| 1 | #include "muscle.h" |
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| 2 | #include "msa.h" |
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| 3 | #include "tree.h" |
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| 4 | #include "clust.h" |
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| 5 | #include "clustsetmsa.h" |
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| 6 | #include "distcalc.h" |
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| 7 | |
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| 8 | static void SaveMSADist(const MSA &msa, MSADist &d, const char *FileName) |
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| 9 | { |
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| 10 | FILE *f = fopen(FileName, "w"); |
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| 11 | if (f == 0) |
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| 12 | Quit("Cannot create %s", FileName); |
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| 13 | |
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| 14 | unsigned n = msa.GetSeqCount(); |
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| 15 | for (unsigned i = 0; i < n; ++i) |
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| 16 | { |
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| 17 | fprintf(f, "%10.10s ", msa.GetSeqName(i)); |
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| 18 | for (unsigned j = 0; j < n; ++j) |
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| 19 | fprintf(f, " %9g", d.ComputeDist(msa, i, j)); |
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| 20 | fprintf(f, "\n"); |
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| 21 | } |
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| 22 | fclose(f); |
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| 23 | } |
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| 24 | |
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| 25 | static void TreeFromMSA_NJ(const MSA &msa, Tree &tree, CLUSTER Cluster, |
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| 26 | DISTANCE Distance, const char *SaveFileName) |
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| 27 | { |
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| 28 | MSADist MD(Distance); |
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| 29 | ClustSetMSA Set(msa, MD); |
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| 30 | |
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| 31 | if (SaveFileName != 0) |
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| 32 | SaveMSADist(msa, MD, SaveFileName); |
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| 33 | |
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| 34 | Clust C; |
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| 35 | C.Create(Set, Cluster); |
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| 36 | |
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| 37 | tree.FromClust(C); |
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| 38 | } |
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| 39 | |
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| 40 | static void SaveDC(const DistCalcMSA &DC, const char *FileName) |
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| 41 | { |
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| 42 | FILE *f = fopen(FileName, "w"); |
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| 43 | if (f == 0) |
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| 44 | Quit("Cannot create %s", FileName); |
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| 45 | |
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| 46 | unsigned n = DC.GetCount(); |
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| 47 | fprintf(f, "%u\n", n); |
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| 48 | float *Dist = new float[n]; |
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| 49 | for (unsigned i = 0; i < n; ++i) |
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| 50 | { |
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| 51 | fprintf(f, "%10.10s ", DC.GetName(i)); |
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| 52 | DC.CalcDistRange(i, Dist); |
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| 53 | for (unsigned j = 0; j < i; ++j) |
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| 54 | fprintf(f, " %9g", Dist[j]); |
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| 55 | fprintf(f, "\n"); |
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| 56 | } |
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| 57 | fclose(f); |
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| 58 | } |
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| 59 | |
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| 60 | static void TreeFromMSA_UPGMA(const MSA &msa, Tree &tree, CLUSTER Cluster, |
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| 61 | DISTANCE Distance, const char *SaveFileName) |
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| 62 | { |
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| 63 | LINKAGE Linkage = LINKAGE_Undefined; |
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| 64 | switch (Cluster) |
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| 65 | { |
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| 66 | case CLUSTER_UPGMA: |
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| 67 | Linkage = LINKAGE_Avg; |
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| 68 | break; |
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| 69 | case CLUSTER_UPGMAMin: |
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| 70 | Linkage = LINKAGE_Min; |
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| 71 | break; |
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| 72 | case CLUSTER_UPGMAMax: |
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| 73 | Linkage = LINKAGE_Max; |
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| 74 | break; |
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| 75 | case CLUSTER_UPGMB: |
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| 76 | Linkage = LINKAGE_Biased; |
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| 77 | break; |
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| 78 | default: |
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| 79 | Quit("TreeFromMSA_UPGMA, CLUSTER_%u not supported", Cluster); |
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| 80 | } |
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| 81 | |
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| 82 | DistCalcMSA DC; |
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| 83 | DC.Init(msa, Distance); |
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| 84 | if (SaveFileName != 0) |
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| 85 | SaveDC(DC, SaveFileName); |
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| 86 | UPGMA2(DC, tree, Linkage); |
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| 87 | } |
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| 88 | |
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| 89 | void TreeFromMSA(const MSA &msa, Tree &tree, CLUSTER Cluster, |
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| 90 | DISTANCE Distance, ROOT Root, const char *SaveFileName) |
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| 91 | { |
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| 92 | if (CLUSTER_NeighborJoining == Cluster) |
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| 93 | TreeFromMSA_NJ(msa, tree, Cluster, Distance, SaveFileName); |
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| 94 | else |
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| 95 | TreeFromMSA_UPGMA(msa, tree, Cluster, Distance, SaveFileName); |
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| 96 | FixRoot(tree, Root); |
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| 97 | } |
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