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R /Kids [315 0 R 472 0 R 748 0 R 907 0 R 1140 0 R 1308 0 R] >> endobj 4299 0 obj << /Type /Pages /Count 36 /Parent 4302 0 R /Kids [1479 0 R 1631 0 R 1747 0 R 1908 0 R 2020 0 R 2123 0 R] >> endobj 4300 0 obj << /Type /Pages /Count 36 /Parent 4302 0 R /Kids [2236 0 R 2302 0 R 2404 0 R 2534 0 R 2639 0 R 2805 0 R] >> endobj 4301 0 obj << /Type /Pages /Count 31 /Parent 4302 0 R /Kids [2920 0 R 3043 0 R 3301 0 R 3631 0 R 3964 0 R 4260 0 R] >> endobj 4302 0 obj << /Type /Pages /Count 139 /Kids [4298 0 R 4299 0 R 4300 0 R 4301 0 R] >> endobj 4303 0 obj << /Type /Outlines /First 7 0 R /Last 279 0 R /Count 69 >> endobj 279 0 obj << /Title 280 0 R /A 277 0 R /Parent 4303 0 R /Prev 275 0 R >> endobj 275 0 obj << /Title 276 0 R /A 273 0 R /Parent 4303 0 R /Prev 271 0 R /Next 279 0 R >> endobj 271 0 obj << /Title 272 0 R /A 269 0 R /Parent 4303 0 R /Prev 267 0 R /Next 275 0 R >> endobj 267 0 obj << /Title 268 0 R /A 265 0 R /Parent 4303 0 R /Prev 263 0 R /Next 271 0 R >> endobj 263 0 obj << /Title 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(Rfn.!=,BString,character.Rdash.method) 1059 0 R (Rfn.!=,XString,XString.Rdash.method) 1061 0 R (Rfn.!=,XString,XStringViews.Rdash.method) 1430 0 R (Rfn.!=,XStringViews,XString.Rdash.method) 1432 0 R (Rfn.!=,XStringViews,XStringViews.Rdash.method) 1433 0 R] /Limits [(Doc-Start) (Rfn.!=,XStringViews,XStringViews.Rdash.method)] >> endobj 4305 0 obj << /Names [(Rfn.!=,XStringViews,character.Rdash.method) 1431 0 R (Rfn.!=,character,BString.Rdash.method) 1060 0 R (Rfn.!=,character,XStringViews.Rdash.method) 1429 0 R (Rfn..Rpcent.in.Rpcent.,XString,XStringSet.Rdash.method) 1194 0 R (Rfn..Rpcent.in.Rpcent.,XStringSet,XStringSet.Rdash.method) 1195 0 R (Rfn..Rpcent.in.Rpcent.,character,XStringSet.Rdash.method) 1193 0 R] /Limits [(Rfn.!=,XStringViews,character.Rdash.method) (Rfn..Rpcent.in.Rpcent.,character,XStringSet.Rdash.method)] >> endobj 4306 0 obj << /Names [(Rfn..inplaceReplaceLetterAt) 2722 0 R (Rfn.==,BString,character.Rdash.method) 1062 0 R (Rfn.==,XString,XString.Rdash.method) 1064 0 R (Rfn.==,XString,XStringViews.Rdash.method) 1435 0 R (Rfn.==,XStringViews,XString.Rdash.method) 1437 0 R (Rfn.==,XStringViews,XStringViews.Rdash.method) 1438 0 R] /Limits [(Rfn..inplaceReplaceLetterAt) (Rfn.==,XStringViews,XStringViews.Rdash.method)] >> endobj 4307 0 obj << /Names [(Rfn.==,XStringViews,character.Rdash.method) 1436 0 R (Rfn.==,character,BString.Rdash.method) 1063 0 R (Rfn.==,character,XStringViews.Rdash.method) 1434 0 R (Rfn.AA.Rul.ALPHABET) 307 0 R (Rfn.AA.Rul.WCP) 964 0 R (Rfn.AA.Rul.WCP.Rdash.class) 965 0 R] /Limits [(Rfn.==,XStringViews,character.Rdash.method) (Rfn.AA.Rul.WCP.Rdash.class)] >> endobj 4308 0 obj << /Names [(Rfn.AAKeySortedData) 1000 0 R (Rfn.AAKeySortedData.Rdash.class) 1001 0 R (Rfn.AAKeySortedDataList) 1028 0 R (Rfn.AAKeySortedDataList.Rdash.class) 1029 0 R (Rfn.AAString) 306 0 R (Rfn.AAString.Rdash.class) 303 0 R] /Limits [(Rfn.AAKeySortedData) (Rfn.AAString.Rdash.class)] >> endobj 4309 0 obj << /Names [(Rfn.AAString.Rdash.class.1) 6 0 R (Rfn.AAStringSet) 911 0 R (Rfn.AAStringSet.Rdash.class) 938 0 R (Rfn.AAStringSetList) 1385 0 R (Rfn.AAStringSetList.Rdash.class) 1386 0 R (Rfn.ACtree2) 664 0 R] /Limits [(Rfn.AAString.Rdash.class.1) (Rfn.ACtree2)] >> endobj 4310 0 obj << /Names [(Rfn.ACtree2.Rdash.class) 665 0 R (Rfn.AMINO.Rul.ACID.Rul.CODE) 318 0 R (Rfn.AMINO.Rul.ACID.Rul.CODE.1) 10 0 R (Rfn.AlignedXStringSet) 336 0 R (Rfn.AlignedXStringSet.Rdash.class) 333 0 R (Rfn.AlignedXStringSet.Rdash.class.1) 14 0 R] /Limits [(Rfn.ACtree2.Rdash.class) (Rfn.AlignedXStringSet.Rdash.class.1)] >> endobj 4311 0 obj << /Names [(Rfn.AlignedXStringSet0) 337 0 R (Rfn.AlignedXStringSet0.Rdash.class) 338 0 R (Rfn.Arithmetic) 1895 0 R (Rfn.B.Rul.WCP) 966 0 R (Rfn.B.Rul.WCP.Rdash.class) 967 0 R (Rfn.BKeySortedData) 1002 0 R] /Limits [(Rfn.AlignedXStringSet0) (Rfn.BKeySortedData)] >> endobj 4312 0 obj << /Names [(Rfn.BKeySortedData.Rdash.class) 1003 0 R (Rfn.BKeySortedDataList) 1030 0 R (Rfn.BKeySortedDataList.Rdash.class) 1031 0 R (Rfn.BLOSUM100) 2905 0 R (Rfn.BLOSUM45) 2906 0 R (Rfn.BLOSUM50) 2907 0 R] /Limits [(Rfn.BKeySortedData.Rdash.class) (Rfn.BLOSUM50)] >> endobj 4313 0 obj << /Names [(Rfn.BLOSUM62) 2908 0 R (Rfn.BLOSUM80) 2909 0 R (Rfn.BOC.Rul.SubjectString) 391 0 R (Rfn.BOC.Rul.SubjectString.Rdash.class) 388 0 R (Rfn.BOC.Rul.SubjectString.Rdash.class.1) 18 0 R (Rfn.BOC2.Rul.SubjectString) 389 0 R] /Limits [(Rfn.BLOSUM62) (Rfn.BOC2.Rul.SubjectString)] >> endobj 4314 0 obj << /Names [(Rfn.BOC2.Rul.SubjectString.Rdash.class) 390 0 R (Rfn.BSgenome) 2706 0 R (Rfn.BSgenome.Rdash.class) 2730 0 R (Rfn.BString) 317 0 R (Rfn.BString.Rdash.class) 1067 0 R (Rfn.BStringSet) 908 0 R] /Limits [(Rfn.BOC2.Rul.SubjectString.Rdash.class) (Rfn.BStringSet)] >> endobj 4315 0 obj << /Names [(Rfn.BStringSet.Rdash.class) 936 0 R (Rfn.BStringSetList) 1387 0 R (Rfn.BStringSetList.Rdash.class) 1388 0 R (Rfn.BStringViews) 1490 0 R (Rfn.BStringViews,ANY.Rdash.method) 1491 0 R (Rfn.BStringViews,XString.Rdash.method) 1493 0 R] /Limits [(Rfn.BStringSet.Rdash.class) (Rfn.BStringViews,XString.Rdash.method)] >> endobj 4316 0 obj << /Names [(Rfn.BStringViews,XStringViews.Rdash.method) 1494 0 R (Rfn.BStringViews,file.Rdash.method) 1492 0 R (Rfn.ByPos.Rul.MIndex.Rdash.class) 513 0 R (Rfn.CharacterToFASTArecords) 1316 0 R (Rfn.CompressedIRangesList) 542 0 R (Rfn.DNA.Rul.ALPHABET) 403 0 R] /Limits [(Rfn.BStringViews,XStringViews.Rdash.method) (Rfn.DNA.Rul.ALPHABET)] >> endobj 4317 0 obj << /Names [(Rfn.DNA.Rul.BASES) 404 0 R (Rfn.DNA.Rul.WCP) 973 0 R (Rfn.DNA.Rul.WCP.Rdash.class) 974 0 R (Rfn.DNAKeySortedData) 1015 0 R (Rfn.DNAKeySortedData.Rdash.class) 1016 0 R (Rfn.DNAKeySortedDataList) 1037 0 R] /Limits [(Rfn.DNA.Rul.BASES) (Rfn.DNAKeySortedDataList)] >> endobj 4318 0 obj << /Names [(Rfn.DNAKeySortedDataList.Rdash.class) 1038 0 R (Rfn.DNAString) 319 0 R (Rfn.DNAString.Rdash.class) 401 0 R (Rfn.DNAString.Rdash.class.1) 22 0 R (Rfn.DNAStringSet) 734 0 R (Rfn.DNAStringSet.Rdash.class) 817 0 R] /Limits [(Rfn.DNAKeySortedDataList.Rdash.class) (Rfn.DNAStringSet.Rdash.class)] >> endobj 4319 0 obj << /Names [(Rfn.DNAStringSetList) 1394 0 R (Rfn.DNAStringSetList.Rdash.class) 1395 0 R (Rfn.DataFrame.Rdash.class) 1047 0 R (Rfn.Dups) 1352 0 R (Rfn.Expanded.Rul.TB.Rul.PDict) 679 0 R (Rfn.Expanded.Rul.TB.Rul.PDict.Rdash.class) 680 0 R] /Limits [(Rfn.DNAStringSetList) (Rfn.Expanded.Rul.TB.Rul.PDict.Rdash.class)] >> endobj 4320 0 obj << /Names [(Rfn.FASTArecordsToBStringViews) 1318 0 R (Rfn.FASTArecordsToCharacter) 1319 0 R (Rfn.FASTArecordsToXStringViews) 1320 0 R (Rfn.GENETIC.Rul.CODE) 367 0 R (Rfn.GENETIC.Rul.CODE.1) 26 0 R (Rfn.Grouping.Rdash.class) 1417 0 R] /Limits [(Rfn.FASTArecordsToBStringViews) (Rfn.Grouping.Rdash.class)] >> endobj 4321 0 obj << /Names [(Rfn.HNF4alpha) 461 0 R (Rfn.HNF4alpha.1) 30 0 R (Rfn.IRanges) 541 0 R (Rfn.IRanges.Rdash.class) 627 0 R (Rfn.IUPAC.Rul.CODE.Rul.MAP) 434 0 R (Rfn.IUPAC.Rul.CODE.Rul.MAP.1) 34 0 R] /Limits [(Rfn.HNF4alpha) (Rfn.IUPAC.Rul.CODE.Rul.MAP.1)] >> endobj 4322 0 obj << /Names [(Rfn.InDel) 491 0 R (Rfn.InDel.Rdash.class) 487 0 R (Rfn.InDel.Rdash.class.1) 38 0 R (Rfn.IntegerList) 1697 0 R (Rfn.MIndex) 524 0 R (Rfn.MIndex.Rdash.class) 512 0 R] /Limits [(Rfn.InDel) (Rfn.MIndex.Rdash.class)] >> endobj 4323 0 obj << /Names [(Rfn.MIndex.Rdash.class.1) 42 0 R (Rfn.MTB.Rul.PDict) 691 0 R (Rfn.MTB.Rul.PDict.Rdash.class) 692 0 R (Rfn.MaskCollection) 629 0 R (Rfn.MaskCollection.Rdash.class) 654 0 R (Rfn.MaskedAAString) 595 0 R] /Limits [(Rfn.MIndex.Rdash.class.1) (Rfn.MaskedAAString)] >> endobj 4324 0 obj << /Names [(Rfn.MaskedAAString.Rdash.class) 596 0 R (Rfn.MaskedBString) 597 0 R (Rfn.MaskedBString.Rdash.class) 598 0 R (Rfn.MaskedDNAString) 599 0 R (Rfn.MaskedDNAString.Rdash.class) 600 0 R (Rfn.MaskedRNAString) 602 0 R] /Limits [(Rfn.MaskedAAString.Rdash.class) (Rfn.MaskedRNAString)] >> endobj 4325 0 obj << /Names [(Rfn.MaskedRNAString.Rdash.class) 603 0 R (Rfn.MaskedXString) 605 0 R (Rfn.MaskedXString.Rdash.class) 569 0 R (Rfn.MaskedXString.Rdash.class.1) 46 0 R (Rfn.N50) 2472 0 R (Rfn.PAM120) 2912 0 R] /Limits [(Rfn.MaskedRNAString.Rdash.class) (Rfn.PAM120)] >> endobj 4326 0 obj << /Names [(Rfn.PAM250) 2913 0 R (Rfn.PAM30) 2914 0 R (Rfn.PAM40) 2915 0 R (Rfn.PAM70) 2916 0 R (Rfn.PDict) 699 0 R (Rfn.PDict,AsIs.Rdash.method) 700 0 R] /Limits [(Rfn.PAM250) (Rfn.PDict,AsIs.Rdash.method)] >> endobj 4327 0 obj << /Names [(Rfn.PDict,DNAStringSet.Rdash.method) 702 0 R (Rfn.PDict,XStringViews.Rdash.method) 704 0 R (Rfn.PDict,character.Rdash.method) 701 0 R (Rfn.PDict,probetable.Rdash.method) 703 0 R (Rfn.PDict.Rdash.class) 626 0 R (Rfn.PDict.Rdash.class.1) 50 0 R] /Limits [(Rfn.PDict,DNAStringSet.Rdash.method) (Rfn.PDict.Rdash.class.1)] >> endobj 4328 0 obj << /Names [(Rfn.PDict3Parts) 705 0 R (Rfn.PDict3Parts.Rdash.class) 706 0 R (Rfn.PWM) 2293 0 R (Rfn.PWM,DNAStringSet.Rdash.method) 2295 0 R (Rfn.PWM,character.Rdash.method) 2294 0 R (Rfn.PWMscore) 2296 0 R] /Limits [(Rfn.PDict3Parts) (Rfn.PWMscore)] >> endobj 4329 0 obj << /Names [(Rfn.PWMscoreStartingAt) 2297 0 R (Rfn.PairwiseAlignedFixedSubject) 787 0 R (Rfn.PairwiseAlignedFixedSubject,XString,XString.Rdash.method) 790 0 R (Rfn.PairwiseAlignedFixedSubject,XStringSet,missing.Rdash.method) 791 0 R (Rfn.PairwiseAlignedFixedSubject,character,character.Rdash.method) 788 0 R (Rfn.PairwiseAlignedFixedSubject,character,missing.Rdash.method) 789 0 R] /Limits [(Rfn.PWMscoreStartingAt) (Rfn.PairwiseAlignedFixedSubject,character,missing.Rdash.method)] >> endobj 4330 0 obj << /Names [(Rfn.PairwiseAlignedFixedSubject.Rdash.class) 792 0 R (Rfn.PairwiseAlignedFixedSubjectSummary) 793 0 R (Rfn.PairwiseAlignedFixedSubjectSummary.Rdash.class) 794 0 R (Rfn.PairwiseAlignedXStringSet) 795 0 R (Rfn.PairwiseAlignedXStringSet,XString,XString.Rdash.method) 798 0 R (Rfn.PairwiseAlignedXStringSet,XStringSet,missing.Rdash.method) 799 0 R] /Limits [(Rfn.PairwiseAlignedFixedSubject.Rdash.class) (Rfn.PairwiseAlignedXStringSet,XStringSet,missing.Rdash.method)] >> endobj 4331 0 obj << /Names [(Rfn.PairwiseAlignedXStringSet,character,character.Rdash.method) 796 0 R (Rfn.PairwiseAlignedXStringSet,character,missing.Rdash.method) 797 0 R (Rfn.PairwiseAlignedXStringSet.Rdash.class) 408 0 R (Rfn.PairwiseAlignedXStringSet.Rdash.class.1) 54 0 R (Rfn.PhredQuality) 1174 0 R (Rfn.PhredQuality.Rdash.class) 1175 0 R] /Limits [(Rfn.PairwiseAlignedXStringSet,character,character.Rdash.method) (Rfn.PhredQuality.Rdash.class)] >> endobj 4332 0 obj << /Names [(Rfn.PreprocessedTB) 707 0 R (Rfn.PreprocessedTB.Rdash.class) 708 0 R (Rfn.QualityAlignedXStringSet) 350 0 R (Rfn.QualityAlignedXStringSet.Rdash.class) 351 0 R (Rfn.QualityScaledAAStringSet) 892 0 R (Rfn.QualityScaledAAStringSet.Rdash.class) 893 0 R] /Limits [(Rfn.PreprocessedTB) (Rfn.QualityScaledAAStringSet.Rdash.class)] >> endobj 4333 0 obj << /Names [(Rfn.QualityScaledBStringSet) 894 0 R (Rfn.QualityScaledBStringSet.Rdash.class) 895 0 R (Rfn.QualityScaledDNAStringSet) 896 0 R (Rfn.QualityScaledDNAStringSet.Rdash.class) 897 0 R (Rfn.QualityScaledRNAStringSet) 898 0 R (Rfn.QualityScaledRNAStringSet.Rdash.class) 899 0 R] /Limits [(Rfn.QualityScaledBStringSet) (Rfn.QualityScaledRNAStringSet.Rdash.class)] >> endobj 4334 0 obj << /Names [(Rfn.QualityScaledXStringSet) 900 0 R (Rfn.QualityScaledXStringSet.Rdash.class) 882 0 R (Rfn.QualityScaledXStringSet.Rdash.class.1) 58 0 R (Rfn.RNA.Rul.ALPHABET) 932 0 R (Rfn.RNA.Rul.BASES) 933 0 R (Rfn.RNA.Rul.GENETIC.Rul.CODE) 431 0 R] /Limits [(Rfn.QualityScaledXStringSet) (Rfn.RNA.Rul.GENETIC.Rul.CODE)] >> endobj 4335 0 obj << /Names [(Rfn.RNA.Rul.WCP) 976 0 R (Rfn.RNA.Rul.WCP.Rdash.class) 977 0 R (Rfn.RNAKeySortedData) 1018 0 R (Rfn.RNAKeySortedData.Rdash.class) 1019 0 R (Rfn.RNAKeySortedDataList) 1039 0 R (Rfn.RNAKeySortedDataList.Rdash.class) 1040 0 R] /Limits [(Rfn.RNA.Rul.WCP) (Rfn.RNAKeySortedDataList.Rdash.class)] >> endobj 4336 0 obj << /Names [(Rfn.RNAString) 320 0 R (Rfn.RNAString.Rdash.class) 435 0 R (Rfn.RNAString.Rdash.class.1) 62 0 R (Rfn.RNAStringSet) 910 0 R (Rfn.RNAStringSet.Rdash.class) 937 0 R (Rfn.RNAStringSetList) 1401 0 R] /Limits [(Rfn.RNAString) (Rfn.RNAStringSetList)] >> endobj 4337 0 obj << /Names [(Rfn.RNAStringSetList.Rdash.class) 1402 0 R (Rfn.Ranges) 544 0 R (Rfn.Ranges.Rdash.utils) 655 0 R (Rfn.RangesList) 543 0 R (Rfn.Rle) 2104 0 R (Rfn.Sequence.Rdash.class) 1418 0 R] /Limits [(Rfn.RNAStringSetList.Rdash.class) (Rfn.Sequence.Rdash.class)] >> endobj 4338 0 obj << /Names [(Rfn.SimpleList.Rdash.class) 1048 0 R (Rfn.SolexaQuality) 1176 0 R (Rfn.SolexaQuality.Rdash.class) 1177 0 R (Rfn.TB.Rul.PDict) 723 0 R (Rfn.TB.Rul.PDict.Rdash.class) 724 0 R (Rfn.Twobit) 725 0 R] /Limits [(Rfn.SimpleList.Rdash.class) (Rfn.Twobit)] >> endobj 4339 0 obj << /Names [(Rfn.Twobit.Rdash.class) 726 0 R (Rfn.Views) 1458 0 R (Rfn.Views,MaskedXString.Rdash.method) 620 0 R (Rfn.Views,PairwiseAlignedFixedSubject.Rdash.method) 812 0 R (Rfn.Views,XString.Rdash.method) 1451 0 R (Rfn.Views,character.Rdash.method) 1450 0 R] /Limits [(Rfn.Twobit.Rdash.class) (Rfn.Views,character.Rdash.method)] >> endobj 4340 0 obj << /Names [(Rfn.Views.Rdash.class) 1480 0 R (Rfn.WCP) 963 0 R (Rfn.WCP.1) 66 0 R (Rfn.WCP.Rdash.class) 979 0 R (Rfn.WCPscoreStartingAt) 2429 0 R (Rfn.XKeySortedData) 999 0 R] /Limits [(Rfn.Views.Rdash.class) (Rfn.XKeySortedData)] >> endobj 4341 0 obj << /Names [(Rfn.XKeySortedData.1) 70 0 R (Rfn.XKeySortedData.Rdash.class) 1020 0 R (Rfn.XKeySortedDataList) 1027 0 R (Rfn.XKeySortedDataList.1) 74 0 R (Rfn.XKeySortedDataList.Rdash.class) 1041 0 R (Rfn.XString) 316 0 R] /Limits [(Rfn.XKeySortedData.1) (Rfn.XString)] >> endobj 4342 0 obj << /Names [(Rfn.XString.Rdash.class) 365 0 R (Rfn.XString.Rdash.class.1) 78 0 R (Rfn.XStringPartialMatches.Rdash.class) 1127 0 R (Rfn.XStringPartialMatches.Rdash.class.1) 82 0 R (Rfn.XStringQuality) 909 0 R (Rfn.XStringQuality.Rdash.class) 939 0 R] /Limits [(Rfn.XString.Rdash.class) (Rfn.XStringQuality.Rdash.class)] >> endobj 4343 0 obj << /Names [(Rfn.XStringQuality.Rdash.class.1) 86 0 R (Rfn.XStringSet) 829 0 R (Rfn.XStringSet.Rdash.class) 409 0 R (Rfn.XStringSet.Rdash.class.1) 90 0 R (Rfn.XStringSet.Rdash.io) 1315 0 R (Rfn.XStringSet.Rdash.io.1) 94 0 R] /Limits [(Rfn.XStringQuality.Rdash.class.1) (Rfn.XStringSet.Rdash.io.1)] >> endobj 4344 0 obj << /Names [(Rfn.XStringSetList) 1407 0 R (Rfn.XStringSetList.Rdash.class) 1303 0 R (Rfn.XStringSetList.Rdash.class.1) 98 0 R (Rfn.XStringSetToFASTArecords) 1332 0 R (Rfn.XStringViews) 545 0 R (Rfn.XStringViews,ANY.Rdash.method) 1495 0 R] /Limits [(Rfn.XStringSetList) (Rfn.XStringViews,ANY.Rdash.method)] >> endobj 4345 0 obj << /Names [(Rfn.XStringViews,XString.Rdash.method) 1496 0 R (Rfn.XStringViews,XStringViews.Rdash.method) 1497 0 R (Rfn.XStringViews.Rdash.class) 628 0 R (Rfn.XStringViews.Rdash.class.1) 102 0 R (Rfn.XStringViews.Rdash.constructors) 1482 0 R (Rfn.XStringViews.Rdash.constructors.1) 106 0 R] /Limits [(Rfn.XStringViews,XString.Rdash.method) (Rfn.XStringViews.Rdash.constructors.1)] >> endobj 4346 0 obj << /Names [(Rfn.XVector) 1275 0 R (Rfn.[,AlignedXStringSet0.Rdash.method) 360 0 R (Rfn.[,PairwiseAlignedXStringSet.Rdash.method) 814 0 R (Rfn.[,QualityScaledXStringSet.Rdash.method) 902 0 R (Rfn.[,XKeySortedData.Rdash.method) 1022 0 R (Rfn.[,XStringPartialMatches.Rdash.method) 1134 0 R] /Limits [(Rfn.XVector) (Rfn.[,XStringPartialMatches.Rdash.method)] >> endobj 4347 0 obj << /Names [(Rfn.[<.Rdash.,AlignedXStringSet0.Rdash.method) 361 0 R (Rfn.[<.Rdash.,PairwiseAlignedXStringSet.Rdash.method) 815 0 R (Rfn.[[,ByPos.Rul.MIndex.Rdash.method) 533 0 R (Rfn.[[,PDict.Rdash.method) 730 0 R (Rfn.[[,XKeySortedData.Rdash.method) 1023 0 R (Rfn.[[,XStringSetList.Rdash.method) 1408 0 R] /Limits [(Rfn.[<.Rdash.,AlignedXStringSet0.Rdash.method) (Rfn.[[,XStringSetList.Rdash.method)] >> endobj 4348 0 obj << /Names [(Rfn.[[<.Rdash.,XStringSetList.Rdash.method) 1409 0 R (Rfn.adjacentViews) 1489 0 R (Rfn.agrep) 2888 0 R (Rfn.align.Rdash.utils) 863 0 R (Rfn.align.Rdash.utils.1) 110 0 R (Rfn.aligned) 334 0 R] /Limits [(Rfn.[[<.Rdash.,XStringSetList.Rdash.method) (Rfn.aligned)] >> endobj 4349 0 obj << /Names [(Rfn.aligned,AlignedXStringSet0.Rdash.method) 335 0 R (Rfn.aligned,PairwiseAlignedFixedSubject.Rdash.method) 772 0 R (Rfn.alphabet) 630 0 R (Rfn.alphabet,ANY.Rdash.method) 1065 0 R (Rfn.alphabetFrequency) 366 0 R (Rfn.alphabetFrequency,DNAString.Rdash.method) 1840 0 R] /Limits [(Rfn.aligned,AlignedXStringSet0.Rdash.method) (Rfn.alphabetFrequency,DNAString.Rdash.method)] >> endobj 4350 0 obj << /Names [(Rfn.alphabetFrequency,DNAStringSet.Rdash.method) 1841 0 R (Rfn.alphabetFrequency,MaskedXString.Rdash.method) 1842 0 R (Rfn.alphabetFrequency,RNAString.Rdash.method) 1843 0 R (Rfn.alphabetFrequency,RNAStringSet.Rdash.method) 1844 0 R (Rfn.alphabetFrequency,XString.Rdash.method) 1845 0 R (Rfn.alphabetFrequency,XStringSet.Rdash.method) 1846 0 R] /Limits [(Rfn.alphabetFrequency,DNAStringSet.Rdash.method) (Rfn.alphabetFrequency,XStringSet.Rdash.method)] >> endobj 4351 0 obj << /Names [(Rfn.alphabetFrequency,XStringViews.Rdash.method) 1847 0 R (Rfn.append,QualityScaledXStringSet,QualityScaledXStringSet.Rdash.method) 883 0 R (Rfn.as.character,AlignedXStringSet0.Rdash.method) 339 0 R (Rfn.as.character,MaskedXString.Rdash.method) 570 0 R (Rfn.as.character,PairwiseAlignedFixedSubject.Rdash.method) 773 0 R (Rfn.as.character,XString.Rdash.method) 1066 0 R] /Limits [(Rfn.alphabetFrequency,XStringViews.Rdash.method) (Rfn.as.character,XString.Rdash.method)] >> endobj 4352 0 obj << /Names [(Rfn.as.character,XStringSet.Rdash.method) 1196 0 R (Rfn.as.character,XStringViews.Rdash.method) 1439 0 R (Rfn.as.complex,DNAString.Rdash.method) 2951 0 R (Rfn.as.integer,PhredQuality.Rdash.method) 1153 0 R (Rfn.as.integer,SolexaQuality.Rdash.method) 1154 0 R (Rfn.as.list,MTB.Rul.PDict.Rdash.method) 666 0 R] /Limits [(Rfn.as.character,XStringSet.Rdash.method) (Rfn.as.list,MTB.Rul.PDict.Rdash.method)] >> endobj 4353 0 obj << /Names [(Rfn.as.matrix,PairwiseAlignedFixedSubject.Rdash.method) 774 0 R (Rfn.as.matrix,XStringSet.Rdash.method) 1197 0 R (Rfn.as.matrix,XStringViews.Rdash.method) 1440 0 R (Rfn.as.numeric,PhredQuality.Rdash.method) 1155 0 R (Rfn.as.numeric,SolexaQuality.Rdash.method) 1156 0 R (Rfn.basecontent) 1575 0 R] /Limits [(Rfn.as.matrix,PairwiseAlignedFixedSubject.Rdash.method) (Rfn.basecontent)] >> endobj 4354 0 obj << /Names [(Rfn.basecontent.1) 114 0 R (Rfn.c) 1894 0 R (Rfn.cDNA) 2983 0 R (Rfn.cat) 1351 0 R (Rfn.ceiling) 3044 0 R (Rfn.chartr) 1609 0 R] /Limits [(Rfn.basecontent.1) (Rfn.chartr)] >> endobj 4355 0 obj << /Names [(Rfn.chartr,ANY,ANY,MaskedXString.Rdash.method) 1610 0 R (Rfn.chartr,ANY,ANY,XString.Rdash.method) 1611 0 R (Rfn.chartr,ANY,ANY,XStringSet.Rdash.method) 1612 0 R (Rfn.chartr,ANY,ANY,XStringViews.Rdash.method) 1613 0 R (Rfn.chartr.1) 118 0 R (Rfn.chisq.test) 1679 0 R] /Limits [(Rfn.chartr,ANY,ANY,MaskedXString.Rdash.method) (Rfn.chisq.test)] >> endobj 4356 0 obj << /Names [(Rfn.class:AA.Rul.WCP) 968 0 R (Rfn.class:AAKeySortedData) 1004 0 R (Rfn.class:AAKeySortedDataList) 1032 0 R (Rfn.class:AAString) 308 0 R (Rfn.class:AAStringSet) 1198 0 R (Rfn.class:AAStringSetList) 1389 0 R] /Limits [(Rfn.class:AA.Rul.WCP) (Rfn.class:AAStringSetList)] >> endobj 4357 0 obj << /Names [(Rfn.class:ACtree2) 667 0 R (Rfn.class:AlignedXStringSet) 340 0 R (Rfn.class:AlignedXStringSet0) 341 0 R (Rfn.class:B.Rul.WCP) 969 0 R (Rfn.class:BKeySortedData) 1005 0 R (Rfn.class:BKeySortedDataList) 1033 0 R] /Limits [(Rfn.class:ACtree2) (Rfn.class:BKeySortedDataList)] >> endobj 4358 0 obj << /Names [(Rfn.class:BOC.Rul.SubjectString) 393 0 R (Rfn.class:BOC2.Rul.SubjectString) 392 0 R (Rfn.class:BString) 1068 0 R (Rfn.class:BStringSet) 1199 0 R (Rfn.class:BStringSetList) 1390 0 R (Rfn.class:ByPos.Rul.MIndex) 514 0 R] /Limits [(Rfn.class:BOC.Rul.SubjectString) (Rfn.class:ByPos.Rul.MIndex)] >> endobj 4359 0 obj << /Names [(Rfn.class:DNA.Rul.WCP) 970 0 R (Rfn.class:DNAKeySortedData) 1006 0 R (Rfn.class:DNAKeySortedDataList) 1034 0 R (Rfn.class:DNAString) 402 0 R (Rfn.class:DNAStringSet) 1200 0 R (Rfn.class:DNAStringSetList) 1391 0 R] /Limits [(Rfn.class:DNA.Rul.WCP) (Rfn.class:DNAStringSetList)] >> endobj 4360 0 obj << /Names [(Rfn.class:Expanded.Rul.TB.Rul.PDict) 668 0 R (Rfn.class:InDel) 488 0 R (Rfn.class:MIndex) 515 0 R (Rfn.class:MTB.Rul.PDict) 669 0 R (Rfn.class:MaskedAAString) 571 0 R (Rfn.class:MaskedBString) 572 0 R] /Limits [(Rfn.class:Expanded.Rul.TB.Rul.PDict) (Rfn.class:MaskedBString)] >> endobj 4361 0 obj << /Names [(Rfn.class:MaskedDNAString) 573 0 R (Rfn.class:MaskedRNAString) 574 0 R (Rfn.class:MaskedXString) 575 0 R (Rfn.class:PDict) 670 0 R (Rfn.class:PDict3Parts) 671 0 R (Rfn.class:PairwiseAlignedFixedSubject) 775 0 R] /Limits [(Rfn.class:MaskedDNAString) (Rfn.class:PairwiseAlignedFixedSubject)] >> endobj 4362 0 obj << /Names [(Rfn.class:PairwiseAlignedFixedSubjectSummary) 776 0 R (Rfn.class:PairwiseAlignedXStringSet) 777 0 R (Rfn.class:PhredQuality) 1157 0 R (Rfn.class:PreprocessedTB) 672 0 R (Rfn.class:QualityAlignedXStringSet) 342 0 R (Rfn.class:QualityScaledAAStringSet) 884 0 R] /Limits [(Rfn.class:PairwiseAlignedFixedSubjectSummary) (Rfn.class:QualityScaledAAStringSet)] >> endobj 4363 0 obj << /Names [(Rfn.class:QualityScaledBStringSet) 885 0 R (Rfn.class:QualityScaledDNAStringSet) 886 0 R (Rfn.class:QualityScaledRNAStringSet) 887 0 R (Rfn.class:QualityScaledXStringSet) 888 0 R (Rfn.class:RNA.Rul.WCP) 971 0 R (Rfn.class:RNAKeySortedData) 1007 0 R] /Limits [(Rfn.class:QualityScaledBStringSet) (Rfn.class:RNAKeySortedData)] >> endobj 4364 0 obj << /Names [(Rfn.class:RNAKeySortedDataList) 1035 0 R (Rfn.class:RNAString) 931 0 R (Rfn.class:RNAStringSet) 1201 0 R (Rfn.class:RNAStringSetList) 1392 0 R (Rfn.class:SolexaQuality) 1158 0 R (Rfn.class:TB.Rul.PDict) 673 0 R] /Limits [(Rfn.class:RNAKeySortedDataList) (Rfn.class:TB.Rul.PDict)] >> endobj 4365 0 obj << /Names [(Rfn.class:Twobit) 674 0 R (Rfn.class:WCP) 972 0 R (Rfn.class:XKeySortedData) 1008 0 R (Rfn.class:XKeySortedDataList) 1036 0 R (Rfn.class:XString) 1069 0 R (Rfn.class:XStringPartialMatches) 1128 0 R] /Limits [(Rfn.class:Twobit) (Rfn.class:XStringPartialMatches)] >> endobj 4366 0 obj << /Names [(Rfn.class:XStringQuality) 1159 0 R (Rfn.class:XStringSet) 1202 0 R (Rfn.class:XStringSetList) 1393 0 R (Rfn.class:XStringViews) 1441 0 R (Rfn.codons) 2984 0 R (Rfn.codons,DNAString.Rdash.method) 2985 0 R] /Limits [(Rfn.class:XStringQuality) (Rfn.codons,DNAString.Rdash.method)] >> endobj 4367 0 obj << /Names [(Rfn.codons,MaskedDNAString.Rdash.method) 2986 0 R (Rfn.codons,MaskedRNAString.Rdash.method) 2987 0 R (Rfn.codons,RNAString.Rdash.method) 2988 0 R (Rfn.coerce,AAString,MaskedAAString.Rdash.method) 576 0 R (Rfn.coerce,BString,MaskedBString.Rdash.method) 577 0 R (Rfn.coerce,BString,PhredQuality.Rdash.method) 1160 0 R] /Limits [(Rfn.codons,MaskedDNAString.Rdash.method) (Rfn.coerce,BString,PhredQuality.Rdash.method)] >> endobj 4368 0 obj << /Names [(Rfn.coerce,BString,SolexaQuality.Rdash.method) 1161 0 R (Rfn.coerce,BStringSet,PhredQuality.Rdash.method) 1162 0 R (Rfn.coerce,BStringSet,SolexaQuality.Rdash.method) 1163 0 R (Rfn.coerce,DNAString,MaskedDNAString.Rdash.method) 578 0 R (Rfn.coerce,MIndex,CompressedIRangesList.Rdash.method) 516 0 R (Rfn.coerce,MaskedAAString,AAString.Rdash.method) 579 0 R] /Limits [(Rfn.coerce,BString,SolexaQuality.Rdash.method) (Rfn.coerce,MaskedAAString,AAString.Rdash.method)] >> endobj 4369 0 obj << /Names [(Rfn.coerce,MaskedBString,BString.Rdash.method) 580 0 R (Rfn.coerce,MaskedDNAString,DNAString.Rdash.method) 581 0 R (Rfn.coerce,MaskedRNAString,RNAString.Rdash.method) 582 0 R (Rfn.coerce,MaskedXString,MaskCollection.Rdash.method) 583 0 R (Rfn.coerce,MaskedXString,MaskedAAString.Rdash.method) 584 0 R (Rfn.coerce,MaskedXString,MaskedBString.Rdash.method) 585 0 R] /Limits [(Rfn.coerce,MaskedBString,BString.Rdash.method) (Rfn.coerce,MaskedXString,MaskedBString.Rdash.method)] >> endobj 4370 0 obj << /Names [(Rfn.coerce,MaskedXString,MaskedDNAString.Rdash.method) 586 0 R (Rfn.coerce,MaskedXString,MaskedRNAString.Rdash.method) 587 0 R (Rfn.coerce,MaskedXString,NormalIRanges.Rdash.method) 588 0 R (Rfn.coerce,MaskedXString,Views.Rdash.method) 589 0 R (Rfn.coerce,MaskedXString,XStringViews.Rdash.method) 590 0 R (Rfn.coerce,PhredQuality,integer.Rdash.method) 1170 0 R] /Limits [(Rfn.coerce,MaskedXString,MaskedDNAString.Rdash.method) (Rfn.coerce,PhredQuality,integer.Rdash.method)] >> endobj 4371 0 obj << /Names [(Rfn.coerce,PhredQuality,numeric.Rdash.method) 1171 0 R (Rfn.coerce,RNAString,MaskedRNAString.Rdash.method) 591 0 R (Rfn.coerce,SolexaQuality,integer.Rdash.method) 1172 0 R (Rfn.coerce,SolexaQuality,numeric.Rdash.method) 1173 0 R (Rfn.coerce,XString,AAString.Rdash.method) 1075 0 R (Rfn.coerce,XString,AAStringSet.Rdash.method) 1208 0 R] /Limits [(Rfn.coerce,PhredQuality,numeric.Rdash.method) (Rfn.coerce,XString,AAStringSet.Rdash.method)] >> endobj 4372 0 obj << /Names [(Rfn.coerce,XString,BString.Rdash.method) 1076 0 R (Rfn.coerce,XString,BStringSet.Rdash.method) 1209 0 R (Rfn.coerce,XString,DNAString.Rdash.method) 1077 0 R (Rfn.coerce,XString,DNAStringSet.Rdash.method) 1210 0 R (Rfn.coerce,XString,RNAString.Rdash.method) 1078 0 R (Rfn.coerce,XString,RNAStringSet.Rdash.method) 1211 0 R] /Limits [(Rfn.coerce,XString,BString.Rdash.method) (Rfn.coerce,XString,RNAStringSet.Rdash.method)] >> endobj 4373 0 obj << /Names [(Rfn.coerce,XString,XStringSet.Rdash.method) 1212 0 R (Rfn.coerce,XStringSet,AAStringSet.Rdash.method) 1213 0 R (Rfn.coerce,XStringSet,BStringSet.Rdash.method) 1214 0 R (Rfn.coerce,XStringSet,DNAStringSet.Rdash.method) 1215 0 R (Rfn.coerce,XStringSet,RNAStringSet.Rdash.method) 1216 0 R (Rfn.coerce,XStringViews,AAStringSet.Rdash.method) 1442 0 R] /Limits [(Rfn.coerce,XString,XStringSet.Rdash.method) (Rfn.coerce,XStringViews,AAStringSet.Rdash.method)] >> endobj 4374 0 obj << /Names [(Rfn.coerce,XStringViews,BStringSet.Rdash.method) 1443 0 R (Rfn.coerce,XStringViews,DNAStringSet.Rdash.method) 1444 0 R (Rfn.coerce,XStringViews,RNAStringSet.Rdash.method) 1445 0 R (Rfn.coerce,XStringViews,XStringSet.Rdash.method) 1446 0 R (Rfn.coerce,character,AAString.Rdash.method) 1070 0 R (Rfn.coerce,character,AAStringSet.Rdash.method) 1203 0 R] /Limits [(Rfn.coerce,XStringViews,BStringSet.Rdash.method) (Rfn.coerce,character,AAStringSet.Rdash.method)] >> endobj 4375 0 obj << /Names [(Rfn.coerce,character,BString.Rdash.method) 1071 0 R (Rfn.coerce,character,BStringSet.Rdash.method) 1204 0 R (Rfn.coerce,character,DNAString.Rdash.method) 1072 0 R (Rfn.coerce,character,DNAStringSet.Rdash.method) 1205 0 R (Rfn.coerce,character,PhredQuality.Rdash.method) 1164 0 R (Rfn.coerce,character,RNAString.Rdash.method) 1073 0 R] /Limits [(Rfn.coerce,character,BString.Rdash.method) (Rfn.coerce,character,RNAString.Rdash.method)] >> endobj 4376 0 obj << /Names [(Rfn.coerce,character,RNAStringSet.Rdash.method) 1206 0 R (Rfn.coerce,character,SolexaQuality.Rdash.method) 1165 0 R (Rfn.coerce,character,XString.Rdash.method) 1074 0 R (Rfn.coerce,character,XStringSet.Rdash.method) 1207 0 R (Rfn.coerce,integer,PhredQuality.Rdash.method) 1166 0 R (Rfn.coerce,integer,SolexaQuality.Rdash.method) 1167 0 R] /Limits [(Rfn.coerce,character,RNAStringSet.Rdash.method) (Rfn.coerce,integer,SolexaQuality.Rdash.method)] >> endobj 4377 0 obj << /Names [(Rfn.coerce,numeric,PhredQuality.Rdash.method) 1168 0 R (Rfn.coerce,numeric,SolexaQuality.Rdash.method) 1169 0 R (Rfn.collapse,MaskedXString.Rdash.method) 592 0 R (Rfn.compact) 1217 0 R (Rfn.compact,XStringSet.Rdash.method) 1218 0 R (Rfn.compareStrings) 1514 0 R] /Limits [(Rfn.coerce,numeric,PhredQuality.Rdash.method) (Rfn.compareStrings)] >> endobj 4378 0 obj << /Names [(Rfn.compareStrings,AlignedXStringSet0,AlignedXStringSet0.Rdash.method) 1515 0 R (Rfn.compareStrings,PairwiseAlignedXStringSet,missing.Rdash.method) 1517 0 R (Rfn.compareStrings,XString,XString.Rdash.method) 1518 0 R (Rfn.compareStrings,XStringSet,XStringSet.Rdash.method) 1519 0 R (Rfn.compareStrings,character,character.Rdash.method) 1516 0 R (Rfn.complement) 1634 0 R] /Limits [(Rfn.compareStrings,AlignedXStringSet0,AlignedXStringSet0.Rdash.method) (Rfn.complement)] >> endobj 4379 0 obj << /Names [(Rfn.complement,DNAString.Rdash.method) 2784 0 R (Rfn.complement,DNAStringSet.Rdash.method) 2785 0 R (Rfn.complement,MaskedDNAString.Rdash.method) 2786 0 R (Rfn.complement,MaskedRNAString.Rdash.method) 2787 0 R (Rfn.complement,RNAString.Rdash.method) 2788 0 R (Rfn.complement,RNAStringSet.Rdash.method) 2789 0 R] /Limits [(Rfn.complement,DNAString.Rdash.method) (Rfn.complement,RNAStringSet.Rdash.method)] >> endobj 4380 0 obj << /Names [(Rfn.complement,XStringViews.Rdash.method) 2790 0 R (Rfn.complementSeq) 1627 0 R (Rfn.complementSeq.1) 122 0 R (Rfn.complementedPalindromeArmLength) 1706 0 R (Rfn.complementedPalindromeArmLength,DNAString.Rdash.method) 1707 0 R (Rfn.complementedPalindromeArmLength,XStringViews.Rdash.method) 1708 0 R] /Limits [(Rfn.complement,XStringViews.Rdash.method) (Rfn.complementedPalindromeArmLength,XStringViews.Rdash.method)] >> endobj 4381 0 obj << /Names [(Rfn.complementedPalindromeLeftArm) 1709 0 R (Rfn.complementedPalindromeLeftArm,DNAString.Rdash.method) 1710 0 R (Rfn.complementedPalindromeLeftArm,XStringViews.Rdash.method) 1711 0 R (Rfn.complementedPalindromeRightArm) 1712 0 R (Rfn.complementedPalindromeRightArm,DNAString.Rdash.method) 1713 0 R (Rfn.complementedPalindromeRightArm,XStringViews.Rdash.method) 1714 0 R] /Limits [(Rfn.complementedPalindromeLeftArm) (Rfn.complementedPalindromeRightArm,XStringViews.Rdash.method)] >> endobj 4382 0 obj << /Names [(Rfn.computeAllFlinks) 675 0 R (Rfn.computeAllFlinks,ACtree2.Rdash.method) 676 0 R (Rfn.consensusMatrix) 860 0 R (Rfn.consensusMatrix,PairwiseAlignedFixedSubject.Rdash.method) 1520 0 R (Rfn.consensusMatrix,XStringSet.Rdash.method) 1851 0 R (Rfn.consensusMatrix,XStringViews.Rdash.method) 1852 0 R] /Limits [(Rfn.computeAllFlinks) (Rfn.consensusMatrix,XStringViews.Rdash.method)] >> endobj 4383 0 obj << /Names [(Rfn.consensusMatrix,character.Rdash.method) 1848 0 R (Rfn.consensusMatrix,list.Rdash.method) 1849 0 R (Rfn.consensusMatrix,matrix.Rdash.method) 1850 0 R (Rfn.consensusString) 861 0 R (Rfn.consensusString,ANY.Rdash.method) 1853 0 R (Rfn.consensusString,BStringSet.Rdash.method) 1854 0 R] /Limits [(Rfn.consensusMatrix,character.Rdash.method) (Rfn.consensusString,BStringSet.Rdash.method)] >> endobj 4384 0 obj << /Names [(Rfn.consensusString,DNAStringSet.Rdash.method) 1855 0 R (Rfn.consensusString,RNAStringSet.Rdash.method) 1857 0 R (Rfn.consensusString,XStringViews.Rdash.method) 1858 0 R (Rfn.consensusString,matrix.Rdash.method) 1856 0 R (Rfn.consmat) 1859 0 R (Rfn.consmat,ANY.Rdash.method) 1860 0 R] /Limits [(Rfn.consensusString,DNAStringSet.Rdash.method) (Rfn.consmat,ANY.Rdash.method)] >> endobj 4385 0 obj << /Names [(Rfn.countIndex) 517 0 R (Rfn.countIndex,ByPos.Rul.MIndex.Rdash.method) 518 0 R (Rfn.countIndex,MIndex.Rdash.method) 519 0 R (Rfn.countPDict) 1934 0 R (Rfn.countPDict,MaskedXString.Rdash.method) 2142 0 R (Rfn.countPDict,XString.Rdash.method) 2143 0 R] /Limits [(Rfn.countIndex) (Rfn.countPDict,XString.Rdash.method)] >> endobj 4386 0 obj << /Names [(Rfn.countPDict,XStringSet.Rdash.method) 2144 0 R (Rfn.countPDict,XStringViews.Rdash.method) 2145 0 R (Rfn.countPWM) 2276 0 R (Rfn.countPWM,DNAString.Rdash.method) 2278 0 R (Rfn.countPWM,MaskedDNAString.Rdash.method) 2279 0 R (Rfn.countPWM,XStringViews.Rdash.method) 2280 0 R] /Limits [(Rfn.countPDict,XStringSet.Rdash.method) (Rfn.countPWM,XStringViews.Rdash.method)] >> endobj 4387 0 obj << /Names [(Rfn.countPWM,character.Rdash.method) 2277 0 R (Rfn.countPattern) 2191 0 R (Rfn.countPattern,BOC2.Rul.SubjectString.Rdash.method) 394 0 R (Rfn.countPattern,MaskedXString.Rdash.method) 2339 0 R (Rfn.countPattern,XString.Rdash.method) 2340 0 R (Rfn.countPattern,XStringSet.Rdash.method) 2341 0 R] /Limits [(Rfn.countPWM,character.Rdash.method) (Rfn.countPattern,XStringSet.Rdash.method)] >> endobj 4388 0 obj << /Names [(Rfn.countPattern,XStringViews.Rdash.method) 2342 0 R (Rfn.countPattern,character.Rdash.method) 2338 0 R (Rfn.countWCP) 2420 0 R (Rfn.countWCP,MaskedXString.Rdash.method) 2422 0 R (Rfn.countWCP,XString.Rdash.method) 2423 0 R (Rfn.countWCP,XStringViews.Rdash.method) 2424 0 R] /Limits [(Rfn.countPattern,XStringViews.Rdash.method) (Rfn.countWCP,XStringViews.Rdash.method)] >> endobj 4389 0 obj << /Names [(Rfn.countWCP,character.Rdash.method) 2421 0 R (Rfn.countbases) 1576 0 R (Rfn.coverage) 1565 0 R (Rfn.coverage,AlignedXStringSet0.Rdash.method) 1521 0 R (Rfn.coverage,MIndex.Rdash.method) 2090 0 R (Rfn.coverage,MaskedXString.Rdash.method) 2089 0 R] /Limits [(Rfn.countWCP,character.Rdash.method) (Rfn.coverage,MaskedXString.Rdash.method)] >> endobj 4390 0 obj << /Names [(Rfn.coverage,PairwiseAlignedFixedSubject.Rdash.method) 862 0 R (Rfn.coverage,PairwiseAlignedFixedSubjectSummary.Rdash.method) 1522 0 R (Rfn.dataKey) 1009 0 R (Rfn.dataKey,XKeySortedData.Rdash.method) 1010 0 R (Rfn.dataTable) 1011 0 R (Rfn.dataTable,XKeySortedData.Rdash.method) 1012 0 R] /Limits [(Rfn.coverage,PairwiseAlignedFixedSubject.Rdash.method) (Rfn.dataTable,XKeySortedData.Rdash.method)] >> endobj 4391 0 obj << /Names [(Rfn.deletion) 489 0 R (Rfn.deletion,InDel.Rdash.method) 490 0 R (Rfn.deletion,PairwiseAlignedXStringSet.Rdash.method) 778 0 R (Rfn.dim,XKeySortedData.Rdash.method) 1013 0 R (Rfn.dimnames,XKeySortedData.Rdash.method) 1014 0 R (Rfn.dinucleotideFrequency) 2522 0 R] /Limits [(Rfn.deletion) (Rfn.dinucleotideFrequency)] >> endobj 4392 0 obj << /Names [(Rfn.dinucleotideFrequencyTest) 1652 0 R (Rfn.dinucleotideFrequencyTest,DNAStringSet.Rdash.method) 1653 0 R (Rfn.dinucleotideFrequencyTest,RNAStringSet.Rdash.method) 1654 0 R (Rfn.dinucleotideFrequencyTest.1) 126 0 R (Rfn.dist) 2887 0 R (Rfn.dna2rna) 2989 0 R] /Limits [(Rfn.dinucleotideFrequencyTest) (Rfn.dna2rna)] >> endobj 4393 0 obj << /Names [(Rfn.duplicated,PDict.Rdash.method) 677 0 R (Rfn.duplicated,PreprocessedTB.Rdash.method) 678 0 R (Rfn.duplicated,XStringSet.Rdash.method) 1219 0 R (Rfn.elementLengths,MIndex.Rdash.method) 520 0 R (Rfn.end,AlignedXStringSet0.Rdash.method) 343 0 R (Rfn.endIndex) 521 0 R] /Limits [(Rfn.duplicated,PDict.Rdash.method) (Rfn.endIndex)] >> endobj 4394 0 obj << /Names [(Rfn.endIndex,ByPos.Rul.MIndex.Rdash.method) 522 0 R (Rfn.errorSubstitutionMatrices) 2910 0 R (Rfn.extractAllMatches) 2146 0 R (Rfn.extractTranscripts) 1673 0 R (Rfn.extractTranscripts.1) 130 0 R (Rfn.extractTranscriptsFromGenome) 1698 0 R] /Limits [(Rfn.endIndex,ByPos.Rul.MIndex.Rdash.method) (Rfn.extractTranscriptsFromGenome)] >> endobj 4395 0 obj << /Names [(Rfn.fasta.info) 1317 0 R (Rfn.fastq.geometry) 1321 0 R (Rfn.findComplementedPalindromes) 1715 0 R (Rfn.findComplementedPalindromes,DNAString.Rdash.method) 1716 0 R (Rfn.findComplementedPalindromes,MaskedXString.Rdash.method) 1717 0 R (Rfn.findComplementedPalindromes,XStringViews.Rdash.method) 1718 0 R] /Limits [(Rfn.fasta.info) (Rfn.findComplementedPalindromes,XStringViews.Rdash.method)] >> endobj 4396 0 obj << /Names [(Rfn.findPalindromes) 1705 0 R (Rfn.findPalindromes,MaskedXString.Rdash.method) 1719 0 R (Rfn.findPalindromes,XString.Rdash.method) 1720 0 R (Rfn.findPalindromes,XStringViews.Rdash.method) 1721 0 R (Rfn.findPalindromes.1) 134 0 R (Rfn.gaps) 1481 0 R] /Limits [(Rfn.findPalindromes) (Rfn.gaps)] >> endobj 4397 0 obj << /Names [(Rfn.gaps,MaskedXString.Rdash.method) 593 0 R (Rfn.gregexpr) 1792 0 R (Rfn.gregexpr2) 1761 0 R (Rfn.gregexpr2.1) 138 0 R (Rfn.hasAllFlinks) 681 0 R (Rfn.hasAllFlinks,ACtree2.Rdash.method) 682 0 R] /Limits [(Rfn.gaps,MaskedXString.Rdash.method) (Rfn.hasAllFlinks,ACtree2.Rdash.method)] >> endobj 4398 0 obj << /Names [(Rfn.hasLetterAt) 1961 0 R (Rfn.hasOnlyBaseLetters) 1861 0 R (Rfn.hasOnlyBaseLetters,DNAString.Rdash.method) 1862 0 R (Rfn.hasOnlyBaseLetters,DNAStringSet.Rdash.method) 1863 0 R (Rfn.hasOnlyBaseLetters,MaskedXString.Rdash.method) 1864 0 R (Rfn.hasOnlyBaseLetters,RNAString.Rdash.method) 1865 0 R] /Limits [(Rfn.hasLetterAt) (Rfn.hasOnlyBaseLetters,RNAString.Rdash.method)] >> endobj 4399 0 obj << /Names [(Rfn.hasOnlyBaseLetters,RNAStringSet.Rdash.method) 1866 0 R (Rfn.hasOnlyBaseLetters,XStringViews.Rdash.method) 1867 0 R (Rfn.head,PDict3Parts.Rdash.method) 683 0 R (Rfn.head,TB.Rul.PDict.Rdash.method) 684 0 R (Rfn.indel) 344 0 R (Rfn.indel,AlignedXStringSet0.Rdash.method) 345 0 R] /Limits [(Rfn.hasOnlyBaseLetters,RNAStringSet.Rdash.method) (Rfn.indel,AlignedXStringSet0.Rdash.method)] >> endobj 4400 0 obj << /Names [(Rfn.indel,PairwiseAlignedXStringSet.Rdash.method) 779 0 R (Rfn.initialize,ACtree2.Rdash.method) 685 0 R (Rfn.initialize,BOC.Rul.SubjectString.Rdash.method) 396 0 R (Rfn.initialize,BOC2.Rul.SubjectString.Rdash.method) 395 0 R (Rfn.initialize,PreprocessedTB.Rdash.method) 686 0 R (Rfn.initialize,Twobit.Rdash.method) 687 0 R] /Limits [(Rfn.indel,PairwiseAlignedXStringSet.Rdash.method) (Rfn.initialize,Twobit.Rdash.method)] >> endobj 4401 0 obj << /Names [(Rfn.injectHardMask) 652 0 R (Rfn.injectHardMask,MaskedXString.Rdash.method) 1785 0 R (Rfn.injectHardMask,XStringViews.Rdash.method) 1786 0 R (Rfn.injectHardMask.1) 142 0 R (Rfn.injectSNPs) 2753 0 R (Rfn.insertion) 492 0 R] /Limits [(Rfn.injectHardMask) (Rfn.insertion)] >> endobj 4402 0 obj << /Names [(Rfn.insertion,InDel.Rdash.method) 493 0 R (Rfn.insertion,PairwiseAlignedXStringSet.Rdash.method) 780 0 R (Rfn.intersect,XStringSet,XStringSet.Rdash.method) 1220 0 R (Rfn.is.unsorted,XStringSet.Rdash.method) 1221 0 R (Rfn.isMatching) 1962 0 R (Rfn.isMatchingAt) 1963 0 R] /Limits [(Rfn.insertion,InDel.Rdash.method) (Rfn.isMatchingAt)] >> endobj 4403 0 obj << /Names [(Rfn.isMatchingEndingAt) 1964 0 R (Rfn.isMatchingEndingAt,XString.Rdash.method) 1966 0 R (Rfn.isMatchingEndingAt,XStringSet.Rdash.method) 1967 0 R (Rfn.isMatchingEndingAt,character.Rdash.method) 1965 0 R (Rfn.isMatchingStartingAt) 1968 0 R (Rfn.isMatchingStartingAt,XString.Rdash.method) 1970 0 R] /Limits [(Rfn.isMatchingEndingAt) (Rfn.isMatchingStartingAt,XString.Rdash.method)] >> endobj 4404 0 obj << /Names [(Rfn.isMatchingStartingAt,XStringSet.Rdash.method) 1971 0 R (Rfn.isMatchingStartingAt,character.Rdash.method) 1969 0 R (Rfn.lcprefix) 2671 0 R (Rfn.lcprefix,XString,XString.Rdash.method) 2675 0 R (Rfn.lcprefix,XString,character.Rdash.method) 2674 0 R (Rfn.lcprefix,character,XString.Rdash.method) 2673 0 R] /Limits [(Rfn.isMatchingStartingAt,XStringSet.Rdash.method) (Rfn.lcprefix,character,XString.Rdash.method)] >> endobj 4405 0 obj << /Names [(Rfn.lcprefix,character,character.Rdash.method) 2672 0 R (Rfn.lcsubstr) 2676 0 R (Rfn.lcsubstr,XString,XString.Rdash.method) 2680 0 R (Rfn.lcsubstr,XString,character.Rdash.method) 2679 0 R (Rfn.lcsubstr,character,XString.Rdash.method) 2678 0 R (Rfn.lcsubstr,character,character.Rdash.method) 2677 0 R] /Limits [(Rfn.lcprefix,character,character.Rdash.method) (Rfn.lcsubstr,character,character.Rdash.method)] >> endobj 4406 0 obj << /Names [(Rfn.lcsuffix) 2681 0 R (Rfn.lcsuffix,XString,XString.Rdash.method) 2685 0 R (Rfn.lcsuffix,XString,character.Rdash.method) 2684 0 R (Rfn.lcsuffix,character,XString.Rdash.method) 2683 0 R (Rfn.lcsuffix,character,character.Rdash.method) 2682 0 R (Rfn.length,AlignedXStringSet0.Rdash.method) 346 0 R] /Limits [(Rfn.lcsuffix) (Rfn.length,AlignedXStringSet0.Rdash.method)] >> endobj 4407 0 obj << /Names [(Rfn.length,MIndex.Rdash.method) 523 0 R (Rfn.length,MaskedXString.Rdash.method) 594 0 R (Rfn.length,PDict.Rdash.method) 688 0 R (Rfn.length,PDict3Parts.Rdash.method) 689 0 R (Rfn.length,PairwiseAlignedFixedSubjectSummary.Rdash.method) 781 0 R (Rfn.length,PairwiseAlignedXStringSet.Rdash.method) 782 0 R] /Limits [(Rfn.length,MIndex.Rdash.method) (Rfn.length,PairwiseAlignedXStringSet.Rdash.method)] >> endobj 4408 0 obj << /Names [(Rfn.length,PreprocessedTB.Rdash.method) 690 0 R (Rfn.length,XKeySortedData.Rdash.method) 1017 0 R (Rfn.length,XString.Rdash.method) 631 0 R (Rfn.length,XStringSetList.Rdash.method) 1396 0 R (Rfn.letter) 364 0 R (Rfn.letter,MaskedXString.Rdash.method) 1814 0 R] /Limits [(Rfn.length,PreprocessedTB.Rdash.method) (Rfn.letter,MaskedXString.Rdash.method)] >> endobj 4409 0 obj << /Names [(Rfn.letter,XString.Rdash.method) 1815 0 R (Rfn.letter,XStringViews.Rdash.method) 1816 0 R (Rfn.letter,character.Rdash.method) 1813 0 R (Rfn.letter.1) 146 0 R (Rfn.letterFrequency) 1839 0 R (Rfn.letterFrequency.1) 150 0 R] /Limits [(Rfn.letter,XString.Rdash.method) (Rfn.letterFrequency.1)] >> endobj 4410 0 obj << /Names [(Rfn.letterFrequencyInSlidingView) 1868 0 R (Rfn.letterFrequencyInSlidingView,XString.Rdash.method) 1869 0 R (Rfn.longestConsecutive) 1947 0 R (Rfn.longestConsecutive.1) 154 0 R (Rfn.lowlevel.Rdash.matching) 1960 0 R (Rfn.lowlevel.Rdash.matching.1) 158 0 R] /Limits [(Rfn.letterFrequencyInSlidingView) (Rfn.lowlevel.Rdash.matching.1)] >> endobj 4411 0 obj << /Names [(Rfn.mask) 2040 0 R (Rfn.maskMotif) 651 0 R (Rfn.maskMotif,MaskedXString,XString.Rdash.method) 2042 0 R (Rfn.maskMotif,MaskedXString,character.Rdash.method) 2041 0 R (Rfn.maskMotif,XString,ANY.Rdash.method) 2043 0 R (Rfn.maskMotif.1) 162 0 R] /Limits [(Rfn.mask) (Rfn.maskMotif.1)] >> endobj 4412 0 obj << /Names [(Rfn.maskedratio,MaskedXString.Rdash.method) 601 0 R (Rfn.maskedwidth,MaskedXString.Rdash.method) 604 0 R (Rfn.masks) 606 0 R (Rfn.masks,MaskedXString.Rdash.method) 607 0 R (Rfn.masks,XString.Rdash.method) 608 0 R (Rfn.masks<.Rdash.) 