added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index c3dfd4884f0d01d6c9dbb98c17aa9a8341a44c5d..2d4947745be0a52fafba4c33f38fb6504ede2288 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -40,7 +40,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                if (m->control_pressed) { return 0; }
 
                ifstream fileHandle;
-               openInputFile(blastfile, fileHandle);
+               m->openInputFile(blastfile, fileHandle);
                
                string firstName, secondName, eScore, currentRow;
                string repeatName = "";
@@ -56,17 +56,17 @@ int ReadBlast::read(NameAssignment* nameMap) {
                if (!hclusterWanted) {
                        matrix = new SparseMatrix();
                }else{
-                       overlapFile = getRootName(blastfile) + "overlap.dist";
-                       distFile = getRootName(blastfile) + "hclusterDists.dist";
+                       overlapFile = m->getRootName(blastfile) + "overlap.dist";
+                       distFile = m->getRootName(blastfile) + "hclusterDists.dist";
                        
-                       openOutputFile(overlapFile, outOverlap);
-                       openOutputFile(distFile, outDist);
+                       m->openOutputFile(overlapFile, outOverlap);
+                       m->openOutputFile(distFile, outDist);
                }
                
                if (m->control_pressed) { 
                        fileHandle.close();
                        if (!hclusterWanted) {  delete matrix; }
-                       else { outOverlap.close(); remove(overlapFile.c_str()); outDist.close(); remove(distFile.c_str());  }
+                       else { outOverlap.close(); m->mothurRemove(overlapFile); outDist.close(); m->mothurRemove(distFile);  }
                        return 0;
                }
                
@@ -79,7 +79,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                if (!fileHandle.eof()) {
                        //read in line from file
                        fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                        
                        currentRow = firstName;
                        lengthThisSeq = numBases;
@@ -90,8 +90,8 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                //convert name to number
                                map<string,int>::iterator itA = nameMap->find(firstName);
                                map<string,int>::iterator itB = nameMap->find(secondName);
-                               if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
-                               if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
+                               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);  }
                                
                                thisRowsBlastScores[itB->second] = score;
                                
@@ -117,7 +117,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                        if (m->control_pressed) { 
                                fileHandle.close();
                                if (!hclusterWanted) {  delete matrix; }
-                               else { outOverlap.close(); remove(overlapFile.c_str()); outDist.close(); remove(distFile.c_str());  }
+                               else { outOverlap.close(); m->mothurRemove(overlapFile); outDist.close(); m->mothurRemove(distFile);  }
                                delete reading;
                                return 0;
                        }
@@ -125,7 +125,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                        //read in line from file
                        fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
                        //cout << firstName << '\t' << secondName << '\t' << percentId << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl;       
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                        
                        string temp = firstName + secondName; //to check if this file has repeat lines, ie. is this a blast instead of a blscreen file
                        
@@ -143,8 +143,8 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                                //convert name to number
                                                map<string,int>::iterator itA = nameMap->find(firstName);
                                                map<string,int>::iterator itB = nameMap->find(secondName);
-                                               if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
-                                               if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
+                                               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);  }
                                                
                                                //save score
                                                thisRowsBlastScores[itB->second] = score;
@@ -210,8 +210,8 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                                //convert name to number
                                                map<string,int>::iterator itA = nameMap->find(firstName);
                                                map<string,int>::iterator itB = nameMap->find(secondName);
-                                               if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
-                                               if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
+                                               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);  }
                                                
                                                thisRowsBlastScores[itB->second] = score;
                                                
@@ -271,7 +271,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                if (m->control_pressed) { 
                                fileHandle.close();
                                if (!hclusterWanted) {  delete matrix; }
-                               else { outOverlap.close(); remove(overlapFile.c_str()); outDist.close(); remove(distFile.c_str());  }
+                               else { outOverlap.close(); m->mothurRemove(overlapFile); outDist.close(); m->mothurRemove(distFile);  }
                                delete reading;
                                return 0;
                }
@@ -286,7 +286,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                if (m->control_pressed) { 
                                fileHandle.close();
                                if (!hclusterWanted) {  delete matrix; }
-                               else {  remove(overlapFile.c_str());  remove(distFile.c_str());  }
+                               else {  m->mothurRemove(overlapFile);  m->mothurRemove(distFile);  }
                                delete reading;
                                return 0;
                }
@@ -311,16 +311,16 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                int num = 1;
                
                ifstream in;
-               openInputFile(blastfile, in);
+               m->openInputFile(blastfile, in);
                
                //ofstream outName;
-               //openOutputFile((blastfile + ".tempOutNames"), outName);
+               //m->openOutputFile((blastfile + ".tempOutNames"), outName);
                
                //read first line
                in >> prevName;
        
                for (int i = 0; i < 11; i++) {  in >> hold;  }
-               gobble(in);
+               m->gobble(in);
                                
                //save name in nameMap
                nameMap->push_back(prevName);
@@ -332,7 +332,7 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                        in >> name;
        
                        for (int i = 0; i < 11; i++) {  in >> hold;  }
-                       gobble(in);
+                       m->gobble(in);
                        
                        //is this a new name?
                        if (name != prevName) {
@@ -345,9 +345,9 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                in.close();
                
                //write out names file
-               //string outNames = getRootName(blastfile) + "names";
+               //string outNames = m->getRootName(blastfile) + "names";
                //ofstream out;
-               //openOutputFile(outNames, out);
+               //m->openOutputFile(outNames, out);
                //nameMap->print(out);
                //out.close();