACTER GEL2(MAXGEL)
PARAMETER (MAXPRM = 32)
CHARACTER PROMPT(9)*(MAXPRM)
INTEGER GCLIN,CHAINL
EXTERNAL GCLIN,CHAINL
WRITE(KBOUT,1000)
1000 FORMAT(
+' Warning:',
+' make a copy first, and check logical consistency after use')
10 CONTINUE
C
C SELECT OPTION
C CALL BELL(1,KBOUT)
C DBMENU now defunct for bap - so we use RADION instead
C CALL DBMENU(4,NOPT,IHELPS,IHELPE,FILEH,IDEVH,
C +KBIN,KBOUT)
PROMPT(1) = 'Line change'
PROMPT(2) = 'Edit gel reading'
PROMPT(3) = 'Delete contig line'
PROMPT(4) = 'Shift'
PROMPT(5) = 'Move gel reading'
PROMPT(6) = 'Rename gel reading'
PROMPT(7) = 'Break a contig'
PROMPT(8) = 'Remove a gel reading'
PROMPT(9) = 'Alter raw data parameters'
NOPT = 1
CALL RADION('Alter relationships', PROMPT, 9, NOPT, IHELPS,
+ IHELPE, FILEH, IDEVH, KBIN, KBOUT)
IF(NOPT.LT.1)RETURN
IF(NOPT.EQ.1)THEN
C LINE CHANGE
MN = 0
MX = IDBSIZ
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of line to change',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.EQ.0) GO TO 10
LNO = IVAL
IF(LNO.EQ.IDBSIZ)GO TO 19
WRITE(KBOUT,*)'Current line'
WRITE(KBOUT,1001)RELPG(LNO),LNGTHG(LNO),LNBR(LNO),RNBR(LNO)
1001 FORMAT(' ',4I6)
MN = 0
MX = 99999
X = RELPG(LNO)
CALL GETINT(MN,MX,X,
+ 'Relative position',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
X = IVAL
MN = -MAXGEL
MX = 99999
L = LNGTHG(LNO)
CALL GETINT(MN,MX,L,
+ 'Length',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
L = IVAL
MN = 0
MX = IDBSIZ
M = LNBR(LNO)
CALL GETINT(MN,MX,M,
+ 'Left neighbour',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
M = IVAL
MN = 0
MX = IDBSIZ
N = RNBR(LNO)
CALL GETINT(MN,MX,N,
+ 'Right neighbour',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
N = IVAL
CALL WRITER(IDEVR,LNO,X,L,M,N)
RELPG(LNO)=X
LNGTHG(LNO)=L
LNBR(LNO)=M
RNBR(LNO)=N
GO TO 10
19 CONTINUE
C NCONTS NGELS LINES
MN = 0
MX = IDBSIZ
LL = NGELS
CALL GETINT(MN,MX,LL,
+ 'Number of gel readings',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
LL = IVAL
MN = 0
MX = IDBSIZ
MM = NCONTS
CALL GETINT(MN,MX,MM,
+ 'Number of contigs',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
MM = IVAL
CALL WRITER(IDEVR,IDBSIZ,LL,MM,LL,MM)
NGELS=LL
NCONTS=MM
GO TO 10
END IF
C
C
IF(NOPT.EQ.4)THEN
MN = 0
MX = NGELS
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of first gel reading to shift',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.LT.1) GO TO 10
LNO = IVAL
I = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,LNO)
IF(I.EQ.0)THEN
WRITE(KBOUT,*)
+ 'Problem with this gel reading. Check logical consistency'
WRITE(KBOUT,*)'of database. Shift not done'
GO TO 10
END IF
NCONTO = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,I)
IF(NCONTO.EQ.0)THEN
WRITE(KBOUT,*)
+ 'No contig line for this contig. Check logical'
WRITE(KBOUT,*)'consistency of database. Shift not done'
GO TO 10
END IF
MN = 1 - RELPG(LNO)
MX = RELPG(NCONTO) - RELPG(LNO)
X = MN
CALL GETINT(MN,MX,X,
+ 'Distance to shift',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
X = IVAL
CALL SHIFTC(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDEVR,
+ IDBSIZ,LNO,NCONTO,X)
WRITE(KBOUT,*)'Shift complete'
GO TO 10
END IF
C
IF(NOPT.EQ.2)THEN
MN = 0
MX = NGELS
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of gel reading to edit',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.LT.1) GO TO 10
LNO = IVAL
IDIM=ABS(LNGTHG(LNO))
C ALLOW EDITING TO BE RELATIVE TO CONTIG POSITION
ISTART=RELPG(LNO)
CALL READW(IDEVW,LNO,GEL,MAXGEL)
C @jkb@
C CALL EDITGL(GEL,GEL2,IDIM,KBIN,KBOUT,MAXGEL,
C + IHELP1,IHELP2,FILEH,IDEVH,ISTART)
CALL WRITEW(IDEVW,LNO,GEL,MAXGEL)
LNGTHG(LNO)=SIGN(IDIM,LNGTHG(LNO))
CALL WRITER(IDEVR,LNO,RELPG(LNO),LNGTHG(LNO),
+ LNBR(LNO),RNBR(LNO))
GO TO 10
END IF
IF(NOPT.EQ.3)THEN
MN=IDBSIZ-NCONTS
MX = IDBSIZ - 1
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of contig line to delete',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
LNO = IVAL
CALL REMCNL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ LNO,IDEVR)
GO TO 10
END IF
IF(NOPT.EQ.6)THEN
MN = 0
MX = NGELS
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of gel reading to rename',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.LT.1) GO TO 10
LNO = IVAL
CALL READN(IDEVN,LNO,NAME)
L = 10
CALL GTSTR('name for gel reading',
+ NAME,NEWNAM,L,KBOUT,KBIN,INFLAG)
IF(L.GT.0)CALL WRITEN(IDEVN,LNO,NEWNAM)
GO TO 10
END IF
IF(NOPT.EQ.5)THEN
MN = 0
MX = NGELS
IFROM = 0
CALL GETINT(MN,MX,IFROM,
+ 'Number of gel reading to move',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.LT.1) GO TO 10
IFROM = IVAL
MN = 0
MX = NGELS
ITO = 0
CALL GETINT(MN,MX,ITO,
+ 'New number for gel reading',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
IF(IVAL.LT.1) GO TO 10
ITO = IVAL
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ GEL,IFROM,ITO,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
GO TO 10
END IF
IF(NOPT.EQ.7)THEN
CALL BREAKC(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,KBIN,KBOUT,IDEVR,IDEVW,IDEVN,
+ IHELPS,IHELPE,IHELP1,IHELP2,FILEH,IDEVH,IOK)
GO TO 10
END IF
IF(NOPT.EQ.8) THEN
CALL REMGD(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ KBIN,KBOUT,GEL,MAXGEL,IDEVR,IDEVW,IDEVN,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
GO TO 10
END IF
IF(NOPT.EQ.9) THEN
CALL FIXRD(IDEVT,IDEVC,IDBSIZ,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH)
GO TO 10
END IF
GO TO 10
END
SUBROUTINE REMGD(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+KBIN,KBOUT,GEL,MAXGEL,IDEVR,IDEVW,IDEVN,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER HELPF*(*),GEL(MAXGEL)
INTEGER REMME,GCLIN,CHAINL
EXTERNAL GCLIN,CHAINL
C assumes db is logical consistent
WRITE(KBOUT,*)'Remove reading from database'
REMME = NGELS
CALL GETINT(1,NGELS,REMME,
+'Number of reading to remove',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
REMME = IVAL
I = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,REMME)
ICONT = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,I)
IF(ICONT.EQ.0) THEN
WRITE(KBOUT,*)'No contig line for this reading'
IOK = 1
RETURN
END IF
CALL REMGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+REMME,ICONT,KBOUT,GEL,MAXGEL,IDEVR,IDEVW,IDEVN)
END
SUBROUTINE REMGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+REMME,ICONT,KBOUT,GEL,MAXGEL,IDEVR,IDEVW,IDEVN)
C Routine to remove a reading from a database
C Cases: 1 left end
C 2 right end
C 3 internal and dispensible
C 4 internal and indispensible
C if 1 change contig lnbr, contig length, lnbr of rnbr of remme, relpgs
C if 2 change contig rnbr, contig length, rnbr of lnbr of remme
C if 3 change contig length, lnbr of rnbr of remme rnbr of lnbr of remme
C if 4 need to break contig, then as for 1
C if 1 and 2 then also remove contig line
C for all cases move gel ngels to remme (if remme/=ngels)
C and update line idbsiz
C
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER REMME,CLEN
LOGICAL LEFTE,RIGHTE,DISPEN
CHARACTER GEL(MAXGEL)
EXTERNAL CLEN
LEFTE = .FALSE.
RIGHTE = .FALSE.
DISPEN = .FALSE.
C
C Left end ?
C
IF(LNBR(REMME).EQ.0) LEFTE = .TRUE.
C
C Right end ?
C
IF(RNBR(REMME).EQ.0) RIGHTE = .TRUE.
C
C If both true remove the contig line, then overwrite the gel
C
IF(LEFTE.AND.RIGHTE) THEN
WRITE(KBOUT,*)'Removing reading and contig'
IFROM = NGELS
NGELS = NGELS - 1
CALL REMCNL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ ICONT,IDEVR)
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
END IF
ELSE IF(LEFTE) THEN
WRITE(KBOUT,*)'Removing reading from left end of contig'
LNBR(ICONT) = RNBR(REMME)
I = 1 - RELPG(RNBR(REMME))
WRITE(KBOUT,*)'Shifting readings in contig by distance=',I
CALL SHIFTC(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDEVR,
+ IDBSIZ,RNBR(REMME),ICONT,I)
I = LNBR(ICONT)
LNBR(I) = 0
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
IFROM = NGELS
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
END IF
NGELS = NGELS - 1
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
ELSE IF(RIGHTE) THEN
WRITE(KBOUT,*)'Removing reading from right end of contig'
RNBR(ICONT) = LNBR(REMME)
I = RNBR(ICONT)
RNBR(I) = 0
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
RELPG(ICONT) = CLEN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,LNBR(ICONT))
CALL WRITER(IDEVR,ICONT,RELPG(ICONT),LNGTHG(ICONT),
+ LNBR(ICONT),RNBR(ICONT))
IFROM = NGELS
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
END IF
NGELS = NGELS - 1
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
ELSE
C Is remme indispensible ?
