Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / muscle / enums.h

diff --git a/website/archive/binaries/mac/src/muscle/enums.h b/website/archive/binaries/mac/src/muscle/enums.h
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+// enums.h\r
+// Define enum types.\r
+// Exploit macro hacks to avoid lots of repetetive typing.\r
+// Generally I am opposed to macro hacks because of the\r
+// highly obscure code that results, but in this case it\r
+// makes maintenance much easier and less error-prone.\r
+// The idea is that this file can be included in different\r
+// places with different definitions of s (Start), c (Case)\r
+// and e (End). See types.h.\r
+\r
+s(ALPHA)\r
+c(ALPHA, Amino)\r
+c(ALPHA, DNA)\r
+c(ALPHA, RNA)\r
+e(ALPHA)\r
+\r
+s(SEQTYPE)\r
+c(SEQTYPE, Protein)\r
+c(SEQTYPE, DNA)\r
+c(SEQTYPE, RNA)\r
+c(SEQTYPE, Auto)\r
+e(SEQTYPE)\r
+\r
+s(ROOT)\r
+c(ROOT, Pseudo)\r
+c(ROOT, MidLongestSpan)\r
+c(ROOT, MinAvgLeafDist)\r
+e(ROOT)\r
+\r
+s(CLUSTER)\r
+c(CLUSTER, UPGMA)\r
+c(CLUSTER, UPGMAMax)\r
+c(CLUSTER, UPGMAMin)\r
+c(CLUSTER, UPGMB)\r
+c(CLUSTER, NeighborJoining)\r
+e(CLUSTER)\r
+\r
+s(JOIN)\r
+c(JOIN, NearestNeighbor)\r
+c(JOIN, NeighborJoining)\r
+e(JOIN)\r
+\r
+s(LINKAGE)\r
+c(LINKAGE, Min)\r
+c(LINKAGE, Avg)\r
+c(LINKAGE, Max)\r
+c(LINKAGE, NeighborJoining)\r
+c(LINKAGE, Biased)\r
+e(LINKAGE)\r
+\r
+s(DISTANCE)\r
+c(DISTANCE, Kmer6_6)\r
+c(DISTANCE, Kmer20_3)\r
+c(DISTANCE, Kmer20_4)\r
+c(DISTANCE, Kbit20_3)\r
+c(DISTANCE, Kmer4_6)\r
+c(DISTANCE, PctIdKimura)\r
+c(DISTANCE, PctIdLog)\r
+c(DISTANCE, PWKimura)\r
+c(DISTANCE, PWScoreDist)\r
+c(DISTANCE, ScoreDist)\r
+c(DISTANCE, Edit)\r
+e(DISTANCE)\r
+\r
+s(PPSCORE)\r
+c(PPSCORE, LE)\r
+c(PPSCORE, SP)\r
+c(PPSCORE, SV)\r
+c(PPSCORE, SPN)\r
+e(PPSCORE)\r
+\r
+s(SEQWEIGHT)\r
+c(SEQWEIGHT, None)\r
+c(SEQWEIGHT, Henikoff)\r
+c(SEQWEIGHT, HenikoffPB)\r
+c(SEQWEIGHT, GSC)\r
+c(SEQWEIGHT, ClustalW)\r
+c(SEQWEIGHT, ThreeWay)\r
+e(SEQWEIGHT)\r
+\r
+s(OBJSCORE)\r
+c(OBJSCORE, SP)                                // Sum of Pairs of sequences\r
+c(OBJSCORE, DP)                                // Dynamic Programming score\r
+c(OBJSCORE, XP)                                // Cross Pairs = sum of pairs between two MSAs\r
+c(OBJSCORE, PS)                                // sum of Prof-Seq score for all seqs in MSA\r
+c(OBJSCORE, SPF)                       // sum of pairs, fast approximation\r
+c(OBJSCORE, SPM)                       // sp if <= 100 seqs, spf otherwise\r
+e(OBJSCORE)\r
+\r
+s(TERMGAPS)\r
+c(TERMGAPS, Full)\r
+c(TERMGAPS, Half)\r
+c(TERMGAPS, Ext)\r
+e(TERMGAPS)\r
+\r
+#undef s\r
+#undef c\r
+#undef e\r