609 0 R] /Limits [(Rfn.maskedratio,MaskedXString.Rdash.method) (Rfn.masks<.Rdash.)] >> endobj 4413 0 obj << /Names [(Rfn.masks<.Rdash.,MaskedXString,MaskCollection.Rdash.method) 610 0 R (Rfn.masks<.Rdash.,MaskedXString,NULL.Rdash.method) 611 0 R (Rfn.masks<.Rdash.,XString,ANY.Rdash.method) 612 0 R (Rfn.masks<.Rdash.,XString,NULL.Rdash.method) 613 0 R (Rfn.match,XString,XStringSet.Rdash.method) 1223 0 R (Rfn.match,XStringSet,XStringSet.Rdash.method) 1224 0 R] /Limits [(Rfn.masks<.Rdash.,MaskedXString,MaskCollection.Rdash.method) (Rfn.match,XStringSet,XStringSet.Rdash.method)] >> endobj 4414 0 obj << /Names [(Rfn.match,character,XStringSet.Rdash.method) 1222 0 R (Rfn.match.Rdash.utils) 1566 0 R (Rfn.match.Rdash.utils.1) 166 0 R (Rfn.matchDNAPattern) 2343 0 R (Rfn.matchLRPatterns) 1766 0 R (Rfn.matchLRPatterns,MaskedXString.Rdash.method) 2117 0 R] /Limits [(Rfn.match,character,XStringSet.Rdash.method) (Rfn.matchLRPatterns,MaskedXString.Rdash.method)] >> endobj 4415 0 obj << /Names [(Rfn.matchLRPatterns,XString.Rdash.method) 2118 0 R (Rfn.matchLRPatterns,XStringViews.Rdash.method) 2119 0 R (Rfn.matchLRPatterns.1) 170 0 R (Rfn.matchPDict) 540 0 R (Rfn.matchPDict,MaskedXString.Rdash.method) 2147 0 R (Rfn.matchPDict,XString.Rdash.method) 2148 0 R] /Limits [(Rfn.matchLRPatterns,XString.Rdash.method) (Rfn.matchPDict,XString.Rdash.method)] >> endobj 4416 0 obj << /Names [(Rfn.matchPDict,XStringSet.Rdash.method) 2149 0 R (Rfn.matchPDict,XStringViews.Rdash.method) 2150 0 R (Rfn.matchPDict.1) 174 0 R (Rfn.matchPDict.Rdash.exact) 2151 0 R (Rfn.matchPDict.Rdash.inexact) 749 0 R (Rfn.matchPDict.Rdash.inexact.1) 178 0 R] /Limits [(Rfn.matchPDict,XStringSet.Rdash.method) (Rfn.matchPDict.Rdash.inexact.1)] >> endobj 4417 0 obj << /Names [(Rfn.matchPWM) 2275 0 R (Rfn.matchPWM,DNAString.Rdash.method) 2282 0 R (Rfn.matchPWM,MaskedDNAString.Rdash.method) 2283 0 R (Rfn.matchPWM,XStringViews.Rdash.method) 2284 0 R (Rfn.matchPWM,character.Rdash.method) 2281 0 R (Rfn.matchPWM.1) 182 0 R] /Limits [(Rfn.matchPWM) (Rfn.matchPWM.1)] >> endobj 4418 0 obj << /Names [(Rfn.matchPattern) 1633 0 R (Rfn.matchPattern,BOC.Rul.SubjectString.Rdash.method) 398 0 R (Rfn.matchPattern,BOC2.Rul.SubjectString.Rdash.method) 397 0 R (Rfn.matchPattern,MaskedXString.Rdash.method) 2345 0 R (Rfn.matchPattern,XString.Rdash.method) 2346 0 R (Rfn.matchPattern,XStringSet.Rdash.method) 2347 0 R] /Limits [(Rfn.matchPattern) (Rfn.matchPattern,XStringSet.Rdash.method)] >> endobj 4419 0 obj << /Names [(Rfn.matchPattern,XStringViews.Rdash.method) 2348 0 R (Rfn.matchPattern,character.Rdash.method) 2344 0 R (Rfn.matchPattern.1) 186 0 R (Rfn.matchProbePair) 1767 0 R (Rfn.matchProbePair,DNAString.Rdash.method) 2398 0 R (Rfn.matchProbePair,MaskedDNAString.Rdash.method) 2399 0 R] /Limits [(Rfn.matchPattern,XStringViews.Rdash.method) (Rfn.matchProbePair,MaskedDNAString.Rdash.method)] >> endobj 4420 0 obj << /Names [(Rfn.matchProbePair,XStringViews.Rdash.method) 2400 0 R (Rfn.matchProbePair.1) 190 0 R (Rfn.matchWCP) 1046 0 R (Rfn.matchWCP,MaskedXString.Rdash.method) 2426 0 R (Rfn.matchWCP,XString.Rdash.method) 2427 0 R (Rfn.matchWCP,XStringViews.Rdash.method) 2428 0 R] /Limits [(Rfn.matchProbePair,XStringViews.Rdash.method) (Rfn.matchWCP,XStringViews.Rdash.method)] >> endobj 4421 0 obj << /Names [(Rfn.matchWCP,character.Rdash.method) 2425 0 R (Rfn.matchWCP.1) 194 0 R (Rfn.matchprobes) 2454 0 R (Rfn.matchprobes.1) 198 0 R (Rfn.maxScore) 2285 0 R (Rfn.maxScore,ANY.Rdash.method) 2286 0 R] /Limits [(Rfn.matchWCP,character.Rdash.method) (Rfn.maxScore,ANY.Rdash.method)] >> endobj 4422 0 obj << /Names [(Rfn.maxWeights) 2287 0 R (Rfn.maxWeights,WCP.Rdash.method) 975 0 R (Rfn.maxWeights,matrix.Rdash.method) 2288 0 R (Rfn.mergeIUPACLetters) 467 0 R (Rfn.minScore) 2289 0 R (Rfn.minScore,ANY.Rdash.method) 2290 0 R] /Limits [(Rfn.maxWeights) (Rfn.minScore,ANY.Rdash.method)] >> endobj 4423 0 obj << /Names [(Rfn.minWeights) 2291 0 R (Rfn.minWeights,matrix.Rdash.method) 2292 0 R (Rfn.misc) 2471 0 R (Rfn.misc.1) 202 0 R (Rfn.mismatch) 2091 0 R (Rfn.mismatch,ANY,XStringViews.Rdash.method) 2092 0 R] /Limits [(Rfn.minWeights) (Rfn.mismatch,ANY,XStringViews.Rdash.method)] >> endobj 4424 0 obj << /Names [(Rfn.mismatch,AlignedXStringSet0,missing.Rdash.method) 1523 0 R (Rfn.mismatchSummary) 1524 0 R (Rfn.mismatchSummary,AlignedXStringSet0.Rdash.method) 1525 0 R (Rfn.mismatchSummary,PairwiseAlignedFixedSubject.Rdash.method) 1526 0 R (Rfn.mismatchSummary,PairwiseAlignedFixedSubjectSummary.Rdash.method) 1527 0 R (Rfn.mismatchSummary,QualityAlignedXStringSet.Rdash.method) 1528 0 R] /Limits [(Rfn.mismatch,AlignedXStringSet0,missing.Rdash.method) (Rfn.mismatchSummary,QualityAlignedXStringSet.Rdash.method)] >> endobj 4425 0 obj << /Names [(Rfn.mismatchTable) 1529 0 R (Rfn.mismatchTable,AlignedXStringSet0.Rdash.method) 1530 0 R (Rfn.mismatchTable,PairwiseAlignedXStringSet.Rdash.method) 1531 0 R (Rfn.mismatchTable,QualityAlignedXStringSet.Rdash.method) 1532 0 R (Rfn.mkAllStrings) 2523 0 R (Rfn.names,MIndex.Rdash.method) 525 0 R] /Limits [(Rfn.mismatchTable) (Rfn.names,MIndex.Rdash.method)] >> endobj 4426 0 obj << /Names [(Rfn.names,PDict.Rdash.method) 693 0 R (Rfn.names,XStringSetList.Rdash.method) 1397 0 R (Rfn.names<.Rdash.,MIndex.Rdash.method) 526 0 R (Rfn.names<.Rdash.,PDict.Rdash.method) 694 0 R (Rfn.names<.Rdash.,XStringSetList.Rdash.method) 1398 0 R (Rfn.narrow) 1250 0 R] /Limits [(Rfn.names,PDict.Rdash.method) (Rfn.narrow)] >> endobj 4427 0 obj << /Names [(Rfn.narrow,QualityScaledXStringSet.Rdash.method) 889 0 R (Rfn.narrow,character.Rdash.method) 1225 0 R (Rfn.nchar,AlignedXStringSet0.Rdash.method) 347 0 R (Rfn.nchar,MaskedXString.Rdash.method) 614 0 R (Rfn.nchar,PairwiseAlignedFixedSubjectSummary.Rdash.method) 783 0 R (Rfn.nchar,PairwiseAlignedXStringSet.Rdash.method) 784 0 R] /Limits [(Rfn.narrow,QualityScaledXStringSet.Rdash.method) (Rfn.nchar,PairwiseAlignedXStringSet.Rdash.method)] >> endobj 4428 0 obj << /Names [(Rfn.nchar,XString.Rdash.method) 1079 0 R (Rfn.nchar,XStringSet.Rdash.method) 1226 0 R (Rfn.nchar,XStringViews.Rdash.method) 1447 0 R (Rfn.nedit) 1533 0 R (Rfn.nedit,PairwiseAlignedFixedSubjectSummary.Rdash.method) 1534 0 R (Rfn.nedit,PairwiseAlignedXStringSet.Rdash.method) 1535 0 R] /Limits [(Rfn.nchar,XString.Rdash.method) (Rfn.nedit,PairwiseAlignedXStringSet.Rdash.method)] >> endobj 4429 0 obj << /Names [(Rfn.neditAt) 1972 0 R (Rfn.neditEndingAt) 1973 0 R (Rfn.neditEndingAt,XString.Rdash.method) 1975 0 R (Rfn.neditEndingAt,XStringSet.Rdash.method) 1976 0 R (Rfn.neditEndingAt,character.Rdash.method) 1974 0 R (Rfn.neditStartingAt) 1977 0 R] /Limits [(Rfn.neditAt) (Rfn.neditStartingAt)] >> endobj 4430 0 obj << /Names [(Rfn.neditStartingAt,XString.Rdash.method) 1979 0 R (Rfn.neditStartingAt,XStringSet.Rdash.method) 1980 0 R (Rfn.neditStartingAt,character.Rdash.method) 1978 0 R (Rfn.needwunsQS) 2488 0 R (Rfn.needwunsQS,XString,XString.Rdash.method) 2492 0 R (Rfn.needwunsQS,XString,character.Rdash.method) 2491 0 R] /Limits [(Rfn.neditStartingAt,XString.Rdash.method) (Rfn.needwunsQS,XString,character.Rdash.method)] >> endobj 4431 0 obj << /Names [(Rfn.needwunsQS,character,XString.Rdash.method) 2490 0 R (Rfn.needwunsQS,character,character.Rdash.method) 2489 0 R (Rfn.needwunsQS.1) 206 0 R (Rfn.nindel) 348 0 R (Rfn.nindel,AlignedXStringSet0.Rdash.method) 349 0 R (Rfn.nindel,PairwiseAlignedFixedSubjectSummary.Rdash.method) 785 0 R] /Limits [(Rfn.needwunsQS,character,XString.Rdash.method) (Rfn.nindel,PairwiseAlignedFixedSubjectSummary.Rdash.method)] >> endobj 4432 0 obj << /Names [(Rfn.nindel,PairwiseAlignedXStringSet.Rdash.method) 786 0 R (Rfn.nmatch) 2093 0 R (Rfn.nmatch,ANY,XStringViews.Rdash.method) 2094 0 R (Rfn.nmatch,PairwiseAlignedFixedSubjectSummary,missing.Rdash.method) 1536 0 R (Rfn.nmatch,PairwiseAlignedXStringSet,missing.Rdash.method) 1537 0 R (Rfn.nmismatch) 2095 0 R] /Limits [(Rfn.nindel,PairwiseAlignedXStringSet.Rdash.method) (Rfn.nmismatch)] >> endobj 4433 0 obj << /Names [(Rfn.nmismatch,ANY,XStringViews.Rdash.method) 2096 0 R (Rfn.nmismatch,AlignedXStringSet0,missing.Rdash.method) 1538 0 R (Rfn.nmismatch,PairwiseAlignedFixedSubjectSummary,missing.Rdash.method) 1539 0 R (Rfn.nmismatch,PairwiseAlignedXStringSet,missing.Rdash.method) 1540 0 R (Rfn.nmismatchEndingAt) 1981 0 R (Rfn.nmismatchStartingAt) 1982 0 R] /Limits [(Rfn.nmismatch,ANY,XStringViews.Rdash.method) (Rfn.nmismatchStartingAt)] >> endobj 4434 0 obj << /Names [(Rfn.nnodes) 695 0 R (Rfn.nnodes,ACtree2.Rdash.method) 696 0 R (Rfn.nucleotideFrequency) 2521 0 R (Rfn.nucleotideFrequency.1) 210 0 R (Rfn.nucleotideFrequencyAt) 1678 0 R (Rfn.nucleotideFrequencyAt,XStringSet.Rdash.method) 2524 0 R] /Limits [(Rfn.nnodes) (Rfn.nucleotideFrequencyAt,XStringSet.Rdash.method)] >> endobj 4435 0 obj << /Names [(Rfn.nucleotideFrequencyAt,XStringViews.Rdash.method) 2525 0 R (Rfn.nucleotideSubstitutionMatrix) 2911 0 R (Rfn.oligonucleotideFrequency) 1933 0 R (Rfn.oligonucleotideFrequency,MaskedXString.Rdash.method) 2526 0 R (Rfn.oligonucleotideFrequency,XString.Rdash.method) 2527 0 R (Rfn.oligonucleotideFrequency,XStringSet.Rdash.method) 2528 0 R] /Limits [(Rfn.nucleotideFrequencyAt,XStringViews.Rdash.method) (Rfn.oligonucleotideFrequency,XStringSet.Rdash.method)] >> endobj 4436 0 obj << /Names [(Rfn.oligonucleotideFrequency,XStringViews.Rdash.method) 2529 0 R (Rfn.oligonucleotideTransitions) 2530 0 R (Rfn.order,XStringSet.Rdash.method) 1227 0 R (Rfn.pairwiseAlignment) 407 0 R (Rfn.pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet.Rdash.method) 2580 0 R (Rfn.pairwiseAlignment,QualityScaledXStringSet,XString.Rdash.method) 2581 0 R] /Limits [(Rfn.oligonucleotideFrequency,XStringViews.Rdash.method) (Rfn.pairwiseAlignment,QualityScaledXStringSet,XString.Rdash.method)] >> endobj 4437 0 obj << /Names [(Rfn.pairwiseAlignment,QualityScaledXStringSet,XStringSet.Rdash.method) 2582 0 R (Rfn.pairwiseAlignment,QualityScaledXStringSet,character.Rdash.method) 2579 0 R (Rfn.pairwiseAlignment,XString,QualityScaledXStringSet.Rdash.method) 2584 