From 9a339a6b007b23c39b7eb20cc777af66dd2cebef Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Thu, 30 Jul 2009 11:25:41 +0000
Subject: [PATCH] pat's edits prior to v.1.5
---
Mothur.xcodeproj/project.pbxproj | 4 ++--
aligncommand.cpp | 4 +++-
libshuffcommand.cpp | 2 +-
mothur.h | 20 +++++++++-----------
nast.cpp | 8 ++------
sharedchao1.cpp | 2 +-
simpson.cpp | 10 +++++-----
trimseqscommand.cpp | 9 ++++-----
8 files changed, 27 insertions(+), 32 deletions(-)
diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index ab3240e..75294bc 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -288,8 +288,8 @@
375AA1360F9E433D008EF9B8 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = SOURCE_ROOT; };
375AA1370F9E433D008EF9B8 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = SOURCE_ROOT; };
375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = SOURCE_ROOT; };
- 377326630FAF16E0007ABB8B /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = "<group>"; };
- 377326640FAF16E0007ABB8B /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = "<group>"; };
+ 377326630FAF16E0007ABB8B /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = SOURCE_ROOT; };
+ 377326640FAF16E0007ABB8B /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = SOURCE_ROOT; };
378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = SOURCE_ROOT; };
378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = SOURCE_ROOT; };
378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = SOURCE_ROOT; };
diff --git a/aligncommand.cpp b/aligncommand.cpp
index d672fc3..958f29b 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -171,6 +171,8 @@ int AlignCommand::execute(){
mothurOutEndLine();
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
+ mothurOut("Aligning sequences...");
+ mothurOutEndLine();
string alignFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align";
string reportFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align.report";
@@ -283,7 +285,7 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
report.setAlignmentParameters(align, alignment);
report.setNastParameters(nast);
-
+
alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
report.print();
diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 73c0a74..e78c00d 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -208,7 +208,7 @@ void LibShuffCommand::printCoverageFile() {
vector<int> prevRow = it->second;
it++;
- for(it;it!=allDistances.end();it++){
+ for(;it!=allDistances.end();it++){
for(int i=0;i<it->second.size();i++){
it->second[i] += prevRow[i];
}
diff --git a/mothur.h b/mothur.h
index 2912433..b27c5ad 100644
--- a/mothur.h
+++ b/mothur.h
@@ -44,20 +44,17 @@
#include <cerrno>
#include <ctime>
#include <limits>
+#include <sys/wait.h>
+#include <unistd.h>
using namespace std;
-#ifdef _WIN32
- #define exp(x) (exp((double) x))
- #define sqrt(x) (sqrt((double) x))
- #define log10(x) (log10((double) x))
- #define log2(x) (log10(x)/log10(2))
- #define isnan(x) ((x) != (x))
- #define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
-#else
- #include <sys/wait.h>
- #include <unistd.h>
-#endif
+#define exp(x) (exp((double) x))
+#define sqrt(x) (sqrt((double) x))
+#define log10(x) (log10((double) x))
+#define log2(x) (log10(x)/log10(2))
+#define isnan(x) ((x) != (x))
+#define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
typedef unsigned long ull;
@@ -96,6 +93,7 @@ inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
throw BadConversion(s);
}
+
//**********************************************************************************************************************
template<typename T>
diff --git a/nast.cpp b/nast.cpp
index 4aed590..804e3c1 100644
--- a/nast.cpp
+++ b/nast.cpp
@@ -53,7 +53,6 @@ void Nast::pairwiseAlignSeqs(){ // Here we call one of the pairwise alignment me
}
else{
-
if(tempAln[0] == '-'){
int pairwiseAlignmentLength = tempAln.length(); // we need to make sure that the candidate sequence alignment
for(int i=0;i<pairwiseAlignmentLength;i++){ // starts where the template sequence alignment starts, if it
