623 lines
22 KiB
Fortran
623 lines
22 KiB
Fortran
C SAP (Sequence assembly program)
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C AUTHOR RODGER STADEN
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C 9-1-90 sent idev instead of kbout to join and enter
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C 16-3-90 removed escape after bpause
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C 2-5-90 Many changes related to introducing graphics
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C 4-5-90 Allowed escape from getreg
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C 9-5-90 Introduced a default gel reading
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C 23-8-90 Added calls to SHOWFU
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C 28-11-90 See dbsys89
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C 22-1-91 Changed use of showfi to include version number
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C 27-1-91 Changed maxsav from 1000 to maxglm
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C 13-04-91 removed initial CLEARV
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C 28-7-91 added extra parameter for quality calc: mxgood, only the parts
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C of reads upto this length are used
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C 21-8-91 Added function to find internal joins
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C 27-8-91 Added buffer flushing for database files
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SUBROUTINE FMAIN()
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INTEGER CHRSIZ,ECHRSZ
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PARAMETER (
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+ NAMLEN = 40,
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+ MAXDEV = 10,
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+ MAXSEQ=50000,
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+ MAXGLM=4096,
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+ MAXGL2=MAXGLM*2,
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+ MINMEN=-3,
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+ CHRSIZ=4,
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+ ECHRSZ = 6,
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+ IDT1=ECHRSZ*MAXGL2,
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+ IDT2=2*CHRSIZ*MAXGL2,
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+ IDT3=2*MAXGL2,
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+ IDT4=2*ECHRSZ*MAXGL2,
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+ MAXDB=1000)
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INTEGER BOTOPT,TOPOPT,DEVNOS(MAXDEV)
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INTEGER RELPG(MAXDB),LREG,RREG,ANS
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INTEGER TEMP1(IDT1),TEMP2(IDT2),TEMP3(IDT4)
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INTEGER LNGTHG(MAXDB),LNBR(MAXDB),RNBR(MAXDB)
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CHARACTER*(NAMLEN) HELPF,POINTF,FILNAM,NAMPRO,FILE,NAMARC,FILMAR
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CHARACTER*(NAMLEN) SHONAM
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CHARACTER GEL(MAXGLM)
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CHARACTER GEL2(MAXGLM),GEL3(MAXGLM),GEL4(MAXGLM)
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PARAMETER (BOTOPT=0,TOPOPT=35)
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PARAMETER (HELPF='SAPHELP')
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PARAMETER (POINTF='SAPHPNT')
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PARAMETER (FILMAR='SAPMARG')
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INTEGER HELPS(BOTOPT:TOPOPT),HELPE(BOTOPT:TOPOPT)
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INTEGER MARGB(TOPOPT),MARGT(TOPOPT)
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CHARACTER SEQ1(MAXSEQ)
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C DBAUTO TEMP3A = TEMP1, SEQ3A = GEL3, SEQ2A = GEL2
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C MATCHA = GEL, SEQ4A = GEL4
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PARAMETER (LENGTH = 6,
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+ MAXCON = 500,
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+ MAXSAV = MAXGLM,
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+ LPOWRC = CHRSIZ**LENGTH)
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INTEGER CONST(LENGTH)
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INTEGER POSNS(MAXSEQ),WORDP(LPOWRC),WORDN(LPOWRC),GELN(MAXGLM)
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INTEGER CENDS(MAXCON),NENDS(MAXCON)
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CHARACTER SEQC2(MAXGLM,2),SEQG2(MAXGLM,2)
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CHARACTER SEQ5(MAXGLM),SEQG3(MAXGLM),SEQC3(MAXGLM)
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INTEGER SAV1(MAXSAV),SAV2(MAXSAV),SAV3(MAXSAV)
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INTEGER WINDOW
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C DBAUTO
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EQUIVALENCE (TEMP2,TEMP1)
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EQUIVALENCE (TEMP1,TEMP3)
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IDM = 5
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CALL INITS
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CALL INITLU(IDM)
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CALL INTHLP('sap', TOPOPT)
