changing command name classify.shared to classifyrf.shared

[mothur.git] / sparsedistancematrix.cpp

diff --git a/sparsedistancematrix.cpp b/sparsedistancematrix.cpp
index 7d505239d88b4d817b3b6c5fd3609c6c18e785b4..417e24ae94e4242db9a56db14fd2987714ab1712 100644 (file)
--- a/sparsedistancematrix.cpp
+++ b/sparsedistancematrix.cpp
@@ -39,8 +39,10 @@ int SparseDistanceMatrix::updateCellCompliment(ull row, ull col){
         ull vcol = 0;
         
         //find the columns entry for this cell as well
-        for (int i = 0; i < seqVec[vrow].size(); i++) {  if (seqVec[vrow][i].index == row) { vcol = i;  break; }  }
-
+        for (int i = 0; i < seqVec[vrow].size(); i++) {  
+            if (seqVec[vrow][i].index == row) { vcol = i;  break; }  
+        }
+       
         seqVec[vrow][vcol].dist = seqVec[row][col].dist;
         
         return 0;
@@ -87,6 +89,30 @@ void SparseDistanceMatrix::addCell(ull row, PDistCell cell){
                exit(1);
        }
 }
+/***********************************************************************/
+int SparseDistanceMatrix::addCellSorted(ull row, PDistCell cell){
+       try {
+               numNodes+=2;
+               if(cell.dist < smallDist){ smallDist = cell.dist; }
+        
+        seqVec[row].push_back(cell);
+        PDistCell temp(row, cell.dist);
+        seqVec[cell.index].push_back(temp);
+        
+        sortSeqVec(row);
+        sortSeqVec(cell.index);
+        
+        int location = -1; //find location of new cell when sorted
+        for (int i = 0; i < seqVec[row].size(); i++) {  if (seqVec[row][i].index == cell.index) { location = i; break; } }
+        
+        return location;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SparseDistanceMatrix", "addCellSorted");
+               exit(1);
+       }
+}
+
 /***********************************************************************/
 
 ull SparseDistanceMatrix::getSmallestCell(ull& row){
@@ -98,7 +124,9 @@ ull SparseDistanceMatrix::getSmallestCell(ull& row){
        
         for (int i = 0; i < seqVec.size(); i++) {
             for (int j = 0; j < seqVec[i].size(); j++) {
- 
+                
+                if (m->control_pressed) { return smallDist; }
+                
                 //already checked everyone else in row
                 if (i < seqVec[i][j].index) {  
                            
@@ -126,7 +154,7 @@ ull SparseDistanceMatrix::getSmallestCell(ull& row){
                return col;
        }
        catch(exception& e) {
-               m->errorOut(e, "SparseMatrix", "getSmallestCell");
+               m->errorOut(e, "SparseDistanceMatrix", "getSmallestCell");
                exit(1);
        }
 }
@@ -141,7 +169,22 @@ int SparseDistanceMatrix::sortSeqVec(){
         return 0;
     }
        catch(exception& e) {
-               m->errorOut(e, "SparseMatrix", "getSmallestCell");
+               m->errorOut(e, "SparseDistanceMatrix", "sortSeqVec");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+int SparseDistanceMatrix::sortSeqVec(int index){
+       try {
+        
+        //saves time in getSmallestCell, by making it so you dont search the repeats
+        sort(seqVec[index].begin(), seqVec[index].end(), compareIndexes);
+        
+        return 0;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "SparseDistanceMatrix", "sortSeqVec");
                exit(1);
        }
 }