precluster command finished

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index 7a092f96cc8b92cd245decd37d388034737a73ed..a6d23e95bfddf71afb20a2d4c2b2d8d1377db71d 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -12,7 +12,7 @@
 
 //********************************************************************************************************************
 //sorts lowest to highest
-inline bool compareOverlap(DistNode left, DistNode right){
+inline bool compareOverlap(seqDist left, seqDist right){
        return (left.dist < right.dist);        
 } 
 /*********************************************************************************************/
@@ -91,7 +91,7 @@ void ReadBlast::read(NameAssignment* nameMap) {
                                //if there is a valid overlap, add it
                                if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
                                        if (!hclusterWanted) {
-                                               DistNode overlapValue(itA->second, itB->second, thisoverlap);
+                                               seqDist overlapValue(itA->second, itB->second, thisoverlap);
                                                overlap.push_back(overlapValue);
                                        }else {
                                                outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
@@ -137,7 +137,7 @@ void ReadBlast::read(NameAssignment* nameMap) {
                                                //if there is a valid overlap, add it
                                                if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
                                                        if (!hclusterWanted) {
-                                                               DistNode overlapValue(itA->second, itB->second, thisoverlap);
+                                                               seqDist overlapValue(itA->second, itB->second, thisoverlap);
                                                                //cout << "overlap = " << itA->second << '\t' << itB->second << '\t' << thisoverlap << endl;
                                                                overlap.push_back(overlapValue);
                                                        }else {
@@ -201,7 +201,7 @@ void ReadBlast::read(NameAssignment* nameMap) {
                                                //if there is a valid overlap, add it
                                                if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
                                                        if (!hclusterWanted) {
-                                                               DistNode overlapValue(itA->second, itB->second, thisoverlap);
+                                                               seqDist overlapValue(itA->second, itB->second, thisoverlap);
                                                                overlap.push_back(overlapValue);
                                                        }else {
                                                                outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;