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CALL UNITNO(KBIN,KBOUT,DEVNOS,MAXDEV)
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CALL OPENGR(DEVNOS(10))
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WRITE(KBOUT,1000)
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1000 FORMAT(
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+' SAP (Sequence assembly program) V5.0 Aug 1991',/,
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+' Author: Rodger Staden')
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IGORT = 0
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IDEV = KBOUT
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C GET SCREEN AND MARGIN SIZES
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CALL GETMRG(ISXMAX,ISYMAX,MARGL,MARGR,MARGB,MARGT,
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+TOPOPT,DEVNOS(5),FILMAR)
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CALL SETHLP(HELPS,HELPE,BOTOPT,TOPOPT,POINTF,DEVNOS(5),KBOUT)
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CALL INITGR(KBIN,KBOUT,HELPS(0),HELPE(0),HELPF,IDEVH)
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IOPEN=1
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LINLEN=50
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PERCD=0.75
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WINDOW = 25
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MXGOOD = MAXGLM
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IGWIND = 1000
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FILE = ' '
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MAXGEL = MAXGLM
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SHONAM = ' '
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CALL SHOWFI(KBOUT,SHONAM)
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ANS = 0
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CALL YESONO(ANS,'Open existing database','Start new database',
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+ HELPS(3),HELPE(3),HELPF,DEVNOS(5),KBIN,KBOUT)
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IF(ANS.LT.0)GO TO 10
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IF(ANS.GT.1)GO TO 10
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MAXGEL = MAXGLM
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IF(IOPEN.EQ.0)THEN
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CLOSE(UNIT=DEVNOS(1))
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CLOSE(UNIT=DEVNOS(2))
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CLOSE(UNIT=DEVNOS(3))
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IOPEN=1
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END IF
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IDBSIZ=MAXDB
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IDBSIS=IDBSIZ
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IF(ANS.EQ.1)THEN
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C CALL SHOWFU(KBOUT,'Start new database')
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CALL DBSTAR(NAMPRO,GEL,IDBSIS,IDBSIZ,KBIN,KBOUT,DEVNOS(1),
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+ DEVNOS(2),DEVNOS(3),IERR,HELPS(NOPT),HELPE(NOPT),
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+ DEVNOS(5),HELPF,MAXGEL,MAXGLM,IDM)
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NGELS=0
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NCONTS=0
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LLINO = 0
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IF(IERR.EQ.0) THEN
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IOPEN=0
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SHONAM = NAMPRO(1:MAX(1,INDEX(NAMPRO,'.'))+1)
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CALL SHOWFI(KBOUT,SHONAM)
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END IF
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CALL INITLU(IDM)
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GO TO 10
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END IF
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IF(ANS.EQ.0)THEN
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C CALL SHOWFU(KBOUT,'Open database')
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NGELS=0
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NCONTS=0
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CALL DBOPEN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,NAMPRO,GEL,
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+ IDBSIS,IDBSIZ,JERR,KBIN,KBOUT,DEVNOS(1),DEVNOS(2),DEVNOS(3),
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+ MAXGEL,MAXGLM,LLINO,IDM,
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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IF(JERR.EQ.0)IOPEN=0
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IF(NGELS.GT.0)CALL DBSTAT(RELPG,LNGTHG,LNBR,RNBR,NGELS,
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+ NCONTS,IDBSIZ,KBOUT)
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CALL INITLU(IDM)
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SHONAM = NAMPRO(1:MAX(1,INDEX(NAMPRO,'.'))+1)
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CALL SHOWFI(KBOUT,SHONAM)
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GO TO 10
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END IF
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MENUN = 0
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10 CONTINUE
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C
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C Flush the database buffers, just in case!
