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
printMatrix(cout);
//sort sequences so they are gathered in groups for processing
- sortGroups();
+ sortGroups(0, numSeqs-1);
cout << "after sort" << endl;
printMatrix(cout);
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); }
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); }
}
/**************************************************************************/
-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);
}
+
}
/**************************************************************************/
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] << " ";
}
using namespace std;
+struct Names {
+ string groupname;
+ string seqName;
+};
+
+
class FullMatrix {
public:
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;
//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
gGroupmap = NULL;
gTree.clear();
labels.clear(); lines.clear(); groups.clear();
+ allLines = 1;
}
//saves help request
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;
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.