0 R (Rfn.pairwiseAlignment,XString,XString.Rdash.method) 2585 0 R (Rfn.pairwiseAlignment,XString,XStringSet.Rdash.method) 2586 0 R (Rfn.pairwiseAlignment,XString,character.Rdash.method) 2583 0 R] /Limits [(Rfn.pairwiseAlignment,QualityScaledXStringSet,XStringSet.Rdash.method) (Rfn.pairwiseAlignment,XString,character.Rdash.method)] >> endobj 4438 0 obj << /Names [(Rfn.pairwiseAlignment,XStringSet,QualityScaledXStringSet.Rdash.method) 2588 0 R (Rfn.pairwiseAlignment,XStringSet,XString.Rdash.method) 2589 0 R (Rfn.pairwiseAlignment,XStringSet,XStringSet.Rdash.method) 2590 0 R (Rfn.pairwiseAlignment,XStringSet,character.Rdash.method) 2587 0 R (Rfn.pairwiseAlignment,character,QualityScaledXStringSet.Rdash.method) 2576 0 R (Rfn.pairwiseAlignment,character,XString.Rdash.method) 2577 0 R] /Limits [(Rfn.pairwiseAlignment,XStringSet,QualityScaledXStringSet.Rdash.method) (Rfn.pairwiseAlignment,character,XString.Rdash.method)] >> endobj 4439 0 obj << /Names [(Rfn.pairwiseAlignment,character,XStringSet.Rdash.method) 2578 0 R (Rfn.pairwiseAlignment,character,character.Rdash.method) 2575 0 R (Rfn.pairwiseAlignment.1) 214 0 R (Rfn.palindromeArmLength) 1722 0 R (Rfn.palindromeArmLength,XString.Rdash.method) 1723 0 R (Rfn.palindromeArmLength,XStringViews.Rdash.method) 1724 0 R] /Limits [(Rfn.pairwiseAlignment,character,XStringSet.Rdash.method) (Rfn.palindromeArmLength,XStringViews.Rdash.method)] >> endobj 4440 0 obj << /Names [(Rfn.palindromeLeftArm) 1725 0 R (Rfn.palindromeLeftArm,XString.Rdash.method) 1726 0 R (Rfn.palindromeLeftArm,XStringViews.Rdash.method) 1727 0 R (Rfn.palindromeRightArm) 1728 0 R (Rfn.palindromeRightArm,XString.Rdash.method) 1729 0 R (Rfn.palindromeRightArm,XStringViews.Rdash.method) 1730 0 R] /Limits [(Rfn.palindromeLeftArm) (Rfn.palindromeRightArm,XStringViews.Rdash.method)] >> endobj 4441 0 obj << /Names [(Rfn.partitioning) 1399 0 R (Rfn.partitioning,XStringSetList.Rdash.method) 1400 0 R (Rfn.paste) 3085 0 R (Rfn.pattern) 1129 0 R (Rfn.pattern,PairwiseAlignedXStringSet.Rdash.method) 800 0 R (Rfn.pattern,XStringPartialMatches.Rdash.method) 1130 0 R] /Limits [(Rfn.partitioning) (Rfn.pattern,XStringPartialMatches.Rdash.method)] >> endobj 4442 0 obj << /Names [(Rfn.patternFrequency) 697 0 R (Rfn.patternFrequency,PDict.Rdash.method) 698 0 R (Rfn.phiX174Phage) 2631 0 R (Rfn.phiX174Phage.1) 218 0 R (Rfn.pid) 864 0 R (Rfn.pid,PairwiseAlignedXStringSet.Rdash.method) 2648 0 R] /Limits [(Rfn.patternFrequency) (Rfn.pid,PairwiseAlignedXStringSet.Rdash.method)] >> endobj 4443 0 obj << /Names [(Rfn.pid.1) 222 0 R (Rfn.pmatchPattern) 2670 0 R (Rfn.pmatchPattern,XString.Rdash.method) 2687 0 R (Rfn.pmatchPattern,XStringViews.Rdash.method) 2688 0 R (Rfn.pmatchPattern,character.Rdash.method) 2686 0 R (Rfn.pmatchPattern.1) 226 0 R] /Limits [(Rfn.pid.1) (Rfn.pmatchPattern.1)] >> endobj 4444 0 obj << /Names [(Rfn.print.needwunsQS) 2493 0 R (Rfn.quPhiX174) 2632 0 R (Rfn.quality) 890 0 R (Rfn.quality,QualityScaledXStringSet.Rdash.method) 891 0 R (Rfn.qualitySubstitutionMatrices) 2917 0 R (Rfn.rank,XStringSet.Rdash.method) 1228 0 R] /Limits [(Rfn.print.needwunsQS) (Rfn.rank,XStringSet.Rdash.method)] >> endobj 4445 0 obj << /Names [(Rfn.read.AAStringSet) 1322 0 R (Rfn.read.BStringSet) 1323 0 R (Rfn.read.BStringViews) 1324 0 R (Rfn.read.DNAStringSet) 1325 0 R (Rfn.read.Mask) 2062 0 R (Rfn.read.RNAStringSet) 1326 0 R] /Limits [(Rfn.read.AAStringSet) (Rfn.read.RNAStringSet)] >> endobj 4446 0 obj << /Names [(Rfn.read.XStringViews) 1327 0 R (Rfn.read.table) 2727 0 R (Rfn.readFASTA) 1350 0 R (Rfn.readFASTA.1) 230 0 R (Rfn.rep,AlignedXStringSet0.Rdash.method) 352 0 R (Rfn.rep,PairwiseAlignedXStringSet.Rdash.method) 801 0 R] /Limits [(Rfn.read.XStringViews) (Rfn.rep,PairwiseAlignedXStringSet.Rdash.method)] >> endobj 4447 0 obj << /Names [(Rfn.replaceLetterAt) 1632 0 R (Rfn.replaceLetterAt,DNAString.Rdash.method) 2723 0 R (Rfn.replaceLetterAt,DNAStringSet.Rdash.method) 2724 0 R (Rfn.replaceLetterAt.1) 234 0 R (Rfn.replaceLetterAtLoc) 2725 0 R (Rfn.rev) 2561 0 R] /Limits [(Rfn.replaceLetterAt) (Rfn.rev)] >> endobj 4448 0 obj << /Names [(Rfn.revcompDNA) 2833 0 R (Rfn.revcompRNA) 2834 0 R (Rfn.reverse,MaskedXString.Rdash.method) 653 0 R (Rfn.reverse,XString.Rdash.method) 1117 0 R (Rfn.reverse,XStringSet.Rdash.method) 2792 0 R (Rfn.reverse,XStringViews.Rdash.method) 2793 0 R] /Limits [(Rfn.revcompDNA) (Rfn.reverse,XStringViews.Rdash.method)] >> endobj 4449 0 obj << /Names [(Rfn.reverse,character.Rdash.method) 2791 0 R (Rfn.reverseComplement) 436 0 R (Rfn.reverseComplement,DNAString.Rdash.method) 2794 0 R (Rfn.reverseComplement,DNAStringSet.Rdash.method) 2795 0 R (Rfn.reverseComplement,MaskedDNAString.Rdash.method) 2796 0 R (Rfn.reverseComplement,MaskedRNAString.Rdash.method) 2797 0 R] /Limits [(Rfn.reverse,character.Rdash.method) (Rfn.reverseComplement,MaskedRNAString.Rdash.method)] >> endobj 4450 0 obj << /Names [(Rfn.reverseComplement,RNAString.Rdash.method) 2798 0 R (Rfn.reverseComplement,RNAStringSet.Rdash.method) 2799 0 R (Rfn.reverseComplement,XStringViews.Rdash.method) 2800 0 R (Rfn.reverseComplement,matrix.Rdash.method) 2298 0 R (Rfn.reverseComplement.1) 238 0 R (Rfn.reverseSeq) 1994 0 R] /Limits [(Rfn.reverseComplement,RNAString.Rdash.method) (Rfn.reverseSeq)] >> endobj 4451 0 obj << /Names [(Rfn.reverseSeq.1) 242 0 R (Rfn.rna2dna) 2990 0 R (Rfn.save.XStringSet) 1328 0 R (Rfn.scan) 2728 0 R (Rfn.score,PairwiseAlignedFixedSubjectSummary.Rdash.method) 802 0 R (Rfn.score,PairwiseAlignedXStringSet.Rdash.method) 803 0 R] /Limits [(Rfn.reverseSeq.1) (Rfn.score,PairwiseAlignedXStringSet.Rdash.method)] >> endobj 4452 0 obj << /Names [(Rfn.setdiff,XStringSet,XStringSet.Rdash.method) 1229 0 R (Rfn.setequal,XStringSet,XStringSet.Rdash.method) 1230 0 R (Rfn.show,ACtree2.Rdash.method) 709 0 R (Rfn.show,AlignedXStringSet0.Rdash.method) 353 0 R (Rfn.show,ByPos.Rul.MIndex.Rdash.method) 527 0 R (Rfn.show,MTB.Rul.PDict.Rdash.method) 710 0 R] /Limits [(Rfn.setdiff,XStringSet,XStringSet.Rdash.method) (Rfn.show,MTB.Rul.PDict.Rdash.method)] >> endobj 4453 0 obj << /Names [(Rfn.show,MaskedXString.Rdash.method) 615 0 R (Rfn.show,PairwiseAlignedFixedSubjectSummary.Rdash.method) 804 0 R (Rfn.show,PairwiseAlignedXStringSet.Rdash.method) 805 0 R (Rfn.show,QualityScaledXStringSet.Rdash.method) 901 0 R (Rfn.show,TB.Rul.PDict.Rdash.method) 711 0 R (Rfn.show,Twobit.Rdash.method) 712 0 R] /Limits [(Rfn.show,MaskedXString.Rdash.method) (Rfn.show,Twobit.Rdash.method)] >> endobj 4454 0 obj << /Names [(Rfn.show,WCP.Rdash.method) 978 0 R (Rfn.show,XString.Rdash.method) 1080 0 R (Rfn.show,XStringPartialMatches.Rdash.method) 1131 0 R (Rfn.show,XStringSet.Rdash.method) 1231 0 R (Rfn.show,XStringSetList.Rdash.method) 1403 0 R (Rfn.show,XStringViews.Rdash.method) 1448 0 R] /Limits [(Rfn.show,WCP.Rdash.method) (Rfn.show,XStringViews.Rdash.method)] >> endobj 4455 0 obj << /Names [(Rfn.sort,XStringSet.Rdash.method) 1232 0 R (Rfn.srPhiX174) 2633 0 R (Rfn.start,AlignedXStringSet0.Rdash.method) 354 0 R (Rfn.startIndex) 528 0 R (Rfn.startIndex,ByPos.Rul.MIndex.Rdash.method) 529 0 R (Rfn.stringDist) 2625 0 R] /Limits [(Rfn.sort,XStringSet.Rdash.method) (Rfn.stringDist)] >> endobj 4456 0 obj << /Names [(Rfn.stringDist,QualityScaledXStringSet.Rdash.method) 2857 0 R (Rfn.stringDist,XStringSet.Rdash.method) 2858 0 R (Rfn.stringDist,character.Rdash.method) 2856 0 R (Rfn.stringDist.1) 246 0 R (Rfn.strrev) 2801 0 R (Rfn.strsplit) 1935 0 R] /Limits [(Rfn.stringDist,QualityScaledXStringSet.Rdash.method) (Rfn.strsplit)] >> endobj 4457 0 obj << /Names [(Rfn.subBString) 2880 0 R (Rfn.subXString) 2879 0 R (Rfn.subXString.1) 250 0 R (Rfn.subject,PairwiseAlignedXStringSet.Rdash.method) 806 0 R (Rfn.subpatterns) 1132 0 R (Rfn.subpatterns,XStringPartialMatches.Rdash.method) 1133 0 R] /Limits [(Rfn.subBString) (Rfn.subpatterns,XStringPartialMatches.Rdash.method)] >> endobj 4458 0 obj << /Names [(Rfn.subseq) 1116 0 R (Rfn.subseq,MaskedXString.Rdash.method) 616 0 R (Rfn.subseq,character.Rdash.method) 1233 0 R (Rfn.subseq<.Rdash.) 1277 0 R (Rfn.subseq<.Rdash.,XStringSet.Rdash.method) 1235 0 R (Rfn.subseq<.Rdash.,character.Rdash.method) 1234 0 R] /Limits [(Rfn.subseq) (Rfn.subseq<.Rdash.,character.Rdash.method)] >> endobj 4459 0 obj << /Names [(Rfn.substitution.matrices) 2510 0 R (Rfn.substitution.matrices.1) 254 0 R (Rfn.substr) 1274 0 R (Rfn.substr,MaskedXString.Rdash.method) 2881 0 R (Rfn.substr,XString.Rdash.method) 2882 0 R (Rfn.substring,MaskedXString.Rdash.method) 2883 0 R] /Limits [(Rfn.substitution.matrices) (Rfn.substring,MaskedXString.Rdash.method)] >> endobj 4460 0 obj << /Names [(Rfn.substring,XString.Rdash.method) 2884 0 R (Rfn.summary,PairwiseAlignedFixedSubject.Rdash.method) 807 0 R (Rfn.tail,PDict3Parts.Rdash.method) 713 0 R (Rfn.tail,TB.Rul.PDict.Rdash.method) 714 0 R (Rfn.tb) 715 0 R (Rfn.tb,PDict3Parts.Rdash.method) 716 0 R] /Limits [(Rfn.substring,XString.Rdash.method) (Rfn.tb,PDict3Parts.Rdash.method)] >> endobj 4461 0 obj << /Names [(Rfn.tb,PreprocessedTB.Rdash.method) 717 0 R (Rfn.tb,TB.Rul.PDict.Rdash.method) 718 0 R (Rfn.tb.width) 719 0 R (Rfn.tb.width,PDict3Parts.Rdash.method) 720 0 R (Rfn.tb.width,PreprocessedTB.Rdash.method) 721 0 R (Rfn.tb.width,TB.Rul.PDict.Rdash.method) 722 0 R] /Limits [(Rfn.tb,PreprocessedTB.Rdash.method) (Rfn.tb.width,TB.Rul.PDict.Rdash.method)] >> endobj 4462 0 obj << /Names [(Rfn.threebands) 1276 0 R (Rfn.threebands,character.Rdash.method) 1236 0 R (Rfn.toComplex) 2950 0 R (Rfn.toComplex,DNAString.Rdash.method) 2952 0 R (Rfn.toComplex.1) 258 0 R (Rfn.toString,AlignedXStringSet0.Rdash.method) 355 0 R] /Limits [(Rfn.threebands) (Rfn.toString,AlignedXStringSet0.Rdash.method)] >> endobj 4463 0 obj << /Names [(Rfn.toString,MaskedXString.Rdash.method) 617 0 R (Rfn.toString,PairwiseAlignedFixedSubject.Rdash.method) 808 0 R (Rfn.toString,XString.Rdash.method) 1081 0 R (Rfn.toString,XStringSet.Rdash.method) 1237 0 R (Rfn.toString,XStringViews.Rdash.method) 1449 0 R (Rfn.toupper) 2476 0 R] /Limits [(Rfn.toString,MaskedXString.Rdash.method) (Rfn.toupper)] >> endobj 4464 0 obj << /Names [(Rfn.transcribe) 2991 0 R (Rfn.transcriptLocs2refLocs) 1674 0 R (Rfn.transcriptWidths) 1675 0 R (Rfn.translate) 455 0 R (Rfn.translate,DNAString.Rdash.method) 2992 0 R (Rfn.translate,DNAStringSet.Rdash.method) 2993 0 R] /Limits [(Rfn.transcribe) (Rfn.translate,DNAStringSet.Rdash.method)] >> endobj 4465 0 obj << /Names [(Rfn.translate,MaskedDNAString.Rdash.method) 2994 0 R (Rfn.translate,MaskedRNAString.Rdash.method) 2995 0 R (Rfn.translate,RNAString.Rdash.method) 2996 0 R (Rfn.translate,RNAStringSet.Rdash.method) 2997 0 R (Rfn.translate.1) 262 0 R (Rfn.trimLRPatterns) 2035 0 R] /Limits [(Rfn.translate,MaskedDNAString.Rdash.method) (Rfn.trimLRPatterns)] >> endobj 4466 0 obj << /Names [(Rfn.trimLRPatterns,XString.Rdash.method) 3019 0 R (Rfn.trimLRPatterns,XStringSet.Rdash.method) 3020 0 R (Rfn.trimLRPatterns,character.Rdash.method) 3018 0 R (Rfn.trimLRPatterns.1) 266 0 R (Rfn.trinucleotideFrequency) 456 0 R (Rfn.type) 809 0 R] /Limits [(Rfn.trimLRPatterns,XString.Rdash.method) (Rfn.type)] >> endobj 4467 0 obj << /Names [(Rfn.type,PairwiseAlignedFixedSubjectSummary.Rdash.method) 810 0 R (Rfn.type,PairwiseAlignedXStringSet.Rdash.method) 811 0 R (Rfn.unaligned) 356 0 R (Rfn.unaligned,AlignedXStringSet0.Rdash.method) 357 0 R (Rfn.union,XStringSet,XStringSet.Rdash.method) 1238 0 R (Rfn.unique,XStringSet.Rdash.method) 1239 0 R] /Limits [(Rfn.type,PairwiseAlignedFixedSubjectSummary.Rdash.method) (Rfn.unique,XStringSet.Rdash.method)] >> endobj 4468 0 obj << /Names [(Rfn.uniqueLetters) 1870 0 R (Rfn.uniqueLetters,MaskedXString.Rdash.method) 1871 0 R (Rfn.uniqueLetters,XString.Rdash.method) 1872 0 R (Rfn.uniqueLetters,XStringSet.Rdash.method) 1873 0 R (Rfn.uniqueLetters,XStringViews.Rdash.method) 1874 0 R (Rfn.unitScale) 2299 0 R] /Limits [(Rfn.uniqueLetters) (Rfn.unitScale)] >> endobj 4469 0 obj << /Names [(Rfn.unlist,MIndex.Rdash.method) 530 0 R (Rfn.unlist,XStringSet.Rdash.method) 1240 0 R (Rfn.unlist,XStringSetList.Rdash.method) 1404 0 R (Rfn.unmasked) 618 0 R (Rfn.unmasked,MaskedXString.Rdash.method) 619 0 R (Rfn.unsplit.list.of.XStringSet) 1241 0 R] /Limits [(Rfn.unlist,MIndex.Rdash.method) (Rfn.unsplit.list.of.XStringSet)] >> endobj 4470 0 obj << /Names [(Rfn.updateObject,XString.Rdash.method) 1082 0 R (Rfn.updateObject,XStringSet.Rdash.method) 1242 0 R (Rfn.vcountPDict) 2152 0 R (Rfn.vcountPDict,MaskedXString.Rdash.method) 2153 0 R (Rfn.vcountPDict,XString.Rdash.method) 2154 0 R (Rfn.vcountPDict,XStringSet.Rdash.method) 2155 0 R] /Limits [(Rfn.updateObject,XString.Rdash.method) (Rfn.vcountPDict,XStringSet.Rdash.method)] >> endobj 4471 0 obj << /Names [(Rfn.vcountPDict,XStringViews.Rdash.method) 2156 0 R (Rfn.vcountPattern) 2193 0 R (Rfn.vcountPattern,MaskedXString.Rdash.method) 2350 0 R (Rfn.vcountPattern,XString.Rdash.method) 2351 0 R (Rfn.vcountPattern,XStringSet.Rdash.method) 2352 0 R (Rfn.vcountPattern,XStringViews.Rdash.method) 2353 0 R] /Limits [(Rfn.vcountPDict,XStringViews.Rdash.method) (Rfn.vcountPattern,XStringViews.Rdash.method)] >> endobj 4472 0 obj << /Names [(Rfn.vcountPattern,character.Rdash.method) 2349 0 R (Rfn.vmatchPDict) 2157 0 R (Rfn.vmatchPDict,ANY.Rdash.method) 2158 0 R (Rfn.vmatchPDict,MaskedXString.Rdash.method) 2159 0 R (Rfn.vmatchPDict,XString.Rdash.method) 2160 0 R (Rfn.vmatchPattern) 2192 0 R] /Limits [(Rfn.vcountPattern,character.Rdash.method) (Rfn.vmatchPattern)] >> endobj 4473 0 obj << /Names [(Rfn.vmatchPattern,MaskedXString.Rdash.method) 2355 0 R (Rfn.vmatchPattern,XString.Rdash.method) 2356 0 R (Rfn.vmatchPattern,XStringSet.Rdash.method) 2357 0 R (Rfn.vmatchPattern,XStringViews.Rdash.method) 2358 0 R (Rfn.vmatchPattern,character.Rdash.method) 2354 0 R (Rfn.vwhichPDict) 2161 0 R] /Limits [(Rfn.vmatchPattern,MaskedXString.Rdash.method) (Rfn.vwhichPDict)] >> endobj 4474 0 obj << /Names [(Rfn.vwhichPDict,MaskedXString.Rdash.method) 2162 0 R (Rfn.vwhichPDict,XString.Rdash.method) 2163 0 R (Rfn.vwhichPDict,XStringSet.Rdash.method) 2164 0 R (Rfn.vwhichPDict,XStringViews.Rdash.method) 2165 0 R (Rfn.which.isMatchingAt) 1983 0 R (Rfn.which.isMatchingEndingAt) 1984 0 R] /Limits [(Rfn.vwhichPDict,MaskedXString.Rdash.method) (Rfn.which.isMatchingEndingAt)] >> endobj 4475 0 obj << /Names [(Rfn.which.isMatchingEndingAt,XString.Rdash.method) 1986 0 R (Rfn.which.isMatchingEndingAt,XStringSet.Rdash.method) 1987 0 R (Rfn.which.isMatchingEndingAt,character.Rdash.method) 1985 0 R (Rfn.which.isMatchingStartingAt) 1988 0 R (Rfn.which.isMatchingStartingAt,XString.Rdash.method) 1990 0 R (Rfn.which.isMatchingStartingAt,XStringSet.Rdash.method) 1991 0 R] /Limits [(Rfn.which.isMatchingEndingAt,XString.Rdash.method) (Rfn.which.isMatchingStartingAt,XStringSet.Rdash.method)] >> endobj 4476 0 obj << /Names [(Rfn.which.isMatchingStartingAt,character.Rdash.method) 1989 0 R (Rfn.whichPDict) 2166 0 R (Rfn.whichPDict,MaskedXString.Rdash.method) 2167 0 R (Rfn.whichPDict,XString.Rdash.method) 2168 0 R (Rfn.whichPDict,XStringSet.Rdash.method) 2169 0 R (Rfn.whichPDict,XStringViews.Rdash.method) 2170 0 R] /Limits [(Rfn.which.isMatchingStartingAt,character.Rdash.method) (Rfn.whichPDict,XStringViews.Rdash.method)] >> endobj 4477 0 obj << /Names [(Rfn.width,AlignedXStringSet0.Rdash.method) 358 0 R (Rfn.width,PDict.Rdash.method) 727 0 R (Rfn.width,PDict3Parts.Rdash.method) 728 0 R (Rfn.width,PreprocessedTB.Rdash.method) 729 0 R (Rfn.width,character.Rdash.method) 1243 0 R (Rfn.width0) 531 0 R] /Limits [(Rfn.width,AlignedXStringSet0.Rdash.method) (Rfn.width0)] >> endobj 4478 0 obj << /Names [(Rfn.width0,MIndex.Rdash.method) 532 0 R (Rfn.write.BStringViews) 1329 0 R (Rfn.write.XStringSet) 1330 0 R (Rfn.write.XStringViews) 1331 0 R (Rfn.write.table) 2729 0 R (Rfn.writeFASTA) 1372 0 R] /Limits [(Rfn.width0,MIndex.Rdash.method) (Rfn.writeFASTA)] >> endobj 4479 0 obj << /Names [(Rfn.wtPhiX174) 2634 0 R (Rfn.xsbasetype,AAString.Rdash.method) 1083 0 R (Rfn.xsbasetype,AlignedXStringSet0.Rdash.method) 359 0 R (Rfn.xsbasetype,BString.Rdash.method) 1084 0 R (Rfn.xsbasetype,DNAString.Rdash.method) 1085 0 R (Rfn.xsbasetype,MaskedXString.Rdash.method) 621 0 R] /Limits [(Rfn.wtPhiX174) (Rfn.xsbasetype,MaskedXString.Rdash.method)] >> endobj 4480 0 obj << /Names [(Rfn.xsbasetype,PairwiseAlignedXStringSet.Rdash.method) 813 0 R (Rfn.xsbasetype,RNAString.Rdash.method) 1086 0 R (Rfn.xsbasetype,WCP.Rdash.method) 980 0 R (Rfn.xsbasetype,XKeySortedData.Rdash.method) 1021 0 R (Rfn.xsbasetype,XKeySortedDataList.Rdash.method) 1042 0 R (Rfn.xsbasetype,XStringSet.Rdash.method) 1244 0 R] /Limits [(Rfn.xsbasetype,PairwiseAlignedXStringSet.Rdash.method) (Rfn.xsbasetype,XStringSet.Rdash.method)] >> endobj 4481 0 obj << /Names [(Rfn.xsbasetype,XStringSetList.Rdash.method) 1405 0 R (Rfn.xsbasetype,XStringViews.Rdash.method) 1452 0 R (Rfn.xsbasetype<.Rdash.,MaskedXString.Rdash.method) 622 0 R (Rfn.xsbasetype<.Rdash.,XString.Rdash.method) 1087 0 R (Rfn.xsbasetype<.Rdash.,XStringSet.Rdash.method) 1245 0 R (Rfn.xsbasetype<.Rdash.,XStringSetList.Rdash.method) 1406 0 R] /Limits [(Rfn.xsbasetype,XStringSetList.Rdash.method) (Rfn.xsbasetype<.Rdash.,XStringSetList.Rdash.method)] >> endobj 4482 0 obj << /Names [(Rfn.xsbasetype<.Rdash.,XStringViews.Rdash.method) 1453 0 R (Rfn.xscat) 3066 0 R (Rfn.xscat.1) 270 0 R (Rfn.yeastSEQCHR1) 3092 0 R (Rfn.yeastSEQCHR1.1) 274 0 R (chapter*.1) 300 0 R] /Limits [(Rfn.xsbasetype<.Rdash.,XStringViews.Rdash.method) (chapter*.1)] >> endobj 4483 0 obj << /Names [(index.0) 278 0 R (page.1) 298 0 R (page.10) 565 0 R (page.100) 2701 0 R (page.101) 2717 0 R (page.102) 2748 0 R] /Limits [(index.0) (page.102)] >> endobj 4484 0 obj << /Names [(page.103) 2779 0 R (page.104) 2822 0 R (page.105) 2832 0 R (page.106) 2843 0 R (page.107) 2855 0 R (page.108) 2873 0 R] /Limits [(page.103) (page.108)] >> endobj 4485 0 obj << /Names [(page.109) 2900 0 R (page.11) 644 0 R (page.110) 2924 0 R (page.111) 2937 0 R (page.112) 2949 0 R (page.113) 2982 0 R] /Limits [(page.109) (page.113)] >> endobj 4486 0 obj << /Names [(page.114) 3015 0 R (page.115) 3041 0 R (page.116) 3061 0 R (page.117) 3079 0 R (page.118) 3091 0 R (page.119) 3169 0 R] /Limits [(page.114) (page.119)] >> endobj 4487 0 obj << /Names [(page.12) 663 0 R (page.120) 3249 0 R (page.121) 3300 0 R (page.122) 3352 0 R (page.123) 3406 0 R (page.124) 3464 0 R] /Limits [(page.12) (page.124)] >> endobj 4488 0 obj << /Names [(page.125) 3521 0 R (page.126) 3577 0 R (page.127) 3630 0 R (page.128) 3685 0 R (page.129) 3738 0 R (page.13) 744 0 R] /Limits [(page.125) (page.13)] >> endobj 4489 0 obj << /Names [(page.130) 3802 0 R (page.131) 3856 0 R (page.132) 3903 0 R (page.133) 3963 0 R (page.134) 4010 0 R (page.135) 4062 0 R] /Limits [(page.130) (page.135)] >> endobj 4490 0 obj << /Names [(page.136) 4118 0 R (page.137) 4173 0 R (page.138) 4230 0 R (page.139) 4259 0 R (page.14) 759 0 R (page.15) 769 0 R] 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(page.46) 1667 0 R (page.47) 1690 0 R (page.48) 1704 0 R] /Limits [(page.43) (page.48)] >> endobj 4497 0 obj << /Names [(page.49) 1743 0 R (page.5) 424 0 R (page.50) 1757 0 R (page.51) 1781 0 R (page.52) 1808 0 R (page.53) 1833 0 R] /Limits [(page.49) (page.53)] >> endobj 4498 0 obj << /Names [(page.54) 1890 0 R (page.55) 1906 0 R (page.56) 1927 0 R (page.57) 1939 0 R (page.58) 1946 0 R (page.59) 1957 0 R] /Limits [(page.54) (page.59)] >> endobj 4499 0 obj << /Names [(page.6) 448 0 R (page.60) 2006 0 R (page.61) 2018 0 R (page.62) 2032 0 R (page.63) 2039 0 R (page.64) 2055 0 R] /Limits [(page.6) (page.64)] >> endobj 4500 0 obj << /Names [(page.65) 2066 0 R (page.66) 2088 0 R (page.67) 2115 0 R (page.68) 2137 0 R (page.69) 2187 0 R (page.7) 460 0 R] /Limits [(page.65) (page.7)] >> endobj 4501 0 obj << /Names [(page.70) 2205 0 R (page.71) 2222 0 R (page.72) 2231 0 R (page.73) 2235 0 R (page.74) 2240 0 R (page.75) 2244 0 R] /Limits [(page.70) (page.75)] >> endobj 4502 0 obj << /Names [(page.76) 2251 0 R (page.77) 2261 0 R (page.78) 2270 0 R (page.79) 2274 0 R (page.8) 481 0 R (page.80) 2311 0 R] /Limits [(page.76) (page.80)] >> endobj 4503 0 obj << /Names [(page.81) 2321 0 R (page.82) 2337 0 R (page.83) 2380 0 R (page.84) 2389 0 R (page.85) 2397 0 R (page.86) 2414 0 R] /Limits [(page.81) (page.86)] >> endobj 4504 0 obj << /Names [(page.87) 2448 0 R (page.88) 2464 0 R (page.89) 2482 0 R (page.9) 510 0 R (page.90) 2502 0 R (page.91) 2520 0 R] /Limits [(page.87) (page.91)] >> endobj 4505 0 obj << /Names [(page.92) 2555 0 R (page.93) 2565 0 R (page.94) 2574 0 R (page.95) 2602 0 R (page.96) 2621 0 R (page.97) 2630 0 R] /Limits [(page.92) (page.97)] >> endobj 4506 0 obj << /Names [(page.98) 2647 