fixed bug in read.tree

[mothur.git] / fullmatrix.cpp

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 6ea2318d740003f8cf46ec7e63815c175e1893ca..66c67b7da0999281af64e9836c9a0f94aff3a698 100644 (file)
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -16,6 +16,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                globaldata = GlobalData::getInstance();
                groupmap = globaldata->gGroupmap;
                
+               float minSoFar = 0.0;
                string name, group;
                filehandle >> numSeqs >> name;
                
@@ -39,9 +40,18 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                        if(isalnum(d)){ 
                                square = true;
                                filehandle.putback(d);
-                               for(int i=0;i<numSeqs;i++){
+                               
+                               if (numSeqs >= 2) {
+                                       //save first distance that is not distance to itself as minimum
+                                       filehandle >> matrix[0][0] >> minSoFar;
+                                       matrix[0][1] = minSoFar;
+                               }
+                               
+                               for(int i=2;i<numSeqs;i++){
                                        filehandle >> matrix[0][i];
+                                       if (matrix[0][i] < minSoFar) { minSoFar = matrix[0][i]; }
                                }
+                               index[0].minDist = minSoFar;
                                break;
                        }
                        
@@ -77,7 +87,8 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                reading = new Progress("Reading matrix:    ", numSeqs * numSeqs);
                
                int count = 0;
-               float distance;
+               float distance, minSoFar;
+               minSoFar = 0.0;
                string group, name;
                
                for(int i=1;i<numSeqs;i++){
@@ -87,15 +98,23 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                        index[i].groupname = group;
                        index[i].seqName = name;
                        
+                       filehandle >> minSoFar;
+                       matrix[i][0] = minSoFar;
+                       
                        if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
                                
-                       for(int j=0;j<numSeqs;j++){
+                       for(int j=1;j<numSeqs;j++){
                                filehandle >> distance;
+                               
+                               if ((distance < minSoFar) && (i != j)) { minSoFar = distance; }
                                        
                                matrix[i][j] = distance;
                                count++;
                                reading->update(count);
                        }
+                       
+                       //save minimum value for each row
+                       index[i].minDist = minSoFar;
                }
                reading->finish();
                delete reading;
@@ -117,7 +136,9 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                reading = new Progress("Reading matrix:    ", numSeqs * (numSeqs - 1) / 2);
                
                int count = 0;
-               float distance;
+               float distance, minSoFar;
+               minSoFar = 0.0;
+
                string group, name;
                
                for(int i=1;i<numSeqs;i++){
@@ -126,16 +147,24 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                        group = groupmap->getGroup(name);
                        index[i].groupname = group;
                        index[i].seqName = name;
+                       
+                       filehandle >> minSoFar;
+                       matrix[i][0] = minSoFar;
        
                        if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl;  exit(1); }
                                
-                       for(int j=0;j<i;j++){
+                       for(int j=1;j<i;j++){
                                filehandle >> distance;
+                               
+                               if (distance < minSoFar)  { minSoFar = distance; }
                                        
                                matrix[i][j] = distance;  matrix[j][i] = distance;
                                count++;
                                reading->update(count);
                        }
+                       
+                       //save minimum value for each row
+                       index[i].minDist = minSoFar;
                }
                reading->finish();
                delete reading;