diff --git a/UserManual.docx b/UserManual.docx
index 92938da..1b4d354 100644
Binary files a/UserManual.docx and b/UserManual.docx differ
diff --git a/UserManual.pdf b/UserManual.pdf
index 30f006b..bdf5ebc 100644
Binary files a/UserManual.pdf and b/UserManual.pdf differ
diff --git a/src/edu/uconn/tripoint/triangulation/Triangulation.java b/src/edu/uconn/tripoint/triangulation/Triangulation.java
index 9892b7d..ffc8c68 100644
--- a/src/edu/uconn/tripoint/triangulation/Triangulation.java
+++ b/src/edu/uconn/tripoint/triangulation/Triangulation.java
@@ -418,7 +418,6 @@ public class Triangulation {
 		}
 		
 		for(int i = 0; i < genes.length; i++){
-			int numnoncoding = noncoding.get(genes[i].getGene()).size();
 			for(Iterator<Pathway> it = _genepathways.get(genes[i].getGene()).iterator(); it.hasNext();){
 				Pathway curpath = it.next();
 				String pathwayid = curpath.getId();
@@ -436,6 +435,7 @@ public class Triangulation {
 					tri = getNormScore(consistencyscore, connparam)+getNormScore(impactscore, impnparam);
 				}
 				if(noncoding != null && noncoding.size() > 0){
+					int numnoncoding = noncoding.get(genes[i].getGene()).size();
 					if(numnoncoding == 0){
 						tri = 0;
 					}
@@ -505,7 +505,6 @@ public class Triangulation {
 		}
 		
 		for(int i = 0; i < genes.length; i++){
-			int numnoncoding = noncoding.get(genes[i].getGene()).size();
 			for(Iterator<Pathway> it = _genepathways.get(genes[i].getGene()).iterator(); it.hasNext();){
 				Pathway curpath = it.next();
 				String pathwayid = curpath.getId();
@@ -523,6 +522,7 @@ public class Triangulation {
 					tri = getNormScore(consistencyscore, connparam)+getNormScore(impactscore, impnparam);
 				}
 				if(noncoding != null && noncoding.size() > 0){
+					int numnoncoding = noncoding.get(genes[i].getGene()).size();
 					if(numnoncoding == 0){
 						tri = 0;
 					}
diff --git a/tripoint.jar b/tripoint.jar
index 058e325..6d3d730 100644
Binary files a/tripoint.jar and b/tripoint.jar differ