229 lines
6.6 KiB
Fortran
229 lines
6.6 KiB
Fortran
INTEGER FUNCTION CONOK(
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+RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
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+SEQ,MAXSEQ,SEQ2,IDBSIZ,TEMP3,
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+ECHRSZ,MAXGL2,KBOUT,IDEVW,IDEV,
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+MAXGEL,IDM,PERCD,CENDS,NENDS,MAXCON)
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INTEGER RELPG(IDBSIZ),LNGTHG(IDBSIZ),LNBR(IDBSIZ),RNBR(IDBSIZ)
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INTEGER ECHRSZ,TEMP3(ECHRSZ,MAXGL2),CENDS(MAXCON),NENDS(MAXCON)
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CHARACTER SEQ(MAXSEQ),SEQ2(MAXGEL),NAMPRO*(*)
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EXTERNAL NOK2
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CONOK = 0
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JOB = 0
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IDIM1 = 0
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CALL ACONSN(RELPG,LNGTHG,LNBR,RNBR,NAMPRO,NGELS,NCONTS,
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+SEQ,MAXSEQ,SEQ2,IDBSIZ,IDIM1,JOB,KDUMM,KDUMM,KDUMM,TEMP3,
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+ECHRSZ,MAXGL2,KBOUT,IDEVW,IFAIL,MAXGEL,IDM,PERCD)
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IF(IFAIL.NE.0) THEN
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CALL ERROM(KBOUT,'Error calculating consensus')
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CONOK = -1
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RETURN
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END IF
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CALL FNDCON(SEQ,IDIM1,CENDS,NENDS,IDCEND,MAXCON,KBOUT)
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IWIN = 20
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NBAD = 15
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DO 10 I=1,IDCEND
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J = CENDS(I) + 20
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IDIM = CENDS(I+1) - J
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K = NOK2(SEQ(J),IDIM,IWIN,NBAD)
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IF (K.LT.IDIM) THEN
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WRITE(IDEV,*)'Problem at position',K,' In contig',NENDS(I)
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CONOK = CONOK + 1
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END IF
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10 CONTINUE
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IF (CONOK.EQ.0) THEN
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WRITE(KBOUT,*)
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+' Consensus has no segments with',NBAD,' dashes in',IWIN
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ELSE
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WRITE(KBOUT,*)
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+ CONOK,' contigs have segments with',NBAD,' dashes in',IWIN
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END IF
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END
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SUBROUTINE DBMENU(MENU,NOPT,KOPT,MAXOPT,
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+IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
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CHARACTER HELPF*(*)
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INTEGER IHELPS(0:MAXOPT),IHELPE(0:MAXOPT)
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1 CONTINUE
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IF(MENU.EQ.0) THEN
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WRITE(KBOUT,5000)
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5000 FORMAT(' Menus and their numbers are',/,
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+ ' m0 = This menu',/,
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+ ' m1 = General',/,
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+ ' m2 = Screen control',/,
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+ ' m3 = Modification',/,
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+ ' ? = Help',/,
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+ ' ! = Quit')
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ELSE IF(MENU.EQ.-1) THEN
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WRITE(KBOUT,1001)
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1001 FORMAT(' General menu',/,
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+' 0 = List of menus',/,
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+' ? = Help',/,
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+' ! = Quit',/,
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+' 3 = Open a database',/,
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+' 5 = Display a contig',/,
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+' 6 = List a text file',/,
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+' 7 = Redirect output',/,
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+' 8 = Calculate a consensus',/,
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+' 17 = Screen against restriction enzymes',/,
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+' 18 = Screen against vector',/,
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+' 19 = Check database',/,
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+' 24 = Copy database',/,
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+' 25 = Show relationships',/,
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+' 27 = Set parameters',/,
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+' 28 = Highlight disagreements',/,
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+' 29 = Examine quality',/,
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+' 35 = Find internal joins')
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ELSE IF(MENU.EQ.-2) THEN
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WRITE(KBOUT,1002)
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1002 FORMAT(' Screen control menu',/,
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+' 0 = List of menus',/,
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+' ? = Help',/,
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+' ! = Quit',/,
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+' 10 = Clear graphics',/,
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+' 11 = Clear text',/,
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+' 12 = Draw ruler',/,
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+' 13 = Use cross hair',/,
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+' 14 = Change margins',/,
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+' 15 = Label diagram',/,
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+' 16 = Plot map',/,
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+' 33 = Plot single contig',/,
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+' 34 = Plot all contigs')
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ELSE IF(MENU.EQ.-3) THEN
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WRITE(KBOUT,1003)
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1003 FORMAT(' Modification menu',/,
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+' 0 = List of menus',/,
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+' ? = Help',/,
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+' ! = Quit',/,
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+' 4 = Edit contig',/,
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+' 9 = Screen edit',/,
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+' 20 = Auto assemble',/,
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+' 21 = Enter new gel reading',/,
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+' 22 = Join contigs',/,
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+' 23 = Complement a contig',/,
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+' 26 = Alter relationships',/,
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+' 30 = Auto edit a contig',/,
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+' 31 = Disassemble readings',/,
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+' 32 = Extract gel readings')
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END IF
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WRITE(KBOUT,1010)
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CALL GETOPT(KBIN,KOPT,NOPT)
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IF((NOPT.LT.-3).OR.(NOPT.GT.MAXOPT).OR.(KOPT.GT.2)) THEN
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MENU = 0
