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
if(isalnum(d)){
square = true;
filehandle.putback(d);
+
for(int i=0;i<numSeqs;i++){
filehandle >> matrix[0][i];
}
if (square == true) { readSquareMatrix(filehandle); }
else { readLTMatrix(filehandle); }
-
-
- printMatrix(cout);
//sort sequences so they are gathered in groups for processing
- sortGroups();
- cout << "after sort" << endl;
- printMatrix(cout);
-
+ sortGroups(0, numSeqs-1);
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
try {
Progress* reading;
- reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
+ reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
int count = 0;
- float distance;
+
string group, name;
for(int i=1;i<numSeqs;i++){
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); }
for(int j=0;j<numSeqs;j++){
- filehandle >> distance;
-
- matrix[i][j] = distance;
+ filehandle >> matrix[i][j];
+
count++;
reading->update(count);
}
void FullMatrix::readLTMatrix(ifstream& filehandle) {
try {
Progress* reading;
- reading = new Progress("Reading matrix: ", numSeqs * (numSeqs - 1) / 2);
+ reading = new Progress("Reading matrix: ", numSeqs * (numSeqs - 1) / 2);
int count = 0;
float distance;
+
string group, name;
for(int i=1;i<numSeqs;i++){
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); }
count++;
reading->update(count);
}
+
}
reading->finish();
delete reading;
}
/**************************************************************************/
-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;
+ float 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;
}
} 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] << " ";
}
}
}
+
/**************************************************************************/
+void FullMatrix::setBounds(){
+ try{
+ numGroups = globaldata->gGroupmap->namesOfGroups.size();
+
+ //sort globaldata->gGroupmap.namesOfGroups so that it will match the matrix
+ sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end());
+
+ //one for each comparision
+ //minsForRows.resize(numGroups*numGroups);
+
+ /*************************************************/
+ //find where in matrix each group starts and stops
+ /*************************************************/
+ bounds.resize(numGroups);
+
+ bounds[0] = 0;
+ bounds[numGroups] = numSeqs;
+
+ //for each group find bounds of subgroup/comparison
+ for (int i = 1; i < numGroups; i++) {
+ getBounds(bounds[i], globaldata->gGroupmap->namesOfGroups[i-1]);
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function getMinsForRowsVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FullMatrix class function getMinsForRowsVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/**************************************************************************/
+vector<float> FullMatrix::getMins(int x) {
+ try{
+ //clear out old data
+ minsForRows.clear();
+
+ /************************************************************/
+ //fill the minsForRows vector for the box the user wants
+ /************************************************************/
+ int count = 0;
+ int lowBoundx = bounds[0]; //where first group starts
+ int lowBoundy = bounds[0];
+ int highBoundx = bounds[1]; //where second group starts
+ int highBoundy = bounds[1];
+
+ int countx = 1; //index in bound
+ int county = 1; //index in bound
+
+ //find the bounds for the box the user wants
+ for (int i = 0; i < (numGroups * numGroups); i++) {
+
+ //are you at the box?
+ if (count == x) { break; }
+ else { count++; }
+
+ //move to next box
+ if (county < numGroups) {
+ county++;
+ highBoundy = bounds[county];
+ lowBoundy = bounds[county-1];
+ }else{ //you are moving to a new row of "boxes"
+ county = 1;
+ countx++;
+ highBoundx = bounds[countx];
+ lowBoundx = bounds[countx-1];
+ highBoundy = bounds[county];
+ lowBoundy = bounds[county-1];
+ }
+ }
+
+ //each row in the box
+ for (int x = lowBoundx; x < highBoundx; x++) {
+ float min4Row = 100000.0;
+ //each entry in that row
+ for (int y = lowBoundy; y < highBoundy; y++) {
+ //if you are not on the diagonal and you are less than previous minimum
+ if ((x != y) && (matrix[x][y] < min4Row)) {
+ min4Row = matrix[x][y];
+ }
+ }
+ //save minimum value for that row in minsForRows vector of vectors
+ minsForRows.push_back(min4Row);
+ }
+
+ return minsForRows;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function getMins. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FullMatrix class function getMins. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************/
+void FullMatrix::getBounds(int& higher, string group) {
+ try{
+ bool gotLower = false;
+
+ //for each group find bounds of subgroup/comparison
+ for (it = index.begin(); it != index.end(); it++) {
+ if (it->second.groupname == group) {
+ gotLower = true;
+ }else if ((gotLower == true) && (it->second.groupname != group)) { higher = it->first; break; }
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function getBounds. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FullMatrix class function getBounds. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/**************************************************************************/
+//print out matrix
+void FullMatrix::printMinsForRows(ostream& out) {
+ try{
+ for (int j = 0; j < minsForRows.size(); j++) {
+ out << minsForRows[j] << " ";
+ }
+ out << endl;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/**************************************************************************/
+//shuffles the sequences in the 2 groups passed in.
