1 #include "muscle.h"
2 #include "textfile.h"
3 #include "msa.h"
4 #include "profile.h"
5 #include "pwpath.h"
6 #include "tree.h"
7
8 #define TRACE 0
9
MSAFromFileName(const char * FileName,MSA & a)10 static void MSAFromFileName(const char *FileName, MSA &a)
11 {
12 TextFile File(FileName);
13 a.FromFile(File);
14 }
15
ProfileFromMSALocal(MSA & msa,Tree & tree)16 static ProfPos *ProfileFromMSALocal(MSA &msa, Tree &tree)
17 {
18 const unsigned uSeqCount = msa.GetSeqCount();
19 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
20 msa.SetSeqId(uSeqIndex, uSeqIndex);
21
22 TreeFromMSA(msa, tree, g_Cluster1, g_Distance1, g_Root1);
23 SetMuscleTree(tree);
24 return ProfileFromMSA(msa);
25 }
26
Local()27 void Local()
28 {
29 if (0 == g_pstrFileName1 || 0 == g_pstrFileName2)
30 Quit("Must specify both -in1 and -in2 for -sw");
31
32 SetSeqWeightMethod(g_SeqWeight1);
33
34 MSA msa1;
35 MSA msa2;
36
37 MSAFromFileName(g_pstrFileName1, msa1);
38 MSAFromFileName(g_pstrFileName2, msa2);
39
40 ALPHA Alpha = ALPHA_Undefined;
41 switch (g_SeqType)
42 {
43 case SEQTYPE_Auto:
44 Alpha = msa1.GuessAlpha();
45 break;
46
47 case SEQTYPE_Protein:
48 Alpha = ALPHA_Amino;
49 break;
50
51 case SEQTYPE_DNA:
52 Alpha = ALPHA_DNA;
53 break;
54
55 case SEQTYPE_RNA:
56 Alpha = ALPHA_RNA;
57 break;
58
59 default:
60 Quit("Invalid SeqType");
61 }
62 SetAlpha(Alpha);
63
64 msa1.FixAlpha();
65 msa2.FixAlpha();
66
67 if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
68 SetPPScore(PPSCORE_SPN);
69
70 const unsigned uSeqCount1 = msa1.GetSeqCount();
71 const unsigned uSeqCount2 = msa2.GetSeqCount();
72 const unsigned uMaxSeqCount = (uSeqCount1 > uSeqCount2 ? uSeqCount1 : uSeqCount2);
73 MSA::SetIdCount(uMaxSeqCount);
74
75 unsigned uLength1 = msa1.GetColCount();
76 unsigned uLength2 = msa2.GetColCount();
77
78 Tree tree1;
79 Tree tree2;
80
81 ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1);
82 ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2);
83
84 PWPath Path;
85 SW(Prof1, uLength1, Prof2, uLength2, Path);
86
87 #if TRACE
88 Path.LogMe();
89 #endif
90
91 MSA msaOut;
92 AlignTwoMSAsGivenPathSW(Path, msa1, msa2, msaOut);
93
94 #if TRACE
95 msaOut.LogMe();
96 #endif
97
98 TextFile fileOut(g_pstrOutFileName, true);
99 msaOut.ToFile(fileOut);
100 }
101