152 lines
6.1 KiB
Fortran
152 lines
6.1 KiB
Fortran
C nipmen
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C 9-7-90 Reorganised lists
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SUBROUTINE MENU(OPT,KOPT,MOPT,MAXOPT,MINMEN,KBIN,KBOUT,
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+IHELPS,IHELPE,HELPF,IDEVH)
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C AUTHOR: RODGER STADEN
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INTEGER IHELPS(0:MAXOPT),IHELPE(0:MAXOPT)
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INTEGER OPT
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CHARACTER HELPF*(*)
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1 CONTINUE
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CALL CLEARV
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IF(MOPT.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 = Statistical analysis of content'/
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+' m4 = Structures and repeats'/
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+' m5 = Translation and codons'/
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+' m6 = Gene search by content'/
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+' m7 = General signals'/
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+' m8 = Specific signals'/
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+' ? = Help'/
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+' ! = Quit')
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1001 FORMAT(
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+' ? Menu or option number=',$)
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ELSE IF(MOPT.EQ.-1)THEN
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WRITE(KBOUT,5001)
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5001 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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1 ' 3 = Read a new sequence'/
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1 ' 4 = Define active region'/
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+ ' 5 = List the sequence'/
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+ ' 6 = List a text file'/
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+ ' 7 = Direct output to disk'/
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+ ' 8 = Write active sequence to disk'/
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+ ' 9 = Edit the sequence'/
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+ ' 17 = Search for restriction enzymes'/
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+ ' 29 = Reverse and complement the active sequence'/
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+ ' 66 = Exchange t and u')
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ELSE IF(MOPT.EQ.-2)THEN
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WRITE(KBOUT,5002)
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5002 FORMAT(' Screen control menu'/
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+ ' 0 = List of menus'/
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+ ' 10 = Clear graphics'/
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+ ' 11 = Clear text'/
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+ ' 12 = Draw a ruler'/
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+ ' 13 = Use crosshair'/
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+ ' 14 = Reposition plots'/
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+ ' 15 = Label diagram'/
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+ ' 16 = Display a map')
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ELSE IF(MOPT.EQ.-3)THEN
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WRITE(KBOUT,5005)
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5005 FORMAT(' Statistical analysis of content'/
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+ ' 0 = List of menus'/
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+ ' 21 = Count bases'/
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+ ' 22 = Count dinucleotides'/
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+ ' 24 = Plot base composition'/
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2 ' 25 = Plot local deviations in base composition'/
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3 ' 26 = Plot local deviations in dinucleotide',
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+ ' composition'/
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4 ' 27 = Plot local deviations in trinucleotide',
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+ ' composition'/
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3 ' 38 = Examine repeats'/
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5 ' 59 = Plot negentropy'/
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6 ' 64 = Plot observed-expected word frequencies')
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ELSE IF(MOPT.EQ.-4)THEN
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WRITE(KBOUT,5007)
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5007 FORMAT(' Structures and repeats menu'/
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+ ' 0 = List of menus'/
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5 ' 30 = Search for hairpin loops'/
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1 ' 31 = Search for long range inverted repeats'/
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1 ' 32 = Search for repeats'/
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1 ' 33 = Search for z dna (total ry,yr)'/
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1 ' 34 = Search for z dna (runs of ry or yr)'/
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1 ' 35 = Search for z dna (best phased value)'/
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1 ' 36 = Search for local similarity or complementarity'/
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3 ' 38 = Examine repeats')
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ELSE IF(MOPT.EQ.-5)THEN
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WRITE(KBOUT,5006)
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5006 FORMAT(' Translation and codon menu'/
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+ ' 0 = List of menus'/
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+ ' 23 = Count codons, amino acids and bases',/,
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+ ' 28 = Calculate codon constraint',/,
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+ ' 37 = Set genetic code'/
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1 ' 39 = Translate and list in up to six phases'/
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5 ' 40 = Translate and write protein sequence to disk'/
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5 ' 41 = Write codon table to disk',/,
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+ ' 54 = Search for open reading frames')
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ELSE IF(MOPT.EQ.-6)THEN
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WRITE(KBOUT,5003)
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5003 FORMAT(' Gene search by content'/
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+ ' 0 = List of menus'/
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1 ' 42 = Codon usage method'/
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5 ' 43 = Positional base preferences method'/
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5 ' 44 = Uneven positional base frequencies method'/
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4 ' 45 = Codon improbability on base composition'/
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4 ' 46 = Codon improbability on amino acid composition'/
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2 ' 47 = Shepherd RNY preference method'/
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3 ' 48 = Ficketts method'/
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5 ' 49 = tRNA gene search')
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ELSE IF(MOPT.EQ.-7)THEN
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WRITE(KBOUT,5004)
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5004 FORMAT(' General signals menu'/
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+ ' 0 = List of menus'/
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+ ' 18 = Compare a short sequence'/
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+ ' 19 = Compare a short sequence using a score matrix'/
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+ ' 20 = Search using a weight matrix'/
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1 ' 50 = Plot start codons'/
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2 ' 51 = Plot stop codons'/
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3 ' 52 = Plot stop codons on the complementary strand'/
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3 ' 53 = Plot stop codons on both strands'/
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+ ' 60 = Search using a dinucleotide weight matrix'/
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+ ' 63 = Search the complementary strand using a ',
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+ 'weight matrix'/
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+ ' 67 = Search for patterns of motifs')
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ELSE IF(MOPT.EQ.-8)THEN
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WRITE(KBOUT,5008)
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5008 FORMAT(' Eukaryotic signal search'/
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+ ' 0 = List of menus'/
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3 ' 55 = Search for E. coli promoters'/
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3 ' 56 = Search for E. coli promoters',
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+ ' on the complementary strand'/
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3 ' 57 = Search for E. coli promoters (-35 and -10)'/
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4 ' 58 = Search for prokaryotic ribosome binding sites'/
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5 ' 61 = Search for eukaryotic ribosome binding sites'/
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6 ' 62 = Search for splice junctions'/
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6 ' 65 = Search for polya sites')
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END IF
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3 CONTINUE
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WRITE(KBOUT,1001)
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CALL GETOPT(KBIN,KOPT,OPT)
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IF((OPT.LT.MINMEN).OR.(OPT.GT.MAXOPT).OR.(KOPT.GT.2)) THEN
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MOPT = 0
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GO TO 1
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END IF
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IF((KOPT.EQ.2).AND.(OPT.GE.0))THEN
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CALL HELP2(IHELPS(OPT),IHELPE(OPT),HELPF,IDEVH,KBIN,KBOUT)
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GO TO 1
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END IF
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IF(OPT.EQ.0) THEN
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MOPT = 0
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GO TO 1
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END IF
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IF(OPT.LT.0) THEN
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MOPT = OPT
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GO TO 1
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END IF
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END
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