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C
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CALL FLUSHL(DEVNOS(1))
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CALL FLUSHL(DEVNOS(2))
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CALL FLUSHL(DEVNOS(3))
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CALL BPAUSE(KBIN,KBOUT,IOK)
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C CALL SHOWFU(KBOUT,' ')
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C IF(IOK.NE.0) GO TO 9999
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C CALL DBMENT(MENU,NOPT,TOPOPT,HELPS(0),HELPE(0),HELPF,DEVNOS(5),
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C +KBIN,KBOUT)
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CALL MENU(NOPT, KOPT, MENUN, TOPOPT, MINMEN, KBIN, KBOUT,
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+ HELPS(0), HELPE(0), HELPF, DEVNOS(5))
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IF(NOPT.EQ.3)THEN
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ANS = 0
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CALL YESONO(ANS,'Open existing database','Start new database',
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+ HELPS(3),HELPE(3),HELPF,DEVNOS(5),KBIN,KBOUT)
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IF(ANS.LT.0)GO TO 10
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IF(ANS.GT.1)GO TO 10
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MAXGEL = MAXGLM
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IF(IOPEN.EQ.0)THEN
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CLOSE(UNIT=DEVNOS(1))
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CLOSE(UNIT=DEVNOS(2))
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CLOSE(UNIT=DEVNOS(3))
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IOPEN=1
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END IF
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IDBSIZ=MAXDB
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IDBSIS=IDBSIZ
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IF(ANS.EQ.1)THEN
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C CALL SHOWFU(KBOUT,'Start a database')
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CALL DBSTAR(NAMPRO,GEL,IDBSIS,IDBSIZ,KBIN,KBOUT,DEVNOS(1),
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+ DEVNOS(2),DEVNOS(3),IERR,HELPS(NOPT),HELPE(NOPT),
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+ DEVNOS(5),HELPF,MAXGEL,MAXGLM,IDM)
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NGELS=0
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NCONTS=0
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IF(IERR.EQ.0)IOPEN=0
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CALL INITLU(IDM)
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SHONAM = NAMPRO(1:MAX(1,INDEX(NAMPRO,'.'))+1)
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CALL SHOWFI(KBOUT,SHONAM)
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GO TO 10
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END IF
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IF(ANS.EQ.0)THEN
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C CALL SHOWFU(KBOUT,'Open database')
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NGELS=0
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NCONTS=0
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CALL DBOPEN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,NAMPRO,GEL,
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+ IDBSIS,IDBSIZ,JERR,KBIN,KBOUT,DEVNOS(1),DEVNOS(2),DEVNOS(3),
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+ MAXGEL,MAXGLM,LLINO,IDM,
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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IF(JERR.EQ.0)IOPEN=0
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IF(NGELS.GT.0)CALL DBSTAT(RELPG,LNGTHG,LNBR,RNBR,NGELS,
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+ NCONTS,IDBSIZ,KBOUT)
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CALL INITLU(IDM)
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SHONAM = NAMPRO(1:MAX(1,INDEX(NAMPRO,'.'))+1)
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CALL SHOWFI(KBOUT,SHONAM)
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GO TO 10
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END IF
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END IF
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C STOP
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IF(NOPT.EQ.2)THEN
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IF(NGELS.GT.0)CALL DBSTAT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ IDBSIZ,KBOUT)
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GO TO 9999
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END IF
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C clear all
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C
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IF(NOPT.EQ.10)THEN
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C CALL SHOWFU(KBOUT,'Clear graphics')
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CALL CLEARG
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GO TO 10
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END IF
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C clear VT100
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C
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IF(NOPT.EQ.11)THEN
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C CALL SHOWFU(KBOUT,'Clear text')
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CALL CLEARV
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GO TO 10
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END IF
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C
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C xhairs
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C
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IF(NOPT.EQ.13) THEN
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C CALL SHOWFU(KBOUT,'Use xhair')
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CALL XHSAP(RELPG,LNGTHG,LNBR,RNBR,
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+ IDBSIZ,NCONTS,LLINO,LINCON,LREG,RREG,
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+ WINDOW,IGWIND,LENCON,IDEPTH,JDEPTH,
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+ MARGL,MARGR,MARGB,MARGT,TOPOPT,ISXMAX,ISYMAX,KBIN,IDEV,
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+ KBOUT,GEL,GEL2,DEVNOS(2),DEVNOS(3),LINLEN,PERCD,MAXGEL,IDM,
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+ SEQ1,MAXSEQ,NGELS,TEMP3,ECHRSZ,MAXGL2,GEL3,GEL4,33,34,29,
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),MXGOOD)
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GO TO 10
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END IF
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C
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C CHANGE MARGINS
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C
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IF(NOPT.EQ.14)THEN
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C CALL SHOWFU(KBOUT,'Change margins')
