X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fullmatrix.cpp;h=4451d6645ea8691b941ebbc991f82cc4ce8b4706;hp=75cb0dfc8a441f510ffbda66b29345d05a6f161f;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=8aaea67a29205b8d3fe787d94d0dc5987858d2e6

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 75cb0df..4451d66 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -9,12 +9,275 @@
 
 #include "fullmatrix.h"
 
+/**************************************************************************/
+//This constructor reads a distance matrix file and stores the data in the matrix.
+FullMatrix::FullMatrix(ifstream& filehandle, GroupMap* g, bool s) : groupmap(g), sim(s) {
+	try{
+		m = MothurOut::getInstance();
+		
+		string name, group;
+		
+		filehandle >> numSeqs >> name;
+	
+		//make the matrix filled with zeros
+		matrix.resize(numSeqs); 
+		for(int i = 0; i < numSeqs; i++) {
+			matrix[i].resize(numSeqs, 0.0);
+		}
+		group = groupmap->getGroup(name);
+		if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+		index.resize(numSeqs);
+		index[0].seqName = name;
+		index[0].groupName = group;
+		
+		//determine if matrix is square or lower triangle
+		//if it is square read the distances for the first sequence
+		char d;
+		bool square;
+		while((d=filehandle.get()) != EOF){
+			
+			//is d a number meaning its square
+			if(isalnum(d)){ 
+				square = true;
+				filehandle.putback(d);
+				
+				for(int i=0;i<numSeqs;i++){
+					filehandle >> matrix[0][i];
+					if (sim) {  matrix[0][i] = 1.0 - matrix[0][i];  }
+				}
+				break;
+			}
+			
+			//is d a line return meaning its lower triangle
+			if(d == '\n'){
+				square = false;
+				break;
+			}
+		}
+	
+		//read rest of matrix
+		if (square == true) {  readSquareMatrix(filehandle); }
+		else {  readLTMatrix(filehandle); }
+		
+		filehandle.close();
+		
+		if (!m->control_pressed) { sortGroups(0, numSeqs-1); }	
+				
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FullMatrix", "FullMatrix");
+		exit(1);
+	}
+}
+/**************************************************************************/
+int FullMatrix::readSquareMatrix(ifstream& filehandle) {
+	try {
+	
+		Progress* reading;
+		reading = new Progress("Reading matrix:     ", numSeqs * numSeqs);
+		
+		int count = 0;
+		
+		string group, name;
+	
+		for(int i=1;i<numSeqs;i++){
+			filehandle >> name;		
+			
+			group = groupmap->getGroup(name);
+			index[i].seqName = name;
+			index[i].groupName = group;
+			
+			if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+				
+			for(int j=0;j<numSeqs;j++){
+				if (m->control_pressed) { delete reading;  return 0; }
+				
+				filehandle >> matrix[i][j];
+				if (sim) {  matrix[i][j] = 1.0 - matrix[i][j];  }
+				
+				count++;
+				reading->update(count);
+			}
+		}
+		
+		if (m->control_pressed) { delete reading;  return 0; }
+		
+		reading->finish();
+		delete reading;
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FullMatrix", "readSquareMatrix");
+		exit(1);
+	}
+} 
+/**************************************************************************/
+int FullMatrix::readLTMatrix(ifstream& filehandle) {
+	try {
+		
+		Progress* reading;
+		reading = new Progress("Reading matrix:     ", numSeqs * (numSeqs - 1) / 2);
+		
+		int count = 0;
+		float distance;
 
-/**************************************************************************
-FullMatrix::FullMatrix(ifstream& in) {
+		string group, name;
+	
+		for(int i=1;i<numSeqs;i++){
+			filehandle >> name;		
+					
+			group = groupmap->getGroup(name);
+			index[i].seqName = name;
+			index[i].groupName = group;
+	
+			if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+				
+			for(int j=0;j<i;j++){
+				if (m->control_pressed) { delete reading;  return 0; }
+				
+				filehandle >> distance;
+				if (sim) {  distance = 1.0 - distance;  }
+				
+				matrix[i][j] = distance;  matrix[j][i] = distance;
+				
+				count++;
+				reading->update(count);
+			}
+		}
+		
+		if (m->control_pressed) { delete reading;  return 0; }
+		
+		reading->finish();
+		delete reading;
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FullMatrix", "readLTMatrix");
+		exit(1);
+	}
+}
+
+/**************************************************************************/
 
+void FullMatrix::sortGroups(int low, int high){
+	try{
+		
+		if (low < high) {
+			int i = low+1;
+			int j = high;
+			int pivot = (low+high) / 2;
+			
+			swapRows(low, pivot);  //puts pivot in final spot
+			
+			/* compare value */
+			//what group does this row belong to
+			string key = index[low].groupName;
+			
+			/* partition */
+			while(i <= j) {
+				/* find member above ... */
+				while((i <= high) && (index[i].groupName <= key))	{  i++;  }  
+				
+				/* find element below ... */
+				while((j >= low) && (index[j].groupName > key))		{  j--;  } 
+								
+				if(i < j) {
+					swapRows(i, j);
+				}
+			} 
+			
+			swapRows(low, j);
+			
+			/* recurse */
+			sortGroups(low, j-1);
+			sortGroups(j+1, high); 
+		}
+	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FullMatrix", "sortGroups");
+		exit(1);
+	}
 }
-~FullMatrix::FullMatrix(){}
+
+/**************************************************************************/	
+void FullMatrix::swapRows(int i, int j) {
+	try {
 	
-	int FullMatrix::getNumSeqs(){}
-*/
\ No newline at end of file
+		float y;
+		string z, name;
+		
+		/* swap rows*/
+		for (int h = 0; h < numSeqs; h++) {
+			y = matrix[i][h];
+			matrix[i][h] = matrix[j][h]; 
+			matrix[j][h] = y;
+		}
+		
+		/* swap columns*/
+		for (int b = 0; b < numSeqs; b++) {
+			y = matrix[b][i];
+			matrix[b][i] = matrix[b][j]; 
+			matrix[b][j] = y;
+		}
+		
+		//swap map elements
+		z = index[i].groupName;
+		index[i].groupName = index[j].groupName;
+		index[j].groupName = z;
+		
+		name = index[i].seqName;
+		index[i].seqName = index[j].seqName;
+		index[j].seqName = name;
+		
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FullMatrix", "swapRows");
+		exit(1);
+	}
+}
+/**************************************************************************/	
+
+float FullMatrix::get(int i, int j){	return matrix[i][j];		}
+
+/**************************************************************************/	
+
+vector<string> FullMatrix::getGroups(){	return groups;		}
+
+/**************************************************************************/	
+
+vector<int> FullMatrix::getSizes(){	return sizes;		}
+
+/**************************************************************************/	
+
+int FullMatrix::getNumGroups(){	return groups.size();		}
+
+/**************************************************************************/	
+
+int FullMatrix::getNumSeqs(){	return numSeqs;		}
+
+/**************************************************************************/
+
+void FullMatrix::printMatrix(ostream& out) {
+	try{
+		for (int i = 0; i < numSeqs; i++) {
+			out << "row " << i << " group = " << index[i].groupName << " name = " << index[i].seqName << endl;
+			for (int j = 0; j < numSeqs; j++) {
+				out << i << '\t' << j << '\t' << matrix[i][j] << endl;
+			}
+			out << endl;
+		}
+		
+		for (int i = 0; i < numSeqs; i++) {  out << i << '\t' <<  index[i].seqName << endl;  }
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FullMatrix", "printMatrix");
+		exit(1);
+	}
+}
+
+/**************************************************************************/
+