NSTART = RELPG(RNBR(REMME))
I = REMME
10 CONTINUE
I = LNBR(I)
IF(I.NE.0) THEN
IF((RELPG(I)+ABS(LNGTHG(I))-1).LT.NSTART) GO TO 10
DISPEN = .TRUE.
END IF
IF(DISPEN) THEN
WRITE(KBOUT,*)
+ 'Removing dispensible reading from middle of contig'
I = LNBR(REMME)
RNBR(I) = RNBR(REMME)
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
I = RNBR(REMME)
LNBR(I) = LNBR(REMME)
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
IFROM = NGELS
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,
+ MAXGEL,KBOUT)
END IF
NGELS = NGELS - 1
RELPG(ICONT) = CLEN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,LNBR(ICONT))
CALL WRITER(IDEVR,ICONT,RELPG(ICONT),LNGTHG(ICONT),
+ LNBR(ICONT),RNBR(ICONT))
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
ELSE
WRITE(KBOUT,*)
+ 'Removing indispensible reading from middle of contig'
WRITE(KBOUT,*)'So breaking contig first'
IR = REMME
IL = LNBR(REMME)
ILO = LNBR(ICONT)
NCONTO = ICONT
NCONTR = IDBSIZ - NCONTS - 1
CALL CBREAK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ KBOUT,IDEVR,IDEVW,IDEVN,IR,IL,ILO,NCONTO,NCONTR,IOK)
IF(IOK.NE.0) RETURN
WRITE(KBOUT,*)'Removing reading from left end of contig'
ICONT = IDBSIZ - NCONTS
LNBR(ICONT) = RNBR(REMME)
I = 1 - RELPG(RNBR(REMME))
WRITE(KBOUT,*)'Shifting readings in contig by distance=',I
CALL SHIFTC(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDEVR,
+ IDBSIZ,RNBR(REMME),ICONT,I)
I = LNBR(ICONT)
LNBR(I) = 0
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
IFROM = NGELS
IF(REMME.NE.IFROM) THEN
WRITE(KBOUT,*)'Renumbering reading',IFROM,' to',REMME
CALL MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,
+ NCONTS,IDBSIZ,GEL,IFROM,REMME,IDEVR,IDEVW,IDEVN,
+ MAXGEL,KBOUT)
END IF
NGELS = NGELS - 1
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
END IF
END IF
END
SUBROUTINE REMCNL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+REMME,IDEVR)
INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
INTEGER REMME
C Routine to remove a contig line from a db
C Loop deals with case of remove top contig
C Move down all lines from above
DO 10 I = REMME,IDBSIZ-NCONTS+1,-1
RELPG(I) = RELPG(I-1)
LNGTHG(I) = LNGTHG(I-1)
LNBR(I) = LNBR(I-1)
RNBR(I) = RNBR(I-1)
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
10 CONTINUE
NCONTS = NCONTS - 1
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
END
SUBROUTINE MOVGEL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+GEL,FROM,TO,IDEVR,IDEVW,IDEVN,MAXGEL,KBOUT)
C Subroutine to move a gel from line from to line to
C Extended 22-5-91
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),FROM,TO
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER NAMGEL*10,GEL(MAXGEL)
INTEGER GCLIN,CHAINL
LOGICAL LEFTE,RIGHTE
EXTERNAL GCLIN,CHAINL
LEFTE = .FALSE.
RIGHTE = .FALSE.
C
C left end ?
C
IF(LNBR(FROM).EQ.0) LEFTE = .TRUE.
C
C right end ?
C
IF(RNBR(FROM).EQ.0) RIGHTE = .TRUE.
C
C if both true remove the contig line, then overwrite the gel
C
IF(LEFTE.AND.RIGHTE) THEN
NCONTO = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,FROM)
IF(NCONTO.EQ.0)THEN
WRITE(KBOUT,*)
+ 'This gel has no left neighbour but does not'
WRITE(KBOUT,*)'appear in a contig line!'
ELSE
LNBR(NCONTO) = TO
RNBR(NCONTO) = TO
CALL WRITER(IDEVR,NCONTO,RELPG(NCONTO),LNGTHG(NCONTO),
+ LNBR(NCONTO),RNBR(NCONTO))
END IF
ELSE IF(LEFTE) THEN
NCONTO = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,FROM)
IF(NCONTO.EQ.0)THEN
WRITE(KBOUT,*)
+ 'This gel has no left neighbour but does not'
WRITE(KBOUT,*)'appear in a contig line!'
ELSE
LNBR(NCONTO) = TO
CALL WRITER(IDEVR,NCONTO,RELPG(NCONTO),LNGTHG(NCONTO),
+ LNBR(NCONTO),RNBR(NCONTO))
END IF
ELSE IF(RIGHTE) THEN
I = CHAINL(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,FROM)
NCONTO = GCLIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ IDBSIZ,I)
IF(NCONTO.EQ.0)THEN
WRITE(KBOUT,*)
+ 'This gel has no right neighbour and does not'
WRITE(KBOUT,*)'appear in a contig!'
ELSE
IF(RNBR(NCONTO).NE.FROM)THEN
WRITE(KBOUT,*)
+ 'This gel has no right neighbour but does not'
WRITE(KBOUT,*)'appear in a contig line!'
ELSE
RNBR(NCONTO) = TO
CALL WRITER(IDEVR,NCONTO,RELPG(NCONTO),LNGTHG(NCONTO),
+ LNBR(NCONTO),RNBR(NCONTO))
END IF
END IF
END IF
RELPG(TO)=RELPG(FROM)
LNGTHG(TO)=LNGTHG(FROM)
LNBR(TO)=LNBR(FROM)
RNBR(TO)=RNBR(FROM)
CALL READW(IDEVW,FROM,GEL,MAXGEL)
CALL WRITEW(IDEVW,TO,GEL,MAXGEL)
CALL READN(IDEVN,FROM,NAMGEL)
CALL WRITEN(IDEVN,TO,NAMGEL)
CALL WRITER(IDEVR,TO,RELPG(TO),LNGTHG(TO),
+LNBR(TO),RNBR(TO))
C Do neighbours
IF(LNBR(FROM).NE.0) THEN
I=LNBR(FROM)
RNBR(I)=TO
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
END IF
IF(RNBR(FROM).NE.0) THEN
I=RNBR(FROM)
LNBR(I)=TO
CALL WRITER(IDEVR,I,RELPG(I),LNGTHG(I),
+ LNBR(I),RNBR(I))
END IF
CALL MOVTAG(FROM,TO)
END
SUBROUTINE DBOPEN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,NAMPRO,GEL,
+IDBSIS,IDBSIZ,IERR,KBIN,KBOUT,
+IDEVR,IDEVW,IDEVN,IDEVT,IDEVC,
+MAXGEL,MAXGLM,LLINO,
+IDM,IHELPS,IHELPE,HELPF,IDEVH)
C AUTHOR: RODGER STADEN
CHARACTER GEL(MAXGLM)
INTEGER RELPG(IDBSIS)
INTEGER LNGTHG(IDBSIS),LNBR(IDBSIS),RNBR(IDBSIS)
CHARACTER NAMPRO*(*),COPYNO*4,HELPF*(*)
INTEGER IWORD,ANS
PARAMETER (IWORD=4)
C NOTE THIS IS THE MACHINES WORD LENGTH IE HOW MANY CHARS PER WORD
CALL FILLI(RELPG,IDBSIS,0)
CALL FILLI(LNGTHG,IDBSIS,0)
CALL FILLI(LNBR,IDBSIS,0)
CALL FILLI(RNBR,IDBSIS,0)
NAMPRO(1:)=' '
IERR=1
1 CONTINUE
L = 0
CALL GTSTR('Project name',' ',NAMPRO,L,KBOUT,KBIN,INFLAG)
IF(L.LT.1) RETURN
LL = L
CALL CCASE(NAMPRO,1)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
GO TO 1
END IF
L = 1
CALL GTSTR('Version','0',COPYNO,L,KBOUT,KBIN,INFLAG)
CALL CCASE(COPYNO,1)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
GO TO 1
END IF
IF(L.LT.1) COPYNO(1:1) = '0'
C GET .ARN FIRST AS IT CONTAINS LENGTH OF OTHER FILES
NAMPRO(LL+1:LL+3)='.AR'
NAMPRO(LL+4:LL+4)=COPYNO(1:1)
CALL OPENRS(IDEVN,NAMPRO,IOK,3,4)
IF(IOK.NE.0)GO TO 100
C ******* PROBLEM HERE READING RECORD 1000 AND INTEGER FROM IDEVN!!!
