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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/textfile.h"
#include "libMUSCLE/msa.h"
#include "libMUSCLE/tree.h"
#include "libMUSCLE/profile.h"
#include "libMUSCLE/objscore.h"
namespace muscle {
bool TreeNeededForWeighting(SEQWEIGHT s)
{
switch (s)
{
case SEQWEIGHT_ClustalW:
case SEQWEIGHT_ThreeWay:
return true;
default:
return false;
}
}
static ProfPos *ProfileFromMSALocal(MSA &msa, Tree &tree)
{
const unsigned uSeqCount = msa.GetSeqCount();
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
msa.SetSeqId(uSeqIndex, uSeqIndex);
if (TreeNeededForWeighting(g_SeqWeight2.get()))
{
TreeFromMSA(msa, tree, g_Cluster2.get(), g_Distance2.get(), g_Root1.get());
SetMuscleTree(tree);
}
return ProfileFromMSA(msa);
}
void SetProfileProfileAlphabet(MSA &msa1, MSA &msa2)
{
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType.get())
{
case SEQTYPE_Auto:
Alpha = msa1.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
default:
Quit("Invalid SeqType");
}
SetAlpha(Alpha);
msa1.FixAlpha();
msa2.FixAlpha();
if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
SetPPScore(PPSCORE_SPN);
}
void ProfileProfile(MSA &msa1, MSA &msa2, MSA &msaOut)
{
unsigned uLength1;
unsigned uLength2;
uLength1 = msa1.GetColCount();
uLength2 = msa2.GetColCount();
Tree tree1;
Tree tree2;
ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1);
ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2);
PWPath Path;
ProfPos *ProfOut;
unsigned uLengthOut;
Progress("Aligning profiles");
AlignTwoProfs(Prof1, uLength1, 1.0, Prof2, uLength2, 1.0, Path, &ProfOut, &uLengthOut);
Progress("Building output");
AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);
delete[] Prof1;
delete[] Prof2;
delete[] ProfOut;
}
// Do profile-profile alignment
void Profile()
{
if ( !g_bProfileOnStdIn.get() && (0 == g_pstrFileName1.get() || 0 == g_pstrFileName2.get()))
Quit("-profile needs -in1 and -in2 or -ProfileOnStdIn");
SetSeqWeightMethod(g_SeqWeight1.get());
MSA msa1;
MSA msa2;
MSA msaOut;
if( !g_bProfileOnStdIn.get() )
{
TextFile file1(g_pstrFileName1.get());
TextFile file2(g_pstrFileName2.get());
msa1.FromFile(file1);
msa2.FromFile(file2);
}else{
TextFile file1("-");
TextFile file2("-");
msa1.FromFile(file1);
msa2.FromFile(file2);
}
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType.get())
{
case SEQTYPE_Auto:
Alpha = msa1.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
default:
Quit("Invalid seq type");
}
SetAlpha(Alpha);
msa1.FixAlpha();
msa2.FixAlpha();
SetPPScore();
const unsigned uSeqCount1 = msa1.GetSeqCount();
const unsigned uSeqCount2 = msa2.GetSeqCount();
//const unsigned uMaxSeqCount = (uSeqCount1 > uSeqCount2 ? uSeqCount1 : uSeqCount2);
//MSA::SetIdCount(uMaxSeqCount);
const unsigned uSumSeqCount = uSeqCount1 + uSeqCount2;
MSA::SetIdCount(uSumSeqCount);
SetProfileProfileAlphabet(msa1, msa2);
if( g_bAnchoredPP.get() )
AnchoredProfileProfile(msa1, msa2, msaOut);
else
ProfileProfile(msa1, msa2, msaOut);
MuscleOutput(msaOut);
}
}
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