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CALL MARGC(ISXMAX,ISYMAX,MARGL,MARGR,MARGB,MARGT,
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+ HELPS(NOPT),HELPE(NOPT),TOPOPT,HELPF,DEVNOS(5),KBIN,KBOUT)
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GO TO 10
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END IF
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C ruler
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C
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IF(NOPT.EQ.12) THEN
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LENCON = RREG - LREG + 1
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IF(LENCON.GT.0) THEN
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C CALL SHOWFU(KBOUT,'Show ruler')
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CALL RULER(LREG,RREG,MARGL,MARGR,
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+ MARGB(NOPT),MARGT(NOPT),ISXMAX,ISYMAX,KBIN,KBOUT,1,
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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GO TO 10
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END IF
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END IF
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C labler
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IF(NOPT.EQ.15)THEN
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C CALL SHOWFU(KBOUT,'Label diagram')
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CALL LABLER(KBIN,KBOUT,ISXMAX,ISYMAX,
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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GO TO 10
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END IF
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IF(NOPT.EQ.16) THEN
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C CALL SHOWFU(KBOUT,'Plot map')
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C map
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LENCON = RREG - LREG + 1
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IF(LENCON.GT.0) THEN
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CALL PLTMAP(DEVNOS(4),FILNAM,LENCON,MARGL,MARGR,MARGB(NOPT),
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+ MARGT(NOPT),ISXMAX,ISYMAX,LREG,RREG,KBIN,KBOUT,
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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END IF
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GO TO 10
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END IF
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IF((NOPT.EQ.21).AND.(IOPEN.EQ.0))THEN
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C CALL SHOWFU(KBOUT,'Enter new gel reading')
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C ENTER
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CALL ENTER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ GEL,GEL2,IDBSIZ,IDEV,KBIN,KBOUT,DEVNOS(1),DEVNOS(2),
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+ DEVNOS(3),DEVNOS(4),LINLEN,PERCD,FILNAM,
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+ HELPS(NOPT),HELPE(NOPT),HELPS(4),HELPE(4),HELPF,DEVNOS(5),
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+ MAXGEL,IDM,LLINO)
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GO TO 10
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END IF
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IF((NOPT.EQ.25).AND.(IOPEN.EQ.0))THEN
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C CALL SHOWFU(KBOUT,'Show relationships')
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C PRINT DB
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CALL DBPRNT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,IDEV,
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+ KBIN,KBOUT,DEVNOS(3),LLINO,
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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GO TO 10
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END IF
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IF((NOPT.EQ.5).AND.(IOPEN.EQ.0))THEN
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C CALL SHOWFU(KBOUT,'Display contig')
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C DISPLAY
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CALL GETLN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON,
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+ LLINO,IERR,IDBSIZ,KBIN,KBOUT,DEVNOS(3),
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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IF(IERR.EQ.0)THEN
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CALL GETREG(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ 1,RELPG(LINCON),LREG,RREG,LINCON,LLINO,IDBSIZ,KBIN,KBOUT,
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),IERR)
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IF(IERR.EQ.0)THEN
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CALL DSPLAY(RELPG,LNGTHG,LNBR,RNBR,
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+ GEL,LLINO,LINCON,LREG,RREG,GEL2,I1,I2,0,I,IDBSIZ,IDEV,KBOUT,
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+ DEVNOS(2),DEVNOS(3),LINLEN,PERCD,MAXGEL,IDM)
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END IF
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END IF
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GO TO 10
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END IF
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200 CONTINUE
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IF((NOPT.EQ.22).AND.(IOPEN.EQ.0))THEN
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C CALL SHOWFU(KBOUT,'Join contigs')
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C JOIN
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WRITE(KBOUT,1006)
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1006 FORMAT(' Which contigs do you want to join ?')
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WRITE(KBOUT,1017)
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1017 FORMAT( ' Left contig')
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LLINOL = 0
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LLINOR = 0
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CALL GETLN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LNCONL,LLINOL,
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+ IERR,IDBSIZ,KBIN,KBOUT,DEVNOS(3),
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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IF(IERR.EQ.0)THEN
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WRITE(KBOUT,1018)
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1018 FORMAT( ' Right contig')
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CALL GETLN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ LNCONR,LLINOR,IERR,IDBSIZ,KBIN,KBOUT,DEVNOS(3),
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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IF(IERR.EQ.0)THEN
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C CHECK TO SEE IF MAKING A CIRCLE!
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IF(LLINOL.EQ.LLINOR)THEN
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WRITE(KBOUT,*)' Making circles is not allowed!'