READ(IDEVN,REC=IDBSIS,ERR=50)IDBSIZ,MAXGEL,IDM
IF(MAXGEL.LT.512)GO TO 50
IF(MAXGEL.GT.MAXGLM)GO TO 50
IF(MOD(MAXGEL,512).NE.0)GO TO 50
20 CONTINUE
IF((IDM.NE.5).AND.(IDM.NE.26))GO TO 51
21 CONTINUE
NAMPRO(LL+2:LL+3)='RL'
CALL OPENRS(IDEVR,NAMPRO,IOK,4,4)
IF(IOK.NE.0)GO TO 100
NAMPRO(LL+2:LL+3)='SQ'
C DEFINE RECORD LENGTH IN TERMS OF NUMBER OF CHARS PER WORD (4 ON VAX)
C AND MAXGEL SIZE
IREC=MAXGEL/IWORD
IF(MOD(MAXGEL,IWORD).NE.0)IREC=IREC+1
CALL OPENRS(IDEVW,NAMPRO,IOK,IREC,4)
IF(IOK.NE.0)GO TO 100
C NAMPRO(LL+2:LL+3) = 'RD'
C CALL OPENRS(IDEVRD,NAMPRO,IOK,7,4)
C IF(IOK.NE.0) IDEVRD = -9
NAMPRO(LL+2:LL+3) = 'TG'
CALL OPENRS(IDEVT,NAMPRO,IOK,5,4)
IF(IOK.NE.0) IDEVT = -1
NAMPRO(LL+2:LL+3) = 'CC'
C COMMENT_LENGTH: 11 = (40 + long)/long
CALL OPENRS(IDEVC,NAMPRO,IOK,11,4)
IF(IOK.NE.0) IDEVC = -1
C READ A LINE FOR LUCK
CALL READW(IDEVW,1,GEL,MAXGEL)
CALL READR(IDEVR,IDBSIZ,NGELS,NCONTS,IDUM1,IDUM2)
WRITE(KBOUT,10011)NGELS,NCONTS,IDBSIZ,MAXGEL
10011 FORMAT(' Number of gel readings=',I3,' Number of contigs=',I3,/,
+' Database size=',I4,' Maximum gel reading length=',I4)
LLINO = 0
IF(NGELS.LT.1)GO TO 5
DO 3 I=1,NGELS
CALL READR(IDEVR,I,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
3 CONTINUE
N=IDBSIZ-NCONTS
MXT = 0
DO 4 I=N,IDBSIZ-1
CALL READR(IDEVR,I,RELPG(I),LNGTHG(I),LNBR(I),RNBR(I))
IF(RELPG(I).GT.MXT) THEN
MXT = RELPG(I)
LLINO = LNBR(I)
END IF
4 CONTINUE
5 CONTINUE
IERR=0
NAMPRO(LL+2:LL+2) = COPYNO(1:1)
RETURN
100 CONTINUE
WRITE(KBOUT,9999)
9999 FORMAT(' Error encountered opening database files')
NAMPRO(LL+2:LL+2) = COPYNO(1:1)
RETURN
50 CONTINUE
WRITE(KBOUT,2000)MAXGLM
2000 FORMAT(' Error reading maximum gel reading length',/,
+' The maximum gel reading length must be a multiple',
+' of 512.',/,' E.G. 512, 1024, 1536, 2048, etc up to',I6)
MN = 512
MX = MAXGLM
MAXIN1 = MN
CALL GETINT(MN,MX,MAXIN1,
+'Maximum gel reading length',
+IVAL,KBIN,KBOUT,IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MAXGEL = IVAL
IF(MOD(MAXGEL,MAXIN1).NE.0)GO TO 50
C PROBLEM WRITING TO RECORD IDBSIZ WITH NO SUBROUTINE CALL!!!!!!!!!!
WRITE(IDEVN,REC=IDBSIS)IDBSIZ,MAXGEL
GO TO 20
51 CONTINUE
WRITE(KBOUT,2003)
2003 FORMAT(' Error reading protein or dna label')
CALL YESNO(ANS,'DNA',
+IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF(ANS.LT.0) RETURN
IF(ANS.EQ.0)IDM = 5
IF(ANS.EQ.1)IDM = 26
C PROBLEM WRITING TO RECORD IDBSIZ WITH NO SUBROUTINE CALL!!!!!!!!!!
WRITE(IDEVN,REC=IDBSIS)IDBSIZ,MAXGEL,IDM
GO TO 21
END
SUBROUTINE DBSTAR(NAMPRO,GEL,IDBSIS,IDBSIZ,KBIN,KBOUT,
+IDEV1,IDEV2,IDEV3,IDEVT,IDEVC,
+IERR,IHELPS,IHELPE,IDEVH,FILEH,
+MAXGEL,MAXGLM,IDM)
CHARACTER GEL(MAXGLM),FILEH*(*)
CHARACTER NAMPRO*(*)
INTEGER IWORD
PARAMETER (IWORD=4)
IERR=1
3 CONTINUE
MN = 0
CALL GTSTR('New project name',' ',NAMPRO,MN,KBOUT,KBIN,INFLAG)
IF(MN.LT.1) RETURN
LL = MIN(12,MN)
CALL CCASE(NAMPRO,1)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 3
END IF
MN = 10
MX = IDBSIS
IDBSIZ = 50
CALL GETINT(MN,MX,IDBSIZ,
+'Database size',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
IDBSIZ = IVAL
5 CONTINUE
MN = 512
MX = MAXGLM
MAXIN1 = MIN(512,MAXGEL)
CALL GETINT(MN,MX,MAXIN1,
+'Maximum gel reading length',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MAXGEL = IVAL
IF(MOD(IVAL,MAXIN1).NE.0) THEN
MAXGEL = 512 + (IVAL/512)*512
WRITE(KBOUT,*)'Maximum set to',MAXGEL
END IF
CALL YESNO(IDM,'Database is for DNA',
+IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
IF(IDM.LT.0) RETURN
IF(IDM.EQ.0)IDM = 5
IF(IDM.EQ.1)IDM = 26
NAMPRO(LL+1:LL+4)='.RL0'
CALL OPENRS(IDEV1,NAMPRO,IOK,4,3)
IF(IOK.NE.0)GO TO 100
C IRAW = 0
C IDEVRT = IDEVRD
C IDEVRD = -9
C CALL YESNO(IRAW,'Create raw data pointer file',
C +IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
C IF(IRAW.LT.0) RETURN
C IF(IRAW.EQ.0) THEN
C NAMPRO(LL+1:LL+4)='.RD0'
C CALL OPENRS(IDEVRT,NAMPRO,IOK,7,3)
C IF(IOK.EQ.0) IDEVRD = IDEVRT
C END IF
WRITE(KBOUT,1004)
1004 FORMAT(' Writing new database files')
J = 0
K = 0
N = 0
M = 0
DO 10 I=1,IDBSIZ
CALL WRITER(IDEV1,I,J,K,M,N)
10 CONTINUE
NAMPRO(LL+2:LL+3)='SQ'
IREC=MAXGEL/IWORD
IF(MOD(MAXGEL,IWORD).NE.0)IREC=IREC+1
CALL OPENRS(IDEV2,NAMPRO,IOK,IREC,3)
IF(IOK.NE.0)GO TO 100
CALL FILLC(GEL,MAXGEL,' ')
CALL WRITEW(IDEV2,IDBSIZ,GEL,MAXGEL)
NAMPRO(LL+2:LL+3)='AR'
CALL OPENRS(IDEV3,NAMPRO,IOK,3,3)
IF(IOK.NE.0)GO TO 100
C NOTE HERE IS A WRITE TO NAMES FILE NOT USING A SUBROUTINE CALL
WRITE(IDEV3,REC=IDBSIS)IDBSIZ,MAXGEL,IDM
C IF(IDEVRD.GT.0) THEN
C NAMFIL = ' '
C MTYPE = ' '
C I = 0
C J = 0
C K = 0
C CALL WRITRD(IDEVRD,IDBSIZ,I,J,K,MTYPE,NAMFIL)
C ENDIF
C CREATE TAG FILES (TAGS AND COMMENTS)
IF (.TRUE.) THEN
NAMPRO(LL+2:LL+3)='TG'
CALL OPENRS(IDEVT,NAMPRO,IOK,5,3)
IF(IOK.NE.0)GO TO 100
CALL WRITTG(IDEVT,IDBSIZ,IDBSIZ,0,0,0,0)
NAMPRO(LL+2:LL+3)='CC'
C COMMENT_LENGTH: 11 = (40 + long)/long
CALL OPENRS(IDEVC,NAMPRO,IOK,11,3)
IF(IOK.NE.0)GO TO 100
CALL WRITCC(IDEVC,1,1,0,' ')
ENDIF
WRITE(KBOUT,1003)NAMPRO(1:LL),IDBSIZ
1003 FORMAT(' Database ',A,' version 0, size',I5,
+' successfully started')
C WRITE(KBOUT,1006)NAMPRO(1:LL)
1006 FORMAT(
+' Note the 3 database files are named ',A,'.AR0, .SQ0, .RL0')
IERR=0
NAMPRO(LL+2:LL+2) = '0'
RETURN
100 CONTINUE
WRITE(KBOUT,9999)
9999 FORMAT(' Error when trying to open database,',
+' database not started')
RETURN
END
SUBROUTINE ENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+GEL,GEL2,IDBSIZ,IDEV,KBIN,KBOUT,IDEVR,IDEVW,IDEVN,IDEVG,
+IDEVT,IDEVC,LINLEN,PERCD,NAMARC,
+HELPS1,HELPE1,HELPS2,HELPE2,FILEH,IDEVH,MAXGEL,IDM,NCONTC)
CHARACTER FILEH*(*)
INTEGER HELPS1,HELPS2,HELPE1,HELPE2
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ)
INTEGER X,Y,ANS
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL),NAMARC*(*)
CHARACTER NAMARK*10
CHARACTER GEL2(MAXGEL)
C WRITE(KBOUT,1000)
C1000 FORMAT(
C +' Enter a new gel reading into the database.',//,
C +' Note that before a gel reading is entered into the',/,
C +' database it must be compared with the database to ',/,
C +' search for overlaps using a function such as auto assemble',/,
C +' The replies to all the questions that follow are given',/,
C +' by these searches',//)
IF((IDBSIZ-(NGELS+NCONTS)).GT.2)GO TO 5
WRITE(KBOUT,1999)IDBSIZ
1999 FORMAT(' Current database size=',I5,' extend with copy')
RETURN
5 CONTINUE
C WRITE(KBOUT,1018)
C1018 FORMAT(
C +' We need the name of the file containing the gel reading')
CALL OPENF1(IDEVG,NAMARC,0,IOK,KBIN,KBOUT,
+'File name of gel reading to enter',
+HELPS1,HELPE1,FILEH,IDEVH)
IF(IOK.NE.0)RETURN
IF(NGELS.GT.0) THEN
DO 10 J=1,NGELS
CALL READN(IDEVN,J,NAMARK)
IF(NAMARC(1:10).NE.NAMARK)GO TO 10
WRITE(KBOUT,1013)J
1013 FORMAT( ' Gel reading already in database (number,',I6,
+ '), entry aborted')
RETURN
10 CONTINUE
END IF
IDIM=MAXGEL
CALL ARRFIM(IDEVG,GEL,IDIM,KBOUT)
CLOSE(UNIT=IDEVG)
NGELS=NGELS+1
LNGTHG(NGELS)=IDIM
NAMARK=NAMARC(1:10)
CALL WRITEN(IDEVN,NGELS,NAMARK)
WRITE(KBOUT,1003)NGELS
1003 FORMAT( ' This gel reading has been given the number ',I6)
IF(IDEVT.GT.0) CALL ENTRD(IDEVG,IDEVRD,NAMARC,NGELS,IOK)
ANS=0
IF(NGELS.GT.1)THEN
C WRITE(KBOUT,1017)
C1017 FORMAT(
C +' We need to know if the gel reading overlaps data already in',
C +' the database')
CALL YESNO(ANS,'New gel overlaps a contig',
+ HELPS1,HELPE1,FILEH,IDEVH,KBIN,KBOUT)
IF(ANS.LT.0) THEN
NGELS = NGELS - 1
RETURN
END IF
IF(ANS.EQ.0)GO TO 100
END IF
C
C DOES NOT OVERLAP SO IT STARTS A CONTIG OF ITS OWN
LNBR(NGELS)=0
RNBR(NGELS)=0
RELPG(NGELS)=1
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
NCONTS=NCONTS+1
N=IDBSIZ-NCONTS
LNBR(N)=NGELS
RNBR(N)=NGELS
RELPG(N)=(IDIM)
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
CALL WRITEW(IDEVW,NGELS,GEL,MAXGEL)
RETURN
C
100 CONTINUE
C WRITE(KBOUT,1019)
C1019 FORMAT(
C +' We need to know if the new gel reading overlaps in the',/,
C +' normal or complementary sense')
C COMPLEMENT GEL IF REQUIRED
CALL YESNO(ANS,'Gel overlaps in normal sense',
+HELPS1,HELPE1,FILEH,IDEVH,KBIN,KBOUT)
IF(ANS.LT.0) THEN
NGELS = NGELS - 1
RETURN
END IF
IF(ANS.EQ.1) THEN
CALL SQREV(GEL,IDIM)
CALL SQCOM(GEL,IDIM)
LNGTHG(NGELS)=-1*LNGTHG(NGELS)
END IF
C WRITE(KBOUT,1020)
C1020 FORMAT(
C +' We need to know which contig the new gel reading overlaps')
CALL GETLN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON,NCONTC,
+IERR,IDBSIZ,KBIN,KBOUT,IDEVN,
+HELPS1,HELPE1,FILEH,IDEVH)
IF(IERR.NE.0) THEN
NGELS=NGELS-1
RETURN
END IF
C WRITE(KBOUT,1014)
C1014 FORMAT(
C +' We need information about the position of the overlap.',/,
C +' First there are two types: those that extend the contig',/,
C +' leftwards and those that start internally.')
