fixed bug with line and label parameters and added all as option for both

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index c61109c78ce2cdcca001455a0408be34692c47d1..64d7b6af2dbe39279164fbe299c86a617af278e7 100644 (file)
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -27,7 +27,8 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                
                group = groupmap->getGroup(name);
                if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
-               index[0] = group; 
+               index[0].groupname = group; 
+               index[0].seqName = name;
                
                //determine if matrix is square or lower triangle
                //if it is square read the distances for the first sequence
@@ -59,7 +60,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                
        printMatrix(cout);
                //sort sequences so they are gathered in groups for processing
-               sortGroups();
+               sortGroups(0, numSeqs-1);
                cout << "after sort" << endl;
        printMatrix(cout);
                
@@ -88,7 +89,8 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                        filehandle >> name;             
                        
                        group = groupmap->getGroup(name);
-                       index[i] = group;
+                       index[i].groupname = group;
+                       index[i].seqName = name;
                        
                        if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
                                
@@ -127,7 +129,8 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                        filehandle >> name;             
                                                
                        group = groupmap->getGroup(name);
-                       index[i] = group;
+                       index[i].groupname = group;
+                       index[i].seqName = name;
        
                        if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl;  exit(1); }
                                
@@ -154,82 +157,76 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
 }
 
 /**************************************************************************/
-void FullMatrix::sortGroups(){
+void FullMatrix::sortGroups(int low, int high){
        try{
-               //sort each row by group and when you do, swap rows too.
-               for (int i = 0; i < numSeqs; i++) {
-                       quicksort(0, numSeqs-1, i);
-               }
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the FullMatrix class function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
-}
-/**************************************************************************/
-//this is a version of quicksort taken from http://www.c.happycodings.com/Sorting_Searching/code13.html
-/* sort everything inbetween `low' <-> `high' */
-void FullMatrix::quicksort(int low, int high, int row) {
-       try {
+       
                int i = low;
                int j = high;
                int y = 0;
+               string name;
                
                /* compare value */
                //what group does this row belong to
-               string z = index[(low + high) / 2];
+               string z = index[(low + high) / 2].groupname;
 
                /* partition */
                do {
                        /* find member above ... */
-                       while(index[i] < z) i++;
+                       while(index[i].groupname < z) i++;
 
                        /* find element below ... */
-                       while(index[j] > z) j--;
+                       while(index[j].groupname > z) j--;
                        
                        if(i <= j) {
-                               /* swap two elements in row*/
-                               y = matrix[row][i];
-                               matrix[row][i] = matrix[row][j]; 
-                               matrix[row][j] = y;
+                               /* swap rows*/
+                               for (int h = 0; h < numSeqs; h++) {
+                                       y = matrix[i][h];
+                                       matrix[i][h] = matrix[j][h]; 
+                                       matrix[j][h] = y;
+                               }
                                
-                               /* swap two elements in column*/
-                               y = matrix[i][row];
-                               matrix[i][row] = matrix[j][row]; 
-                               matrix[j][row] = 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];
-                               index[i] = index[j];
-                               index[j] = z;
+                               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;
+
                                
                                i++; 
                                j--;
-//cout << "swapping elements " << i << " " << j << endl;
-//printMatrix(cout); cout << endl;
+cout << "swapping rows " << i << " " << j << endl;
+printMatrix(cout); cout << endl;
                        }
                } while(i <= j);
 
                /* recurse */
                if(low < j) 
-               quicksort(low, j, row);
+               sortGroups(low, j);
 
                if(i < high) 
-               quicksort(i, high, row); 
+               sortGroups(i, high); 
+
+       
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
        catch(...) {
-               cout << "An unknown error has occurred in the FullMatrix class function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "An unknown error has occurred in the FullMatrix class function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
+
 }
 
 /**************************************************************************/   
@@ -239,7 +236,7 @@ int FullMatrix::getNumSeqs(){ return numSeqs; }
 void FullMatrix::printMatrix(ostream& out) {
        try{
                for (int i = 0; i < numSeqs; i++) {
-                       out << "row " << i << " group = " << index[i] << endl;
+                       out << "row " << i << " group = " << index[i].groupname << " name = " << index[i].seqName << endl;
                        for (int j = 0; j < numSeqs; j++) {
                                out << matrix[i][j] << " ";
                        }

diff --git a/fullmatrix.h b/fullmatrix.h
index f3ad0e73dfb2615e4fbeb5bbd96f1a025c6a0ae6..0ab1d7175dce3b9bdef4758b83dffc26ace8079b 100644 (file)
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -16,6 +16,12 @@
 
 using namespace std;
 
+struct Names {
+       string  groupname;
+       string          seqName;
+};
+
+
 class FullMatrix {
        
        public:
@@ -27,12 +33,11 @@ class FullMatrix {
                void printMatrix(ostream&);
        
        private:
-               void sortGroups();  //this function sorts the sequences within the matrix.
-               void quicksort(int, int, int);//row of matrix, low, high and row number
+               void sortGroups(int, int);  //this function sorts the sequences within the matrix.
                void readSquareMatrix(ifstream&);  
                void readLTMatrix(ifstream&);
                vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
-               map<int, string> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
+               map<int, Names> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
                GroupMap* groupmap;  //maps sequences to groups they belong to.
                GlobalData* globaldata;
                int numSeqs;

diff --git a/globaldata.cpp b/globaldata.cpp
index 3ddd02e5c24dc03cd8ff7549b6b03a32982562e9..17b4908515179211b792a6d06801d2dc878a7bca 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -20,7 +20,6 @@ GlobalData* GlobalData::getInstance() {
 //This function parses through the option string of the command to remove its parameters
 void GlobalData::parseGlobalData(string commandString, string optionText){
        try {
-               allLines = 1;
                commandName = commandString; //save command name to be used by other classes
                
                //set all non filename paramters to default
@@ -32,6 +31,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        gGroupmap = NULL;
                        gTree.clear();
                        labels.clear(); lines.clear(); groups.clear();
+                       allLines = 1;
                }
                
                //saves help request
@@ -122,16 +122,17 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                lines.clear();
                                line = value;
                                label = "";
-                               splitAtDash(value, lines);
-                               allLines = 0;
+                               if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
+                               else { allLines = 1;  }
                        }
                        if (key == "label") {//stores lines to be used in a vector
                                labels.clear();
                                label = value;
                                line = "";
-                               splitAtDash(value, labels);
-                               allLines = 0;
+                               if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
+                               else { allLines = 1;  }
                        }
+                       
                        if (key == "groups") {//stores groups to be used in a vector
                                        Groups.clear();
                                        groups = value;
@@ -274,8 +275,6 @@ void GlobalData::reset() {
        cutoff                  =       "10.00";
        precision               =       "100";
        iters                   =       "1000"; 
-       line                    =   "";
-       label                   =       "";
        groups                  =       "";
        jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
        randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.