| 1 | #include "muscle.h" |
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| 2 | #include "seqvect.h" |
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| 3 | #include "distfunc.h" |
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| 4 | #include "clust.h" |
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| 5 | #include "clustsetdf.h" |
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| 6 | #include "tree.h" |
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| 7 | #include "clust.h" |
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| 8 | #include "distcalc.h" |
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| 9 | #include <math.h> |
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| 10 | |
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| 11 | static void TreeFromSeqVect_NJ(const DistFunc &DF, CLUSTER Cluster, Tree &tree) |
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| 12 | { |
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| 13 | ClustSetDF CSD(DF); |
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| 14 | |
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| 15 | Clust C; |
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| 16 | C.Create(CSD, Cluster); |
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| 17 | |
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| 18 | tree.FromClust(C); |
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| 19 | } |
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| 20 | |
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| 21 | static void TreeFromSeqVect_UPGMA(const DistFunc &DF, CLUSTER Cluster, Tree &tree) |
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| 22 | { |
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| 23 | LINKAGE Linkage = LINKAGE_Undefined; |
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| 24 | switch (Cluster) |
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| 25 | { |
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| 26 | case CLUSTER_UPGMA: |
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| 27 | Linkage = LINKAGE_Avg; |
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| 28 | break; |
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| 29 | case CLUSTER_UPGMAMin: |
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| 30 | Linkage = LINKAGE_Min; |
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| 31 | break; |
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| 32 | case CLUSTER_UPGMAMax: |
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| 33 | Linkage = LINKAGE_Max; |
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| 34 | break; |
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| 35 | case CLUSTER_UPGMB: |
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| 36 | Linkage = LINKAGE_Biased; |
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| 37 | break; |
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| 38 | default: |
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| 39 | Quit("TreeFromSeqVect_UPGMA, CLUSTER_%u not supported", Cluster); |
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| 40 | } |
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| 41 | |
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| 42 | DistCalcDF DC; |
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| 43 | DC.Init(DF); |
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| 44 | UPGMA2(DC, tree, Linkage); |
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| 45 | } |
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| 46 | |
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| 47 | static void SaveDF(const SeqVect &v, DistFunc &d, const char *FileName) |
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| 48 | { |
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| 49 | FILE *f = fopen(FileName, "w"); |
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| 50 | if (f == 0) |
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| 51 | Quit("Cannot create %s", FileName); |
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| 52 | |
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| 53 | unsigned n = v.GetSeqCount(); |
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| 54 | fprintf(f, "%u\n", n); |
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| 55 | for (unsigned i = 0; i < n; ++i) |
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| 56 | { |
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| 57 | fprintf(f, "%10.10s ", v.GetSeqName(i)); |
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| 58 | for (unsigned j = 0; j < i; ++j) |
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| 59 | fprintf(f, " %9g", d.GetDist(i, j)); |
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| 60 | fprintf(f, "\n"); |
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| 61 | } |
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| 62 | fclose(f); |
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| 63 | } |
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| 64 | |
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| 65 | void TreeFromSeqVect(const SeqVect &v, Tree &tree, CLUSTER Cluster, |
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| 66 | DISTANCE Distance, ROOT Root, const char *SaveFileName) |
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| 67 | { |
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| 68 | DistFunc DF; |
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| 69 | DistUnaligned(v, Distance, DF); |
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| 70 | if (SaveFileName != 0) |
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| 71 | SaveDF(v, DF, SaveFileName); |
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| 72 | if (CLUSTER_NeighborJoining == Cluster) |
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| 73 | TreeFromSeqVect_NJ(DF, Cluster, tree); |
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| 74 | else |
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| 75 | TreeFromSeqVect_UPGMA(DF, Cluster, tree); |
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| 76 | FixRoot(tree, Root); |
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| 77 | } |
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