From: westcott <westcott>
Date: Mon, 21 Mar 2011 11:08:28 +0000 (+0000)
Subject: fixed get.lienage and remove.lineage bug with confidence scores that are floats....
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=a4f05f09c250323132a4b9427f41a3ededaec634;p=mothur.git
fixed get.lienage and remove.lineage bug with confidence scores that are floats. fixed bug with pairwiase.seqs that was caused by using nast.
---
diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 5a30e1e..2a5505f 100644
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -571,7 +571,7 @@ int GetLineageCommand::readTax(){
//bool wroteSomething = false;
bool taxonsHasConfidence = false;
- vector< map<string, int> > searchTaxons;
+ vector< map<string, float> > searchTaxons;
string noConfidenceTaxons = taxons;
int hasConPos = taxons.find_first_of('(');
if (hasConPos != string::npos) {
@@ -629,7 +629,7 @@ int GetLineageCommand::readTax(){
if (pos != string::npos) { //if yes, then are the confidences okay
bool good = true;
- vector< map<string, int> > usersTaxon = getTaxons(newtax);
+ vector< map<string, float> > usersTaxon = getTaxons(newtax);
//the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
//we want to "line them up", so we will find the the index where the searchstring starts
@@ -691,10 +691,10 @@ int GetLineageCommand::readTax(){
}
}
/**************************************************************************************************/
-vector< map<string, int> > GetLineageCommand::getTaxons(string tax) {
+vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
try {
- vector< map<string, int> > t;
+ vector< map<string, float> > t;
string taxon = "";
int taxLength = tax.length();
for(int i=0;i<taxLength;i++){
@@ -711,10 +711,10 @@ vector< map<string, int> > GetLineageCommand::getTaxons(string tax) {
newtaxon = taxon;
confidence = "0";
}
- int con = 0;
+ float con = 0;
convert(confidence, con);
- map<string, int> temp;
+ map<string, float> temp;
temp[newtaxon] = con;
t.push_back(temp);
diff --git a/getlineagecommand.h b/getlineagecommand.h
index 45b51a8..5b7c43e 100644
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -40,7 +40,7 @@ class GetLineageCommand : public Command {
int readList();
int readTax();
string removeConfidences(string);
- vector< map<string, int> > getTaxons(string);
+ vector< map<string, float> > getTaxons(string);
};
#endif
diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index e3f8852..1e7a338 100644
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -14,7 +14,6 @@
#include "needlemanoverlap.hpp"
#include "blastalign.hpp"
#include "noalign.hpp"
-#include "nast.hpp"
#include "ignoregaps.h"
#include "eachgapdist.h"
@@ -605,16 +604,16 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
- Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+ Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+ Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
- Nast(alignment, seqI, seqJ);
+ alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+ seqI.setAligned(alignment->getSeqAAln());
+ seqJ.setAligned(alignment->getSeqBAln());
- distCalculator->calcDist(*seqI, *seqJ);
+ distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
- delete seqI; delete seqJ;
-
if(dist <= cutoff){
if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
}
@@ -673,15 +672,15 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
- Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+ Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+ Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
- Nast(alignment, seqI, seqJ);
+ alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+ seqI.setAligned(alignment->getSeqAAln());
+ seqJ.setAligned(alignment->getSeqBAln());
- distCalculator->calcDist(*seqI, *seqJ);
+ distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
-
- delete seqI; delete seqJ;
outFile << dist << '\t';
}
@@ -728,16 +727,16 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI,
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
- Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+ Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+ Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
- Nast(alignment, seqI, seqJ);
+ alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+ seqI.setAligned(alignment->getSeqAAln());
+ seqJ.setAligned(alignment->getSeqBAln());
- distCalculator->calcDist(*seqI, *seqJ);
+ distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
- delete seqI; delete seqJ;
-
if(dist <= cutoff){
outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
}
@@ -809,16 +808,16 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
- Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+ Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+ Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
- Nast(alignment, seqI, seqJ);
+ alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+ seqI.setAligned(alignment->getSeqAAln());
+ seqJ.setAligned(alignment->getSeqBAln());
- distCalculator->calcDist(*seqI, *seqJ);
+ distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
- delete seqI; delete seqJ;
-
outputString += toString(dist) + "\t";
}
@@ -885,16 +884,16 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
- Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+ Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+ Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
- Nast(alignment, seqI, seqJ);
+ alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+ seqI.setAligned(alignment->getSeqAAln());
+ seqJ.setAligned(alignment->getSeqBAln());
- distCalculator->calcDist(*seqI, *seqJ);
+ distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
- delete seqI; delete seqJ;
-
outputString += toString(dist) + "\t";
}
diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 893b210..ef1e77e 100644
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -556,7 +556,7 @@ int RemoveLineageCommand::readTax(){
bool wroteSomething = false;
bool taxonsHasConfidence = false;
- vector< map<string, int> > searchTaxons;
+ vector< map<string, float> > searchTaxons;
string noConfidenceTaxons = taxons;
int hasConPos = taxons.find_first_of('(');
if (hasConPos != string::npos) {
@@ -618,7 +618,7 @@ int RemoveLineageCommand::readTax(){
if (pos != string::npos) { //if yes, then are the confidences okay
bool remove = false;
- vector< map<string, int> > usersTaxon = getTaxons(newtax);
+ vector< map<string, float> > usersTaxon = getTaxons(newtax);
//the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
//we want to "line them up", so we will find the the index where the searchstring starts
@@ -686,10 +686,10 @@ int RemoveLineageCommand::readTax(){
}
}
/**************************************************************************************************/
-vector< map<string, int> > RemoveLineageCommand::getTaxons(string tax) {
+vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
try {
- vector< map<string, int> > t;
+ vector< map<string, float> > t;
string taxon = "";
int taxLength = tax.length();
for(int i=0;i<taxLength;i++){
@@ -706,10 +706,10 @@ vector< map<string, int> > RemoveLineageCommand::getTaxons(string tax) {
newtaxon = taxon;
confidence = "0";
}
- int con = 0;
+ float con = 0;
convert(confidence, con);
- map<string, int> temp;
+ map<string, float> temp;
temp[newtaxon] = con;
t.push_back(temp);
diff --git a/removelineagecommand.h b/removelineagecommand.h
index 60712c9..02a4440 100644
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -40,7 +40,7 @@ class RemoveLineageCommand : public Command {
int readList();
int readTax();
string removeConfidences(string);
- vector< map<string, int> > getTaxons(string);
+ vector< map<string, float> > getTaxons(string);
};
#endif