X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readphylip.cpp;h=6de23e83279482127f5f261c53f94c345585455d;hp=5f92275eb9e6d4c8e3ee21241bbd6f626a295bc1;hb=615301e57c25e241356a9c2380648d117709458d;hpb=832d53a9dfac6b1795735eec643d8cf627b0d8e3 diff --git a/readphylip.cpp b/readphylip.cpp index 5f92275..6de23e8 100644 --- a/readphylip.cpp +++ b/readphylip.cpp @@ -14,22 +14,35 @@ ReadPhylipMatrix::ReadPhylipMatrix(string distFile){ - successOpen = openInputFile(distFile, fileHandle); + successOpen = m->openInputFile(distFile, fileHandle); + sim=false; } +/***********************************************************************/ + +ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){ + + successOpen = m->openInputFile(distFile, fileHandle); + sim=s; +} + /***********************************************************************/ -void ReadPhylipMatrix::read(NameAssignment* nameMap){ +int ReadPhylipMatrix::read(NameAssignment* nameMap){ try { float distance; - int square, nseqs; + int square, nseqs; string name; vector matrixNames; - - fileHandle >> nseqs >> name; - + + string numTest; + fileHandle >> numTest >> name; + + if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); } + else { convert(numTest, nseqs); } + matrixNames.push_back(name); if(nameMap == NULL){ @@ -38,7 +51,7 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } else{ list = new ListVector(nameMap->getListVector()); - if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); } + if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); } } char d; @@ -59,7 +72,8 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } Progress* reading; - + DMatrix->resize(nseqs); + if(square == 0){ reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2); @@ -67,21 +81,28 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ int index = 0; for(int i=1;icontrol_pressed) { fileHandle.close(); delete reading; return 0; } + fileHandle >> name; matrixNames.push_back(name); + //there's A LOT of repeated code throughout this method... if(nameMap == NULL){ list->set(i, name); for(int j=0;jcontrol_pressed) { delete reading; fileHandle.close(); return 0; } + fileHandle >> distance; if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. if(distance < cutoff){ - PCell value(i, j, distance); - D->addCell(value); + PDistCell value(i, distance); + DMatrix->addCell(j, value); } index++; reading->update(index); @@ -89,16 +110,19 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } else{ - if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); } + if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); } for(int j=0;j> distance; + + if (m->control_pressed) { delete reading; fileHandle.close(); return 0; } if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. if(distance < cutoff){ - PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance); - D->addCell(value); + PDistCell value(nameMap->get(matrixNames[i]), distance); + DMatrix->addCell(nameMap->get(matrixNames[j]), value); } index++; reading->update(index); @@ -115,17 +139,22 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ for(int i=1;i> name; matrixNames.push_back(name); + + if(nameMap == NULL){ list->set(i, name); for(int j=0;j> distance; - + + if (m->control_pressed) { fileHandle.close(); delete reading; return 0; } + if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. if(distance < cutoff && j < i){ - PCell value(i, j, distance); - D->addCell(value); + PDistCell value(i, distance); + DMatrix->addCell(j, value); } index++; reading->update(index); @@ -133,16 +162,19 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } else{ - if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); } + if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); } for(int j=0;j> distance; - - if (distance == -1) { distance = 1000000; } + + if (m->control_pressed) { fileHandle.close(); delete reading; return 0; } + + if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. - if(distance < cutoff && j < i){ - PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance); - D->addCell(value); + if(distance < cutoff && j < i){ + PDistCell value(nameMap->get(matrixNames[i]), distance); + DMatrix->addCell(nameMap->get(matrixNames[j]), value); } index++; reading->update(index); @@ -150,32 +182,213 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } } } + + if (m->control_pressed) { fileHandle.close(); delete reading; return 0; } + reading->finish(); delete reading; - + list->setLabel("0"); fileHandle.close(); - /* if(nameMap != NULL){ - for(int i=0;ierase(matrixNames[i]); - } - if(nameMap->size() > 0){ - //should probably tell them what is missing if we missed something - mothurOut("missed something\t" + toString(nameMap->size())); mothurOutEndLine(); - } - } */ + + return 1; } catch(exception& e) { - errorOut(e, "ReadPhylipMatrix", "read"); + m->errorOut(e, "ReadPhylipMatrix", "read"); exit(1); } } - /***********************************************************************/ -ReadPhylipMatrix::~ReadPhylipMatrix(){ - // delete D; - // delete list; +int ReadPhylipMatrix::read(CountTable* countTable){ + try { + + float distance; + int square, nseqs; + string name; + vector matrixNames; + + string numTest; + fileHandle >> numTest >> name; + + if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); } + else { convert(numTest, nseqs); } + + matrixNames.push_back(name); + + if(countTable == NULL){ + list = new ListVector(nseqs); + list->set(0, name); + } + else{ list = new ListVector(countTable->getListVector()); } + + if (m->control_pressed) { return 0; } + + char d; + while((d=fileHandle.get()) != EOF){ + + if(isalnum(d)){ + square = 1; + fileHandle.putback(d); + for(int i=0;i> distance; + } + break; + } + if(d == '\n'){ + square = 0; + break; + } + } + + Progress* reading; + DMatrix->resize(nseqs); + + if(square == 0){ + + reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2); + + int index = 0; + + for(int i=1;icontrol_pressed) { fileHandle.close(); delete reading; return 0; } + + fileHandle >> name; + matrixNames.push_back(name); + + + //there's A LOT of repeated code throughout this method... + if(countTable == NULL){ + list->set(i, name); + + for(int j=0;jcontrol_pressed) { delete reading; fileHandle.close(); return 0; } + + fileHandle >> distance; + + if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. + + if(distance < cutoff){ + PDistCell value(i, distance); + DMatrix->addCell(j, value); + } + index++; + reading->update(index); + } + + } + else{ + for(int j=0;j> distance; + + if (m->control_pressed) { delete reading; fileHandle.close(); return 0; } + + if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. + + if(distance < cutoff){ + int iIndex = countTable->get(matrixNames[i]); + int jIndex = countTable->get(matrixNames[j]); + + if (m->control_pressed) { delete reading; fileHandle.close(); return 0; } + if (iIndex < jIndex) { + PDistCell value(jIndex, distance); + DMatrix->addCell(iIndex, value); + }else { + PDistCell value(iIndex, distance); + DMatrix->addCell(jIndex, value); + + } + } + index++; + reading->update(index); + } + } + } + } + else{ + + reading = new Progress("Reading matrix: ", nseqs * nseqs); + + int index = nseqs; + + for(int i=1;i> name; + matrixNames.push_back(name); + + + + if(countTable == NULL){ + list->set(i, name); + for(int j=0;j> distance; + + if (m->control_pressed) { fileHandle.close(); delete reading; return 0; } + + if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. + + if(distance < cutoff && j < i){ + PDistCell value(i, distance); + DMatrix->addCell(j, value); + } + index++; + reading->update(index); + } + + } + else{ + for(int j=0;j> distance; + + if (m->control_pressed) { fileHandle.close(); delete reading; return 0; } + + if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. + + if(distance < cutoff && j < i){ + int iIndex = countTable->get(matrixNames[i]); + int jIndex = countTable->get(matrixNames[j]); + + if (m->control_pressed) { delete reading; fileHandle.close(); return 0; } + if (iIndex < jIndex) { + PDistCell value(jIndex, distance); + DMatrix->addCell(iIndex, value); + }else { + PDistCell value(iIndex, distance); + DMatrix->addCell(jIndex, value); + + } + } + index++; + reading->update(index); + } + } + } + } + + if (m->control_pressed) { fileHandle.close(); delete reading; return 0; } + + reading->finish(); + delete reading; + + list->setLabel("0"); + fileHandle.close(); + + + return 1; + + } + catch(exception& e) { + m->errorOut(e, "ReadPhylipMatrix", "read"); + exit(1); + } } +/***********************************************************************/ +ReadPhylipMatrix::~ReadPhylipMatrix(){} +/***********************************************************************/ +