added out.hierarchy command

[mothur.git] / chimeracheckrdp.cpp

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index 07fb8ab65019b9a45d7556fbd75d50310c5c0b98..12785137232677e3a056a43fd31b705f9b618734 100644 (file)
--- a/chimeracheckrdp.cpp
+++ b/chimeracheckrdp.cpp
@@ -43,7 +43,7 @@ void ChimeraCheckRDP::print(ostream& out) {
                                        out << IS[i][k].score << '\t'; 
                                        //if (IS[i][k].score > chimeraCutoff) {  isChimeric[i] = true;   lastChimericWindowFound = k;           }                       
                                }
-                               
+                               out << endl;
                                //if (isChimeric[i]) { 
                                        //mothurOut(querySeqs[i]->getName() + "\tIS: " + toString(IS[i][lastChimericWindowFound].score) + "\tbreakpoint: " + toString(IS[i][lastChimericWindowFound].midpoint) + "\tleft parent: " + IS[i][lastChimericWindowFound].leftParent + "\tright parent: " + IS[i][lastChimericWindowFound].rightParent); mothurOutEndLine();
                                        //out << endl << "chimera: YES" << endl;
@@ -65,6 +65,7 @@ void ChimeraCheckRDP::print(ostream& out) {
                                }
                }
                
+               mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); mothurOutEndLine();
        }
        catch(exception& e) {
                errorOut(e, "ChimeraCheckRDP", "print");
@@ -73,7 +74,7 @@ void ChimeraCheckRDP::print(ostream& out) {
 }
 
 //***************************************************************************************************************
-void ChimeraCheckRDP::getChimeras() {
+int ChimeraCheckRDP::getChimeras() {
        try {
                
                //read in query sequences and subject sequences
@@ -82,7 +83,7 @@ void ChimeraCheckRDP::getChimeras() {
                querySeqs = readSeqs(fastafile);
                mothurOut("Done."); 
                //templateSeqs = readSeqs(templateFile);
-               templateDB = new AlignmentDB(templateFile, "kmer", kmerSize, 0,0,0,0);
+               templateDB = new AlignmentDB(templateFile, "kmer", kmerSize, 0.0,0.0,0.0,0.0);
                mothurOutEndLine();
                
                int numSeqs = querySeqs.size();
@@ -134,7 +135,7 @@ void ChimeraCheckRDP::getChimeras() {
                //free memory
                for (int i = 0; i < lines.size(); i++)                                  {       delete lines[i];        }
        
-                       
+               return 0;
        }
        catch(exception& e) {
                errorOut(e, "ChimeraCheckRDP", "getChimeras");