/**************************************************************************/
//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;
- 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<numSeqs;j++){
- filehandle >> distance;
-
- matrix[i][j] = distance;
+ 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;
- int 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";
+ m->errorOut(e, "FullMatrix", "sortGroups");
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);
- }
-
}
/**************************************************************************/
-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;
+void FullMatrix::swapRows(int i, int j) {
+ try {
+
+ float y;
+ string z, name;
+
+ /* 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 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::getMinsForRowsVectors(){
- try{
- numGroups = globaldata->gGroupmap->namesOfGroups.size();
- numUserGroups = globaldata->Groups.size();
- //sort globaldata->gGroupmap.namesOfGroups so that it will match the matrix
- sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end());
+ /* swap columns*/
+ for (int b = 0; b < numSeqs; b++) {
+ y = matrix[b][i];
+ matrix[b][i] = matrix[b][j];
+ matrix[b][j] = y;
+ }
- /*************************************************/
- //find where in matrix each group starts and stops
- /*************************************************/
- vector<int> bounds; //bounds[0] = 0, bounds[1] = starting row in matrix from group B, bounds[2] = starting row in matrix from group C, bounds[3] = no need to find C because its numSeqs.
- bounds.resize(numGroups);
+ //swap map elements
+ z = index[i].groupName;
+ index[i].groupName = index[j].groupName;
+ index[j].groupName = z;
- bounds[numGroups] = numSeqs;
- //for each group find bounds of subgroup/comparison
- for (int i = 0; i < numGroups; i++) {
- getBounds(bounds[i], globaldata->gGroupmap->namesOfGroups[i]);
- }
+ name = index[i].seqName;
+ index[i].seqName = index[j].seqName;
+ index[j].seqName = name;
- /************************************************************/
- //fill the minsForRows vectors for each group the user wants
- /************************************************************/
- int countx = bounds[0]; //where second group starts
- int county = bounds[0];
- //go through the entire matrix
- for (int x = 0; x < numSeqs; x++) {
- for (int y = 0; y < numSeqs; y++) {
- //if have not changed groups
- if ((x < countx) && (y < county)) {
- if (inUsersGroups(index[x].groupname, globaldata->Groups)) {
- }
- }
- }
- }
-
-
-
-
}
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";
+ m->errorOut(e, "FullMatrix", "swapRows");
exit(1);
}
-
}
+/**************************************************************************/
+
+float FullMatrix::get(int i, int j){ return matrix[i][j]; }
+
+/**************************************************************************/
+
+vector<string> FullMatrix::getGroups(){ return groups; }
+
+/**************************************************************************/
+
+vector<int> FullMatrix::getSizes(){ return sizes; }
+
+/**************************************************************************/
+
+int FullMatrix::getNumGroups(){ return groups.size(); }
+
+/**************************************************************************/
+
+int FullMatrix::getNumSeqs(){ return numSeqs; }
/**************************************************************************/
-void FullMatrix::getBounds(int& higher, string group) {
+
+void FullMatrix::printMatrix(ostream& out) {
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) {
- if (gotLower != true) { gotLower = true; }
- }else if ((gotLower == true) && (it->second.groupname != group)) { higher = it->first; break; }
+ 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;
+ }
+ 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 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";
+ m->errorOut(e, "FullMatrix", "printMatrix");
exit(1);
}
-
}
+/**************************************************************************/
+
projects / mothur.git / blobdiff