de.hpi.fgis.dude.similarityfunction.contentbased.util
Class SmithWatermanDistance

java.lang.Object
  uk.ac.shef.wit.simmetrics.similaritymetrics.AbstractStringMetric
      de.hpi.fgis.dude.similarityfunction.contentbased.util.SmithWatermanDistance

All Implemented Interfaces:

Serializable, uk.ac.shef.wit.simmetrics.similaritymetrics.InterfaceStringMetric

public final class SmithWatermanDistance
extends uk.ac.shef.wit.simmetrics.similaritymetrics.AbstractStringMetric
implements Serializable

SmithWatermanDistance implements the Smith-Waterman distance.

Author:

Ziawasch Abedjan

See Also:

Serialized Form

Constructor Summary

SmithWatermanDistance()
constructor - default (empty).

SmithWatermanDistance(uk.ac.shef.wit.simmetrics.similaritymetrics.costfunctions.AbstractSubstitutionCost costFunc)
constructor.

SmithWatermanDistance(float costG)
constructor.

SmithWatermanDistance(float costG, uk.ac.shef.wit.simmetrics.similaritymetrics.costfunctions.AbstractSubstitutionCost costFunc)
constructor.

Method Summary

uk.ac.shef.wit.simmetrics.similaritymetrics.costfunctions.AbstractSubstitutionCost	getdCostFunc() get the d(i,j) cost function.
float	getGapCost() gets the gap cost for the distance function.
String	getLongDescriptionString() returns the long string identifier for the metric.
String	getShortDescriptionString() returns the string identifier for the metric .
float	getSimilarity(String string1, String string2) gets the similarity of the two strings using Needleman Wunch distance.
String	getSimilarityExplained(String string1, String string2) gets a div class xhtml similarity explaining the operation of the metric.
float	getSimilarityTimingEstimated(String string1, String string2) gets the estimated time in milliseconds it takes to perform a similarity timing.
float	getUnNormalisedSimilarity(String s, String t) implements the Smith-Waterman distance function //see http://www.gen.tcd.ie/molevol/nwswat.html for details .
void	setdCostFunc(uk.ac.shef.wit.simmetrics.similaritymetrics.costfunctions.AbstractSubstitutionCost dCostFunc) sets the d(i,j) cost function used.
void	setGapCost(float gapCost) sets the gap cost for the distance function.

Methods inherited from class uk.ac.shef.wit.simmetrics.similaritymetrics.AbstractStringMetric

batchCompareSet, batchCompareSets, getSimilarityTimingActual

Methods inherited from class java.lang.Object

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

Constructor Detail

SmithWatermanDistance

public SmithWatermanDistance()

constructor - default (empty).

SmithWatermanDistance

public SmithWatermanDistance(float costG)

constructor.

Parameters:

costG - - the cost of a gap

SmithWatermanDistance

public SmithWatermanDistance(float costG,
                             uk.ac.shef.wit.simmetrics.similaritymetrics.costfunctions.AbstractSubstitutionCost costFunc)

constructor.

Parameters:

costG - - the cost of a gap

costFunc - - the cost function to use

SmithWatermanDistance

public SmithWatermanDistance(uk.ac.shef.wit.simmetrics.similaritymetrics.costfunctions.AbstractSubstitutionCost costFunc)

constructor.

Parameters:

costFunc - - the cost function to use

Method Detail

getGapCost

public float getGapCost()

gets the gap cost for the distance function.

Returns:

the gap cost for the distance function

setGapCost

public void setGapCost(float gapCost)

sets the gap cost for the distance function.

Parameters:

gapCost - the cost of a gap

getdCostFunc

public uk.ac.shef.wit.simmetrics.similaritymetrics.costfunctions.AbstractSubstitutionCost getdCostFunc()

get the d(i,j) cost function.

Returns:

AbstractSubstitutionCost cost function used

setdCostFunc

public void setdCostFunc(uk.ac.shef.wit.simmetrics.similaritymetrics.costfunctions.AbstractSubstitutionCost dCostFunc)

sets the d(i,j) cost function used.

Parameters:

dCostFunc - - the cost function to use

getShortDescriptionString

public String getShortDescriptionString()

returns the string identifier for the metric .

Specified by:

getShortDescriptionString in interface uk.ac.shef.wit.simmetrics.similaritymetrics.InterfaceStringMetric

Specified by:

getShortDescriptionString in class uk.ac.shef.wit.simmetrics.similaritymetrics.AbstractStringMetric

Returns:

the string identifier for the metric

getLongDescriptionString

public String getLongDescriptionString()

returns the long string identifier for the metric.

Specified by:

getLongDescriptionString in interface uk.ac.shef.wit.simmetrics.similaritymetrics.InterfaceStringMetric

Specified by:

getLongDescriptionString in class uk.ac.shef.wit.simmetrics.similaritymetrics.AbstractStringMetric

Returns:

the long string identifier for the metric

getSimilarityExplained

public String getSimilarityExplained(String string1,
                                     String string2)

gets a div class xhtml similarity explaining the operation of the metric.

Specified by:

getSimilarityExplained in interface uk.ac.shef.wit.simmetrics.similaritymetrics.InterfaceStringMetric

Specified by:

getSimilarityExplained in class uk.ac.shef.wit.simmetrics.similaritymetrics.AbstractStringMetric

Parameters:

string1 - string 1

string2 - string 2

Returns:

a div class html section detailing the metric operation.

getSimilarityTimingEstimated

public float getSimilarityTimingEstimated(String string1,
                                          String string2)

gets the estimated time in milliseconds it takes to perform a similarity timing.

Specified by:

getSimilarityTimingEstimated in interface uk.ac.shef.wit.simmetrics.similaritymetrics.InterfaceStringMetric

Specified by:

getSimilarityTimingEstimated in class uk.ac.shef.wit.simmetrics.similaritymetrics.AbstractStringMetric

Parameters:

string1 - string 1

string2 - string 2

Returns:

the estimated time in milliseconds taken to perform the similarity measure

getSimilarity

public float getSimilarity(String string1,
                           String string2)

gets the similarity of the two strings using Needleman Wunch distance.

Specified by:

getSimilarity in interface uk.ac.shef.wit.simmetrics.similaritymetrics.InterfaceStringMetric

Specified by:

getSimilarity in class uk.ac.shef.wit.simmetrics.similaritymetrics.AbstractStringMetric

Parameters:

string1 -

string2 -

Returns:

a value between 0-1 of the similarity

getUnNormalisedSimilarity

public float getUnNormalisedSimilarity(String s,
                                       String t)

implements the Smith-Waterman distance function //see http://www.gen.tcd.ie/molevol/nwswat.html for details .

Specified by:

getUnNormalisedSimilarity in class uk.ac.shef.wit.simmetrics.similaritymetrics.AbstractStringMetric

Parameters:

s -

t -

Returns:

the Smith-Waterman distance for the given strings