X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readcolumn.cpp;h=e14125cc6d94f563e37d5ea1cea8235a5c8df04b;hp=665dcabd5db7fd17513d912bab974ae4087d449f;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=0cefb55a2616975bd4a144fc345693695ffc9bb6

diff --git a/readcolumn.cpp b/readcolumn.cpp
index 665dcab..e14125c 100644
--- a/readcolumn.cpp
+++ b/readcolumn.cpp
@@ -48,13 +48,17 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
 		while(fileHandle && lt == 1){  //let's assume it's a triangular matrix...
 
 		
-			fileHandle >> firstName >> secondName >> distance;	// get the row and column names and distance
+			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);  }
 
@@ -106,7 +110,9 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
 			m->openInputFile(distFile, fileHandle);  //let's start over
 
 			while(fileHandle){
-				fileHandle >> firstName >> secondName >> distance;
+				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; }
 		
@@ -144,6 +150,128 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
 		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(){}