created mothurOut class to handle logfiles

[mothur.git] / fullmatrix.cpp

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 5612041528a00e9e0e441422662c6d3738bcb07c..0255d07f00bbcfef3a9c62658149ec39fd6fc5bf 100644 (file)
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -13,6 +13,7 @@
 //This constructor reads a distance matrix file and stores the data in the matrix.
 FullMatrix::FullMatrix(ifstream& filehandle) {
        try{
+               m = MothurOut::getInstance();
                globaldata = GlobalData::getInstance();
                groupmap = globaldata->gGroupmap;
                
@@ -25,7 +26,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                        matrix[i].resize(numSeqs, 0.0);
                }
                group = groupmap->getGroup(name);
-               if(group == "not found") {      mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+               if(group == "not found") {      m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
                index.resize(numSeqs);
                index[0].seqName = name;
                index[0].groupName = group;
@@ -62,7 +63,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                                
        }
        catch(exception& e) {
-               errorOut(e, "FullMatrix", "FullMatrix");
+               m->errorOut(e, "FullMatrix", "FullMatrix");
                exit(1);
        }
 }
@@ -84,7 +85,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                        index[i].seqName = name;
                        index[i].groupName = group;
                        
-                       if(group == "not found") {      mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+                       if(group == "not found") {      m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
                                
                        for(int j=0;j<numSeqs;j++){
                                filehandle >> matrix[i][j];
@@ -97,7 +98,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                delete reading;
        }
        catch(exception& e) {
-               errorOut(e, "FullMatrix", "readSquareMatrix");
+               m->errorOut(e, "FullMatrix", "readSquareMatrix");
                exit(1);
        }
 } 
@@ -119,7 +120,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                        index[i].seqName = name;
                        index[i].groupName = group;
        
-                       if(group == "not found") {      mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
+                       if(group == "not found") {      m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
                                
                        for(int j=0;j<i;j++){
                                filehandle >> distance;
@@ -133,7 +134,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                delete reading;
        }
        catch(exception& e) {
-               errorOut(e, "FullMatrix", "readLTMatrix");
+               m->errorOut(e, "FullMatrix", "readLTMatrix");
                exit(1);
        }
 }
@@ -176,7 +177,7 @@ void FullMatrix::sortGroups(int low, int high){
        
        }
        catch(exception& e) {
-               errorOut(e, "FullMatrix", "sortGroups");
+               m->errorOut(e, "FullMatrix", "sortGroups");
                exit(1);
        }
 }
@@ -214,7 +215,7 @@ void FullMatrix::swapRows(int i, int j) {
                
        }
        catch(exception& e) {
-               errorOut(e, "FullMatrix", "swapRows");
+               m->errorOut(e, "FullMatrix", "swapRows");
                exit(1);
        }
 }
@@ -253,7 +254,7 @@ void FullMatrix::printMatrix(ostream& out) {
                for (int i = 0; i < numSeqs; i++) {  out << i << '\t' <<  index[i].seqName << endl;  }
        }
        catch(exception& e) {
-               errorOut(e, "FullMatrix", "printMatrix");
+               m->errorOut(e, "FullMatrix", "printMatrix");
                exit(1);
        }
 }