Adds filter to improve time in pre.cluster

#220

source/calculators/filters.h

@@ -62,6 +62,18 @@ class Filters {
 		}
 	
 	}
+    
+    void doVerticalAllBases() {
+        
+        for(int i=0;i<alignmentLength;i++){
+            if(gap[i] == numSeqs)       {	filter[i] = '0';	}
+            else if(a[i] == numSeqs)	{	filter[i] = '0';	}
+            else if(t[i] == numSeqs)	{	filter[i] = '0';	}
+            else if(c[i] == numSeqs)	{	filter[i] = '0';	}
+            else if(g[i] == numSeqs)	{	filter[i] = '0';	}
+        }
+        
+    }
 	
 	void doTrump(Sequence seq) {
 	

source/commands/preclustercommand.cpp

@@ -691,8 +691,8 @@ int PreClusterCommand::process(string newMapFile){
                                 chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n";
                                 
                                 alignSeqs[j].active = 0;
-                                //alignSeqs[j].numIdentical = 0;
-                                //alignSeqs[j].diffs = mismatch;
+                                alignSeqs[j].numIdentical = 0;
+                                alignSeqs[j].diffs = mismatch;
                                 count++;
                             }
                         }//end if j active
@@ -860,11 +860,11 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
 			}
 		}
     
+        length = *(lengths.begin());
+        
         if (lengths.size() > 1) { method = "unaligned"; }
         else if (lengths.size() == 1) {  method = "aligned"; filterSeqs(); }
         
-        length = *(lengths.begin());
-        
 		//sanity check
 		if (error) { m->control_pressed = true; }
 		
@@ -1041,28 +1041,24 @@ int PreClusterCommand::filterSeqs(){
         string filterString = "";
         Filters F;
         
-        F.setTrump('.');
         F.setLength(length);
         F.initialize();
         F.setFilter(string(length, '1'));
         
         for (int i = 0; i < alignSeqs.size(); i++) {
-            F.doTrump(alignSeqs[i].seq);
             F.getFreqs(alignSeqs[i].seq);
         }
         
         F.setNumSeqs(alignSeqs.size());
-        F.doVertical();
+        F.doVerticalAllBases();
         filterString = F.getFilter();
         
         //run filter
         for (int i = 0; i < alignSeqs.size(); i++) {
             alignSeqs[i].filteredSeq = "";
             string align = alignSeqs[i].seq.getAligned();
             for(int j=0;j<length;j++){
-                if(filterString[j] == '1'){
-                    alignSeqs[i].filteredSeq += align[j];
-                }
+                if(filterString[j] == '1'){ alignSeqs[i].filteredSeq += align[j]; }
             }
         }