+void FullMatrix::shuffle(string groupA, string groupB){
+ try{
+ vector<int> rows2Swap;
+ vector<int> shuffled;
+ float y = 0;
+ string name = "";
+
+
+ /********************************/
+ //save rows you want to randomize
+ /********************************/
+ //go through the matrix map to find the rows from groups you want to randomize
+ for (it = index.begin(); it != index.end(); it++) {
+ //is this row from group A or B?
+ if ((it->second.groupname == groupA) || (it->second.groupname == groupB)) {
+ rows2Swap.push_back(it->first);
+ shuffled.push_back(it->first);
+ }
+ }
+
+ //randomize rows to shuffle in shuffled
+ random_shuffle(shuffled.begin(), shuffled.end());
+
+ /***************************************/
+ //swap rows and columns to randomize box
+ /***************************************/
+ for (int i = 0; i < shuffled.size(); i++) {
+
+ //record the swaps you are making so you can undo them in restore function
+ restoreIndex[i].a = shuffled[i];
+ restoreIndex[i].b = rows2Swap[i];
+
+ /* swap rows*/
+ for (int h = 0; h < numSeqs; h++) {
+ y = matrix[shuffled[i]][h];
+ matrix[shuffled[i]][h] = matrix[rows2Swap[i]][h];
+ matrix[rows2Swap[i]][h] = y;
+ }
+
+ /* swap columns */
+ for (int b = 0; b < numSeqs; b++) {
+ y = matrix[b][shuffled[i]];
+ matrix[b][shuffled[i]] = matrix[b][rows2Swap[i]];
+ matrix[b][rows2Swap[i]] = y;
+ }
+
+ //swap map elements
+ name = index[shuffled[i]].seqName;
+ index[shuffled[i]].seqName = index[rows2Swap[i]].seqName;
+ index[rows2Swap[i]].seqName = name;
+
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function shuffle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FullMatrix class function shuffle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************/
+//unshuffles the matrix.
+void FullMatrix::restore(){
+ try{
+ float y = 0;
+ string name = "";
+
+ //reverse iterate through swaps and undo them to restore original matrix and index map.
+ for(it2 = restoreIndex.rbegin(); it2 != restoreIndex.rend(); it2++) {
+ /* swap rows */
+
+ for (int h = 0; h < numSeqs; h++) {
+ y = matrix[it2->second.a][h];
+ matrix[it2->second.a][h] = matrix[it2->second.b][h];
+ matrix[it2->second.b][h] = y;
+ }
+
+ /* swap columns */
+ for (int b = 0; b < numSeqs; b++) {
+ y = matrix[b][it2->second.a];
+ matrix[b][it2->second.a] = matrix[b][it2->second.b];
+ matrix[b][it2->second.b] = y;
+ }
+
+
+ //swap map elements
+ name = index[it2->second.a].seqName;
+ index[it2->second.a].seqName = index[it2->second.b].seqName;
+ index[it2->second.b].seqName = name;
+
+ }
+
+ //clear restore for next shuffle
+ restoreIndex.clear();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FullMatrix class function restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************/
+void FullMatrix::getDist(vector<float>& distances) {
+ try{
+ map<float, float> dist; //holds the distances for the integral form
+ map<float, float>::iterator it;
+
+ /************************************************************/
+ //fill the minsForRows vectors for each group the user wants
+ /************************************************************/
+ int lowBoundx = bounds[0]; //where first group starts
+ int lowBoundy = bounds[0];
+ int highBoundx = bounds[1]; //where second group starts
+ int highBoundy = bounds[1];
+
+ int countx = 1; //index in bound
+ int county = 1; //index in bound
+
+ //go through each "box" in the matrix
+ for (int i = 0; i < (numGroups * numGroups); i++) {
+ //each row in the box
+ for (int x = lowBoundx; x < highBoundx; x++) {
+ float min4Row = 100000.0;
+ //each entry in that row
+ for (int y = lowBoundy; y < highBoundy; y++) {
+ //if you are not on the diagonal and you are less than previous minimum
+ if ((x != y) && (matrix[x][y] < min4Row)){
+ min4Row = matrix[x][y];
+ }
+ }
+ //save minimum value
+ dist[min4Row] = min4Row;
+ }
+
+ //****** reset bounds to process next "box" ********
+ //if you still have more "boxes" in that row
+ if (county < numGroups) {
+ county++;
+ highBoundy = bounds[county];
+ lowBoundy = bounds[county-1];
+ }else{ //you are moving to a new row of "boxes"
+ county = 1;
+ countx++;
+ highBoundx = bounds[countx];
+ lowBoundx = bounds[countx-1];
+ highBoundy = bounds[county];
+ lowBoundy = bounds[county-1];
+ }
+ }
+
+ //store distances in users vector
+ for (it = dist.begin(); it != dist.end(); it++) {
+ distances.push_back(it->first);
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FullMatrix class function restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
projects / mothur.git / blobdiff