added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / sparsedistancematrix.cpp

diff --git a/sparsedistancematrix.cpp b/sparsedistancematrix.cpp
new file mode 100644 (file)
index 0000000..8035e13
--- /dev/null
+++ b/sparsedistancematrix.cpp
@@ -0,0 +1,149 @@
+//
+//  sparsedistancematrix.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 7/16/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "sparsedistancematrix.h"
+
+
+/***********************************************************************/
+
+SparseDistanceMatrix::SparseDistanceMatrix() : numNodes(0), smallDist(1e6){  m = MothurOut::getInstance(); sorted=false; aboveCutoff = 1e6; }
+
+/***********************************************************************/
+
+int SparseDistanceMatrix::getNNodes(){
+       return numNodes; 
+}
+/***********************************************************************/
+
+void SparseDistanceMatrix::clear(){
+    for (int i = 0; i < seqVec.size(); i++) {  seqVec[i].clear();  }
+    seqVec.clear();
+}
+
+/***********************************************************************/
+
+float SparseDistanceMatrix::getSmallDist(){
+       return smallDist;
+}
+/***********************************************************************/
+
+int SparseDistanceMatrix::updateCellCompliment(ull row, ull col){
+    try {
+        
+        ull vrow = seqVec[row][col].index;
+        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; }  }
+
+        seqVec[vrow][vcol].dist = seqVec[row][col].dist;
+        
+        return 0;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "SparseDistanceMatrix", "updateCellCompliment");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+int SparseDistanceMatrix::rmCell(ull row, ull col){
+       try {
+        numNodes-=2;
+ 
+        ull vrow = seqVec[row][col].index;
+        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; }  }
+        
+        seqVec[vrow].erase(seqVec[vrow].begin()+vcol);
+        seqVec[row].erase(seqVec[row].begin()+col);
+ 
+               return(0);
+    }
+       catch(exception& e) {
+               m->errorOut(e, "SparseDistanceMatrix", "rmCell");
+               exit(1);
+       }
+}
+/***********************************************************************/
+void SparseDistanceMatrix::addCell(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);
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SparseDistanceMatrix", "addCell");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+ull SparseDistanceMatrix::getSmallestCell(ull& row){
+       try {
+        if (!sorted) { sortSeqVec(); sorted = true; }
+        
+        vector<PDistCellMin> mins;
+        smallDist = 1e6;
+       
+        for (int i = 0; i < seqVec.size(); i++) {
+            for (int j = 0; j < seqVec[i].size(); j++) {
+ 
+                //already checked everyone else in row
+                if (i < seqVec[i][j].index) {  
+                           
+                    float dist = seqVec[i][j].dist;
+                  
+                    if(dist < smallDist){  //found a new smallest distance
+                        mins.clear();
+                        smallDist = dist;
+                        PDistCellMin temp(i, seqVec[i][j].index);
+                        mins.push_back(temp);  
+                    }
+                    else if(dist == smallDist){  //if a subsequent distance is the same as mins distance add the new iterator to the mins vector
+                        PDistCellMin temp(i, seqVec[i][j].index);
+                        mins.push_back(temp); 
+                    }
+                }else { j+=seqVec[i].size(); } //stop looking 
+                       }
+               }
+        
+               random_shuffle(mins.begin(), mins.end());  //randomize the order of the iterators in the mins vector
+        
+        row = mins[0].row;
+        ull col = mins[0].col;
+
+               return col;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SparseMatrix", "getSmallestCell");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+int SparseDistanceMatrix::sortSeqVec(){
+       try {
+        
+        //saves time in getSmallestCell, by making it so you dont search the repeats
+        for (int i = 0; i < seqVec.size(); i++) {  sort(seqVec[i].begin(), seqVec[i].end(), compareIndexes); }
+    
+        return 0;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "SparseMatrix", "getSmallestCell");
+               exit(1);
+       }
+}
+/***********************************************************************/
+