/**************************************************************************/
//This constructor reads a distance matrix file and stores the data in the matrix.
-FullMatrix::FullMatrix(ifstream& filehandle) {
+FullMatrix::FullMatrix(ifstream& filehandle, GroupMap* g, bool s) : groupmap(g), sim(s) {
try{
- globaldata = GlobalData::getInstance();
- groupmap = globaldata->gGroupmap;
+ m = MothurOut::getInstance();
string name, group;
- filehandle >> numSeqs >> name;
+ filehandle >> numSeqs >> name;
+
//make the matrix filled with zeros
matrix.resize(numSeqs);
for(int i = 0; i < numSeqs; i++) {
- matrix[i].resize(numSeqs, 0);
+ matrix[i].resize(numSeqs, 0.0);
}
-
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;
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+ index.resize(numSeqs);
index[0].seqName = name;
+ index[0].groupName = group;
//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
for(int i=0;i<numSeqs;i++){
filehandle >> matrix[0][i];
+ if (sim) { matrix[0][i] = 1.0 - matrix[0][i]; }
}
break;
}
break;
}
}
-
+
//read rest of matrix
- if (square == true) { readSquareMatrix(filehandle); }
- else { readLTMatrix(filehandle); }
+ if (square == true) { readSquareMatrix(filehandle); }
+ else { readLTMatrix(filehandle); }
- //sort sequences so they are gathered in groups for processing
- sortGroups(0, numSeqs-1);
-
+ filehandle.close();
+
+ if (!m->control_pressed) { 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";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the FullMatrix class function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FullMatrix", "FullMatrix");
exit(1);
}
}
/**************************************************************************/
-void FullMatrix::readSquareMatrix(ifstream& filehandle) {
+int FullMatrix::readSquareMatrix(ifstream& filehandle) {
try {
Progress* reading;
- reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
+ reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
int count = 0;
string group, name;
-
+
for(int i=1;i<numSeqs;i++){
filehandle >> name;
group = groupmap->getGroup(name);
- index[i].groupname = group;
index[i].seqName = name;
+ index[i].groupName = group;
- if(group == "not found") { cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
for(int j=0;j<numSeqs;j++){
+ if (m->control_pressed) { delete reading; return 0; }
+
filehandle >> matrix[i][j];
+ if (sim) { matrix[i][j] = 1.0 - matrix[i][j]; }
count++;
reading->update(count);
}
}
+
+ if (m->control_pressed) { delete reading; return 0; }
+
reading->finish();
delete reading;
+
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the FullMatrix class function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FullMatrix", "readSquareMatrix");
exit(1);
}
-
}
/**************************************************************************/
-void FullMatrix::readLTMatrix(ifstream& filehandle) {
+int 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].groupname = group;
index[i].seqName = name;
+ index[i].groupName = group;
- if(group == "not found") { cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
for(int j=0;j<i;j++){
+ if (m->control_pressed) { delete reading; return 0; }
+
filehandle >> distance;
-
+ if (sim) { distance = 1.0 - distance; }
+
matrix[i][j] = distance; matrix[j][i] = distance;
+
count++;
reading->update(count);
}
-
}
+
+ if (m->control_pressed) { delete reading; return 0; }
+
reading->finish();
delete reading;
+
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the FullMatrix class function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FullMatrix", "readLTMatrix");
exit(1);
}
-
}
/**************************************************************************/
+
void FullMatrix::sortGroups(int low, int high){
try{
-
- int i = low;
- int j = high;
- float y = 0;
- string name;
- /* compare value */
- //what group does this row belong to
- string z = index[(low + high) / 2].groupname;
-
- /* partition */
- do {
- /* find member above ... */
- while(index[i].groupname < z) i++;
-
- /* find element below ... */
- while(index[j].groupname > z) j--;
+ if (low < high) {
+ int i = low+1;
+ int j = high;
+ int pivot = (low+high) / 2;
- if(i <= j) {
- /* swap rows*/
- for (int h = 0; h < numSeqs; h++) {
- y = matrix[i][h];
- matrix[i][h] = matrix[j][h];
- matrix[j][h] = y;
- }
+ swapRows(low, pivot); //puts pivot in final spot
+
+ /* compare value */
