# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1411118709 -7200
# Node ID 9018657a9f7383f93cc20faad3dae1c9cb61da20
# Parent  0ff22eec3e4b72b2ea9b96f8e46021ca187b1c27
Added "Membership cutoff (0.0 - 1.0)" option

diff -r 0ff22eec3e4b -r 9018657a9f73 MsClust.jar
Binary file MsClust.jar has changed
diff -r 0ff22eec3e4b -r 9018657a9f73 msclust.xml
--- a/msclust.xml	Thu Sep 18 14:29:57 2014 +0200
+++ b/msclust.xml	Fri Sep 19 11:25:09 2014 +0200
@@ -27,8 +27,10 @@
 		-pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope
 		-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
+		-rtDistanceConfidence $potDensFuncType.pdf_scan_conf
+		#if $clusteringType.type == "original"
+			-clustMembershipCutoff $clusteringType.clust_membership_cutoff
+		#end if  
 		-centrotypesOut $centrotypesOut 
 		-simOut $simOut
 		-micOut $micOut
@@ -98,13 +100,9 @@
 		      	</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])" />
@@ -128,7 +126,9 @@
 		      <option value="fuzzyCMeans">(experimental) Fuzzy C-Means - Fuzzy clustering, optimize centers</option>
 		    </param>
 		    <when value="original">
-		    <!-- nothing -->
+		    	<param name="clust_membership_cutoff" type="float" size="10" value=""
+		    	       label="Membership cutoff (0.0 - 1.0)"
+		    	       help="Items with membership below this value are NOT added to the cluster"/>
 			</when>
 		    <!-- one idea would be to have clustering specific tolerance values, not reusing the centrotype selection ones
 		    <when value="originalNewTol">