added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / readphylip.cpp

diff --git a/readphylip.cpp b/readphylip.cpp
index fe278ab14856f085a9a61bfc09e40522dcf96d03..d256f92a816b03c101a01c12fdf19f4cace6678a 100644 (file)
--- 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;
+                        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;
@@ -59,29 +72,37 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                         }
         
                         Progress* reading;
+                        DMatrix->resize(nseqs);
         
                         if(square == 0){
 
                                 reading = new Progress("Reading matrix:     ", nseqs * (nseqs - 1) / 2);
                 
                                 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);
-                                                                D->addCell(value);
+                                                            PDistCell value(i, distance);
+                                                            DMatrix->addCell(j, value);
                                                         }
                                                         index++;
                                                         reading->update(index);
@@ -89,16 +110,19 @@ 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);
-                                                                D->addCell(value);
+                                                            PDistCell value(nameMap->get(matrixNames[i]), distance);
+                                                            DMatrix->addCell(nameMap->get(matrixNames[j]), value);
                                                         }
                                                         index++;
                                                         reading->update(index);
@@ -115,17 +139,22 @@ 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);
-                                                                D->addCell(value);
+                                                            PDistCell value(i, distance);
+                                                            DMatrix->addCell(j, value);
                                                         }
                                                         index++;
                                                         reading->update(index);
@@ -133,16 +162,19 @@ 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){
-                                                                PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
-                                                                D->addCell(value);
+                                                                                                               if(distance < cutoff && j < i){
+                                                            PDistCell value(nameMap->get(matrixNames[i]), distance);
+                                                            DMatrix->addCell(nameMap->get(matrixNames[j]), value);
                                                         }
                                                         index++;
                                                         reading->update(index);
@@ -150,32 +182,26 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                                         }
                                 }
                         }
+                                               
+                                               if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+                                               
                         reading->finish();
                         delete reading;
-
+            
                         list->setLabel("0");
                         fileHandle.close();
 
-                        if(nameMap != NULL){
-                                for(int i=0;i<matrixNames.size();i++){
-                                        nameMap->erase(matrixNames[i]);
-                                }
-                                if(nameMap->size() > 0){
-                                        //should probably tell them what is missing if we missed something
-                                        mothurOut("missed something\t" + toString(nameMap->size())); mothurOutEndLine();
-                                }
-                        }
+                                                               
+                                               return 1;
 
                 }
         catch(exception& e) {
-               errorOut(e, "ReadPhylipMatrix", "read");
+               m->errorOut(e, "ReadPhylipMatrix", "read");
                 exit(1);
         }
        }
 
 /***********************************************************************/
+ReadPhylipMatrix::~ReadPhylipMatrix(){}
+/***********************************************************************/
 
-ReadPhylipMatrix::~ReadPhylipMatrix(){
-       // delete D;
-       // delete list;
-}