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java.lang.Objectmethods.clustering.MCLClusterer
public class MCLClusterer
Performs clustering using the Markov Cluster Algorithm as proposed in the PhD thesis Graph Clustering by Flow Simulation by Stijn van Dongen.
Note: This class does not contain an actual implementation
but an interface to the binaries of the mcl algorithm. Thus it requires
the mcl
program to be installed on the system it is executed on.
See also: http://micans.org/mcl/
Field Summary | |
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static String |
DEFAULT_BINARY
Default MCL binary: mcl , requires this binary in the
current PATH |
Constructor Summary | |
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MCLClusterer()
Creates an MCL cluster with default parameters . |
|
MCLClusterer(MCLParameters params)
Creates an MCL clusterer with a given set of parameters. |
Method Summary | |
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ComplexSet |
cluster(ProteinNetwork net)
Perform MCL clustering. |
MCLParameters |
getParamemeters()
Returns the mcl parameters for this clusterer |
static void |
setMCLBinary(String path)
Sets the path to the mcl binary to be used. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String DEFAULT_BINARY
mcl
, requires this binary in the
current PATH
Constructor Detail |
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public MCLClusterer()
parameters
.
public MCLClusterer(MCLParameters params)
params
- MCL parameters to be used for this clustererMethod Detail |
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public MCLParameters getParamemeters()
mcl parameters
for this clusterer
public ComplexSet cluster(ProteinNetwork net)
mcl
binary is in the
current PATH
or set the path to that binary using
setMCLBinary(String)
cluster
in interface Clusterer
net
- similarity network which will be clustered
LibraryNameException
- if and error occurs during the execution
of the mcl binarypublic static void setMCLBinary(String path)
mcl
binary to be used. This method is
static and the binary valid for all MCL clusterer objects.
path
- mcl
binary to be used
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