added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / readcolumn.cpp

diff --git a/readcolumn.cpp b/readcolumn.cpp
index 53a8c4263dddc4687acc5a64cf7c5b1d27aac647..665dcabd5db7fd17513d912bab974ae4087d449f 100644 (file)
--- a/readcolumn.cpp
+++ b/readcolumn.cpp
@@ -34,7 +34,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                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);
@@ -63,33 +63,34 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                        
                        if(distance < cutoff && itA != itB){
                                if(itA->second > itB->second){
-                                       PCell value(itA->second, itB->second, distance);
-                       
+                    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;
-                                               D->addCell(value);
+                                               DMatrix->addCell(itB->second, value);
                                        }
                                        else if(refRow == itA->second && refCol == itB->second){
                                                lt = 0;
                                        }
                                        else{
-                                               D->addCell(value);
+                                               DMatrix->addCell(itB->second, value);
                                        }
                                }
                                else if(itA->second < itB->second){
-                                       PCell value(itB->second, itA->second, distance);
+                                       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;
-                                               D->addCell(value);
+                                               DMatrix->addCell(itA->second, value);
                                        }
                                        else if(refRow == itB->second && refCol == itA->second){
                                                lt = 0;
                                        }
                                        else{
-                                               D->addCell(value);
+                                               DMatrix->addCell(itA->second, value);
                                        }
                                }
                                reading->update(itA->second * nseqs);
@@ -100,7 +101,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                if(lt == 0){  // oops, it was square
        
                        fileHandle.close();  //let's start over
-                       D->clear();  //let's start over
+                       DMatrix->clear();  //let's start over
                   
                        m->openInputFile(distFile, fileHandle);  //let's start over
 
@@ -119,8 +120,8 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                                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){
-                                       PCell value(itA->second, itB->second, distance);
-                                       D->addCell(value);
+                    PDistCell value(itA->second, distance);
+                                       DMatrix->addCell(itB->second, value);
                                        reading->update(itA->second * nseqs);
                                }
                
@@ -145,10 +146,6 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
 }
 
 /***********************************************************************/
-
-ReadColumnMatrix::~ReadColumnMatrix(){
-       //delete D;
-       //delete list;
-}
-
+ReadColumnMatrix::~ReadColumnMatrix(){}
+/***********************************************************************/