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GO TO 200
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END IF
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CALL JOIN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ LNCONL,LLINOL,LNCONR,LLINOR,GEL,GEL2,
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+ IDBSIZ,IDEV,KBIN,KBOUT,DEVNOS(1),DEVNOS(2),
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+ DEVNOS(3),LINLEN,PERCD,
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+ HELPS(NOPT),HELPE(NOPT),HELPS(4),HELPE(4),HELPF,DEVNOS(5),
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+ MAXGEL,IDM)
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END IF
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END IF
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GO TO 10
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END IF
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IF((NOPT.EQ.23).AND.(IOPEN.EQ.0))THEN
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C CALL SHOWFU(KBOUT,'Complement contig')
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C COMPLEMENT
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CALL GETLN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ LINCON,LLINO,IERR,IDBSIZ,KBIN,KBOUT,DEVNOS(3),
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
|
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IF(IERR.EQ.0)THEN
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CALL CMPLMT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ LINCON,LLINO,GEL,IDBSIZ,KBOUT,DEVNOS(1),DEVNOS(2),
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+ MAXGEL)
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END IF
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GO TO 10
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END IF
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C EDIT
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IF((NOPT.EQ.4).AND.(IOPEN.EQ.0))THEN
|
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C EDIT DB
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CALL GETLN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON,
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+ LLINO,IERR,IDBSIZ,KBIN,KBOUT,DEVNOS(3),
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
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IF(IERR.EQ.0)THEN
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CALL DBEDIT(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ GEL,LINCON,0,0,IDBSIZ,KBIN,KBOUT,DEVNOS(1),DEVNOS(2),
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),MAXGEL)
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END IF
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GO TO 10
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END IF
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C PLOT SINGLE CONTIG
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IF((NOPT.EQ.33).AND.(IOPEN.EQ.0))THEN
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CALL GETLN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON,
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+ LLINO,IERR,IDBSIZ,KBIN,KBOUT,DEVNOS(3),
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
|
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IF(IERR.EQ.0)THEN
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CALL GETREG(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ 1,RELPG(LINCON),LREG,RREG,LINCON,LLINO,IDBSIZ,KBIN,KBOUT,
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+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),IERR)
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IF(IERR.EQ.0)THEN
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LENCON = RREG - LREG + 1
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CALL FDEPTH(RELPG,LNGTHG,LNBR,RNBR,
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+ IDBSIZ,LLINO,LREG,RREG,LENCON,
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+ MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),ISXMAX,ISYMAX)
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END IF
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END IF
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GO TO 10
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END IF
|
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IF((NOPT.EQ.26).AND.(IOPEN.EQ.0))THEN
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C CALL SHOWFU(KBOUT,'Alter relationships')
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C FIX
