changes while testing

[mothur.git] / fullmatrix.cpp

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 0255d07f00bbcfef3a9c62658149ec39fd6fc5bf..4451d6645ea8691b941ebbc991f82cc4ce8b4706 100644 (file)
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -11,15 +11,14 @@
 
 /**************************************************************************/
 //This constructor reads a distance matrix file and stores the data in the matrix.
-FullMatrix::FullMatrix(ifstream& filehandle) {
+FullMatrix::FullMatrix(ifstream& filehandle, GroupMap* g, bool s) : groupmap(g), sim(s) {
        try{
                m = MothurOut::getInstance();
-               globaldata = GlobalData::getInstance();
-               groupmap = globaldata->gGroupmap;
                
                string name, group;
-               filehandle >> numSeqs >> name;
                
+               filehandle >> numSeqs >> name;
+       
                //make the matrix filled with zeros
                matrix.resize(numSeqs); 
                for(int i = 0; i < numSeqs; i++) {
@@ -44,6 +43,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                                
                                for(int i=0;i<numSeqs;i++){
                                        filehandle >> matrix[0][i];
+                                       if (sim) {  matrix[0][i] = 1.0 - matrix[0][i];  }
                                }
                                break;
                        }
@@ -54,12 +54,14 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                                break;
                        }
                }
-               
+       
                //read rest of matrix
-               if (square == true) { readSquareMatrix(filehandle); }
-               else { readLTMatrix(filehandle); }
+               if (square == true) {  readSquareMatrix(filehandle); }
+               else {  readLTMatrix(filehandle); }
                
-               sortGroups(0, numSeqs-1);       
+               filehandle.close();
+               
+               if (!m->control_pressed) { sortGroups(0, numSeqs-1); }  
                                
        }
        catch(exception& e) {
@@ -68,7 +70,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
        }
 }
 /**************************************************************************/
-void FullMatrix::readSquareMatrix(ifstream& filehandle) {
+int FullMatrix::readSquareMatrix(ifstream& filehandle) {
        try {
        
                Progress* reading;
@@ -77,7 +79,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                int count = 0;
                
                string group, name;
-               
+       
                for(int i=1;i<numSeqs;i++){
                        filehandle >> name;             
                        
@@ -88,14 +90,22 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                        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++){
+                               if (m->control_pressed) { delete reading;  return 0; }
+                               
                                filehandle >> matrix[i][j];
+                               if (sim) {  matrix[i][j] = 1.0 - matrix[i][j];  }
                                
                                count++;
                                reading->update(count);
                        }
                }
+               
+               if (m->control_pressed) { delete reading;  return 0; }
+               
                reading->finish();
                delete reading;
+               
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "FullMatrix", "readSquareMatrix");
@@ -103,8 +113,9 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
        }
 } 
 /**************************************************************************/
-void FullMatrix::readLTMatrix(ifstream& filehandle) {
+int FullMatrix::readLTMatrix(ifstream& filehandle) {
        try {
+               
                Progress* reading;
                reading = new Progress("Reading matrix:     ", numSeqs * (numSeqs - 1) / 2);
                
@@ -123,15 +134,24 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                        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++){
+                               if (m->control_pressed) { delete reading;  return 0; }
+                               
                                filehandle >> distance;
+                               if (sim) {  distance = 1.0 - distance;  }
+                               
                                matrix[i][j] = distance;  matrix[j][i] = distance;
+                               
                                count++;
                                reading->update(count);
                        }
                }
-
+               
+               if (m->control_pressed) { delete reading;  return 0; }
+               
                reading->finish();
                delete reading;
+               
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "FullMatrix", "readLTMatrix");