CALL YESNO(ANS,'Left end of gel reading is inside contig',
+ HELPS1,HELPE1,FILEH,IDEVH,KBIN,KBOUT)
IF(ANS.LT.0)THEN
NGELS=NGELS-1
RETURN
END IF
IF(ANS.EQ.1)GO TO 400
C RIGHT END OR INTERNAL OVERLAP
C
C WRITE(KBOUT,1015)
C1015 FORMAT(' Now we need to know the exact position of the overlap')
160 CONTINUE
MN = 1
MX = RELPG(LINCON)
X = 0
CALL GETINT(MN,MX,X,
+'Position in contig of left end of gel reading',
+IVAL,KBIN,KBOUT,
+HELPS1,HELPE1,FILEH,IDEVH,IOK)
IF(IOK.NE.0) THEN
NGELS = NGELS - 1
RETURN
END IF
X = IVAL
IF(X.EQ.0)GO TO 160
N=NCONTC
200 CONTINUE
IF(RELPG(N).GT.X)GO TO 250
IF(RNBR(N).EQ.0)GO TO 350
N=RNBR(N)
GO TO 200
250 CONTINUE
C GEL LIES BETWEEN N AND LNBR(N)
C DISPLAY JOINT
NOPT = 1
C @jkb@
C CALL BEDIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
C +GEL,GEL2,LINCON,NCONTC,NOPT,X,IDBSIZ,IDEV,KBIN,KBOUT,
C +IDEVR,IDEVW,IDEVN,LINLEN,PERCD,
C +HELPS1,HELPE1,HELPS2,HELPE2,FILEH,IDEVH,MAXGEL,IDM)
C CHECK ON RESULT
IF(NOPT.EQ.1)GO TO 160
IF(NOPT.EQ.3)GO TO 260
C COCKUP
NGELS=NGELS-1
RETURN
260 CONTINUE
CALL WRITEW(IDEVW,NGELS,GEL,MAXGEL)
LNBR(NGELS)=LNBR(N)
RNBR(NGELS)=N
RELPG(NGELS)=X
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
RNBR(LNBR(N))=NGELS
K=LNBR(N)
CALL WRITER(IDEVR,K,RELPG(K),LNGTHG(K),
+LNBR(K),RNBR(K))
LNBR(N)=NGELS
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
IDIM=ABS(LNGTHG(NGELS))
Y=X+(IDIM)-1
IF(Y.LE.RELPG(LINCON))RETURN
RELPG(LINCON)=Y
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
RETURN
350 CONTINUE
C MUST BE A RIGHT END OVERLAP
C DSPLAY JOINT
NOPT = 1
C @jkb@
C CALL BEDIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
C +GEL,GEL2,LINCON,NCONTC,NOPT,X,IDBSIZ,IDEV,KBIN,KBOUT,
C +IDEVR,IDEVW,IDEVN,LINLEN,PERCD,
C +HELPS1,HELPE1,HELPS2,HELPE2,FILEH,IDEVH,MAXGEL,IDM)
IF(NOPT.EQ.1)GO TO 160
IF(NOPT.EQ.3)GO TO 360
C COCKUP
NGELS=NGELS-1
RETURN
360 CONTINUE
CALL WRITEW(IDEVW,NGELS,GEL,MAXGEL)
LNBR(NGELS)=N
RNBR(NGELS)=0
RELPG(NGELS)=X
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
RNBR(N)=NGELS
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
RNBR(LINCON)=NGELS
IDIM=ABS(LNGTHG(NGELS))
Y=X+(IDIM)-1
RELPG(LINCON)=MAX(RELPG(LINCON),Y)
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
RETURN
C
400 CONTINUE
C
C ADDING TO LEFT END
C WRITE(KBOUT,1015)
410 CONTINUE
MN = 1
MX = IDIM
X = 0
CALL GETINT(MN,MX,X,
+'Position in new gel reading of left end of contig',
+IVAL,KBIN,KBOUT,
+HELPS1,HELPE1,FILEH,IDEVH,IOK)
IF(IOK.NE.0) THEN
NGELS = NGELS - 1
RETURN
END IF
X = IVAL
IF(X.EQ.0)GO TO 410
C SET FLAG TO SHOW LEFT END OVERLAP
NOPT=2
C @jkb@
C CALL BEDIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
C +GEL,GEL2,LINCON,NCONTC,NOPT,X,IDBSIZ,IDEV,KBIN,KBOUT,
C +IDEVR,IDEVW,IDEVN,LINLEN,PERCD,
C +HELPS1,HELPE1,HELPS2,HELPE2,FILEH,IDEVH,MAXGEL,IDM)
IF(NOPT.EQ.1)GO TO 400
IF(NOPT.EQ.3)GO TO 420
C COCKUP
NGELS=NGELS-1
RETURN
420 CONTINUE
CALL WRITEW(IDEVW,NGELS,GEL,MAXGEL)
RELPG(NGELS)=1
RNBR(NGELS)=NCONTC
LNBR(NGELS)=0
CALL WRITER(IDEVR,NGELS,RELPG(NGELS),LNGTHG(NGELS),
+LNBR(NGELS),RNBR(NGELS))
LNBR(NCONTC)=NGELS
RELPG(NCONTC)=X
CALL WRITER(IDEVR,NCONTC,RELPG(NCONTC),LNGTHG(NCONTC),
+LNBR(NCONTC),RNBR(NCONTC))
RELPG(LINCON)=RELPG(LINCON)+X-1
IDIM=ABS(LNGTHG(NGELS))
Y=IDIM
IF(Y.GT.RELPG(LINCON))RELPG(LINCON)=Y
LNBR(LINCON)=NGELS
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
CALL WRITER(IDEVR,IDBSIZ,NGELS,NCONTS,NGELS,NCONTS)
N=NCONTC
440 CONTINUE
IF(RNBR(N).EQ.0)RETURN
N=RNBR(N)
RELPG(N)=RELPG(N)+X-1
CALL WRITER(IDEVR,N,RELPG(N),LNGTHG(N),
+LNBR(N),RNBR(N))
GO TO 440
END
C SUBROUTINE XENTRD(IDEVG,IDEVRD,NAMARC,NGEL,IOK)
C CHARACTER NAMARC*(*),NAMFIL*12,MTYPE*4
CC Enters raw data info into database
C IOK = 0
C IF(IDEVRD.GT.0) THEN
C CALL OPENRS(IDEVG,NAMARC,IOK,LRECL,2)
CC IF(IOK.EQ.0) THEN
C CALL RRD(IDEVG,LENR,LCUT,LENW,MTYPE,NAMFIL)
C CALL WRITRD(IDEVRD,NGEL,LENR,LCUT,LENW,MTYPE,NAMFIL)
CC END IF
C END IF
C END
SUBROUTINE FIXRD(IDEVT,IDEVC,IDBSIZ,KBIN,KBOUT,
+IHELPS,IHELPE,FILEH,IDEVH)
C FILE_NAME_LENGTH
CHARACTER NAMFIL*18,NEWNAM*18,MTYPE*4,NEWMT*4,FILEH*(*)
IF(IDEVRD.LT.0) THEN
WRITE(KBOUT,*)'No raw data file!'
