fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / readphylipvector.cpp

diff --git a/readphylipvector.cpp b/readphylipvector.cpp
new file mode 100644 (file)
index 0000000..f8907cc
--- /dev/null
+++ b/readphylipvector.cpp
@@ -0,0 +1,184 @@
+/*
+ *  readphylipvector.cpp
+ *  mothur
+ *
+ *  Created by westcott on 1/11/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "readphylipvector.h"
+
+/***********************************************************************/
+ReadPhylipVector::ReadPhylipVector(string d) {
+       try {
+               m = MothurOut::getInstance();
+               distFile = d;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadPhylipVector", "ReadPhylipVector");
+               exit(1);
+       }
+}
+/***********************************************************************/
+vector<string> ReadPhylipVector::read(vector< vector<double> >& matrix) {
+       try {
+               vector<string> names;
+               
+               ifstream in;
+               m->openInputFile(distFile, in);
+               
+               //check whether matrix is square
+               char d;
+               int square = 1;
+               int numSeqs;
+               string name;
+               
+               in >> numSeqs >> name; 
+               
+               while((d=in.get()) != EOF){
+                       
+                       //is d a number meaning its square
+                       if(isalnum(d)){ 
+                               square = 1; 
+                               break; 
+                       }
+                       
+                       //is d a line return meaning its lower triangle
+                       if(d == '\n'){
+                               square = 2;
+                               break;
+                       }
+               }
+               in.close();
+               
+               
+               //reopen and read now that you know whether you are square
+               ifstream f;
+               m->openInputFile(distFile, f);
+               
+               int rank;
+               f >> rank;
+               
+               names.resize(rank);
+               matrix.resize(rank);
+               if(square == 1){
+                       for(int i=0;i<rank;i++)
+                               matrix[i].resize(rank);
+                       for(int i=0;i<rank;i++) {
+                               f >> names[i];
+                               for(int j=0;j<rank;j++) {
+                                       if (m->control_pressed) { return names; }
+                                       
+                                       f >> matrix[i][j];
+                                       if (matrix[i][j] == -0.0000)
+                                               matrix[i][j] = 0.0000;
+                               }
+                       }
+               }
+               else if(square == 2){
+                       for(int i=0;i<rank;i++){
+                               matrix[i].resize(rank);
+                       }
+                       matrix[0][0] = 0.0000;
+                       f >> names[0];
+                       for(int i=1;i<rank;i++){
+                               f >> names[i];
+                               matrix[i][i]=0.0000;
+                               for(int j=0;j<i;j++){
+                                       if (m->control_pressed) { return names; }
+                                       f >> matrix[i][j];
+                                       if (matrix[i][j] == -0.0000)
+                                               matrix[i][j] = 0.0000;
+                                       matrix[j][i]=matrix[i][j];
+                               }
+                       }
+               }
+               
+               return names;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadPhylipVector", "read");
+               exit(1);
+       }
+}
+/***********************************************************************/
+vector<string> ReadPhylipVector::read(vector<seqDist>& matrix) {
+       try {
+               vector<string> names;
+               
+               ifstream in;
+               m->openInputFile(distFile, in);
+               
+               //check whether matrix is square
+               char d;
+               int square = 1;
+               int numSeqs;
+               string name;
+               
+               in >> numSeqs >> name; 
+               
+               while((d=in.get()) != EOF){
+                       
+                       //is d a number meaning its square
+                       if(isalnum(d)){ 
+                               square = 1; 
+                               break; 
+                       }
+                       
+                       //is d a line return meaning its lower triangle
+                       if(d == '\n'){
+                               square = 2;
+                               break;
+                       }
+               }
+               in.close();
+               
+               
+               //reopen and read now that you know whether you are square
+               ifstream f;
+               m->openInputFile(distFile, f);
+               
+               int rank;
+               float temp;
+               f >> rank;
+               
+               names.resize(rank);
+               if(square == 1){
+                       for(int i=0;i<rank;i++) {
+                               f >> names[i];
+                               for(int j=0;j<rank;j++) {
+                                       if (m->control_pressed) { return names; }
+                                       
+                                       f >> temp;
+                                       
+                                       if (j < i) { //only save lt
+                                               seqDist dist(i, j, temp);
+                                               matrix.push_back(dist);
+                                       }
+                               }
+                       }
+               }
+               else if(square == 2){
+                       f >> names[0];
+                       for(int i=1;i<rank;i++){
+                               f >> names[i];
+                               for(int j=0;j<i;j++){
+                                       if (m->control_pressed) { return names; }
+                                       f >> temp;
+                                       seqDist dist(i, j, temp);
+                                       matrix.push_back(dist);
+                               }
+                       }
+               }
+               
+               return names;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadPhylipVector", "read");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+