X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readcolumn.cpp;h=e14125cc6d94f563e37d5ea1cea8235a5c8df04b;hp=59c3bd5520929f40086279d744c666ab18fe6d8b;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc

diff --git a/readcolumn.cpp b/readcolumn.cpp
index 59c3bd5..e14125c 100644
--- a/readcolumn.cpp
+++ b/readcolumn.cpp
@@ -14,147 +14,266 @@
 
 ReadColumnMatrix::ReadColumnMatrix(string df) : distFile(df){
 	
-	successOpen = openInputFile(distFile, fileHandle);
+	successOpen = m->openInputFile(distFile, fileHandle);
+	sim = false;
 	
 }
+/***********************************************************************/
+
+ReadColumnMatrix::ReadColumnMatrix(string df, bool s) : distFile(df){
+	
+	successOpen = m->openInputFile(distFile, fileHandle);
+	sim = s;
+}
 
 /***********************************************************************/
 
-void ReadColumnMatrix::read(NameAssignment* nameMap){
+int ReadColumnMatrix::read(NameAssignment* nameMap){
 	try {		
+
+		string firstName, secondName;
+		float distance;
+		int nseqs = nameMap->size();
+        DMatrix->resize(nseqs);
+		list = new ListVector(nameMap->getListVector());
 	
-			string firstName, secondName;
-			float distance;
-			int nseqs = nameMap->size();
+		Progress* reading = new Progress("Reading matrix:     ", nseqs * 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...
 	
-			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
+		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; }
 	
-			//need to see if this is a square or a triangular matrix...
-			while(fileHandle && lt == 1){  //let's assume it's a triangular matrix...
+			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.
 			
-				fileHandle >> firstName >> secondName >> distance;	// get the row and column names and distance
-		
-				if(nameMap->count(firstName)==0){
-					cerr << "AError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
+			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);
+					}
 				}
-				if(nameMap->count(secondName)==0){
-					cerr << "AError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
+				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 (distance == -1) { distance = 1000000; }
+				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(distance < cutoff && nameMap->get(firstName) != nameMap->get(secondName)){
-					if(nameMap->get(firstName) > nameMap->get(secondName)){
-						PCell value(nameMap->get(firstName), nameMap->get(secondName), distance);
+				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(refRow == refCol){		// in other words, if we haven't loaded refRow and refCol...
-							refRow = nameMap->get(firstName);
-							refCol = nameMap->get(secondName);
-							D->addCell(value);
-						}
-						else if(refRow == nameMap->get(firstName) && refCol == nameMap->get(secondName)){
-							lt = 0;
-						}
-						else{
-							D->addCell(value);
-						}
-					}
-					else if(nameMap->get(firstName) < nameMap->get(secondName)){
-						PCell value(nameMap->get(secondName), nameMap->get(firstName), 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(refRow == refCol){		// in other words, if we haven't loaded refRow and refCol...
-							refRow = nameMap->get(firstName);
-							refCol = nameMap->get(secondName);
-							D->addCell(value);
-						}
-						else if(refRow == nameMap->get(secondName) && refCol == nameMap->get(firstName)){
-							lt = 0;
-						}
-						else{
-							D->addCell(value);
-						}
-					}
-					reading->update(nameMap->get(firstName) * nseqs);
+				if(distance < cutoff && itA->second > itB->second){
+                    PDistCell value(itA->second, distance);
+					DMatrix->addCell(itB->second, value);
+					reading->update(itA->second * nseqs);
 				}
-				gobble(fileHandle);
+		
+				m->gobble(fileHandle);
 			}
+		}
+		
+		if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+		
+		reading->finish();
+		fileHandle.close();
 
-			if(lt == 0){  // oops, it was square
-				fileHandle.close();  //let's start over
-				D->clear();  //let's start over
-			   
-				openInputFile(distFile, fileHandle);  //let's start over
+		list->setLabel("0");
+		
+		return 1;
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadColumnMatrix", "read");
+		exit(1);
+	}
+}
+/***********************************************************************/
 
-				while(fileHandle){
-					fileHandle >> firstName >> secondName >> distance;
+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(nameMap->count(firstName)==0){
-						cerr << "BError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
+			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);
 					}
-					if(nameMap->count(secondName)==0){
-						cerr << "BError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
+					else if(refRow == itA && refCol == itB){
+						lt = 0;
 					}
-					
-					if (distance == -1) { distance = 1000000; }
-					
-					if(distance < cutoff && nameMap->get(firstName) > nameMap->get(secondName)){
-						PCell value(nameMap->get(firstName), nameMap->get(secondName), distance);
-						D->addCell(value);
-						reading->update(nameMap->get(firstName) * nseqs);
+					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);
 					}
-			
-					gobble(fileHandle);
 				}
+				reading->update(itA * nseqs);
 			}
-		//	else if(lt == 0){
-		//		while(fileHandle){
-		//			fileHandle >> firstName >> secondName >> distance;
-		//			
-		//			if(nameMap->count(firstName)==0){
-		//				cerr << "CError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
-		//			}
-		//			if(nameMap->count(secondName)==0){
-		//				cerr << "CError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
-		//			}
-		//			if (distance == -1) { distance = 1000000; }
+			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(distance < cutoff && (*nameMap)[firstName].second < (*nameMap)[secondName].second){
-		////				cout << (*nameMap)[secondName] << ' ' << (*nameMap)[firstName] << ' ' << distance << endl;
-		//				D->addCell(Cell((*nameMap)[secondName].second, (*nameMap)[firstName].second, distance));
-		//				reading->update((*nameMap)[secondName].second * nseqs);
-		//			}
-		//
-		//			gobble(fileHandle);
-		//		}
-		//	}	
-			reading->finish();
-			fileHandle.close();
-	
-			list->setLabel("0");
-	
+		if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+		
+		reading->finish();
+		fileHandle.close();
+        
+		list->setLabel("0");
+		
+		return 1;
+        
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReadColumnMatrix class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ReadColumnMatrix", "read");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReadColumnMatrix class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }
 
 /***********************************************************************/
-
-ReadColumnMatrix::~ReadColumnMatrix(){
-	//delete D;
-	//delete list;
-}
-
+ReadColumnMatrix::~ReadColumnMatrix(){}
+/***********************************************************************/