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Consegna progetto bioinformatica 2 #7

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126ee5b
Fixed Profile
andreanasari Jun 25, 2015
413f667
Fixed Profile (reverted from commit 126ee5b6533eedc536217a762a87f5b44…
andreanasari Sep 2, 2015
af1cb22
Added Phylogenesis package, fixed Align2
andreanasari Sep 2, 2015
9e8fe5f
fixed PhylogeneticTrees help
andreanasari Sep 2, 2015
eb8bc02
Fixed clustal output
andreanasari Sep 2, 2015
57c9c85
Refixed clustal output
andreanasari Sep 2, 2015
ff7d310
Fixed memory leak.
andreanasari Sep 17, 2015
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39 changes: 24 additions & 15 deletions Align2/APPS/subali.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@
#include <AtchleyDistance.h>
#include <AtchleyCorrelation.h>
#include <NWAlign.h>
#include <NWGAlign.h>
#include <SWAlign.h>
#include <FSAlign.h>
#include <SubMatrix.h>
Expand Down Expand Up @@ -101,6 +102,7 @@ sShowHelp() {
<< "\n \t --sf=8: AtchleyCorrelation."
<< "\n"
<< "\n [--global] \t Needleman-Wunsch global alignment (default)"
<< "\n [--gotoh] \t Needleman-Wunsch-Gotoh global alignment"
<< "\n [--local] \t Smith-Waterman local alignment"
<< "\n [--freeshift] \t Free-shift alignment"
<< "\n [-n <int>] \t Number of suboptimal alignments (default = 1)"
Expand Down Expand Up @@ -156,7 +158,7 @@ main(int argc, char **argv) {
double weightHelix, weightStrand, weightBuried, weightStraight, weightSpace;
double cSeq, cStr;
unsigned int weightingScheme, scoringFunction, suboptNum, gapFunction, extensionType, structure;
bool fasta, global, local, freeshift, verbose;
bool fasta, global, gotoh, local, freeshift, verbose;
struct tm* newtime;
time_t t;

Expand All @@ -182,9 +184,10 @@ main(int argc, char **argv) {
getArg("-sf", scoringFunction, argc, argv, 1);

global = getArg("-global", argc, argv);
gotoh = getArg("-gotoh", argc, argv);
local = getArg("-local", argc, argv);
freeshift = getArg("-freeshift", argc, argv);
if (!local && !freeshift)
if (!local && !freeshift && !gotoh)
global = true;
getArg("n", suboptNum, argc, argv, 1);
getArg("p", suboptPenaltyMul, argc, argv, 1.00);
Expand Down Expand Up @@ -539,20 +542,26 @@ main(int argc, char **argv) {
Align *a;

if (global) {
cout << "\nSuboptimal Needleman-Wunsch alignments:\n" << endl;
a = new NWAlign(ad, gf, ss);
cout << "\nSuboptimal Needleman-Wunsch alignments:\n" << endl;
a = new NWAlign(ad, gf, ss);
} else
if (local) {
cout << "\nSuboptimal Smith-Waterman alignments:\n" << endl;
a = new SWAlign(ad, gf, ss);
} else {
cout << "\nSuboptimal free-shift alignments:\n" << endl;
try {
a = new FSAlign(ad, gf, ss);
} catch (const char* a) {
cout << "FSAlign error!\n";
}
}
if (local) {
cout << "\nSuboptimal Smith-Waterman alignments:\n" << endl;
a = new SWAlign(ad, gf, ss);
}
else
if (gotoh) {
cout << "\nSuboptimal Needleman-Wunsch-Gotoh alignments:\n" << endl;
a = new NWGAlign(ad, gf, ss);
}
else {
cout << "\nSuboptimal free-shift alignments:\n" << endl;
try {
a = new FSAlign(ad, gf, ss);
} catch (const char* a) {
cout << "FSAlign error!\n";
}
}
time(&t);
newtime = localtime(&t);
cout << "object FSAlign created " << newtime->tm_hour << "/" << newtime->tm_min << endl;
Expand Down
4 changes: 2 additions & 2 deletions Align2/Sources/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ SOURCES = Alignment.cc AlignmentBase.cc \
PssmInput.cc Profile.cc HenikoffProfile.cc PSICProfile.cc SeqDivergenceProfile.cc \
LogAverage.cc CrossProduct.cc DotPFreq.cc DotPOdds.cc Pearson.cc JensenShannon.cc EDistance.cc AtchleyDistance.cc AtchleyCorrelation.cc Panchenko.cc Zhou.cc \
ThreadingInput.cc Ss2Input.cc ProfInput.cc Sec.cc Threading.cc Ss2.cc Prof.cc ThreadingSs2.cc ThreadingProf.cc \
ReverseScore.cc stringtools.cc
ReverseScore.cc stringtools.cc NWGAlign.cc