|
|
CALL DBFIX(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
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+ GEL,GEL2,IDBSIZ,KBIN,KBOUT,DEVNOS(1),DEVNOS(2),DEVNOS(3),
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+ HELPS(NOPT),HELPE(NOPT),
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+ HELPS(4),HELPE(4),HELPF,DEVNOS(5),MAXGEL)
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GO TO 10
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END IF
|
|
IF((NOPT.EQ.24).AND.(IOPEN.EQ.0))THEN
|
|
C CALL SHOWFU(KBOUT,'Copy database')
|
|
C COPY
|
|
CALL DBCOPY(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,GEL,
|
|
+ NAMPRO,DEVNOS(4),IDBSIZ,JERR,KBIN,KBOUT,DEVNOS(1),
|
|
+ DEVNOS(2),DEVNOS(3),
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),MAXGEL,MAXDB,IDM)
|
|
GO TO 10
|
|
END IF
|
|
IF((NOPT.EQ.19).AND.(IOPEN.EQ.0))THEN
|
|
C CALL SHOWFU(KBOUT,'Check database for consistency')
|
|
C CHECK
|
|
CALL DBCHEK(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,IDBSIZ,
|
|
+ TEMP1,IERR,KBOUT)
|
|
GO TO 10
|
|
END IF
|
|
IF((NOPT.EQ.29).AND.(IOPEN.EQ.0))THEN
|
|
C CALL SHOWFU(KBOUT,'Examine quality')
|
|
C SCAN
|
|
IDIM1=MAXSEQ
|
|
CALL DBSCAN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,SEQ1,
|
|
+ IDIM1,GEL,IDBSIZ,TEMP3,2,ECHRSZ,MAXGL2,
|
|
+ KBIN,KBOUT,DEVNOS(2),IDEV,LINLEN,PERCD,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),MAXGEL,GEL3,GEL4,
|
|
+ MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),ISXMAX,ISYMAX,DEVNOS(3),
|
|
+ LLINO,LINCON,LREG,RREG,MXGOOD)
|
|
GO TO 10
|
|
END IF
|
|
IF((NOPT.EQ.8).AND.(IOPEN.EQ.0))THEN
|
|
C CALL SHOWFU(KBOUT,'Make consensus')
|
|
C CONSENSUS
|
|
IDIM1=MAXSEQ
|
|
CALL CONSEN(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,SEQ1,
|
|
+ IDIM1,GEL,IDBSIZ,TEMP1,ECHRSZ,MAXGL2,
|
|
+ KBIN,KBOUT,DEVNOS(2),DEVNOS(4),FILNAM,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),MAXGEL,IDM,PERCD,
|
|
+ DEVNOS(3),LLINO)
|
|
CLOSE(UNIT=DEVNOS(4))
|
|
GO TO 10
|
|
END IF
|
|
IF(NOPT.EQ.7)THEN
|
|
C CALL SHOWFU(KBOUT,'Redirect output')
|
|
CALL REDIR(IDEV,DEVNOS(6),DEVNOS(10),IGORT,FILNAM,KBIN,KBOUT,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),KOPT)
|
|
GO TO 10
|
|
END IF
|
|
C HELP
|
|
IF(NOPT.EQ.1)THEN
|
|
C CALL SHOWFU(KBOUT,'Help')
|
|
C HELP
|
|
CALL HELP(HELPS,HELPE,BOTOPT,TOPOPT,
|
|
+ HELPF,DEVNOS(5),KBIN,KBOUT)
|
|
GO TO 10
|
|
END IF
|
|
IF(NOPT.EQ.27)THEN
|
|
C CALL SHOWFU(KBOUT,'Set parameters')
|
|
C SET DISPLAY PARAMETERS
|
|
MN = 10
|
|
MX = 100
|
|
CALL GETINT(MN,MX,LINLEN,'Display line length',
|
|
+ IVAL,KBIN,KBOUT,HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),IOK)
|
|
IF(IOK.EQ.0) LINLEN = IVAL
|
|
IPCMIN = 51
|
|
IPCMAX = 100
|
|
IPCD = INT(PERCD*100.)
|
|
CALL GETINT(IPCMIN,IPCMAX,IPCD,
|
|
+ 'Percentage score for consensus',
|
|
+ IPVAL,KBIN,KBOUT,HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),IOK)
|
|
IF(IOK.EQ.0) THEN
|
|
PERCD = REAL(IPVAL)/100.
|
|
END IF
|
|
MN = 1
|
|
MX = MAXGLM
|
|
CALL GETINT(MN,MX,MXGOOD,
|
|
+ 'Maximum read length for quality analysis',
|
|
+ IVAL,KBIN,KBOUT,HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),IOK)
|
|
IF(IOK.EQ.0) MXGOOD = IVAL
|
|
MN = 1
|
|
MX = MAXSEQ
|
|
CALL GETINT(MN,MX,WINDOW,'Text window length',
|
|
+ IVAL,KBIN,KBOUT,HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),IOK)
|
|
IF(IOK.EQ.0) WINDOW = IVAL
|
|
MN = 1
|
|
MX = MAXSEQ
|
|
CALL GETINT(MN,MX,IGWIND,'Graphics window length',
|
|
+ IVAL,KBIN,KBOUT,HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),IOK)
|
|
IF(IOK.EQ.0) IGWIND = IVAL
|
|
GO TO 10
|
|
END IF
|
|
IF(NOPT.EQ.6)THEN
|
|
C CALL SHOWFU(KBOUT,'Display text file')
|
|
CALL TTEXT(DEVNOS(4),FILNAM,KBIN,KBOUT,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
|
|
CLOSE(UNIT=DEVNOS(4))
|
|
GO TO 10
|
|
END IF
|
|
IF(NOPT.EQ.28) THEN
|
|
C CALL SHOWFU(KBOUT,'Highlight disagreements')
|
|
CALL HIGHLT(SEQ1,SEQ1(6001),SEQ1(10001),KBIN,KBOUT,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),DEVNOS(7),
|
|
+ DEVNOS(8),FILE,IOK)
|
|
CLOSE(UNIT=DEVNOS(7))
|
|
CLOSE(UNIT=DEVNOS(8))
|
|
GO TO 10
|
|
END IF
|
|
IF((NOPT.EQ.34).AND.(IOPEN.EQ.0))THEN
|
|
C CALL SHOWFU(KBOUT,'Plot contigs')
|
|
C PLOT ALL CONTIGS
|
|
CALL PLC(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,0,0,
|
|
+ NCONTS,MARGL,MARGR,MARGB(NOPT),MARGT(NOPT),ISXMAX,ISYMAX)
|
|
GO TO 10
|
|
END IF
|
|
C AUTO EDIT
|
|
IF((NOPT.EQ.30).AND.(IOPEN.EQ.0))THEN
|
|
C CALL SHOWFU(KBOUT,'AutoEdit a contig')
|
|
WRITE(KBOUT,*)'Make a copy first!'
