X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readphylip.cpp;h=6de23e83279482127f5f261c53f94c345585455d;hp=174b7e3c510c1492043e21b3f94d3eb1cad76ee0;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037

diff --git a/readphylip.cpp b/readphylip.cpp
index 174b7e3..6de23e8 100644
--- a/readphylip.cpp
+++ b/readphylip.cpp
@@ -13,174 +13,382 @@
 /***********************************************************************/
 
 ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
-	
-	successOpen = openInputFile(distFile, fileHandle);
-	
+        
+        successOpen = m->openInputFile(distFile, fileHandle);
+		sim=false;
+        
 }
-
 /***********************************************************************/
 
-void ReadPhylipMatrix::read(NameAssignment* nameMap){
-	try {
+ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){
 	
-			float distance;
-			int square, nseqs;
-			string name;
-			vector<string> matrixNames;
-	
-			fileHandle >> nseqs >> name;
+	successOpen = m->openInputFile(distFile, fileHandle);
+	sim=s;
+}
 
-			matrixNames.push_back(name);
 
-			if(nameMap == NULL){
-				list = new ListVector(nseqs);
-				list->set(0, name);
-			}
-			else{
-				list = new ListVector(nameMap->getListVector());
-				if(nameMap->count(name)==0){	cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
-			}
-	
-			char d;
-			while((d=fileHandle.get()) != EOF){
-		
-				if(isalnum(d)){
-					square = 1;
-					fileHandle.putback(d);
-					for(int i=0;i<nseqs;i++){
-						fileHandle >> distance;
-					}
-					break;
-				}
-				if(d == '\n'){
-					square = 0;
-					break;
-				}
-			}
-	
-			Progress* reading;
-	
-			if(square == 0){
+/***********************************************************************/
 
-				reading = new Progress("Reading matrix:     ", nseqs * (nseqs - 1) / 2);
-		
-				int	index = 0;
-		
-				for(int i=1;i<nseqs;i++){
-					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++){
-							fileHandle >> distance;
-						
-							if (distance == -1) { distance = 1000000; }
+int ReadPhylipMatrix::read(NameAssignment* nameMap){
+        try {
+        
+                        float distance;
+                        int square, nseqs; 
+                        string name;
+                        vector<string> matrixNames;
 						
-							if(distance < cutoff){
-								PCell value(i, j, distance);
-								D->addCell(value);
-							}
-							index++;
-							reading->update(index);
-						}
-				
-					}
-					else{
-						if(nameMap->count(name)==0){	cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
-				
-						for(int j=0;j<i;j++){
-							fileHandle >> distance;
-				
-							if (distance == -1) { distance = 1000000; }
-							
-							if(distance < cutoff){
-								PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
-								D->addCell(value);
-							}
-							index++;
-							reading->update(index);
-						}
-					}
-				}
-			}
-			else{
-
-				reading = new Progress("Reading matrix:     ", nseqs * nseqs);
+						string numTest;
+						fileHandle >> numTest >> name;
 			
-				int index = nseqs;
-		
-				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 (distance == -1) { distance = 1000000; }
-							
-							if(distance < cutoff && j < i){
-								PCell value(i, j, distance);
-								D->addCell(value);
-							}
-							index++;
-							reading->update(index);
-						}
-					
-					}
-					else{
-						if(nameMap->count(name)==0){	cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
-				
-						for(int j=0;j<nseqs;j++){
-							fileHandle >> distance;
+						if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+						else { convert(numTest, nseqs); }
 			
-							if (distance == -1) { distance = 1000000; }
-							
-							if(distance < cutoff && j < i){
-								PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
-								D->addCell(value);
-							}
-							index++;
-							reading->update(index);
-						}
-					}
-				}
-			}
-			reading->finish();
-			delete reading;
+                        matrixNames.push_back(name);
 
-			list->setLabel("0");
-			fileHandle.close();
+                        if(nameMap == NULL){
+                                list = new ListVector(nseqs);
+                                list->set(0, name);
+                        }
+                        else{
+                                list = new ListVector(nameMap->getListVector());
+                                if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
+                        }
+        
+                        char d;
+                        while((d=fileHandle.get()) != EOF){
+                
+                                if(isalnum(d)){
+                                        square = 1;
+                                        fileHandle.putback(d);
+                                        for(int i=0;i<nseqs;i++){
+                                                fileHandle >> distance;
+                                        }
+                                        break;
+                                }
+                                if(d == '\n'){
+                                        square = 0;
+                                        break;
+                                }
+                        }
+        
+                        Progress* reading;
+                        DMatrix->resize(nseqs);
+        
+                        if(square == 0){
 