OBJECTS = Alignment.o AlignmentBase.o \
Align.o NWAlign.o SWAlign.o FSAlign.o NWAlignNoTermGaps.o \
Expand All @@ -46,7 +46,7 @@ OBJECTS = Alignment.o AlignmentBase.o \
PssmInput.o Profile.o HenikoffProfile.o PSICProfile.o SeqDivergenceProfile.o \
LogAverage.o CrossProduct.o DotPFreq.o DotPOdds.o Pearson.o JensenShannon.o EDistance.o AtchleyDistance.o AtchleyCorrelation.o Panchenko.o Zhou.o \
ThreadingInput.o Ss2Input.o ProfInput.o Sec.o Threading.o Ss2.o Prof.o ThreadingSs2.o ThreadingProf.o \
ReverseScore.o stringtools.o
ReverseScore.o stringtools.o NWGAlign.o

TARGETS =

Expand Down
24 changes: 12 additions & 12 deletions Align2/Sources/NWAlign.cc
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Expand Up @@ -125,14 +125,14 @@ namespace Victor { namespace Align2{

for (int i = 1; i <= static_cast<int> (n); i++) {
if (update)
F[i][0] = -gf->getOpenPenalty(0) -
gf->getExtensionPenalty(0) * (i - 1);
F[i][0] = -gf->getOpenPenalty(1) -
gf->getExtensionPenalty(i) * (i - 1);
B[i][0] = Traceback(i - 1, 0);
}

for (int j = 1; j <= static_cast<int> (m); j++) {
if (update)
F[0][j] = -gf->getOpenPenalty(j) -
F[0][j] = -gf->getOpenPenalty(1) -
gf->getExtensionPenalty(j) * (j - 1);
B[0][j] = Traceback(0, j - 1);
}
Expand All @@ -144,12 +144,12 @@ namespace Victor { namespace Align2{

if ((i != 1) && (j != 1)) {
if (B[i - 1][j].j == j)
extI = F[i - 1][j] - gf->getExtensionPenalty(j);
extI = F[i - 1][j] - gf->getExtensionPenalty(i);
else
if (B[i - 1][j].j == (j - 1))
extI = F[i - 1][j] - gf->getOpenPenalty(j);
extI = F[i - 1][j] - gf->getOpenPenalty(i);
} else
extI = F[i - 1][j] - gf->getOpenPenalty(j);
extI = F[i - 1][j] - gf->getOpenPenalty(i);

if ((i != 1) && (j != 1)) {
if (B[i][j - 1].i == i)
Expand Down Expand Up @@ -202,14 +202,14 @@ namespace Victor { namespace Align2{

for (int i = 1; i <= static_cast<int> (n); i++) {
if (update)
F[i][0] = -gf->getOpenPenalty(0) -
gf->getExtensionPenalty(0) * (i - 1);
F[i][0] = -gf->getOpenPenalty(1) -
gf->getExtensionPenalty(i) * (i - 1);
B[i][0] = Traceback(i - 1, 0);
}

for (int j = 1; j <= static_cast<int> (m); j++) {
if (update)
F[0][j] = -gf->getOpenPenalty(j) -
F[0][j] = -gf->getOpenPenalty(1) -
gf->getExtensionPenalty(j) * (j - 1);
B[0][j] = Traceback(0, j - 1);
}
Expand All @@ -229,12 +229,12 @@ namespace Victor { namespace Align2{

if ((i != 1) && (j != 1)) {
if (B[i - 1][j].j == j)
extI = F[i - 1][j] - gf->getExtensionPenalty(j);
extI = F[i - 1][j] - gf->getExtensionPenalty(i);
else
if (B[i - 1][j].j == (j - 1))
extI = F[i - 1][j] - gf->getOpenPenalty(j);
extI = F[i - 1][j] - gf->getOpenPenalty(i);
} else
extI = F[i - 1][j] - gf->getOpenPenalty(j);
extI = F[i - 1][j] - gf->getOpenPenalty(i);

if ((i != 1) && (j != 1)) {
if (B[i][j - 1].i == i)
Expand Down
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