|
|
CALL GETLN(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,LINCON,
|
|
+ LLINO,IERR,IDBSIZ,KBIN,KBOUT,DEVNOS(3),
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
|
|
IF(IERR.EQ.0)THEN
|
|
CALL GETREG(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,
|
|
+ 1,RELPG(LINCON),LREG,RREG,LINCON,LLINO,IDBSIZ,KBIN,KBOUT,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),IERR)
|
|
IF(IERR.EQ.0) THEN
|
|
IDIM1=MAXSEQ
|
|
CALL SUMMER(RELPG,LNGTHG,LNBR,RNBR,NGELS,NCONTS,SEQ1,IDIM1,
|
|
+ GEL,LREG,RREG,LLINO,IDBSIZ,TEMP1,ECHRSZ,MAXGL2,
|
|
+ DEVNOS(2),MAXGEL,IDM,PERCD)
|
|
CALL AEDIT(RELPG,LNGTHG,LNBR,RNBR,IDBSIZ,LLINO,LINCON,
|
|
+ GEL,MAXGEL,SEQ1,IDIM1,DEVNOS(2),DEVNOS(1),LREG,RREG,
|
|
+ KBOUT)
|
|
END IF
|
|
END IF
|
|
GO TO 10
|
|
END IF
|
|
IF((NOPT.EQ.9).AND.(IOPEN.EQ.0)) THEN
|
|
C CALL SHOWFU(KBOUT,'Screen Edit a contig')
|
|
CALL CEDT(KBIN,KBOUT,
|
|
+ POSNS(1),POSNS(1001),POSNS(2001),
|
|
+ MAXDB,POSNS(3001),POSNS(3101),50,
|
|
+ RELPG,LNGTHG,LNBR,RNBR,
|
|
+ IDBSIZ,NGELS,NCONTS,GEL,GEL2,MAXGEL,LINCON,PERCD,IDM,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),DEVNOS(4),
|
|
+ DEVNOS(1),DEVNOS(2),DEVNOS(3),LINLEN,FILNAM,LLINO,IOK)
|
|
GO TO 10
|
|
END IF
|
|
IF(NOPT.EQ.17) THEN
|
|
C CALL SHOWFU(KBOUT,'Screen for restriction sites')
|
|
CALL SCRENR(GEL2,MAXGEL,GEL3,NAMARC,FILE,
|
|
+ DEVNOS(4),DEVNOS(7),DEVNOS(8),DEVNOS(9),IDEV,KBIN,KBOUT,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
|
|
CLOSE(UNIT=DEVNOS(4))
|
|
CLOSE(UNIT=DEVNOS(7))
|
|
CLOSE(UNIT=DEVNOS(8))
|
|
CLOSE(UNIT=DEVNOS(9))
|
|
GO TO 10
|
|
END IF
|
|
IF(NOPT.EQ.18) THEN
|
|
C CALL SHOWFU(KBOUT,'Screen against vector')
|
|
CALL SCRENV(MAXGEL,WORDP,WORDN,LPOWRC,POSNS,GELN,
|
|
+ SEQ1,MAXSEQ,GEL2,GEL3,GEL4,LENGTH,
|
|
+ SAV1,SAV2,SAV3,MAXSAV,CENDS,NENDS,MAXCON,CONST,
|
|
+ KBIN,KBOUT,DEVNOS(4),DEVNOS(7),DEVNOS(8),DEVNOS(9),IDEV,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),NAMARC,FILE,IOK)
|
|
CLOSE(UNIT=DEVNOS(4))
|
|
CLOSE(UNIT=DEVNOS(7))
|
|
CLOSE(UNIT=DEVNOS(8))
|
|
CLOSE(UNIT=DEVNOS(9))
|
|
GO TO 10
|
|
END IF
|
|
IF((NOPT.EQ.20).AND.(IOPEN.EQ.0)) THEN