0 R (page.99) 2668 0 R (section*.10) 330 0 R (section*.100) 881 0 R (section*.101) 903 0 R (section*.102) 904 0 R] /Limits [(page.98) (section*.102)] >> endobj 4507 0 obj << /Names [(section*.103) 905 0 R (section*.104) 906 0 R (section*.105) 925 0 R (section*.106) 926 0 R (section*.107) 927 0 R (section*.108) 928 0 R] /Limits [(section*.103) (section*.108)] >> endobj 4508 0 obj << /Names [(section*.109) 930 0 R (section*.11) 331 0 R (section*.110) 934 0 R (section*.111) 935 0 R (section*.112) 957 0 R (section*.113) 958 0 R] /Limits [(section*.109) (section*.113)] >> endobj 4509 0 obj << /Names [(section*.114) 959 0 R (section*.115) 960 0 R (section*.116) 961 0 R (section*.117) 962 0 R (section*.118) 981 0 R (section*.119) 997 0 R] /Limits [(section*.114) (section*.119)] >> endobj 4510 0 obj << /Names [(section*.12) 332 0 R (section*.120) 998 0 R (section*.121) 1024 0 R (section*.122) 1025 0 R (section*.123) 1026 0 R (section*.124) 1043 0 R] /Limits [(section*.12) (section*.124)] >> endobj 4511 0 obj << /Names [(section*.125) 1044 0 R (section*.126) 1045 0 R (section*.127) 1088 0 R (section*.128) 1089 0 R (section*.129) 1090 0 R (section*.13) 362 0 R] /Limits [(section*.125) (section*.13)] >> endobj 4512 0 obj << /Names [(section*.130) 1091 0 R (section*.131) 1092 0 R (section*.132) 1109 0 R (section*.133) 1110 0 R (section*.134) 1112 0 R (section*.135) 1113 0 R] /Limits [(section*.130) (section*.135)] >> endobj 4513 0 obj << /Names [(section*.136) 1115 0 R (section*.137) 1135 0 R (section*.138) 1136 0 R (section*.139) 1137 0 R (section*.14) 363 0 R (section*.140) 1138 0 R] /Limits [(section*.136) (section*.140)] >> endobj 4514 0 obj << /Names [(section*.141) 1139 0 R (section*.142) 1178 0 R (section*.143) 1179 0 R (section*.144) 1180 0 R (section*.145) 1181 0 R (section*.146) 1182 0 R] /Limits [(section*.141) (section*.146)] >> endobj 4515 0 obj << /Names [(section*.147) 1183 0 R (section*.148) 1184 0 R (section*.149) 1246 0 R (section*.15) 372 0 R (section*.150) 1247 0 R (section*.151) 1248 0 R] /Limits [(section*.147) (section*.151)] >> endobj 4516 0 obj << /Names [(section*.152) 1249 0 R (section*.153) 1271 0 R (section*.154) 1272 0 R (section*.155) 1273 0 R (section*.156) 1284 0 R (section*.157) 1285 0 R] /Limits [(section*.152) (section*.157)] >> endobj 4517 0 obj << /Names [(section*.158) 1286 0 R (section*.159) 1287 0 R (section*.16) 373 0 R (section*.160) 1288 0 R (section*.161) 1299 0 R (section*.162) 1300 0 R] /Limits [(section*.158) (section*.162)] >> endobj 4518 0 obj << /Names [(section*.163) 1301 0 R (section*.164) 1302 0 R (section*.165) 1333 0 R (section*.166) 1334 0 R (section*.167) 1349 0 R (section*.168) 1368 0 R] /Limits [(section*.163) (section*.168)] >> endobj 4519 0 obj << /Names [(section*.169) 1369 0 R (section*.17) 385 0 R (section*.170) 1371 0 R (section*.171) 1410 0 R (section*.172) 1411 0 R (section*.173) 1413 0 R] /Limits [(section*.169) (section*.173)] >> endobj 4520 0 obj << /Names [(section*.174) 1414 0 R (section*.175) 1415 0 R (section*.176) 1416 0 R (section*.177) 1454 0 R (section*.178) 1455 0 R (section*.179) 1456 0 R] /Limits [(section*.174) (section*.179)] >> endobj 4521 0 obj << /Names [(section*.18) 386 0 R (section*.180) 1457 0 R (section*.181) 1474 0 R (section*.182) 1475 0 R (section*.183) 1476 0 R (section*.184) 1478 0 R] /Limits [(section*.18) (section*.184)] >> endobj 4522 0 obj << /Names [(section*.185) 1498 0 R (section*.186) 1499 0 R (section*.187) 1509 0 R (section*.188) 1510 0 R (section*.189) 1511 0 R (section*.19) 387 0 R] /Limits [(section*.185) (section*.19)] >> endobj 4523 0 obj << /Names [(section*.190) 1512 0 R (section*.191) 1513 0 R (section*.192) 1541 0 R (section*.193) 1542 0 R (section*.194) 1561 0 R (section*.195) 1562 0 R] /Limits [(section*.190) (section*.195)] >> endobj 4524 0 obj << /Names [(section*.196) 1563 0 R (section*.197) 1574 0 R (section*.198) 1577 0 R (section*.199) 1578 0 R (section*.2) 309 0 R (section*.20) 399 0 R] /Limits [(section*.196) (section*.20)] >> endobj 4525 0 obj << /Names [(section*.200) 1579 0 R (section*.201) 1580 0 R (section*.202) 1581 0 R (section*.203) 1582 0 R (section*.204) 1607 0 R (section*.205) 1608 0 R] /Limits [(section*.200) (section*.205)] >> endobj 4526 0 obj << /Names [(section*.206) 1614 0 R (section*.207) 1615 0 R (section*.208) 1616 0 R (section*.209) 1617 0 R (section*.21) 400 0 R (section*.210) 1623 0 R] /Limits [(section*.206) (section*.210)] >> endobj 4527 0 obj << /Names [(section*.211) 1624 0 R (section*.212) 1626 0 R (section*.213) 1628 0 R (section*.214) 1629 0 R (section*.215) 1630 0 R (section*.216) 1641 0 R] /Limits [(section*.211) (section*.216)] >> endobj 4528 0 obj << /Names [(section*.217) 1642 0 R (section*.218) 1643 0 R (section*.219) 1644 0 R (section*.22) 405 0 R (section*.220) 1645 0 R (section*.221) 1655 0 R] /Limits [(section*.217) (section*.221)] >> endobj 4529 0 obj << /Names [(section*.222) 1656 0 R (section*.223) 1657 0 R (section*.224) 1658 0 R (section*.225) 1668 0 R (section*.226) 1669 0 R (section*.227) 1670 0 R] /Limits [(section*.222) (section*.227)] >> endobj 4530 0 obj << /Names [(section*.228) 1671 0 R (section*.229) 1672 0 R (section*.23) 406 0 R (section*.230) 1676 0 R (section*.231) 1677 0 R (section*.232) 1691 0 R] /Limits [(section*.228) (section*.232)] >> endobj 4531 0 obj << /Names [(section*.233) 1692 0 R (section*.234) 1693 0 R (section*.235) 1694 0 R (section*.236) 1696 0 R (section*.237) 1731 0 R (section*.238) 1732 0 R] /Limits [(section*.233) (section*.238)] >> endobj 4532 0 obj << /Names [(section*.239) 1744 0 R (section*.24) 425 0 R (section*.240) 1745 0 R (section*.241) 1746 0 R (section*.242) 1758 0 R (section*.243) 1759 0 R] /Limits [(section*.239) (section*.243)] >> endobj 4533 0 obj << /Names [(section*.244) 1760 0 R (section*.245) 1762 0 R (section*.246) 1763 0 R (section*.247) 1764 0 R (section*.248) 1765 0 R (section*.249) 1782 0 R] /Limits [(section*.244) (section*.249)] >> endobj 4534 0 obj << /Names [(section*.25) 426 0 R (section*.250) 1783 0 R (section*.251) 1784 0 R (section*.252) 1787 0 R (section*.253) 1788 0 R (section*.254) 1789 0 R] /Limits [(section*.25) (section*.254)] >> endobj 4535 0 obj << /Names [(section*.255) 1790 0 R (section*.256) 1809 0 R (section*.257) 1810 0 R (section*.258) 1811 0 R (section*.259) 1812 0 R (section*.26) 427 0 R] /Limits [(section*.255) (section*.26)] >> endobj 4536 0 obj << /Names [(section*.260) 1817 0 R (section*.261) 1818 0 R (section*.262) 1834 0 R (section*.263) 1835 0 R (section*.264) 1836 0 R (section*.265) 1837 0 R] /Limits [(section*.260) (section*.265)] >> endobj 4537 0 obj << /Names [(section*.266) 1838 0 R (section*.267) 1875 0 R (section*.268) 1891 0 R (section*.269) 1892 0 R (section*.27) 428 0 R (section*.270) 1907 0 R] /Limits [(section*.266) (section*.270)] >> endobj 4538 0 obj << /Names [(section*.271) 1928 0 R (section*.272) 1929 0 R (section*.273) 1930 0 R (section*.274) 1932 0 R (section*.275) 1948 0 R (section*.276) 1949 0 R] /Limits [(section*.271) (section*.276)] >> endobj 4539 0 obj << /Names [(section*.277) 1950 0 R (section*.278) 1951 0 R (section*.279) 1952 0 R (section*.28) 429 0 R (section*.280) 1953 0 R (section*.281) 1958 0 R] /Limits [(section*.277) (section*.281)] >> endobj 4540 0 obj << /Names [(section*.282) 1959 0 R (section*.283) 1992 0 R (section*.284) 1993 0 R (section*.285) 2007 0 R (section*.286) 2008 0 R (section*.287) 2019 0 R] /Limits [(section*.282) (section*.287)] >> endobj 4541 0 obj << /Names [(section*.288) 2033 0 R (section*.289) 2034 0 R (section*.29) 430 0 R (section*.290) 2044 0 R (section*.291) 2056 0 R (section*.292) 2057 0 R] /Limits [(section*.288) (section*.292)] >> endobj 4542 0 obj << /Names [(section*.293) 2058 0 R (section*.294) 2059 0 R (section*.295) 2060 0 R (section*.296) 2061 0 R (section*.297) 2097 0 R (section*.298) 2098 0 R] /Limits [(section*.293) (section*.298)] >> endobj 4543 0 obj << /Names [(section*.299) 2099 0 R (section*.3) 310 0 R (section*.30) 432 0 R (section*.300) 2100 0 R (section*.301) 2101 0 R (section*.302) 2102 0 R] /Limits [(section*.299) (section*.302)] >> endobj 4544 0 obj << /Names [(section*.303) 2116 0 R (section*.304) 2120 0 R (section*.305) 2121 0 R (section*.306) 2122 0 R (section*.307) 2138 0 R (section*.308) 2139 0 R] /Limits [(section*.303) (section*.308)] >> endobj 4545 0 obj << /Names [(section*.309) 2140 0 R (section*.31) 433 0 R (section*.310) 2141 0 R (section*.311) 2188 0 R (section*.312) 2189 0 R (section*.313) 2190 0 R] /Limits [(section*.309) (section*.313)] >> endobj 4546 0 obj << /Names [(section*.314) 2207 0 R (section*.315) 2208 0 R (section*.316) 2223 0 R (section*.317) 2224 0 R (section*.318) 2225 0 R (section*.319) 2227 0 R] /Limits [(section*.314) (section*.319)] >> endobj 4547 0 obj << /Names [(section*.32) 449 0 R (section*.320) 2252 0 R (section*.321) 2262 0 R (section*.322) 2263 0 R (section*.323) 2264 0 R (section*.324) 2265 0 R] /Limits [(section*.32) (section*.324)] >> endobj 4548 0 obj << /Names [(section*.325) 2266 0 R (section*.326) 2300 0 R (section*.327) 2301 0 R (section*.328) 2312 0 R (section*.329) 2313 0 R (section*.33) 450 0 R] /Limits [(section*.325) (section*.33)] >> endobj 4549 0 obj << /Names [(section*.330) 2322 0 R (section*.331) 2323 0 R (section*.332) 2324 0 R (section*.333) 2325 0 R (section*.334) 2326 0 R (section*.335) 2359 0 R] /Limits [(section*.330) (section*.335)] >> endobj 4550 0 obj << /Names [(section*.336) 2360 0 R (section*.337) 2361 0 R (section*.338) 2381 0 R (section*.339) 2382 0 R (section*.34) 451 0 R (section*.340) 2383 0 R] /Limits [(section*.336) (section*.340)] >> endobj 4551 0 obj << /Names [(section*.341) 2384 0 R (section*.342) 2385 0 R (section*.343) 2401 0 R (section*.344) 2402 0 R (section*.345) 2403 0 R (section*.346) 2415 0 R] /Limits [(section*.341) (section*.346)] >> endobj 4552 0 obj << /Names [(section*.347) 2416 0 R (section*.348) 2417 0 R (section*.349) 2418 0 R (section*.35) 452 0 R (section*.350) 2419 0 R (section*.351) 2430 0 R] /Limits [(section*.347) (section*.351)] >> endobj 4553 0 obj << /Names [(section*.352) 2449 0 R (section*.353) 2450 0 R (section*.354) 2451 0 R (section*.355) 2452 0 R (section*.356) 2453 0 R (section*.357) 2455 0 R] 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