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GO TO 1
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END IF
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IF((KOPT.EQ.2).AND.(NOPT.GE.0))THEN
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CALL HELP2(IHELPS(NOPT),IHELPE(NOPT),HELPF,IDEVH,KBIN,KBOUT)
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GO TO 1
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END IF
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IF(NOPT.EQ.0) THEN
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MENU = 0
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GO TO 1
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END IF
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IF(NOPT.LT.0) THEN
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MENU = NOPT
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GO TO 1
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END IF
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1010 FORMAT(
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+' ? Option number=',$)
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RETURN
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END
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SUBROUTINE DBMENT(MENU,NOPT,KOPT,IHELPS,IHELPE,HELPF,IDEVH,
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+KBIN,KBOUT)
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CHARACTER HELPF*(*)
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INTEGER IHELPS,IHELPE
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1 CONTINUE
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IF(MENU.EQ.2)THEN
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20 CONTINUE
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CALL BPAUSE(KBIN,KBOUT,IOK)
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WRITE(KBOUT,1002)
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1002 FORMAT( ' Enter menu options are:',/,
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+' ? = Help',/,
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+' ! = Give up',/,
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+' 3 = Complete entry',/,
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+' 4 = Edit contig',/,
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+' 5 = Display',/,
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+' 6 = Edit new gel reading')
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WRITE(KBOUT,1010)
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CALL GETOPT(KBIN,KOPT,NOPT)
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MAXOPT = 6
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IF((NOPT.LT.0).OR.(NOPT.GT.MAXOPT).OR.(KOPT.GT.2)) THEN
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GO TO 20
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END IF
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IF((KOPT.EQ.2).AND.(NOPT.GE.0))THEN
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CALL HELP2(IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
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GO TO 20
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END IF
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ELSE IF(MENU.EQ.3)THEN
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30 CONTINUE
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CALL BPAUSE(KBIN,KBOUT,IOK)
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WRITE(KBOUT,1003)
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1003 FORMAT( ' Join menu options are:'/
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+' ? = Help',/,
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+' ! = Give up',/,
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+' 3 = Complete join',/,
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+' 4 = Edit left contig',/,
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+' 5 = Display join',/,
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+' 6 = Edit right contig',/,
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+' 7 = Move join')
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WRITE(KBOUT,1010)
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CALL GETOPT(KBIN,KOPT,NOPT)
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MAXOPT = 7
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IF((NOPT.LT.0).OR.(NOPT.GT.MAXOPT).OR.(KOPT.GT.2)) THEN
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GO TO 30
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END IF
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IF((KOPT.EQ.2).AND.(NOPT.GE.0))THEN
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CALL HELP2(IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
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GO TO 30
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END IF
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ELSE IF(MENU.EQ.4)THEN
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40 CONTINUE
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CALL BPAUSE(KBIN,KBOUT,IOK)
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WRITE(KBOUT,1004)
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1004 FORMAT(' Alter relationships menu options are:'/
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+' ? = Help',/,
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+' ! = Quit',/,
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+' 3 = Line change',/,
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+' 4 = Check logical consistency',/,
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+' 5 = Remove a contig',/,
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+' 6 = Shift',/,
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+' 7 = Move gel reading',/,
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+' 8 = Rename gel reading',/,
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+' 9 = Break a contig',/,
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+' 10 = Remove a gel reading')
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WRITE(KBOUT,1010)
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CALL GETOPT(KBIN,KOPT,NOPT)
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MAXOPT = 10
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IF((NOPT.LT.0).OR.(NOPT.GT.MAXOPT).OR.(KOPT.GT.2)) THEN
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GO TO 40
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END IF
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IF((KOPT.EQ.2).AND.(NOPT.GE.0))THEN
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CALL HELP2(IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
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GO TO 40
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END IF
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ELSE IF(MENU.EQ.5)THEN
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50 CONTINUE
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CALL BPAUSE(KBIN,KBOUT,IOK)
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WRITE(KBOUT,1005)
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1005 FORMAT(
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+' Edit options are:',/,
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+' ? = Help',/,
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+' ! = Quit',/,
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+' 3 = Insert',/,
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+' 4 = Delete',/,
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+' 5 = Change')
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WRITE(KBOUT,1010)
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CALL GETOPT(KBIN,KOPT,NOPT)
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MAXOPT = 5
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IF((NOPT.LT.0).OR.(NOPT.GT.MAXOPT).OR.(KOPT.GT.2)) THEN
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GO TO 50
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END IF
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IF((KOPT.EQ.2).AND.(NOPT.GE.0))THEN
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CALL HELP2(IHELPS,IHELPE,HELPF,IDEVH,KBIN,KBOUT)
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GO TO 50
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END IF
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END IF
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1010 FORMAT(
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+' ? Option number=',$)
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IF(NOPT.LE.0) GO TO 1
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RETURN
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END
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