|
|
C CALL SHOWFU(KBOUT,'Auto assemble sequences')
|
|
CALL DBAUTO(RELPG,LNGTHG,LNBR,RNBR,MAXDB,IDBSIZ,
|
|
+NGELS,NCONTS,MAXGEL,
|
|
+TEMP1,WORDP,WORDN,LPOWRC,POSNS,GELN,
|
|
+SEQ1,MAXSEQ,GEL2,GEL3,GEL4,SEQ5,SEQC2,SEQG2,GEL,
|
|
+MAXGLM,MAXGL2,CHRSIZ,ECHRSZ,LENGTH,
|
|
+SAV1,SAV2,SAV3,MAXSAV,CENDS,NENDS,MAXCON,CONST,
|
|
+KBIN,KBOUT,DEVNOS(1),DEVNOS(2),DEVNOS(3),
|
|
+DEVNOS(4),DEVNOS(7),DEVNOS(8),IDEV,
|
|
+HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),NAMARC,NAMPRO,FILE,
|
|
+PERCD,IOPEN,IDM,SEQG3,SEQC3,IOK)
|
|
CLOSE(UNIT=DEVNOS(4))
|
|
CLOSE(UNIT=DEVNOS(7))
|
|
CLOSE(UNIT=DEVNOS(8))
|
|
GO TO 10
|
|
END IF
|
|
IF((NOPT.EQ.35).AND.(IOPEN.EQ.0).AND.(IDM.EQ.5)) THEN
|
|
C CALL SHOWFU(KBOUT,'Find internal joins')
|
|
CALL AUTOJ(RELPG,LNGTHG,LNBR,RNBR,MAXDB,IDBSIZ,
|
|
+NGELS,NCONTS,MAXGEL,
|
|
+TEMP1,WORDP,WORDN,LPOWRC,POSNS,GELN,
|
|
+SEQ1,MAXSEQ,GEL2,GEL3,GEL4,SEQ5,SEQC2,SEQG2,GEL,
|
|
+MAXGLM,MAXGL2,CHRSIZ,ECHRSZ,LENGTH,
|
|
+SAV1,SAV2,SAV3,MAXSAV,CENDS,NENDS,MAXCON,CONST,
|
|
+KBIN,KBOUT,DEVNOS(1),DEVNOS(2),DEVNOS(3),
|
|
+DEVNOS(4),DEVNOS(7),DEVNOS(8),IDEV,
|
|
+HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),NAMARC,NAMPRO,FILE,
|
|
+PERCD,IOPEN,IDM,SEQG3,SEQC3,IOK)
|
|
CLOSE(UNIT=DEVNOS(4))
|
|
CLOSE(UNIT=DEVNOS(7))
|
|
CLOSE(UNIT=DEVNOS(8))
|
|
GO TO 10
|
|
END IF
|
|
IF((NOPT.EQ.32).AND.(IOPEN.EQ.0)) THEN
|
|
C CALL SHOWFU(KBOUT,'Extract gel readings')
|
|
CALL GELOUT(RELPG,LNGTHG,LNBR,RNBR,MAXDB,IDBSIZ,NGELS,
|
|
+ NCONTS,GEL,MAXGEL,DEVNOS(2),DEVNOS(3),DEVNOS(4),DEVNOS(7),
|
|
+ KBIN,KBOUT,
|
|
+ HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5),FILE)
|
|
CLOSE(UNIT=DEVNOS(4))
|
|
GO TO 10
|
|
END IF
|
|
IF(NOPT.EQ.31) THEN
|
|
C CALL SHOWFU(KBOUT,'Type in gel readings')
|
|
CALL BATIN(SEQ1,MAXSEQ,KBIN,KBOUT,
|
|
+ DEVNOS(4),DEVNOS(7),IDEV,
|
|
+ FILNAM,HELPS(NOPT),HELPE(NOPT),HELPF,DEVNOS(5))
|
|
GO TO 10
|
|
END IF
|
|
IF((NOPT.GT.3).AND.(IOPEN.NE.0))THEN
|
|
WRITE(KBOUT,1012)
|
|
1012 FORMAT(' You have not opened a database!')
|
|
GO TO 10
|
|
END IF
|
|
GO TO 10
|
|
9999 CONTINUE
|
|
CALL SHUTD
|
|
END
|