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formatted classes in package org.corehunter.objectives.distance
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@hdbeukel
hdbeukel committed Jan 18, 2016
1 parent 62a3262 commit 14e81e4
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Showing 3 changed files with 202 additions and 172 deletions.
95 changes: 50 additions & 45 deletions ...c/main/java/org/corehunter/objectives/distance/AbstractGenotypeVariantDistanceMetric.java
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Original file line number Diff line number Diff line change
@@ -1,13 +1,22 @@
/*******************************************************************************
* Copyright 2014 Herman De Beukelaer, Guy Davenport Licensed under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with the
* License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law
* or agreed to in writing, software distributed under the License is
* distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the specific language
* governing permissions and limitations under the License.
*******************************************************************************/
/*--------------------------------------------------------------*/
/* Licensed to the Apache Software Foundation (ASF) under one */
/* or more contributor license agreements. See the NOTICE file */
/* distributed with this work for additional information */
/* regarding copyright ownership. The ASF licenses this file */
/* to you under the Apache License, Version 2.0 (the */
/* "License"); you may not use this file except in compliance */
/* with the License. You may obtain a copy of the License at */
/* */
/* http://www.apache.org/licenses/LICENSE-2.0 */
/* */
/* Unless required by applicable law or agreed to in writing, */
/* software distributed under the License is distributed on an */
/* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY */
/* KIND, either express or implied. See the License for the */
/* specific language governing permissions and limitations */
/* under the License. */
/*--------------------------------------------------------------*/

package org.corehunter.objectives.distance;

import java.util.Set;
Expand All @@ -18,39 +27,35 @@
* @author Guy Davenport
*/
public abstract class AbstractGenotypeVariantDistanceMetric<GenotypeVariantDataType extends GenotypeVariantData>
implements GenotypeVariantDistanceMetric<GenotypeVariantDataType>
{
private GenotypeVariantDataType data;

public AbstractGenotypeVariantDistanceMetric(GenotypeVariantDataType data)
{
super();

setData(data);
}

/*
* (non-Javadoc)
* @see org.jamesframework.core.problems.datatypes.SubsetData#getIDs()
*/
@Override
public final Set<Integer> getIDs()
{
return data.getIDs();
}

/*
* (non-Javadoc)
* @see org.corehunter.objectives.distance.GenotypeVariantDistanceMetric.SubsetData#getData()
*/
@Override
public final GenotypeVariantDataType getData()
{
return data;
}

protected final void setData(GenotypeVariantDataType data)
{
this.data = data;
}
implements GenotypeVariantDistanceMetric<GenotypeVariantDataType> {

private GenotypeVariantDataType data;

public AbstractGenotypeVariantDistanceMetric(GenotypeVariantDataType data) {
super();

setData(data);
}

/*
* (non-Javadoc)
* @see org.jamesframework.core.problems.datatypes.SubsetData#getIDs()
*/
@Override
public final Set<Integer> getIDs() {
return data.getIDs();
}

/*
* (non-Javadoc)
* @see org.corehunter.objectives.distance.GenotypeVariantDistanceMetric.SubsetData#getData()
*/
@Override
public final GenotypeVariantDataType getData() {
return data;
}

protected final void setData(GenotypeVariantDataType data) {
this.data = data;
}
}
251 changes: 128 additions & 123 deletions ...unter-base/src/main/java/org/corehunter/objectives/distance/AverageDistanceObjective.java
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Original file line number Diff line number Diff line change
@@ -1,13 +1,22 @@
/*******************************************************************************
* Copyright 2014 Herman De Beukelaer, Guy Davenport Licensed under the Apache
* License, Version 2.0 (the "License"); you may not use this file except in
* compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law
* or agreed to in writing, software distributed under the License is
* distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the specific language
* governing permissions and limitations under the License.
*******************************************************************************/
/*--------------------------------------------------------------*/
/* Licensed to the Apache Software Foundation (ASF) under one */
/* or more contributor license agreements. See the NOTICE file */
/* distributed with this work for additional information */
/* regarding copyright ownership. The ASF licenses this file */
/* to you under the Apache License, Version 2.0 (the */
/* "License"); you may not use this file except in compliance */
/* with the License. You may obtain a copy of the License at */
/* */
/* http://www.apache.org/licenses/LICENSE-2.0 */
/* */
/* Unless required by applicable law or agreed to in writing, */
/* software distributed under the License is distributed on an */
/* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY */
/* KIND, either express or implied. See the License for the */
/* specific language governing permissions and limitations */
/* under the License. */
/*--------------------------------------------------------------*/

package org.corehunter.objectives.distance;

import java.util.ArrayList;
Expand All @@ -24,119 +33,115 @@
import org.jamesframework.core.subset.neigh.moves.SubsetMove;

public class AverageDistanceObjective implements
Objective<SubsetSolution, DistanceMatrixData>
{
/**
* Evaluates the given subset solution using the given data, by computing the
* average distance between all pairs of selected items. If less than two
* items are selected, this method always returns 0.
*
* @param solution
* the subset solution to be evaluated
* @param data
* the distance matrix
*/
@Override
public Evaluation evaluate(SubsetSolution solution, DistanceMatrixData data)
{
double value = 0.0;
if(solution.getNumSelectedIDs() >= 2){
// at least two items selected: compute average distance
int numDist = 0;
double sumDist = 0.0;
Integer[] selected = new Integer[solution.getNumSelectedIDs()];
solution.getSelectedIDs().toArray(selected);
for(int i=0; i<selected.length; i++){
for(int j=i+1; j<selected.length; j++){
sumDist += data.getDistance(selected[i], selected[j]);
numDist++;
Objective<SubsetSolution, DistanceMatrixData> {

