1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
|
#include "libMUSCLE/muscle.h"
#include "libMUSCLE/msa.h"
#include "libMUSCLE/params.h"
#include "libMUSCLE/textfile.h"
namespace muscle {
static void DoOutput(MSA &msa)
{
bool AnyOutput = false;
// Value options
if (g_pstrFASTAOutFileName.get())
{
TextFile File(g_pstrFASTAOutFileName.get(), true);
msa.ToFASTAFile(File);
AnyOutput = true;
}
if (g_pstrMSFOutFileName.get())
{
TextFile File(g_pstrMSFOutFileName.get(), true);
msa.ToMSFFile(File);
AnyOutput = true;
}
if (g_pstrClwOutFileName.get())
{
TextFile File(g_pstrClwOutFileName.get(), true);
msa.ToAlnFile(File);
AnyOutput = true;
}
if (g_pstrClwStrictOutFileName.get())
{
g_bClwStrict.get() = true;
TextFile File(g_pstrClwStrictOutFileName.get(), true);
msa.ToAlnFile(File);
AnyOutput = true;
}
if (g_pstrHTMLOutFileName.get())
{
TextFile File(g_pstrHTMLOutFileName.get(), true);
msa.ToHTMLFile(File);
AnyOutput = true;
}
if (g_pstrPHYIOutFileName.get())
{
TextFile File(g_pstrPHYIOutFileName.get(), true);
msa.ToPhyInterleavedFile(File);
AnyOutput = true;
}
if (g_pstrPHYSOutFileName.get())
{
TextFile File(g_pstrPHYSOutFileName.get(), true);
msa.ToPhySequentialFile(File);
AnyOutput = true;
}
// Flag options, at most one used (because only one -out filename)
TextFile fileOut(g_pstrOutFileName.get(), true);
if (g_bFASTA.get())
{
msa.ToFASTAFile(fileOut);
AnyOutput = true;
}
else if (g_bMSF.get())
{
msa.ToMSFFile(fileOut);
AnyOutput = true;
}
else if (g_bAln.get())
{
msa.ToAlnFile(fileOut);
AnyOutput = true;
}
else if (g_bHTML.get())
{
msa.ToHTMLFile(fileOut);
AnyOutput = true;
}
else if (g_bPHYI.get())
{
msa.ToPhyInterleavedFile(fileOut);
AnyOutput = true;
}
else if (g_bPHYS.get())
{
msa.ToPhySequentialFile(fileOut);
AnyOutput = true;
}
// If -out option was given but no flags, output as FASTA
if (!AnyOutput && strcmp(g_pstrOutFileName.get(), "-") != 0)
msa.ToFASTAFile(fileOut);
fileOut.Close();
if (0 != g_pstrScoreFileName.get())
WriteScoreFile(msa);
}
void MuscleOutput(MSA &msa)
{
if( strcmp(g_pstrOutFileName.get(),"-")==0 )
g_bFASTA.get() = true;
MHackEnd(msa);
if (g_bStable.get())
{
MSA msaStable;
Stabilize(msa, msaStable);
msa.Clear(); // save memory
DoOutput(msaStable);
}
else
DoOutput(msa);
}
}
|