+ //what group does this row belong to
+ string key = index[low].groupName;
+
+ /* partition */
+ while(i <= j) {
+ /* find member above ... */
+ while((i <= high) && (index[i].groupName <= key)) { i++; }
- /* swap columns*/
- for (int b = 0; b < numSeqs; b++) {
- y = matrix[b][i];
- matrix[b][i] = matrix[b][j];
- matrix[b][j] = y;
+ /* find element below ... */
+ while((j >= low) && (index[j].groupName > key)) { j--; }
+
+ if(i < j) {
+ swapRows(i, j);
}
-
- //swap map elements
- 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--;
- }
- } while(i <= j);
-
- /* recurse */
- if(low < j)
- sortGroups(low, j);
-
- if(i < high)
- sortGroups(i, high);
-
+ }
+
+ swapRows(low, j);
+
+ /* recurse */
+ sortGroups(low, j-1);
+ sortGroups(j+1, high);
+ }
}
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";
+ m->errorOut(e, "FullMatrix", "sortGroups");
exit(1);
}
-
}
/**************************************************************************/
-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);
+void FullMatrix::swapRows(int i, int j) {
+ try {
+
+ float y;
+ string z, name;
- 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]);
+ /* swap rows*/
+ for (int h = 0; h < numSeqs; h++) {
+ y = matrix[i][h];
+ matrix[i][h] = matrix[j][h];
+ matrix[j][h] = y;
}
- }
- 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();
+ /* swap columns*/
+ for (int b = 0; b < numSeqs; b++) {
+ y = matrix[b][i];
+ matrix[b][i] = matrix[b][j];
+ matrix[b][j] = y;
+ }
- /************************************************************/
- //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];
+ //swap map elements
+ z = index[i].groupName;
+ index[i].groupName = index[j].groupName;
+ index[j].groupName = z;
- int countx = 1; //index in bound
- int county = 1; //index in bound
+ name = index[i].seqName;
+ index[i].seqName = index[j].seqName;
+ index[j].seqName = name;
- //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";
+ m->errorOut(e, "FullMatrix", "swapRows");
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);
- }
+/**************************************************************************/
-}
+float FullMatrix::get(int i, int j){ return matrix[i][j]; }
-/**************************************************************************/
-//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);
- }
+vector<string> FullMatrix::getGroups(){ return groups; }
-}
-/**************************************************************************/
-//shuffles the sequences in the 2 groups passed in.
-void FullMatrix::shuffle(int box){
- try{
- vector<int> rows2Swap;
- vector<int> shuffled;
- float y = 0;
- string name = "";
-
- /****************************/
- //find the box the user wants
- /****************************/
- int count = 0;
- int lowBoundy = bounds[0]; //where first group starts
- int highBoundy = bounds[1]; //where second group starts
- 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 == box) { 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;
- highBoundy = bounds[county];
- lowBoundy = bounds[county-1];
- }
- }
-
- /************************/
- //save its rows locations
- /************************/
- //go through the matrix map to find the rows from groups you want to randomize
- for (int y = lowBoundy; y < highBoundy; y++) {
- rows2Swap.push_back(y);
- shuffled.push_back(y);
- }
-
- //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;
- }
+vector<int> FullMatrix::getSizes(){ return sizes; }
+
+/**************************************************************************/
+
+int FullMatrix::getNumGroups(){ return groups.size(); }
+
+/**************************************************************************/
+
+int FullMatrix::getNumSeqs(){ return numSeqs; }
- //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];
+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 << i << '\t' << j << '\t' << matrix[i][j] << endl;
}
- }
-
- //store distances in users vector
- for (it = dist.begin(); it != dist.end(); it++) {
- distances.push_back(it->first);
+ out << endl;
}
+ for (int i = 0; i < numSeqs; i++) { out << i << '\t' << index[i].seqName << endl; }
}
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";
+ m->errorOut(e, "FullMatrix", "printMatrix");
exit(1);
}
}
+/**************************************************************************/
+
projects / mothur.git / blobdiff