RETURN
END IF
10 CONTINUE
C Change raw data record
MN = 0
MX = IDBSIZ-1
LNO = 0
CALL GETINT(MN,MX,LNO,
+ 'Number of line to change',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
IF(IVAL.EQ.0) RETURN
LNO = IVAL
CALL READRD(IDEVT,IDEVC,LNO,LENR,LCUT,LENW,MTYPE,NAMFIL)
WRITE(KBOUT,*)'Current line'
WRITE(KBOUT,1001)LENR,LCUT,LENW,MTYPE,NAMFIL
1001 FORMAT(' ',3I6,' ',A,' ',A)
MN = 1
MX = 9999
LX = LENR
CALL GETINT(MN,MX,LX,
+ 'Length raw sequence',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
LX = IVAL
MN = 1
MX = LX
L = LCUT
CALL GETINT(MN,MX,L,
+ 'Left cutoff',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) GO TO 10
L = IVAL
MN = 1
MX = LX
M = LENW
CALL GETINT(MN,MX,M,
+ 'Length of original working sequence',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,FILEH,IDEVH,IOK)
IF(IOK.NE.0) RETURN
M = IVAL
20 CONTINUE
LNAM = 4
CALL GTSTR('Machine type',
+ MTYPE,NEWMT,LNAM,KBOUT,KBIN,INFLAG)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 20
END IF
IF(INFLAG.EQ.3) NEWMT = MTYPE
30 CONTINUE
C FILE_NAME_LENGTH
LNAM = 18
CALL GTSTR('Name for raw data file',
+ NAMFIL,NEWNAM,LNAM,KBOUT,KBIN,INFLAG)
IF(INFLAG.EQ.2) RETURN
IF(INFLAG.EQ.1) THEN
CALL HELP2(IHELPS,IHELPE,FILEH,IDEVH,KBIN,KBOUT)
GO TO 30
END IF
IF(INFLAG.EQ.3) NEWNAM = NAMFIL
WRITE(KBOUT,1001)LX,L,M,NEWMT,NEWNAM
CALL WRITRD(IDEVT,IDEVC,LNO,LX,L,M,NEWMT,NEWNAM)
WRITE(KBOUT,*)'New record written to disk'
GO TO 10
END
C SUBROUTINE READRD(IDEVT,IDEVC,NGEL,LENR,LCUT,LENW,MTYPE,NAMFIL)
C CHARACTER MTYPE*(*),NAMFIL*(*)
C IF(IDEVT.GT.0)READ(IDEVRD,REC=NGEL)LENR,LCUT,LENW,MTYPE,NAMFIL
C END
C SUBROUTINE RRD(IDEVG,LENR,LCUT,LENW,MTYPE,NAMFIL)
C CHARACTER LINE*80,NAMFIL*(*),MTYPE*(*)
C Reads raw data info from reading file assuming it starts with ;
C 1 CONTINUE
C READ(IDEVG,1000,END=100,ERR=100)LINE
C 1000 FORMAT(A)
C IF(LINE(1:1).NE.';') GO TO 1
C READ(LINE,1001,ERR=100)LENR,LCUT,LENW,MTYPE,NAMFIL
C 1001 FORMAT(1X,3I6,A,A)
C RETURN
C 100 CONTINUE
C LENR = 0
C LCUT = 0
C LENW = 0
C MTYPE = ' '
C NAMFIL = ' '
C END
C SUBROUTINE WRITRD(IDEVT,IDEVC,NGEL,LENR,LCUT,LENW,MTYPE,NAMFIL)
C CHARACTER MTYPE*(*),NAMFIL*(*)
C IF(IDEVT.GT.0)WRITE(IDEVRD,REC=NGEL)LENR,LCUT,LENW,MTYPE,NAMFIL
C END
SUBROUTINE READRD(IDEVT,IDEVC,NGEL,LENR,LCUT,LENW,MTYPE,NAMFIL)
CHARACTER MTYPE*(*),NAMFIL*(*)
C COMMENT_LENGTH
CHARACTER NOTE*40
IF(IDEVT.GT.0)THEN
CALL READTG(IDEVT,NGEL,LPOS,LLEN,LCOM,LTYPE,NEXT)
CALL READCC(IDEVC,LCOM,ICNT,NEXT,NOTE)
READ(NOTE,1001,ERR=100)LENR,LCUT,LENW,MTYPE,NAMFIL
1001 FORMAT(3I6,A,A)
ENDIF
RETURN
100 CONTINUE
LENR = 0
LCUT = 0
LENW = 0
MTYPE = ' '
NAMFIL = ' '
END
SUBROUTINE WRITRD(IDEVT,IDEVC,NGEL,LENR,LCUT,LENW,MTYPE,NAMFIL)
CHARACTER MTYPE*(*),NAMFIL*(*)
INTEGER FREECC
C COMMENT_LENGTH
CHARACTER NOTE*40
IF(IDEVT.GT.0)THEN
CALL READTG(IDEVT,NGEL,LPOS,LLEN,LCOM,LTYPE,NEXT)
IF(LCOM.EQ.0)THEN
LCOM = FREECC(IDEVC)
ENDIF
WRITE(NOTE,1001,ERR=100)LENR,LCUT,LENW,MTYPE,NAMFIL
1001 FORMAT(3I6,A,A)
NEXT = 0
CALL WRITCC(IDEVC,LCOM,ICNT,NEXT,NOTE)
ENDIF
RETURN
100 CONTINUE
END
SUBROUTINE READTG(IDEVT,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
IF(IDEVT.GT.0) THEN
READ(IDEVT,REC=I)LPOS,LLEN,LCOM,LTYPE,NEXT
ENDIF
END
SUBROUTINE WRITTG(IDEVT,I,LPOS,LLEN,LCOM,LTYPE,NEXT)
IF (IDEVT.GT.0) THEN
WRITE(IDEVT,REC=I)LPOS,LLEN,LCOM,LTYPE,NEXT
ENDIF
END
SUBROUTINE READCC(IDEVC,I,ICNT,NEXT,NOTE)
C COMMENT_LENGTH
CHARACTER NOTE*40
C COMMENT_LENGTH - 4
CHARACTER DUMM*36
IF(IDEVC.GT.0)THEN
READ(IDEVC,REC=1)NEXT,ICNT,DUMM
IF(I.EQ.0.OR.I.GT.ICNT)THEN
NEXT = 0
NOTE = ' '
ELSE
READ(IDEVC,REC=I)NEXT,NOTE
ENDIF
ENDIF
END
SUBROUTINE WRITCC(IDEVC,I,ICNT,NEXT,NOTE)
C COMMENT_LENGTH
CHARACTER NOTE*40
C COMMENT_LENGTH - 4
CHARACTER DUMM*36
IF(IDEVC.GT.0)THEN
IF(I.EQ.1) THEN
WRITE(IDEVC,REC=1)NEXT,ICNT,DUMM
ELSE
READ(IDEVC,REC=1)IDUM,ICNT,DUMM
IF(I.LE.ICNT) WRITE(IDEVC,REC=I)NEXT,NOTE
ENDIF
ENDIF
END
SUBROUTINE PADCON(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+GEL,LINCON,POSN,NC,IDBSIZ,IDEVR,IDEVW,MAXGEL,KBOUT)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),POSN,X
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL)
CHARACTER PAD
SAVE PAD
DATA PAD/'*'/
C NOW FIND FIRST CHAR THAT OVERLAPS REGION
LLINO=LNBR(LINCON)
30 CONTINUE
X=RELPG(LLINO)+ABS(LNGTHG(LLINO))-1
IF(X.GE.POSN)GO TO 40
C NOT IN REGION
LLINO=RNBR(LLINO)
GO TO 30
40 CONTINUE
C NOW GET THIS GEL FROM DISK
C READ(IDEVW,REC=LLINO)GEL
CALL READW(IDEVW,LLINO,GEL,MAXGEL)
C CALC POSN IN THIS GEL TO EDIT
X=POSN-RELPG(LLINO)+1
K=X
C MOVE THE DATA RIGHT
M=ABS(LNGTHG(LLINO))
LNGTHG(LLINO)=LNGTHG(LLINO)+SIGN(NC,LNGTHG(LLINO))
C CHECK FOR OVER END OF ARRAY
N=ABS(LNGTHG(LLINO))
IF(N.GT.MAXGEL)THEN
WRITE(KBOUT,1000)LLINO
1000 FORMAT(
+' Data pushed off end of gel',I4,' during padding')
M=M-(N-MAXGEL)
N=MAXGEL
LNGTHG(LLINO)=SIGN(MAXGEL,LNGTHG(LLINO))
END IF
J=M-K+1
DO 55 I=1,J
GEL(N)=GEL(M)
N=N-1
M=M-1
55 CONTINUE
C PERFORM THE INSERTION
DO 60 I=K,MIN(MAXGEL,K+NC-1)
GEL(I)=PAD
60 CONTINUE
C WRITE BACK TO DISK
CALL WRITEW(IDEVW,LLINO,GEL,MAXGEL)
C WRITE(IDEVW,REC=LLINO)GEL
C WRITE NEW LINE
CALL WRITER(IDEVR,LLINO,RELPG(LLINO),LNGTHG(LLINO),
+LNBR(LLINO),RNBR(LLINO))
C WRITE(IDEVR,REC=LLINO)
C 1RELPG(LLINO),LNGTHG(LLINO),LNBR(LLINO),RNBR(LLINO)
C
C NOW UPDATE TAG FILES ACCORDINGLY
CALL PADTAG(LLINO,K,NC,LNGTHG(LLINO))
C
65 CONTINUE
C NOW GET NEXT GEL
LLINO=RNBR(LLINO)
C LAST GEL?
IF(LLINO.EQ.0)GO TO 70
C DOES IT HAVE DATA IN REGION?
C IE DO RELPG AND RELPG+LNGTHG-1 LIE EITHER SIDE OF POSN?
