X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readphylip.cpp;h=1c529b26f15fdfa172c8a0f7ebcf20187e87b03b;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=5f92275eb9e6d4c8e3ee21241bbd6f626a295bc1;hpb=832d53a9dfac6b1795735eec643d8cf627b0d8e3;p=mothur.git

diff --git a/readphylip.cpp b/readphylip.cpp
index 5f92275..1c529b2 100644
--- a/readphylip.cpp
+++ b/readphylip.cpp
@@ -14,22 +14,35 @@
 
 ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
         
-        successOpen = openInputFile(distFile, fileHandle);
+        successOpen = m->openInputFile(distFile, fileHandle);
+		sim=false;
         
 }
+/***********************************************************************/
+
+ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){
+	
+	successOpen = m->openInputFile(distFile, fileHandle);
+	sim=s;
+}
+
 
 /***********************************************************************/
 
-void ReadPhylipMatrix::read(NameAssignment* nameMap){
+int ReadPhylipMatrix::read(NameAssignment* nameMap){
         try {
         
                         float distance;
                         int square, nseqs;
                         string name;
                         vector<string> matrixNames;
-        
-                        fileHandle >> nseqs >> name;
-
+						
+						string numTest;
+						fileHandle >> numTest >> name;
+			
+						if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+						else { convert(numTest, nseqs); }
+			
                         matrixNames.push_back(name);
 
                         if(nameMap == NULL){
@@ -38,7 +51,7 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                         }
                         else{
                                 list = new ListVector(nameMap->getListVector());
-                                if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+                                if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
                         }
         
                         char d;
@@ -67,17 +80,25 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                                 int        index = 0;
                
                                 for(int i=1;i<nseqs;i++){
+										if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+										
                                         fileHandle >> name;
                                         matrixNames.push_back(name);
+						
         
                                         //there's A LOT of repeated code throughout this method...
                                         if(nameMap == NULL){
                                                 list->set(i, name);
                                         
                                                 for(int j=0;j<i;j++){
+												
+														if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
+														
                                                         fileHandle >> distance;
+											
                                                 
                                                         if (distance == -1) { distance = 1000000; }
+														else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                                 
                                                         if(distance < cutoff){
                                                                 PCell value(i, j, distance);
@@ -89,12 +110,15 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                                 
                                         }
                                         else{
-                                                if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+                                                if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
                                 
                                                 for(int j=0;j<i;j++){
                                                         fileHandle >> distance;
+														
+														if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
                                 
                                                         if (distance == -1) { distance = 1000000; }
+														else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                                         
                                                         if(distance < cutoff){
                                                                 PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
@@ -115,13 +139,18 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                                 for(int i=1;i<nseqs;i++){
                                         fileHandle >> name;                
                                         matrixNames.push_back(name);
+										
+										
         
                                         if(nameMap == NULL){
                                                 list->set(i, name);
                                                 for(int j=0;j<nseqs;j++){
                                                         fileHandle >> distance;
-                                        
+														
+														if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+														
                                                         if (distance == -1) { distance = 1000000; }
+														else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                                         
                                                         if(distance < cutoff && j < i){
                                                                 PCell value(i, j, distance);
@@ -133,14 +162,17 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                                         
                                         }
                                         else{
-                                                if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+                                                if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
                                 
                                                 for(int j=0;j<nseqs;j++){
                                                         fileHandle >> distance;
-                        
-                                                        if (distance == -1) { distance = 1000000; }
+														
+														if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+														
+                                                       if (distance == -1) { distance = 1000000; }
+														else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.                                                        
                                                         
-                                                        if(distance < cutoff && j < i){
+														if(distance < cutoff && j < i){
                                                                 PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
                                                                 D->addCell(value);
                                                         }
@@ -150,6 +182,9 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                                         }
                                 }
                         }
+						
+						if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+						
                         reading->finish();
                         delete reading;
 
@@ -162,13 +197,15 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                                 }
                                 if(nameMap->size() > 0){
                                         //should probably tell them what is missing if we missed something
-                                        mothurOut("missed something\t" + toString(nameMap->size())); mothurOutEndLine();
+                                        m->mothurOut("missed something\t" + toString(nameMap->size())); m->mothurOutEndLine();
                                 }
                         } */
+						
+						return 1;
 
                 }
         catch(exception& e) {
-               errorOut(e, "ReadPhylipMatrix", "read");
+               m->errorOut(e, "ReadPhylipMatrix", "read");
                 exit(1);
         }
 	}