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| 1 | // enums.h |
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| 2 | // Define enum types. |
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| 3 | // Exploit macro hacks to avoid lots of repetetive typing. |
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| 4 | // Generally I am opposed to macro hacks because of the |
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| 5 | // highly obscure code that results, but in this case it |
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| 6 | // makes maintenance much easier and less error-prone. |
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| 7 | // The idea is that this file can be included in different |
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| 8 | // places with different definitions of s (Start), c (Case) |
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| 9 | // and e (End). See types.h. |
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| 10 | |
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| 11 | s(ALPHA) |
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| 12 | c(ALPHA, Amino) |
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| 13 | c(ALPHA, DNA) |
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| 14 | c(ALPHA, RNA) |
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| 15 | e(ALPHA) |
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| 16 | |
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| 17 | s(SEQTYPE) |
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| 18 | c(SEQTYPE, Protein) |
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| 19 | c(SEQTYPE, DNA) |
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| 20 | c(SEQTYPE, RNA) |
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| 21 | c(SEQTYPE, Auto) |
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| 22 | e(SEQTYPE) |
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| 23 | |
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| 24 | s(ROOT) |
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| 25 | c(ROOT, Pseudo) |
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| 26 | c(ROOT, MidLongestSpan) |
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| 27 | c(ROOT, MinAvgLeafDist) |
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| 28 | e(ROOT) |
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| 29 | |
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| 30 | s(CLUSTER) |
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| 31 | c(CLUSTER, UPGMA) |
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| 32 | c(CLUSTER, UPGMAMax) |
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| 33 | c(CLUSTER, UPGMAMin) |
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| 34 | c(CLUSTER, UPGMB) |
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| 35 | c(CLUSTER, NeighborJoining) |
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| 36 | e(CLUSTER) |
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| 37 | |
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| 38 | s(JOIN) |
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| 39 | c(JOIN, NearestNeighbor) |
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| 40 | c(JOIN, NeighborJoining) |
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| 41 | e(JOIN) |
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| 42 | |
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| 43 | s(LINKAGE) |
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| 44 | c(LINKAGE, Min) |
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| 45 | c(LINKAGE, Avg) |
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| 46 | c(LINKAGE, Max) |
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| 47 | c(LINKAGE, NeighborJoining) |
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| 48 | c(LINKAGE, Biased) |
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| 49 | e(LINKAGE) |
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| 50 | |
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| 51 | s(DISTANCE) |
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| 52 | c(DISTANCE, Kmer6_6) |
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| 53 | c(DISTANCE, Kmer20_3) |
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| 54 | c(DISTANCE, Kmer20_4) |
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| 55 | c(DISTANCE, Kbit20_3) |
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| 56 | c(DISTANCE, Kmer4_6) |
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| 57 | c(DISTANCE, PctIdKimura) |
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| 58 | c(DISTANCE, PctIdLog) |
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| 59 | c(DISTANCE, PWKimura) |
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| 60 | c(DISTANCE, PWScoreDist) |
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| 61 | c(DISTANCE, ScoreDist) |
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| 62 | c(DISTANCE, Edit) |
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| 63 | e(DISTANCE) |
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| 64 | |
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| 65 | s(PPSCORE) |
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| 66 | c(PPSCORE, LE) |
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| 67 | c(PPSCORE, SP) |
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| 68 | c(PPSCORE, SV) |
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| 69 | c(PPSCORE, SPN) |
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| 70 | e(PPSCORE) |
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| 71 | |
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| 72 | s(SEQWEIGHT) |
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| 73 | c(SEQWEIGHT, None) |
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| 74 | c(SEQWEIGHT, Henikoff) |
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| 75 | c(SEQWEIGHT, HenikoffPB) |
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| 76 | c(SEQWEIGHT, GSC) |
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| 77 | c(SEQWEIGHT, ClustalW) |
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| 78 | c(SEQWEIGHT, ThreeWay) |
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| 79 | e(SEQWEIGHT) |
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| 80 | |
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| 81 | s(OBJSCORE) |
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| 82 | c(OBJSCORE, SP) // Sum of Pairs of sequences |
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| 83 | c(OBJSCORE, DP) // Dynamic Programming score |
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| 84 | c(OBJSCORE, XP) // Cross Pairs = sum of pairs between two MSAs |
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| 85 | c(OBJSCORE, PS) // sum of Prof-Seq score for all seqs in MSA |
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| 86 | c(OBJSCORE, SPF) // sum of pairs, fast approximation |
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| 87 | c(OBJSCORE, SPM) // sp if <= 100 seqs, spf otherwise |
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| 88 | e(OBJSCORE) |
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| 89 | |
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| 90 | s(TERMGAPS) |
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| 91 | c(TERMGAPS, Full) |
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| 92 | c(TERMGAPS, Half) |
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| 93 | c(TERMGAPS, Ext) |
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| 94 | e(TERMGAPS) |
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| 95 | |
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| 96 | #undef s |
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| 97 | #undef c |
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| 98 | #undef e |
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