-/*\r
- * readcolumn.cpp\r
- * Mothur\r
- *\r
- * Created by Sarah Westcott on 4/21/09.\r
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.\r
- *\r
- */\r
-\r
-#include "readcolumn.h"\r
-#include "progress.hpp"\r
-\r
-/***********************************************************************/\r
-\r
-ReadColumnMatrix::ReadColumnMatrix(string df) : distFile(df){\r
- \r
- successOpen = openInputFile(distFile, fileHandle);\r
- \r
-}\r
-\r
-/***********************************************************************/\r
-\r
-int ReadColumnMatrix::read(NameAssignment* nameMap){\r
- try { \r
-\r
- string firstName, secondName;\r
- float distance;\r
- int nseqs = nameMap->size();\r
-\r
- list = new ListVector(nameMap->getListVector());\r
- \r
- Progress* reading = new Progress("Reading matrix: ", nseqs * nseqs);\r
-\r
- int lt = 1;\r
- int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose\r
- int refCol = 0; //shows up later - Cell(refCol,refRow). If it does, then its a square matrix\r
-\r
- //need to see if this is a square or a triangular matrix...\r
- \r
- while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...\r
-\r
- \r
- fileHandle >> firstName >> secondName >> distance; // get the row and column names and distance\r
- \r
- if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }\r
- \r
- map<string,int>::iterator itA = nameMap->find(firstName);\r
- map<string,int>::iterator itB = nameMap->find(secondName);\r
- \r
- if(itA == nameMap->end()){\r
- cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);\r
- }\r
- if(itB == nameMap->end()){\r
- cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);\r
- }\r
-\r
- if (distance == -1) { distance = 1000000; }\r
- \r
- if(distance < cutoff && itA != itB){\r
- if(itA->second > itB->second){\r
- PCell value(itA->second, itB->second, distance);\r
- \r
- if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...\r
- refRow = itA->second;\r
- refCol = itB->second;\r
- D->addCell(value);\r
- }\r
- else if(refRow == itA->second && refCol == itB->second){\r
- lt = 0;\r
- }\r
- else{\r
- D->addCell(value);\r
- }\r
- }\r
- else if(itA->second < itB->second){\r
- PCell value(itB->second, itA->second, distance);\r
- \r
- if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...\r
- refRow = itA->second;\r
- refCol = itB->second;\r
- D->addCell(value);\r
- }\r
- else if(refRow == itB->second && refCol == itA->second){\r
- lt = 0;\r
- }\r
- else{\r
- D->addCell(value);\r
- }\r
- }\r
- reading->update(itA->second * nseqs);\r
- }\r
- gobble(fileHandle);\r
- }\r
-\r
- if(lt == 0){ // oops, it was square\r
- fileHandle.close(); //let's start over\r
- D->clear(); //let's start over\r
- \r
- openInputFile(distFile, fileHandle); //let's start over\r
-\r
- while(fileHandle){\r
- fileHandle >> firstName >> secondName >> distance;\r
- \r
- if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }\r
- \r
- map<string,int>::iterator itA = nameMap->find(firstName);\r
- map<string,int>::iterator itB = nameMap->find(secondName);\r
- \r
- if(itA == nameMap->end()){\r
- cerr << "BError: Sequence '" << firstName << "' was not found in the names file, please correct\n";\r
- }\r
- if(itB == nameMap->end()){\r
- cerr << "BError: Sequence '" << secondName << "' was not found in the names file, please correct\n";\r
- }\r
- \r
- if (distance == -1) { distance = 1000000; }\r
- \r
- if(distance < cutoff && itA->second > itB->second){\r
- PCell value(itA->second, itB->second, distance);\r
- D->addCell(value);\r
- reading->update(itA->second * nseqs);\r
- }\r
- \r
- gobble(fileHandle);\r
- }\r
- }\r
- \r
- if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }\r
- \r
- reading->finish();\r
- fileHandle.close();\r
-\r
- list->setLabel("0");\r
- \r
- return 1;\r
-\r
- }\r
- catch(exception& e) {\r
- m->errorOut(e, "ReadColumnMatrix", "read");\r
- exit(1);\r
- }\r
-}\r
-\r
-/***********************************************************************/\r
-\r
-ReadColumnMatrix::~ReadColumnMatrix(){\r
- //delete D;\r
- //delete list;\r
-}\r
-\r
-\r
+/*
+ * readcolumn.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 4/21/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "readcolumn.h"
+#include "progress.hpp"
+
+/***********************************************************************/
+
+ReadColumnMatrix::ReadColumnMatrix(string df) : distFile(df){
+
+ successOpen = m->openInputFile(distFile, fileHandle);
+ sim = false;
+
+}
+/***********************************************************************/
+
+ReadColumnMatrix::ReadColumnMatrix(string df, bool s) : distFile(df){
+
+ successOpen = m->openInputFile(distFile, fileHandle);
+ sim = s;
+}
+
+/***********************************************************************/
+
+int ReadColumnMatrix::read(NameAssignment* nameMap){
+ try {
+
+ string firstName, secondName;
+ float distance;
+ int nseqs = nameMap->size();
+ DMatrix->resize(nseqs);
+ list = new ListVector(nameMap->getListVector());
+
+ Progress* reading = new Progress("Reading matrix: ", nseqs * nseqs);
+
+ int lt = 1;
+ int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
+ int refCol = 0; //shows up later - Cell(refCol,refRow). If it does, then its a square matrix
+
+ //need to see if this is a square or a triangular matrix...