IF(RELPG(LLINO).GT.POSN)GO TO 70
X=RELPG(LLINO)+ABS(LNGTHG(LLINO))-1
IF(X.LT.POSN)GO TO 65
C WITHIN
GO TO 40
70 CONTINUE
C INSERTS FINISHED SO NEED TO INCREMENT ALL THOSE GELS TO RIGHT
LLINO=LNBR(LINCON)
75 CONTINUE
IF(RELPG(LLINO).GT.POSN)GO TO 80
76 CONTINUE
LLINO=RNBR(LLINO)
IF(LLINO.EQ.0)GO TO 90
GO TO 75
80 CONTINUE
RELPG(LLINO)=RELPG(LLINO)+NC
C WRITE NEW LINE
CALL WRITER(IDEVR,LLINO,RELPG(LLINO),LNGTHG(LLINO),
+LNBR(LLINO),RNBR(LLINO))
C WRITE(IDEVR,REC=LLINO)
C 1RELPG(LLINO),LNGTHG(LLINO),LNBR(LLINO),RNBR(LLINO)
GO TO 76
90 CONTINUE
C NEED TO INCREMENT CONTIG LINE
RELPG(LINCON)=RELPG(LINCON)+NC
CALL WRITER(IDEVR,LINCON,RELPG(LINCON),LNGTHG(LINCON),
+LNBR(LINCON),RNBR(LINCON))
C WRITE(IDEVR,REC=LINCON)RELPG(LINCON),LNGTHG(LINCON),LNBR(LINCON),
C 1RNBR(LINCON)
RETURN
END
SUBROUTINE AUTOJ(RELPG,LNGTHG,LNBR,RNBR,MAXDB,IDBSIZ,
+NGELS,NCONTS,MAXGEL,
+TEMP3,WORDP,WORDN,LPOWRC,POSNS,GELN,
+SEQ1,MAXSEQ,SEQ2,SEQ3,SEQ4,SEQ5,SEQC2,SEQG2,MATCH,
+MAXGLM,MAXGL2,CHRSIZ,ECHRSZ,LENGTH,
+SAV1,SAV2,SAV3,MAXSAV,CENDS,NENDS,MAXCON,CONST,
+KBIN,KBOUT,IDEV1,IDEV2,IDEV3,IDEV4,IDEV7,IDEV8,IDEV,
+IHELPS,IHELPE,HELPF,IDEVH,NAMARC,NAMPRO,FILE,
+PERCD,IOPEN,IDM,SEQG3,SEQC3,IOK)
INTEGER CHRSIZ,ECHRSZ
INTEGER RELPG(MAXDB)
INTEGER LNGTHG(MAXDB),LNBR(MAXDB),RNBR(MAXDB)
INTEGER JOINT(2),ITOTPC(2),ITOTPG(2),IDIM22(2),IDOUT(2)
INTEGER LLINO(2),ITYPE(2),IFAIL(2)
INTEGER ILEFTS(2),ILC(2),IPOSC(2),IPOSG(2),ISENSE(2)
INTEGER ANS,WINDOW
INTEGER TEMP3(ECHRSZ,MAXGL2),CONST(LENGTH)
INTEGER POSNS(MAXSEQ),WORDP(LPOWRC),WORDN(LPOWRC),GELN(MAXGLM)
INTEGER CENDS(MAXCON),NENDS(MAXCON)
CHARACTER SEQ3(MAXGLM),SEQC2(MAXGLM,2),SEQG2(MAXGLM,2)
CHARACTER SEQ1(MAXSEQ),SEQ2(MAXGLM),MATCH(MAXGLM),SEQ4(MAXGLM)
INTEGER SAV1(MAXSAV),SAV2(MAXSAV),SAV3(MAXSAV)
CHARACTER NAMARC*(*),NAMPRO*(*),FILE*(*)
CHARACTER SEQ5(MAXGLM),HELPF*(*),SEQG3(MAXGLM),SEQC3(MAXGLM)
CALL DBCHEK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
+ TEMP3,IERR,KBOUT)
IF(IERR.GT.1) RETURN
IFAIL(1) = 0
IF(NGELS.LT.1) RETURN
MN = LENGTH*2
MX = MAXGLM + 1
MINMAT = MAX(15,MN)
CALL GETINT(MN,MX,MINMAT,
+'Minimum initial match',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MINMAT = IVAL
MN = 2
MX = 5
MINSLI = MAX(3,MN)
CALL GETINT(MN,MX,MINSLI,
+'Minimum alignment block',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MINSLI = IVAL
MN = 0
MX = 50
MAXPG = 8
CALL GETINT(MN,MX,MAXPG,
+'Maximum pads per sequence',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
MAXPG = IVAL
MAXPC = IVAL
RMN = 0.
RMX = 100.
PERMAX = 8.
CALL GETRL(RMN,RMX,PERMAX,
+ 'Maximum percent mismatch after alignment',
+ VAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
PERMAX = VAL
MN = MINMAT
MX = MAXGEL
WINDOW = 100
CALL GETINT(MN,MX,WINDOW,
+'Probe length',
+IVAL,KBIN,KBOUT,
+IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
WINDOW = IVAL
IOK = 1
I = 0
CALL YESNO(I,'Use clipped data',
+ IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
IF(I.LT.0) RETURN
IWING = 0
IF(I.EQ.0) THEN
MN = 1
MX = MAXGEL
IWING = 100
CALL GETINT(MN,MX,IWING,
+ 'Window size for good data scan',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
IWING = IVAL
MN = 1
MX = MIN(100,IWING)
C Note nbad must be compatible with nok2
NBAD = MIN(IWING,5)
CALL GETINT(MN,MX,NBAD,
+ 'Maximum number of dashes in scan window',
+ IVAL,KBIN,KBOUT,
+ IHELPS,IHELPE,HELPF,IDEVH,IOK)
IF(IOK.NE.0) RETURN
NBAD = IVAL
END IF
IDIM1=0
MAXOVR=MAXGEL-3*MAX(MAXPC,MAXPG)
ANS=0
CALL JCONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,MAXSEQ,SEQ2,IDBSIZ,IDIM1,ANS,KDUMM,KDUMM,KDUMM,TEMP3,
+ECHRSZ,MAXGL2,KBOUT,IDEV2,IFAIL(1),MAXGEL,IDM,PERCD,SEQ5,
+CENDS,NENDS,MAXCON,IWING,NBAD)
IDIM2=MAXGEL
C
C Note I am doing something horrible here to save space:
C sending cends and nends to jcons to get the extension lengths
C then swapping them with temp3 by sending temp to ajoin and
C receiving them as cends and nends, and sending cends nends
C and receiving them as iladd,iradd
CALL AUTOJN(SEQ1,IDIM1,SEQ2,IDIM2,ILEFTS,ILC,IPOSC,
+IPOSG,ISENSE,LLINO,IMATC,IFCOMP,MINMAT,POSNS,WORDP,WORDN,
+CONST,LENGTH,LPOWRC,IDEV,MATCH,MAXGEL,MAXGLM,SEQ5,GELN,
+SAV1,SAV2,SAV3,MAXSAV,TEMP3,TEMP3(MAXCON+1,1),MAXCON,
+SEQG2,SEQC2,SEQ4,IDOUT,IDIM22,ITOTPG,ITOTPC,JOINT,IFAIL,
+ITYPE,MAXPC,MAXPG,PERMAX,MINSLI,SEQG3,SEQC3,KFAIL,
+WINDOW,CENDS,NENDS,RELPG,LNBR,IDBSIZ,NCONTS)
END
SUBROUTINE AUTOJN(SEQ1,IDIMIN,GEL,IDIMGI,ILEFTS,ILC,IPOSC,
+IPOSG,ISENSE,LLINO,IMATC,IFCOMP,MINMAT,POSNS,WORDP,WORDN,
+CONST,LENGTH,LPOWRC,KBOUT,MATCH,MAXGEL,MAXGLM,GELCOP,GELN,
+SAVPS,SAVPG,SAVL,MAXSAV,CENDS,NENDS,MAXCON,
+SEQG2,SEQC2,SEQ4,IDOUT,IDIM22,ITOTPG,ITOTPC,JOINT,IFAIL,
+ITYPE,MAXPC,MAXPG,PERMAX,MINSLI,SEQG3,SEQC3,KFAIL,
+WINDOW,ILADD,IRADD,RELPG,LNBR,IDBSIZ,NCONTS)
C AUTHOR: RODGER STADEN
INTEGER ILEFTS(2),ILC(2),IPOSC(2),IPOSG(2),ISENSE(2),LLINO(2)
INTEGER POSNS(IDIMIN),GELN(MAXGLM),WORDP(LPOWRC),SAVPS(MAXSAV)
INTEGER SAVPG(MAXSAV),SAVL(MAXSAV)
INTEGER WORDN(LPOWRC),RELPG(IDBSIZ),LNBR(IDBSIZ)
CHARACTER GELCOP(MAXGLM),MATCH(MAXGLM)
INTEGER CENDS(MAXCON),NENDS(MAXCON),ILADD(MAXCON),IRADD(MAXCON)
INTEGER CONST(LENGTH)
CHARACTER SEQ1(IDIMIN),GEL(MAXGLM)
CHARACTER SEQG2(MAXGLM,2),SEQC2(MAXGLM,2),SEQ4(MAXGLM)
INTEGER IDOUT(2),IDIM22(2),ITOTPG(2),ITOTPC(2),JOINT(2)
INTEGER IFAIL(2),ITYPE(2)
PARAMETER (MAXC = 10)
CHARACTER SEQG3(MAXGLM),SEQC3(MAXGLM)
INTEGER JLEFTS(MAXC),JLC(MAXC),JPOSC(MAXC),JPOSG(MAXC),MCON(MAXC)
INTEGER JSENSE(MAXC),JLLINO(MAXC),WINDOW
IFAIL(1) = 1
IFAIL(2) = 1
KFAIL = 0
IDCEND=MAXCON
CALL FNDCON(SEQ1,IDIMIN,CENDS,NENDS,IDCEND,MAXCON,KBOUT)
