working on pam

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index 66f1db23d633eb83b3706bd15f6deb48e8c7cb5b..84fddcf263cfdeb572f72ff3bd658325f31271e0 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -54,7 +54,8 @@ int ReadBlast::read(NameAssignment* nameMap) {
                
                //create objects needed for read
                if (!hclusterWanted) {
-                       matrix = new SparseMatrix();
+                       matrix = new SparseDistanceMatrix();
+            matrix->resize(nseqs);
                }else{
                        overlapFile = m->getRootName(blastfile) + "overlap.dist";
                        distFile = m->getRootName(blastfile) + "hclusterDists.dist";
@@ -66,7 +67,7 @@ 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);  }
                        return 0;
                }
                
@@ -110,14 +111,14 @@ int ReadBlast::read(NameAssignment* nameMap) {
                        }
                }else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
 
-                               
+       
                //read file
                while(!fileHandle.eof()){  
                
                        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;
                        }
@@ -185,9 +186,14 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                                        //is this distance below cutoff
                                                        if (distance < cutoff) {
                                                                if (!hclusterWanted) {
-                                                                       PCell value(itA->second, it->first, distance);
-                                                                       matrix->addCell(value);
-                                                               }else{
+                                    if (itA->second < it->first) {
+                                        PDistCell value(it->first, distance);
+                                        matrix->addCell(itA->second, value);
+                                    }else {
+                                        PDistCell value(itA->second, distance);
+                                        matrix->addCell(it->first, value);
+                                    }
+                                }else{
                                                                        outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
                                                                }
                                                        }
@@ -252,8 +258,13 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                //is this distance below cutoff
                                if (distance < cutoff) {
                                        if (!hclusterWanted) {
-                                               PCell value(itA->second, it->first, distance);
-                                               matrix->addCell(value);
+                                               if (itA->second < it->first) {
+                            PDistCell value(it->first, distance);
+                            matrix->addCell(itA->second, value);
+                        }else {
+                            PDistCell value(itA->second, distance);
+                            matrix->addCell(it->first, value);
+                        }
                                        }else{
                                                outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
                                        }
@@ -271,7 +282,7 @@ 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 +297,7 @@ 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;
                }
@@ -337,7 +348,12 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                        //is this a new name?
                        if (name != prevName) {
                                prevName = name;
-                               nameMap->push_back(name);
+                
+                if (nameMap->get(name) != -1) { m->mothurOut("[ERROR]: trying to exact names from blast file, and I found dups.  Are you sequence names unique? quitting.\n"); m->control_pressed = true; }
+                else {
+                    nameMap->push_back(name);
+                }
+                //outName << name << '\t' << name << endl;
                                num++;
                        }
                }