com.chemaxon.overlap.wui

Class SlowUnguardedComparator<T>

java.lang.Object

com.chemaxon.overlap.wui.SlowUnguardedComparator<T>

All Implemented Interfaces:

UnguardedDissimilarityCalculator<T>, Serializable

public final class SlowUnguardedComparator<T>
extends Object
implements UnguardedDissimilarityCalculator<T>

Diagnostic tool to introduce slow execution speed to similarity search.

Usage:

 # Import MMS
 bin/createMms.sh -in data/molecules/drugbank/drugbank-common_name.smi.gz -out mms.bin

 # Calculate fingerprint; inject slow comparator wrapper as the default comparison
 # Note that the similarity search internally will further group pages together
 # Specify pagesize 1 in order to avoid grouping all targets together a single page
 bin/buildStorage.sh \
     -in data/molecules/drugbank/drugbank-common_name.smi.gz  \
     -out fp.bin \
     -context createSimpleCfp7Context \
     -contextjs 'ctx.pagesize(1).unguarded(
         ctx.getUnguardedExtractor(),
         new Packages.com.chemaxon.overlap.wui.SlowUnguardedComparator(
             ctx.getUnguardedDissimilarityCalculator(), 1
         )
     );'

 # Launch embedded server
 # Specify to use only a single working thread for search execution
 bin/gui.sh \
     -tp 1 \
     -allowedOrigins "*,*" -nobrowse -port 8085\
     -mols -mms:mms.bin:-name:m \
     -desc -desc:fp.bin:-name:slow-fp:-mols:m


 

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
SlowUnguardedComparator(UnguardedDissimilarityCalculator<T> base, long delay)

Method Summary

Modifier and Type	Method and Description
double	denormalize(double d) Calculate raw value for a normalized dissimilarity value.
double	dissimilarity(T t, T t1) Compare dissimilarity of two objects.
double	normalize(double d) Normalize dissimilarity value returned by UnguardedDissimilarityCalculator.dissimilarity(java.lang.Object, java.lang.Object).
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SlowUnguardedComparator

public SlowUnguardedComparator(UnguardedDissimilarityCalculator<T> base,
                               long delay)

Method Detail

dissimilarity

public double dissimilarity(T t,
                            T t1)

Description copied from interface: UnguardedDissimilarityCalculator

Compare dissimilarity of two objects. Raw dissimilarity score is returned which

Note that implementations might not check even basic consistency of compared objects.

Implementations must return valid real numbers which are smaller than Double.MAX_VALUE.

Specified by:

dissimilarity in interface UnguardedDissimilarityCalculator<T>

Parameters:

t - Target to compare

t1 - Query to compare

Returns:

Raw score. Lower score represents more similar object

normalize

public double normalize(double d)

Description copied from interface: UnguardedDissimilarityCalculator

Normalize dissimilarity value returned by UnguardedDissimilarityCalculator.dissimilarity(java.lang.Object, java.lang.Object).

Specified by:

normalize in interface UnguardedDissimilarityCalculator<T>

Parameters:

d - Raw dissimilarity value

Returns:

Normalized value

denormalize

public double denormalize(double d)

Description copied from interface: UnguardedDissimilarityCalculator

Calculate raw value for a normalized dissimilarity value. This function can be used where a cutoff defined in terms of dissimilarity is implemented.

Specified by:

denormalize in interface UnguardedDissimilarityCalculator<T>

Parameters:

d - Normalized dissimilarity value

Returns:

Raw value

toString

public String toString()

Overrides:

toString in class Object