Package chemaxon.clustering
Class JarvisPatrick
- java.lang.Object
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- chemaxon.clustering.Common
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- chemaxon.clustering.NearestNeighbors
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- chemaxon.clustering.JarvisPatrick
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@PublicAPI public class JarvisPatrick extends NearestNeighbors
Performs variable-length Jarvis-Patrick clustering based on binary fingerprints (bits strings) and/or other data stored in a database table or a file. It can also be used for calculating diversity measures, like average and minimum dissimilarity of a compound library.
This class can be used from command-line or from the API.
See the documentation for details.An example for running JarvisPatrick:
ConnectionHandler ch; String selectString; ... JarvisPatrick jp=new JarvisPatrick(); jp.setInput(ch, selectString ); jp.setOutput(System.out); jp.setDimensions(0); jp.setFpSize(512); jp.setStatNeeded(true); jp.setOnlyStat(false); jp.setStatStream(System.out); jp.setIdGeneration(true); jp.setThreshold(0.1f); jp.setCentralShown(true); jp.setMinCommonRatio(0.1f); jp.setSingletonNegative(true); jp.run();
- Since:
- JChem 1.6.2
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Constructor Summary
Constructors Constructor Description JarvisPatrick()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description float
getMinCommonRatio()
Gets the minimum ratio of common neighbors of two compounds.boolean
isCentralShown()
Indicates whether central objects are displayed.boolean
isSingletonNegative()
Indicates whether singeltons get negative cluster id-s.static void
main(String[] args)
The command line version entry point.void
run()
Starts processing.void
setCentralShown(boolean b)
Specifies if cluster centers should be diplayed.void
setMinCommonRatio(float ratio)
Sets the minimum ratio of common neighbors of two compounds.void
setSingletonNegative(boolean b)
Specifies whether singletons get negative cluste id-s.-
Methods inherited from class chemaxon.clustering.NearestNeighbors
getThreshold, setInput, setInput, setInput, setInput, setThreshold
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Methods inherited from class chemaxon.clustering.Common
getDimensions, getElapsedTime, getFpSize, getIdGeneration, getStartTime, getStatStream, getWeights, isOnlyStat, isStatNeeded, setDimensions, setFpSize, setIdGeneration, setOnlyStat, setOutput, setOutput, setOutput, setOutput, setStatNeeded, setStatStream, setWeights
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Method Detail
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setMinCommonRatio
public void setMinCommonRatio(float ratio)
Sets the minimum ratio of common neighbors of two compounds.- Parameters:
ratio
- the ratio to be set- Since:
- JChem 1.6.2
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getMinCommonRatio
public float getMinCommonRatio()
Gets the minimum ratio of common neighbors of two compounds.- Returns:
- the ratio
- Since:
- JChem 1.6.2
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setSingletonNegative
public void setSingletonNegative(boolean b)
Specifies whether singletons get negative cluste id-s.- Parameters:
b
- If set totrue
, singeltons get negative cluster id-s.- Since:
- JChem 1.6.2
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isSingletonNegative
public boolean isSingletonNegative()
Indicates whether singeltons get negative cluster id-s.- Returns:
true
, if singeltons get negative cluster id-s.- Since:
- JChem 1.6.2
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setCentralShown
public void setCentralShown(boolean b)
Specifies if cluster centers should be diplayed.- Parameters:
b
- if set totrue
, central objects are calculated and shown in output.- Since:
- JChem 1.6.2
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isCentralShown
public boolean isCentralShown()
Indicates whether central objects are displayed.- Returns:
true
if central objects are calculated and shown in output.- Since:
- JChem 1.6.2
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run
public void run() throws chemaxon.clustering.ClusteringException, IOException, SQLException, chemaxon.clustering.InvalidLicenseKeyException
Starts processing.- Overrides:
run
in classNearestNeighbors
- Throws:
chemaxon.clustering.ClusteringException
IOException
SQLException
chemaxon.clustering.InvalidLicenseKeyException
- Since:
- JChem 1.6.2
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main
public static void main(String[] args)
The command line version entry point. Parameter parsing, initialization then start.
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