C find possible missed joins
C we have consensus in seq1 in order first contig,second contig etc
C compare the ends in reverse order, simultaneously shortening the consensus
IDIM = IDIMIN
DO 200 JCON = IDCEND,2,-1
IDIM = CENDS(JCON) - 1
CALL ENCO(SEQ1,IDIM,POSNS,CONST,LENGTH)
CALL ENCONA(POSNS,IDIM,WORDP,WORDN,LPOWRC,LENGTH)
JS = CENDS(JCON) + 20
JE = CENDS(JCON+1) - 1
IEND = 1
IDIMG = MIN(WINDOW,JE-JS+1)
C check for case where contig is shorter than probe (window)
C in which case only compare the left hand end
IF(JE-JS+1.LE.WINDOW) IEND = 2
C WRITE(*,*)JCON,JS,JE,IDIMG
1 CONTINUE
IMATC = 0
IF(IEND.EQ.1) THEN
CALL SQCOPY(SEQ1(JE-IDIMG+1),GEL,IDIMG)
ELSE
CALL SQCOPY(SEQ1(JS),GEL,IDIMG)
END IF
CALL SQCOPY(GEL,GELCOP,IDIMG)
ISTRAN=1
2 CONTINUE
CALL ENCO(GEL,IDIMG,GELN,CONST,LENGTH)
IDSAV=MAXSAV
CALL CFGEL(GELN,IDIMG,POSNS,IDIM,WORDP,WORDN,LENGTH,LPOWRC,
+SAVPG,SAVPS,SAVL,
+IDSAV,SEQ1,GEL,MINMAT,IFCOMP,KBOUT)
IF(IFCOMP.NE.0) THEN
CALL ERROM(KBOUT,'Error in CFGEL')
RETURN
END IF
IF(IDSAV.NE.0)THEN
CALL ADISM5(IDIM,IDIMG,SAVPS,SAVPG,IDSAV,CENDS,NENDS,
+ IDCEND,MAXCON,JLEFTS,JLC,JPOSC,JPOSG,JSENSE,JLLINO,
+ IMATC,ISTRAN,MAXC,KBOUT,MCON)
END IF
ISTRAN=ISTRAN+1
IF(ISTRAN.EQ.2) THEN
CALL SQCOPY(GELCOP,GEL,IDIMG)
CALL SQREV(GEL,IDIMG)
CALL SQCOM(GEL,IDIMG)
GO TO 2
END IF
CALL SQCOPY(GELCOP,GEL,IDIMG)
KSENSE = 0
C WRITE(KBOUT,*)'Total matches found',IMATC
IF(IMATC.NE.0) THEN
JMATC = 0
DO 100 I = 1,IMATC
IF(JSENSE(I).EQ.-1) THEN
IF(KSENSE.EQ.0) THEN
CALL SQREV(GEL,IDIMG)
CALL SQCOM(GEL,IDIMG)
KSENSE = 1
END IF
END IF
JDIM22 = IDIMG
JDOUT = MAXGEL
IDSAV = MAXSAV
C IF(IEND.EQ.1) WRITE(KBOUT,*)'Left end of Contig',NENDS(JCON)
C IF(IEND.EQ.2) WRITE(KBOUT,*)'Right end of Contig',NENDS(JCON)
C WRITE(KBOUT,*)'Trying to align with contig',JLLINO(I)
CALL ALINEJ(SEQ1(JLEFTS(I)),GEL,SEQG3,SEQC3,
+ SAVPS,SAVPG,SAVL,IDSAV,JLC(I),JDIM22,JDOUT,
+ JPOSC(I),JPOSG(I),MINSLI,JJOINT,JTOTPC,JTOTPG,
+ JFAIL,JTYPE,MAXPC,MAXPG,PERMAX,KBOUT,SEQ4,MAXGEL,PERMS,
+ NENDS(JCON),IEND,JLLINO(I),JSENSE(I),ILADD,IRADD,MAXCON,MCON(I),
+ JCON,RELPG,LNBR,IDBSIZ,NCONTS,WINDOW)
100 CONTINUE
END IF
IEND = IEND + 1
IF(IEND.EQ.2) GO TO 1
C IDIM = CENDS(JCON)-1
200 CONTINUE
END
SUBROUTINE ALINEJ(SEQ1,SEQ2,SEQG2,SEQC2,ISAV1,ISAV2,ISAV3,
+IDSAV,IDC,IDIM2,IDOUT,IC1,IG1,MINSLI,JOINT,
+ITOTPC,ITOTPG,IFAIL,ITYPE,MAXPC,MAXPG,PERMAX,KBOUT,SEQ3,MAXGEL,
+PERCM,JCONN,IEND,NCON,JSENSE,ILADD,IRADD,MAXCON,MCON,JCON,
+RELPG,LNBR,IDBSIZ,NCONTS,WINDOW)
C AUTHOR: RODGER STADEN
CHARACTER SEQ1(IDC),SEQ2(IDIM2),SEQG2(IDOUT),SEQC2(IDOUT)
CHARACTER SEQ3(MAXGEL)
INTEGER ISAV1(IDSAV),ISAV2(IDSAV),ISAV3(IDSAV)
INTEGER ILADD(MAXCON),IRADD(MAXCON)
INTEGER RELPG(IDBSIZ),LNBR(IDBSIZ),WINDOW
MINSLT=MINSLI
C SAVE SEQ2
CALL SQCOPY(SEQ2,SEQ3,IDIM2)
CALL MSTLKL(SEQ3,IDIM2)
IFAIL=1
C FIND MATCHES
IPP=IDSAV
CALL SLIDER(SEQ1,IDC,SEQ3,IDIM2,IC1,IG1,MAXPG,MAXPC,MINSLT,
+ISAV1,ISAV2,ISAV3,IPP)
IF(IPP.GT.IDSAV)RETURN
IF(IPP.LT.1)RETURN
CALL REMOVL(ISAV2,ISAV3,ISAV1,IPP)
CALL BUB3AS(ISAV2,ISAV3,ISAV1,IPP)
C DO TOPOLOGICAL CHECK
CALL TPCHEK(ISAV2,ISAV3,ISAV1,IPP)
IFAIL=0
CALL LINEUP(SEQ2,SEQ1,SEQG2,SEQC2,IDC,IDIM2,IDOUT,ISAV3,ISAV2,
+ISAV1,IPP,ITOTPC,ITOTPG,JOINT,ITYPE,KBOUT,MAXGEL,IFAIL)
IF(IFAIL.NE.0)RETURN
C IDIM2 IS NOW LENGTH OF ALIGNED GEL
C WRITE(KBOUT,1052)ITOTPC,ITOTPG
C1052 FORMAT(' Padding in contig= ',I4,' and in gel= ',I4)
CALL JALIGN(SEQC2,SEQG2,SEQ3,MAXGEL,IDOUT,IDIM2,JOINT,
+ITYPE,PERCM,KBOUT,IFAIL,PERMAX,JCONN,IEND,NCON,JSENSE,
+ILADD,IRADD,MAXCON,MCON,JCON,RELPG,LNBR,IDBSIZ,NCONTS,WINDOW)
C ARE ALL CHECKS OK?
IF(ITOTPC.GT.MAXPC)IFAIL=1
IF(ITOTPG.GT.MAXPG)IFAIL=1
IF(PERCM.GT.PERMAX)IFAIL=1
END
C SUBROUTINE DALIGN
C
C COUNTS MISMATCHES AND DISPLAYS OVERLAP.
SUBROUTINE JALIGN(SEQC2,SEQG2,SEQ3,MAXGEL,IDOUT,IDIM2,
+JOINT,ITYPE,X,KBOUT,IFAIL,PERMAX,JCONN,IEND,NCON,JSENSE,
+ILADD,IRADD,MAXCON,MCON,JCON,RELPG,LNBR,IDBSIZ,NCONTS,WINDOW)
C AUTHOR: RODGER STADEN
CHARACTER SEQC2(MAXGEL),SEQG2(MAXGEL),SEQ3(MAXGEL)
CHARACTER PAD,DASH,STRAND,NAME1*6,NAME2*6
INTEGER ILADD(MAXCON),IRADD(MAXCON),RELPG(IDBSIZ),LNBR(IDBSIZ)
INTEGER CLINNO,WINDOW
EXTERNAL CLINNO
SAVE PAD,DASH
DATA PAD,DASH/',','-'/
C
C where are the overlaps?
C
C
C
C if ITYPE is 1 the overlap starts within the reading at JOINT
C else it starts at the left end of the reading at JOINT in the contig
IENDG=1
IENDC=JOINT
C ONLY LOOK AT OVERLAP WHICH IS FROM JOINT FOR LEFT TYPE JOIN
IF(ITYPE.EQ.1)THEN
IENDG=JOINT
IENDC=1
END IF
100 CONTINUE
C LENGTH OF OVERLAP?
LG=IDIM2-IENDG+1
LO=MIN(IDOUT,LG)
C SAVE RAW DATA
CALL SQCOPY(SEQG2,SEQ3,IDIM2)
CALL MSTLKL(SEQ3,IDIM2)
X=FLOAT(LO)
Y=X
K=IENDG+LO-1
C POINT TO CONSENSUS
J=0
C CHECK FOR OVERFLOW
IF(K.GT.MAXGEL)THEN
WRITE(KBOUT,1001)
1001 FORMAT(
+' Matching region too long for routine dalign. Alignment aborted')
IFAIL=1
RETURN
END IF
DO 200 I=IENDG,K
J=J+1
IF(SEQC2(J).EQ.SEQ3(I))GO TO 200
C IF(SEQ3(I).EQ.DASH)GO TO 200
C IF(SEQC2(J).EQ.DASH)GO TO 200
C IF(SEQC2(J).EQ.PAD)GO TO 200
X=X-1.
200 CONTINUE
X=(Y-X)*100./Y
IF(X.LT.PERMAX) THEN
IC = CLINNO(LNBR,IDBSIZ,NCONTS,JCONN)
IF(IC.EQ.0) THEN
IFAIL = 99
RETURN
END IF
IF(JSENSE.EQ.-1) THEN
STRAND = '-'
IF(IEND.EQ.1) THEN
C
C probe is complement of right hand end of contig. Give posns assuming
C this contig is complemented.
C
IENDGT = IENDG - IRADD(JCON)
C
C Next line gives posns relative to original orientation
C IENDGT = RELPG(IC) + IRADD(JCON) - IENDG + 1
ELSE
C
C probe is complement of left end of contig. Give posns assuming this
C contig is going to be complemented.
