# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1411043397 -7200
# Node ID 0ff22eec3e4b72b2ea9b96f8e46021ca187b1c27
# Parent  e79a7c32b011405c37cce5c508eff0056e7265f7
added peak_width_max for better performance

diff -r e79a7c32b011 -r 0ff22eec3e4b MsClust.jar
Binary file MsClust.jar has changed
diff -r e79a7c32b011 -r 0ff22eec3e4b msclust.xml
--- a/msclust.xml	Wed Sep 17 11:31:34 2014 +0200
+++ b/msclust.xml	Thu Sep 18 14:29:57 2014 +0200
@@ -7,7 +7,7 @@
 	       
 	       TODO in command below: add conditionals according to options of using or NOT the tolerances/thresholds from previous steps 
 	    -->
-	<command interpreter="java -jar -Xmx58g ">
+	<command interpreter="java -jar ">
 	    MsClust.jar 
 	   	-peaksFileName $inputPeaks 
 	   	-dataType $dataType
@@ -28,6 +28,7 @@
 		-rtDistTolUnit $potDensFuncType.rt_dist_tol_unit.type
 		-rtDistTol $potDensFuncType.rt_dist_tol_unit.pdf_rt_toler
 		-rtDistanceConfidence $potDensFuncType.pdf_scan_conf  
+		-peakWidthMax $potDensFuncType.rt_dist_tol_unit.peak_width_max
 		-centrotypesOut $centrotypesOut 
 		-simOut $simOut
 		-micOut $micOut
@@ -97,9 +98,13 @@
 		      	</param>
 		      	<when value="1">
 		      		<param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans"  />
+		      		<param name="peak_width_max" type="float" size="10" value="30" label="MAX Peak Width, in scans"  help="This parameter is to avoid calculations of correlation 
+		      		between peaks that are too far apart anyway" />
 		      	</when>
 		      	<when value="2">
 		      		<param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" />
+		      		<param name="peak_width_max" type="float" size="10" value="300000" label="MAX Peak Width, in micro minutes"  help="This parameter is to avoid calculations of correlation 
+		      		between peaks that are too far apart anyway" />
 		      	</when>
 		      </conditional>
 		      <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />