| Previous changeset 35:0ff22eec3e4b (2014-09-18) Next changeset 37:2398cbcac2cb (2014-09-19) |
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Commit message:
Added "Membership cutoff (0.0 - 1.0)" option |
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modified:
MsClust.jar msclust.xml |
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| diff -r 0ff22eec3e4b -r 9018657a9f73 MsClust.jar |
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| Binary file MsClust.jar has changed |
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| 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 |
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| @@ -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"> |