From 5ca05ed0a8311b2943c1c0a1fad825785db484d6 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Wed, 25 Nov 2009 16:50:42 +0000
Subject: [PATCH] a few changes to chimera classes

---
 ccode.cpp           | 6 +++---
 chimeracheckrdp.cpp | 3 ++-
 chimeraslayer.cpp   | 6 ++----
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/ccode.cpp b/ccode.cpp
index a43a5a1..0a9214e 100644
--- a/ccode.cpp
+++ b/ccode.cpp
@@ -423,15 +423,15 @@ vector<int> Ccode::findWindows(int query) {
 		it = trim[query].begin();
 		
 		int length = it->second - it->first;
-		
+	
 		//default is wanted = 10% of total length
 		if (windowSizes[query] > length) { 
 			mothurOut("You have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.");
 			windowSizes[query] = length / 10;
 		}else if (windowSizes[query] == 0) { windowSizes[query] = length / 10;  }
-		else if (windowSizes[query] > (length / 20)) {
+		else if (windowSizes[query] > (length * 0.20)) {
 			mothurOut("You have selected a window that is larger than 20% of your sequence length.  This is not recommended, but I will continue anyway."); mothurOutEndLine();
-		}else if (windowSizes[query] < (length / 5)) {
+		}else if (windowSizes[query] < (length * 0.05)) {
 			mothurOut("You have selected a window that is smaller than 5% of your sequence length.  This is not recommended, but I will continue anyway."); mothurOutEndLine();
 		}
 		
diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index f9b2319..dcd2ef3 100644
--- 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");
diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 86ed532..0b7c221 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -38,7 +38,7 @@ void ChimeraSlayer::print(ostream& out) {
 					out << querySeqs[i]->getName() << "\tyes" << endl;
 				}else {
 					out << querySeqs[i]->getName() << "\tno" << endl;
-					mothurOut(querySeqs[i]->getName() + "\tno"); mothurOutEndLine();
+					//mothurOut(querySeqs[i]->getName() + "\tno"); mothurOutEndLine();
 				}
 
 				printBlock(chimeraResults[i][0], out, i);
@@ -46,7 +46,7 @@ void ChimeraSlayer::print(ostream& out) {
 				out << endl;
 			}else{
 				out << querySeqs[i]->getName() << "\tno" << endl;
-				mothurOut(querySeqs[i]->getName() + "\tno"); mothurOutEndLine();
+				//mothurOut(querySeqs[i]->getName() + "\tno"); mothurOutEndLine();
 			}
 		}
 				
@@ -212,8 +212,6 @@ void ChimeraSlayer::getChimeras() {
 		if (seqMask != "") {
 			delete decalc; 
 		}
-
-			
 	}
 	catch(exception& e) {
 		errorOut(e, "ChimeraSlayer", "getChimeras");
-- 
2.39.2