/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.api;
import static org.openbel.framework.common.BELUtilities.hasItems;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.openbel.framework.api.Kam.KamEdge;
import org.openbel.framework.api.Kam.KamNode;
import org.openbel.framework.common.InvalidArgument;
/**
* Utility class for operating on Kams
*
* @author julianjray
*
*/
public final class KamUtils {
private KamUtils() {
// only static methods; no instantiation
}
/**
*
* @param kam
* @return
* @throws InvalidArgument Thrown if {@code kam} is null
*/
public static Kam newInstance(Kam kam) {
if (kam == null) {
throw new InvalidArgument("kam", kam);
}
return new KamImpl(kam.getKamInfo());
}
/**
*
* @param kam
* @param edgeFilter
* @return
* @throws InvalidArgument
*/
public static Kam filter(Kam kam, EdgeFilter edgeFilter)
throws InvalidArgument {
Kam newKam = newInstance(kam);
newKam.union(kam.getEdges(edgeFilter));
return newKam;
}
/**
*
* @param kam1
* @param kam2
* @return
* @throws InvalidArgument
*/
public static Kam intersection(Kam kam1, Kam kam2) throws InvalidArgument {
if (!kam1.getKamInfo().equals(kam2.getKamInfo())) {
throw new InvalidArgument(
"Kam1 and Kam2 must reference the same kam in the KamStore");
}
List<KamEdge> kamEdges = new ArrayList<KamEdge>();
// Check for edges in Kam1 that are also in Kam2
for (KamEdge kamEdge : kam1.getEdges()) {
if (kam2.contains(kamEdge)) {
kamEdges.add(kamEdge);
}
}
// Create a new Kam with the difference set from both Kams
Kam newKam = newInstance(kam1);
newKam.union(kamEdges);
return newKam;
}
/**
*
* @param kam
* @param kamEdges
* @return
* @throws InvalidArgument
*/
public static Kam intersection(Kam kam, List<KamEdge> kamEdges)
throws InvalidArgument {
// Make sure that all the edges in the edge list are associated with the Kam
for (KamEdge kamEdge : kamEdges) {
if (!kamEdge.getKam().getKamInfo().equals(kam.getKamInfo())) {
throw new InvalidArgument(
"Kamedges do not reference the same Kam.");
}
}
// Check for edges in Kam1 that are also in the list
List<KamEdge> intersectionKamEdges = new ArrayList<KamEdge>();
for (KamEdge kamEdge : kamEdges) {
if (kam.contains(kamEdge)) {
intersectionKamEdges.add(kamEdge);
}
}
return union(kam, intersectionKamEdges);
}
/**
*
* @param kam
* @param kamEdges
* @return
* @throws InvalidArgument
*/
public static Kam difference(Kam kam, List<KamEdge> kamEdges)
throws InvalidArgument {
// Make sure that all the edges in the edge list are associated with the Kam
for (KamEdge kamEdge : kamEdges) {
if (!kamEdge.getKam().getKamInfo().equals(kam.getKamInfo())) {
throw new InvalidArgument(
"Kamedges do not reference the same Kam.");
}
}
// Create a new kam instance and add the edges
Kam kam2 = newInstance(kam);
kam2.union(kamEdges);
// perform a kam to kam difference
return difference(kam, kam2);
}
/**
*
* @param kam1
* @param kam2
* @return
* @throws InvalidArgument
*/
public static Kam union(Kam kam1, Kam kam2) throws InvalidArgument {
if (!kam1.getKamInfo().equals(kam2.getKamInfo())) {
throw new InvalidArgument(
"Kam1 and Kam2 must reference the same kam in the KamStore");
}
Kam newKam = newInstance(kam1);
newKam.union(kam1.getEdges());
newKam.union(kam2.getEdges());
return newKam;
}
/**
*
* @param kam1
* @param edges
* @return
* @throws InvalidArgument
*/
public static Kam union(Kam kam1, List<KamEdge> kamEdges)
throws InvalidArgument {
Kam newKam = newInstance(kam1);
newKam.union(kam1.getEdges());
newKam.union(kamEdges);
return newKam;
}
/**
*
* @param kam1
* @param kam2
* @return
* @throws InvalidArgument
*/
public static Kam difference(Kam kam1, Kam kam2) throws InvalidArgument {
if (!kam1.getKamInfo().equals(kam2.getKamInfo())) {
throw new InvalidArgument(
"Kam1 and Kam2 must reference the same kam in the KamStore");
}
List<KamEdge> kamEdges = new ArrayList<KamEdge>();
// First check for edges in Kam1 that are not in Kam2
for (KamEdge kamEdge : kam1.getEdges()) {
if (!kam2.contains(kamEdge)) {
kamEdges.add(kamEdge);
}
}
// Now check for edges in Kam2 that are not in Kam1
for (KamEdge kamEdge : kam2.getEdges()) {
if (!kam1.contains(kamEdge)) {
kamEdges.add(kamEdge);
}
}
// Create a new Kam with the difference set from both Kams
Kam newKam = newInstance(kam1);
newKam.union(kamEdges);
return newKam;
}
/**
* Copy the {@link Kam} by creating a new {@link KamImpl} instance with
* new {@link KamNode}s and {@link KamEdge}s.
*
* @param kam {@link Kam}
* @return the new instance {@link Kam}
*/
public static Kam copy(final Kam kam) {
if (kam == null) {
return null;
}
final Kam copy = new KamImpl(kam.getKamInfo());
final Collection<KamNode> nodes = kam.getNodes();
if (hasItems(nodes)) {
for (final KamNode node : nodes) {
copy.createNode(node.getId(), node.getFunctionType(),
node.getLabel());
}
}
final Collection<KamEdge> edges = kam.getEdges();
if (hasItems(edges)) {
for (final KamEdge edge : edges) {
final KamNode source = copy.findNode(edge.getSourceNode()
.getId());
final KamNode target = copy.findNode(edge.getTargetNode()
.getId());
assert source != null;
assert target != null;
copy.createEdge(edge.getId(), source,
edge.getRelationshipType(), target);
}
}
return copy;
}
}