C
IENDGT = RELPG(IC) - WINDOW + ILADD(JCON) + IENDG
END IF
ELSE
STRAND = '+'
IF(IEND.EQ.2) THEN
C
C probe is left hand end of contig in original sense
C
IENDGT = IENDG - ILADD(JCON)
ELSE
C
C probe is right hand end of contig in original sense
C
IENDGT = RELPG(IC) + IRADD(JCON) - WINDOW + IENDG
END IF
END IF
IENDCT = IENDC - ILADD(MCON)
WRITE(KBOUT,*)
+ ' Possible join between contig ',JCONN,' in the ',
+ STRAND,' sense and contig ',NCON
WRITE(KBOUT,1000)X
1000 FORMAT(' Percentage mismatch after alignment = ',F4.1)
WRITE(NAME1,1002)JCONN
WRITE(NAME2,1002)NCON
1002 FORMAT(I6)
CALL FMT4LP(SEQC2(1),SEQG2(IENDG),LO,IENDCT,IENDGT,KBOUT,
+ NAME2,NAME1)
END IF
IFAIL=0
END
SUBROUTINE ADISM5(IDIM,IDIMG,SAVPS,SAVPG,IDSAV,
+CENDS,NENDS,IDCEND,MAXCON,ILEFTS,ILC,IPOSC,IPOSG,ISENSE,
+LLINO,IMATC,ISTRAN,MAXC,KBOUT,MCON)
C AUTHOR: RODGER STADEN
INTEGER ILEFTS(MAXC),ILC(MAXC),IPOSC(MAXC),IPOSG(MAXC)
INTEGER ISENSE(MAXC),LLINO(MAXC),MCON(MAXC)
INTEGER CENDS(MAXCON)
INTEGER NENDS(MAXCON)
INTEGER SAVPS(IDSAV),SAVPG(IDSAV)
NEXTC=IDIM+1
CALL BUB2AS(SAVPS,SAVPG,IDSAV)
IMATC=IMATC+1
CALL ADISM6(SAVPS(1),SAVPG(1),CENDS,NENDS,IDCEND,MAXCON,
+ ILEFTS,ILC,IPOSC,IPOSG,ISENSE,LLINO,IMATC,ISTRAN,NEXTC,MAXC,
+ KBOUT,MCON)
LEND=IDIMG-SAVPG(1)+SAVPS(1)
DO 10 I=2,IDSAV
IF((SAVPS(I).LT.LEND).AND.(SAVPS(I).LT.NEXTC))GO TO 10
IMATC=IMATC+1
CALL ADISM6(SAVPS(I),SAVPG(I),CENDS,NENDS,IDCEND,MAXCON,
+ ILEFTS,ILC,IPOSC,IPOSG,ISENSE,LLINO,IMATC,ISTRAN,NEXTC,MAXC,
+ KBOUT,MCON)
LEND=IDIMG-SAVPG(I)+SAVPS(I)
10 CONTINUE
IMATC = MIN(IMATC,MAXC)
END
SUBROUTINE ADISM6(ISAVPS,SAVPG,CENDS,NENDS,
+IDCEND,MAXCON,ILEFTS,ILC,IPOSC,IPOSG,ISENSE,LLINO,IMATC,ISTRAN,
+NEXTC,MAXC,KBOUT,MCON)
C AUTHOR: RODGER STADEN
INTEGER ILEFTS(MAXC),ILC(MAXC),IPOSC(MAXC),IPOSG(MAXC)
INTEGER ISENSE(MAXC),LLINO(MAXC),MCON(MAXC)
INTEGER SAVPS,SAVPG,CENDS(MAXCON)
INTEGER NENDS(MAXCON)
SAVPS=ISAVPS-19
JJ=1
DO 5 J=2,IDCEND
IF(SAVPS.GT.CENDS(J))GO TO 5
JJ=J-1
GO TO 6
5 CONTINUE
JJ=IDCEND
6 CONTINUE
C new bit need to save contig number for alinej
SAVPS=SAVPS-1
LCL=SAVPS-CENDS(JJ)
LCR=CENDS(JJ+1)-ISAVPS-1
NEXTC=CENDS(JJ+1)+20
IF(IMATC.LE.MAXC) THEN
MCON(IMATC) = JJ
ILEFTS(IMATC)=CENDS(JJ)+20
ILC(IMATC)=LCL+LCR+1
IPOSC(IMATC)=LCL+1
IPOSG(IMATC)=SAVPG
LLINO(IMATC)=NENDS(JJ)
ISENSE(IMATC)=1
IF(ISTRAN.EQ.2)ISENSE(IMATC)=-1
ELSE
CALL ERROM(KBOUT,'Warning: too many overlaps')
END IF
END
C JCONS
SUBROUTINE JCONS(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
+SEQ1,IDIM1,GEL,IDBSIZ,ISTART,ANS,LLINO,LREG,RREG,TEMP,
+CHRSIZ,MAXGL2,KBOUT,
+IDEVW,IFAIL,MAXGEL,IDM,PERCD,TGEL,ILADD,IRADD,MAXCON,
+IWIN,NBAD)
C AUTHOR: RODGER STADEN
INTEGER RELPG(IDBSIZ),ANS,CHRSIZ,ILADD(MAXCON),IRADD(MAXCON)
INTEGER LREG,RREG,X,Y,TEMP(CHRSIZ,MAXGL2)
CHARACTER SEQ1(IDIM1)
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
CHARACTER GEL(MAXGEL),TGEL(MAXGEL)
CHARACTER NAMPRO*(*)
CALL BUSY(KBOUT)
C IF(IWIN.GT.0) PERC = REAL(NBAD)/REAL(IWIN)
IEND = 1
IFAIL=0
N=IDBSIZ-NCONTS
NCONS = 0
DO 110 I=N,IDBSIZ-1
J=LNBR(I)
X=1
Y=RELPG(I)
ISTART=ISTART+1
IF((ISTART+19+Y+2*MAXGEL).GT.IDIM1)THEN
WRITE(KBOUT,1009)IDIM1
1009 FORMAT(
+ ' Maximum consensus length(',I6,') exceeded',/,
+ ' calculation aborted')
IFAIL=1
RETURN
END IF
CALL ADDTIT(SEQ1(ISTART),NAMPRO,J,ISTART)
NCONS = NCONS + 1
IDIN = 0
IF(IWIN.GT.0) THEN
IDIN = MAXGEL
CALL GETEX(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,I,1,
+ GEL,TGEL,IDIN,IWIN,NBAD)
IF(IDIN.GT.0)CALL SQCOPY(GEL,SEQ1(ISTART),IDIN)
END IF
ILADD(NCONS) = IDIN
ISTART = ISTART + IDIN
CALL SUMMER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
+ SEQ1(ISTART),Y,GEL,X,Y,J,IDBSIZ,TEMP,CHRSIZ,MAXGL2,IDEVW,MAXGEL,
+ IDM,PERCD)
ISTART=ISTART+Y-1
IDIN = 0
IF(IWIN.GT.0) THEN
IDIN = MAXGEL
CALL GETEX(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,I,2,
+ GEL,TGEL,IDIN,IWIN,NBAD)
IF(IDIN.GT.0)CALL SQCOPY(GEL,SEQ1(ISTART+1),IDIN)
END IF
IRADD(NCONS) = IDIN
ISTART = ISTART + IDIN
110 CONTINUE
END
SUBROUTINE GETEX(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,ICONT,IEND,
+GEL,GELT,ID,IWIN,NBAD)
INTEGER LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ),RELPG(IDBSIZ)
CHARACTER GEL(ID),GELT(ID)
EXTERNAL NOK2
MAXGEL = ID
IDT = 0
C routine to find a possible extension to a contig by looking in a tag file
C contig ICONT end IEND = 1 =left 2=right
C return data in GEL, of length ID
C The worst aspect of this is that if we dont choose the very end reading
C we dont know where it lies relative to the consensus. For now just assume
C there are no length difference between the extension and the consensus
C and just add it on the end
IF(IEND.EQ.1) THEN
LMOST = 1
IGEL = LNBR(ICONT)
10 CONTINUE
IF(IGEL.EQ.0) GO TO 100
IF(RELPG(IGEL).GT.MAXGEL) GO TO 100
IF(LNGTHG(IGEL).LT.0) THEN
ID = MAXGEL
CALL GETEXT(IGEL,GELT,ID,IOK)
IF(IOK.EQ.0) THEN
C look for number of n's here and change id accordingly
K = NOK2(GELT,ID,IWIN,NBAD)
LT = MIN(LMOST,RELPG(IGEL)-K)
IF(LT.LT.LMOST) THEN
IS = RELPG(IGEL)
N = K - IS + 1
CALL SQCOPY(GELT(IS),GEL,N)
CALL SQREV(GEL,N)
CALL SQCOM(GEL,N)
IDT = N
LMOST = LT
END IF
ELSE
C WRITE(*,*)'COCKUP IN GETEXT, gel',IGEL
END IF
END IF
IGEL = RNBR(IGEL)
GO TO 10
ELSE
IGEL = RNBR(ICONT)
LMOST = RELPG(ICONT)
IDC = RELPG(ICONT)
20 CONTINUE
IF(IGEL.EQ.0) GO TO 100
IF(LMOST-RELPG(IGEL).GT.MAXGEL) GO TO 100
IF(LNGTHG(IGEL).GT.0) THEN
ID = MAXGEL
CALL GETEXT(IGEL,GELT,ID,IOK)
IF(IOK.EQ.0) THEN
K = NOK2(GELT,ID,IWIN,NBAD)
LT = MAX(LMOST,RELPG(IGEL)+LNGTHG(IGEL)+K-1)
IF(LT.GT.LMOST) THEN
IS = RELPG(ICONT) - (RELPG(IGEL) + LNGTHG(IGEL)) + 2
N = K - IS + 1
CALL SQCOPY(GELT(IS),GEL,N)
IDT = N
LMOST = LT
END IF
ELSE
C WRITE(*,*)'COCKUP IN GETEXT, GEL',IGEL
END IF
END IF
IGEL = LNBR(IGEL)
GO TO 20
END IF
100 CONTINUE
ID = IDT
END
INTEGER FUNCTION NOK2(GEL,ID,IWIN,NBADIN)
CHARACTER GEL(ID)
PARAMETER (MAXPOS = 101)
INTEGER POSNS(MAXPOS),R
EXTERNAL KWRAP
C count N's over a window of iwin, return position
C when over NBAD
C INIT
NBAD = NBADIN + 1
I = 0
N = 0
NOK2 = ID
L = 1
R = 0
IF(NBAD.GT.MAXPOS)THEN
WRITE(*,*)'Scream: nok2 not happy'
RETURN
END IF
10 CONTINUE
I = I + 1
IF(I.GT.ID) RETURN
IF(GEL(I).EQ.'-') THEN
N = N + 1
R = KWRAP(R,NBAD)
POSNS(R) = I
IF(N.GE.NBAD) THEN
IF(POSNS(R)-POSNS(L)+1.LT.IWIN) THEN
NOK2 = POSNS(L)
RETURN
END IF
L = KWRAP(L,NBAD)
END IF
END IF
GO TO 10
END
INTEGER FUNCTION KWRAP(I,J)
IT = I + 1
IF(IT.GT.J) IT = 1
KWRAP = IT
END
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