#include "fullmatrix.h"
/**************************************************************************/
-
//This constructor reads a distance matrix file and stores the data in the matrix.
FullMatrix::FullMatrix(ifstream& filehandle) {
try{
//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") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
index.resize(numSeqs);
- index[0].groupName = group;
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
if (square == true) { readSquareMatrix(filehandle); }
else { readLTMatrix(filehandle); }
- //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++;
- }
- }
-
+ sortGroups(0, numSeqs-1);
+
}
catch(exception& e) {
errorOut(e, "FullMatrix", "FullMatrix");
filehandle >> name;
group = groupmap->getGroup(name);
- index[i].groupName = group;
index[i].seqName = name;
+ index[i].groupName = group;
if(group == "not found") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
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") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
for(int j=0;j<i;j++){
filehandle >> distance;
-
matrix[i][j] = distance; matrix[j][i] = distance;
count++;
reading->update(count);
}
-
}
+
reading->finish();
delete reading;
}
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) {
}
}
+/**************************************************************************/
+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;
+ }
+
+ /* 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].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;
+
+
+ }
+ catch(exception& e) {
+ errorOut(e, "FullMatrix", "swapRows");
+ exit(1);
+ }
+}
/**************************************************************************/
float FullMatrix::get(int i, int j){ return matrix[i][j]; }
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 << 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) {
errorOut(e, "FullMatrix", "printMatrix");