+
+ while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
+
+
+ fileHandle >> firstName; m->gobble(fileHandle);
+ fileHandle >> secondName; m->gobble(fileHandle);
+ fileHandle >> distance; // get the row and column names and distance
+
+ if (m->debug) { cout << firstName << '\t' << secondName << '\t' << distance << endl; }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ map<string,int>::iterator itA = nameMap->find(firstName);
+ map<string,int>::iterator itB = nameMap->find(secondName);
+
+ if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
+ if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
+
+ 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 && itA != itB){
+ if(itA->second > itB->second){
+ PDistCell value(itA->second, distance);
+
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = itA->second;
+ refCol = itB->second;
+ DMatrix->addCell(itB->second, value);
+ }
+ else if(refRow == itA->second && refCol == itB->second){
+ lt = 0;
+ }
+ else{
+ DMatrix->addCell(itB->second, value);
+ }
+ }
+ else if(itA->second < itB->second){
+ PDistCell value(itB->second, distance);
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = itA->second;
+ refCol = itB->second;
+ DMatrix->addCell(itA->second, value);
+ }
+ else if(refRow == itB->second && refCol == itA->second){
+ lt = 0;
+ }
+ else{
+ DMatrix->addCell(itA->second, value);
+ }
+ }
+ reading->update(itA->second * nseqs);
+ }
+ m->gobble(fileHandle);
+ }
+
+ if(lt == 0){ // oops, it was square
+
+ fileHandle.close(); //let's start over
+ DMatrix->clear(); //let's start over
+
+ m->openInputFile(distFile, fileHandle); //let's start over
+
+ while(fileHandle){
+ fileHandle >> firstName; m->gobble(fileHandle);
+ fileHandle >> secondName; m->gobble(fileHandle);
+ fileHandle >> distance; // get the row and column names and distance
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ map<string,int>::iterator itA = nameMap->find(firstName);
+ map<string,int>::iterator itB = nameMap->find(secondName);
+
+ if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
+ if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
+
+ 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 && itA->second > itB->second){
+ PDistCell value(itA->second, distance);
+ DMatrix->addCell(itB->second, value);
+ reading->update(itA->second * nseqs);
+ }
+
+ m->gobble(fileHandle);
+ }
+ }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ reading->finish();
+ fileHandle.close();
+
+ list->setLabel("0");
+
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadColumnMatrix", "read");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+int ReadColumnMatrix::read(CountTable* countTable){
+ try {
+
+ string firstName, secondName;
+ float distance;
+ int nseqs = countTable->size();
+
+ DMatrix->resize(nseqs);
+ list = new ListVector(countTable->getListVector());
+
+ Progress* reading = new Progress("Reading matrix: ", nseqs * nseqs);
+
+ int lt = 1;
+ int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
+ int refCol = 0; //shows up later - Cell(refCol,refRow). If it does, then its a square matrix
+
+ //need to see if this is a square or a triangular matrix...
+
+ while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
+
+
+ fileHandle >> firstName; m->gobble(fileHandle);
+ fileHandle >> secondName; m->gobble(fileHandle);
+ fileHandle >> distance; // get the row and column names and distance
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ int itA = countTable->get(firstName);
+ int itB = countTable->get(secondName);
+
+ if (m->control_pressed) { exit(1); }
+
+ 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 && itA != itB){
+ if(itA > itB){
+ PDistCell value(itA, distance);
+
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = itA;
+ refCol = itB;
+ DMatrix->addCell(itB, value);
+ }
+ else if(refRow == itA && refCol == itB){
+ lt = 0;
+ }
+ else{
+ DMatrix->addCell(itB, value);
+ }
+ }
+ else if(itA < itB){
+ PDistCell value(itB, distance);
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = itA;
+ refCol = itB;
+ DMatrix->addCell(itA, value);
+ }
+ else if(refRow == itB && refCol == itA){
+ lt = 0;
+ }
+ else{
+ DMatrix->addCell(itA, value);
+ }
+ }
+ reading->update(itA * nseqs);
+ }
+ m->gobble(fileHandle);
+ }
+
+ if(lt == 0){ // oops, it was square
+
+ fileHandle.close(); //let's start over
+ DMatrix->clear(); //let's start over
+
+ m->openInputFile(distFile, fileHandle); //let's start over
+
+ while(fileHandle){
+ fileHandle >> firstName; m->gobble(fileHandle);
+ fileHandle >> secondName; m->gobble(fileHandle);
+ fileHandle >> distance; // get the row and column names and distance
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ int itA = countTable->get(firstName);
+ int itB = countTable->get(secondName);
+
+
+ if (m->control_pressed) { exit(1); }
+
+ 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 && itA > itB){
+ PDistCell value(itA, distance);
+ DMatrix->addCell(itB, value);
+ reading->update(itA * nseqs);
+ }
+
+ m->gobble(fileHandle);
+ }
+ }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ reading->finish();
+ fileHandle.close();
+
+ list->setLabel("0");
+
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadColumnMatrix", "read");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+ReadColumnMatrix::~ReadColumnMatrix(){}
+/***********************************************************************/
+
projects / mothur.git / blobdiff