-			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
-					cout << "missed something" << '\t' << nameMap->size() << endl;
-				}
-			}
+                                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){
+                                                            PDistCell value(i, distance);
+                                                            DMatrix->addCell(j, value);
+                                                        }
+                                                        index++;
+                                                        reading->update(index);
+                                                }
+                                
+                                        }
+                                        else{
+                                                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){
+                                                            PDistCell value(nameMap->get(matrixNames[i]), distance);
+                                                            DMatrix->addCell(nameMap->get(matrixNames[j]), value);
+                                                        }
+                                                        index++;
+                                                        reading->update(index);
+                                                }
+                                        }
+                                }
+                        }
+                        else{
 
-		}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReadPhylipMatrix class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReadPhylipMatrix class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-}
+                                reading = new Progress("Reading matrix:     ", nseqs * nseqs);
+                        
+                                int index = nseqs;
+                
+                                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){
+                                                            PDistCell value(i, distance);
+                                                            DMatrix->addCell(j, value);
+                                                        }
+                                                        index++;
+                                                        reading->update(index);
+                                                }
+                                        
+                                        }
+                                        else{
+                                                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 (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){
+                                                            PDistCell value(nameMap->get(matrixNames[i]), distance);
+                                                            DMatrix->addCell(nameMap->get(matrixNames[j]), value);
+                                                        }
+                                                        index++;
+                                                        reading->update(index);
+                                                }
+                                        }
+                                }
+                        }
+						
+						if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+						
+                        reading->finish();
+                        delete reading;
+            
+                        list->setLabel("0");
+                        fileHandle.close();
+
+                    						
+						return 1;
 
+                }
+        catch(exception& e) {
+               m->errorOut(e, "ReadPhylipMatrix", "read");
+                exit(1);
+        }
+	}
 /***********************************************************************/
 
-ReadPhylipMatrix::~ReadPhylipMatrix(){
-	delete D;
-	delete list;
+int ReadPhylipMatrix::read(CountTable* countTable){
+    try {
+        
+        float distance;
+        int square, nseqs; 
+        string name;
+        vector<string> matrixNames;
+        
+        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(countTable == NULL){
+            list = new ListVector(nseqs);
+            list->set(0, name);
+        }
+        else{  list = new ListVector(countTable->getListVector()); }
+        
+        if (m->control_pressed) { return 0; }
+        
+        char d;
+        while((d=fileHandle.get()) != EOF){
+            
+            if(isalnum(d)){
+                square = 1;
+                fileHandle.putback(d);
+                for(int i=0;i<nseqs;i++){
+                    fileHandle >> distance;
+                }
+                break;
+            }
+            if(d == '\n'){
+                square = 0;
+                break;
+            }
+        }
+        
+        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(countTable == 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){
+                            PDistCell value(i, distance);
+                            DMatrix->addCell(j, value);
+                        }
+                        index++;
+                        reading->update(index);
+                    }
+                    
+                }
+                else{
+                    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){
+                            int iIndex = countTable->get(matrixNames[i]);
+                            int jIndex = countTable->get(matrixNames[j]);
+                            
+                            if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
+                            if (iIndex < jIndex) { 
+                                PDistCell value(jIndex, distance);
+                                DMatrix->addCell(iIndex, value);
+                            }else {
+                                PDistCell value(iIndex, distance);
+                                DMatrix->addCell(jIndex, value);
+
+                            }
+                        }
+                        index++;
+                        reading->update(index);
+                    }
+                }
+            }
+        }
+        else{
+            
+            reading = new Progress("Reading matrix:     ", nseqs * nseqs);
+            
+            int index = nseqs;
+            
+            for(int i=1;i<nseqs;i++){
+                fileHandle >> name;                
+                matrixNames.push_back(name);
+                
+                
+                
+                if(countTable == 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){
+                            PDistCell value(i, distance);
+                            DMatrix->addCell(j, value);
+                        }
+                        index++;
+                        reading->update(index);
+                    }
+                    
+                }
+                else{
+                    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){
+                            int iIndex = countTable->get(matrixNames[i]);
+                            int jIndex = countTable->get(matrixNames[j]);
+                            
+                            if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
+                            if (iIndex < jIndex) { 
+                                PDistCell value(jIndex, distance);
+                                DMatrix->addCell(iIndex, value);
+                            }else {
+                                PDistCell value(iIndex, distance);
+                                DMatrix->addCell(jIndex, value);
+                                
+                            }
+                        }
+                        index++;
+                        reading->update(index);
+                    }
+                }
+            }
+        }
+        
+        if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+        
+        reading->finish();
+        delete reading;
+        
+        list->setLabel("0");
+        fileHandle.close();
+        
+        
+        return 1;
+        
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ReadPhylipMatrix", "read");
+        exit(1);
+    }
 }
+/***********************************************************************/
+ReadPhylipMatrix::~ReadPhylipMatrix(){}
+/***********************************************************************/