@@ -64,7 +63,6 @@ void Nast::pairwiseAlignSeqs(){ // Here we call one of the pairwise alignment me
}
}
}
-
int pairwiseAlignmentLength = tempAln.length();
if(tempAln[pairwiseAlignmentLength-1] == '-'){ // we need to make sure that the candidate sequence alignment
for(int i=pairwiseAlignmentLength-1; i>=0; i--){// ends where the template sequence alignment ends, if it runs
@@ -113,8 +111,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
break;
}
}
-
-
+
for(rightIndex=i+1;rightIndex<longAlignmentLength-1;rightIndex++){
if(!isalpha(candAln[rightIndex])){
rightRoom = 1; //count how far it is to the nearest gap on the RIGHT side of the anomaly
@@ -207,7 +204,6 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
errorOut(e, "Nast", "removeExtraGaps");
exit(1);
}
-
}
/**************************************************************************************************/
@@ -239,7 +235,7 @@ void Nast::regapSequences(){ //This is essentially part B in Fig 2. of DeSantis
newTemplateAlign += tempAln[fullAlignIndex];// pairwise sequences
fullAlignIndex++;
}
-
+
string lastLoop = "";
while(pairwiseAlignIndex<pairwiseLength){
diff --git a/sharedchao1.cpp b/sharedchao1.cpp
index 803e953..cbb5192 100644
--- a/sharedchao1.cpp
+++ b/sharedchao1.cpp
@@ -50,7 +50,7 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
//calculate chao1, (numleaves-1) because numleaves contains the ++ values.
bool bias;
for(int i=0;i<numLeaves;i++){
- if ((f2leaves[i]->lvalue == 0) || (f2leaves[i]->rvalue == 0)) { bias = true; }// break;}
+ if (f2leaves[i]->lvalue == 0 || f2leaves[i]->rvalue == 0) { bias = true;}// break;}
}
if(bias){
diff --git a/simpson.cpp b/simpson.cpp
index d260800..8e176cf 100644
--- a/simpson.cpp
+++ b/simpson.cpp
@@ -19,8 +19,8 @@ EstOutput Simpson::getValues(SAbundVector* rank){
double ci = 0;
double maxRank = (double)rank->getMaxRank();
- int sampled = rank->getNumSeqs();
- int sobs = rank->getNumBins();
+ double sampled = (double)rank->getNumSeqs();
+ double sobs = (double)rank->getNumBins();
double firstTerm = 0;
double secondTerm = 0;
@@ -31,8 +31,8 @@ EstOutput Simpson::getValues(SAbundVector* rank){
for(int i=1;i<=maxRank;i++){
simnum += (double)(rank->get(i)*i*(i-1));
}
-
- simpson = simnum / (double)(sampled*(sampled-1));
+
+ simpson = simnum / (sampled*(sampled-1));
for(int i=1;i<=maxRank;i++){
double piI = (double) i / (double)sampled;
@@ -40,7 +40,7 @@ EstOutput Simpson::getValues(SAbundVector* rank){
secondTerm += rank->get(i) * pow(piI, 2);
}
- double var = (4.0 / (double)sampled) * (firstTerm - secondTerm*secondTerm);
+ double var = (4.0 / sampled) * (firstTerm - secondTerm*secondTerm);
ci = 1.95 * pow(var, 0.5);
}
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 937b130..2a982c7 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -171,7 +171,6 @@ int TrimSeqsCommand::execute(){
if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
if(!success) { trashCode += 'q'; }
- qFile.close();
}
if(barcodes.size() != 0){
success = stripBarcode(currSeq, group);
@@ -221,6 +220,7 @@ int TrimSeqsCommand::execute(){
outFASTA.close();
scrapFASTA.close();
outGroups.close();
+ if(qFileName != "") { qFile.close(); }
for(int i=0;i<fastaFileNames.size();i++){
fastaFileNames[i]->close();
@@ -548,7 +548,8 @@ bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
string name;
qFile >> name;
- if (name.length() != 0) { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine(); } }
+ if (name[0] == '>') { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); mothurOutEndLine(); } }
+
while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
float score;
@@ -559,7 +560,7 @@ bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
average += score;
}
average /= seqLength;
-
+
if(average >= qAverage) { success = 1; }
else { success = 0; }
@@ -572,5 +573,3 @@ bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
}
//***************************************************************************************************************
-
-
--
2.39.5