/**
* Evaluates the given subset solution using the given data, by computing the average distance between all pairs of
* selected items. If less than two items are selected, this method always returns 0.
*
* @param solution the subset solution to be evaluated
* @param data the distance matrix
*/
@Override
public Evaluation evaluate(SubsetSolution solution, DistanceMatrixData data) {
double value = 0.0;
if (solution.getNumSelectedIDs() >= 2) {
// at least two items selected: compute average distance
int numDist = 0;
double sumDist = 0.0;
Integer[] selected = new Integer[solution.getNumSelectedIDs()];
solution.getSelectedIDs().toArray(selected);
for (int i = 0; i < selected.length; i++) {
for (int j = i + 1; j < selected.length; j++) {
sumDist += data.getDistance(selected[i], selected[j]);
numDist++;
}
}
value = sumDist / numDist;
}
return SimpleEvaluation.WITH_VALUE(value);
}

@Override
public Evaluation evaluate(Move move, SubsetSolution curSolution,
Evaluation curEvaluation, DistanceMatrixData data) {
// check move type
if (!(move instanceof SubsetMove)) {
throw new IncompatibleDeltaEvaluationException("Core subset objective should be used in combination "
+ "with neighbourhoods that generate moves of type SubsetMove.");
}
// cast move
SubsetMove subsetMove = (SubsetMove) move;

// get current evaluation
double curEval = curEvaluation.getValue();
// undo average to get sum of distances
int numSelected = curSolution.getNumSelectedIDs();
int numDistances = numSelected * (numSelected - 1) / 2;
double sumDist = curEval * numDistances;

// get set of added and removed IDs
Set<Integer> added = subsetMove.getAddedIDs();
Set<Integer> removed = subsetMove.getDeletedIDs();
// infer list of retained IDs
List<Integer> retained = new ArrayList<>(curSolution.getSelectedIDs());
retained.removeAll(removed);

// subtract distances from removed items to retained items
for (int rem : removed) {
for (int ret : retained) {
sumDist -= data.getDistance(rem, ret);
numDistances--;
}
}

// subtract distances from removed to other removed items
for (int rem1 : removed) {
for (int rem2 : removed) {
// account for each distinct pair only once
if (rem1 < rem2) {
sumDist -= data.getDistance(rem1, rem2);
numDistances--;
}
}
}
value = sumDist/numDist;

// add distances from new items to retained items
for (int add : added) {
for (int ret : retained) {
sumDist += data.getDistance(add, ret);
numDistances++;
}
}

// add distances from new items to other new items
for (int add1 : added) {
for (int add2 : added) {
// account for each distinct pair only once
if (add1 < add2) {
sumDist += data.getDistance(add1, add2);
numDistances++;
}
}
}

double newEval;
if (numDistances > 0) {
// take average based on updated number of distances
newEval = sumDist / numDistances;
} else {
// no distances (less than two items remain selected)
newEval = 0.0;
}

// return new evaluation
return SimpleEvaluation.WITH_VALUE(newEval);

}
return SimpleEvaluation.WITH_VALUE(value);
}

public Evaluation evaluate(Move move, SubsetSolution curSolution, Evaluation curEvaluation, DistanceMatrixData data) {
// check move type
if(!(move instanceof SubsetMove)){
throw new IncompatibleDeltaEvaluationException("Core subset objective should be used in combination "
+ "with neighbourhoods that generate moves of type SubsetMove.");
}
// cast move
SubsetMove subsetMove = (SubsetMove) move;

// get current evaluation
double curEval = curEvaluation.getValue();
// undo average to get sum of distances
int numSelected = curSolution.getNumSelectedIDs();
int numDistances = numSelected * (numSelected-1) / 2;
double sumDist = curEval * numDistances;

// get set of added and removed IDs
Set<Integer> added = subsetMove.getAddedIDs();
Set<Integer> removed = subsetMove.getDeletedIDs();
// infer list of retained IDs
List<Integer> retained = new ArrayList<>(curSolution.getSelectedIDs());
retained.removeAll(removed);

// subtract distances from removed items to retained items
for(int rem : removed){
for(int ret : retained){
sumDist -= data.getDistance(rem, ret);
numDistances--;
}
}

// subtract distances from removed to other removed items
for(int rem1 : removed){
for(int rem2 : removed){
// account for each distinct pair only once
if(rem1 < rem2){
sumDist -= data.getDistance(rem1, rem2);
numDistances--;
}
}
}

// add distances from new items to retained items
for(int add : added){
for(int ret : retained){
sumDist += data.getDistance(add, ret);
numDistances++;
}
}

// add distances from new items to other new items
for(int add1 : added){
for(int add2 : added){
// account for each distinct pair only once
if(add1 < add2){
sumDist += data.getDistance(add1, add2);
numDistances++;
}
}
}

double newEval;
if(numDistances > 0){
// take average based on updated number of distances
newEval = sumDist / numDistances;
} else {
// no distances (less than two items remain selected)
newEval = 0.0;
}

// return new evaluation
return SimpleEvaluation.WITH_VALUE(newEval);

}


@Override
public boolean isMinimizing()
{
return false;
}

}

@Override
public boolean isMinimizing() {
return false;
}

}
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