#include "fullmatrix.h"
/**************************************************************************/
+
//This constructor reads a distance matrix file and stores the data in the matrix.
FullMatrix::FullMatrix(ifstream& filehandle) {
try{
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].groupname = group;
+ index.resize(numSeqs);
+ 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
char d;
+ bool square;
while((d=filehandle.get()) != EOF){
//is d a number meaning its square
//sort sequences so they are gathered in groups for processing
sortGroups(0, numSeqs-1);
-
+
+ groups.push_back(index[0].groupName);
+ sizes.push_back(1);
+ int groupCount = 0;
+
+ for(int i=1;i<numSeqs;i++){
+ if(index[i].groupName == index[i-1].groupName){ sizes[groupCount]++; }
+ else{
+ sizes.push_back(1);
+ groups.push_back(index[i].groupName);
+ groupCount++;
+ }
+ }
+
}
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";
filehandle >> name;
group = groupmap->getGroup(name);
- index[i].groupname = 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].groupname = 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(int low, int high){
try{
/* compare value */
//what group does this row belong to
- string z = index[(low + high) / 2].groupname;
+ string z = index[(low + high) / 2].groupName;
/* partition */
do {
/* find member above ... */
- while(index[i].groupname < z) i++;
+ while(index[i].groupName < z) i++;
/* find element below ... */
- while(index[j].groupname > z) j--;
+ while(index[j].groupName > z) j--;
if(i <= j) {
/* swap rows*/
}
//swap map elements
- z = index[i].groupname;
- index[i].groupname = index[j].groupname;
- index[j].groupname = 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;
}
/**************************************************************************/
-int FullMatrix::getNumSeqs(){ return numSeqs; }
-/**************************************************************************/
-//print out matrix
-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 << matrix[i][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);
- }
-
-}
-/**************************************************************************/
-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;
+float FullMatrix::get(int i, int j){ return matrix[i][j]; }
- //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);
- }
+vector<string> FullMatrix::getGroups(){ return groups; }
-}
+/**************************************************************************/
-/**************************************************************************/
-//print out matrix
-void FullMatrix::printMinsForRows(ostream& out) {
- try{
- for (int j = 0; j < minsForRows.size(); j++) {
- out << minsForRows[j] << " ";
- }
- out << endl;
+vector<int> FullMatrix::getSizes(){ return sizes; }
- }
- 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);
- }
+/**************************************************************************/
-}
+int FullMatrix::getNumGroups(){ return groups.size(); }
-/**************************************************************************/
-//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;
+int FullMatrix::getNumSeqs(){ return numSeqs; }
- }
- }
- 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) {
+void FullMatrix::printMatrix(ostream& out) {
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];
+ 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 << matrix[i][j] << " ";
}
+ out << endl;
}
-
- //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";
+ 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 restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
+
}
+/**************************************************************************/
+
projects / mothur.git / blobdiff