/**
* 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.compiler;
import static java.util.Collections.emptyList;
import java.util.ArrayList;
import java.util.List;
import org.openbel.framework.common.InvalidArgument;
import org.openbel.framework.common.enums.FunctionEnum;
import org.openbel.framework.common.model.Document;
import org.openbel.framework.common.model.Statement;
import org.openbel.framework.common.protonetwork.model.ProtoNetwork;
import org.openbel.framework.common.protonetwork.model.ProtoNetworkError;
import org.openbel.framework.core.protonetwork.ProtoNetworkDescriptor;
/**
* BEL compiler phase three interface.
* <p>
* Phase three compilation consists of:
* <ol>
* <li><b>Stage 1 -- Gene Scaffolding Injection</b><br>
* Injects gene scaffolding into the source proto-network.<br>
* (TODO more info into how the source proto-network changes</li>
* <li><b>Stage 2 -- Protein Family Injection</b><br>
* Injects protein families into the source proto-network.<br>
* (TODO more info into how the source proto-network changes)</li>
* </ol>
* </p>
*/
public interface DefaultPhaseThree {
/**
* Prunes the protein families document of statements that are not relevant
* to the input proto-network.
* <p>
* Note: This method will modify the provided BEL document.
* </p>
*
* @param expand When {@code true}, members of a protein family found within
* the proto-network will result in protein family injection. Without
* expansion (i.e., {@code false}, only the protein family itself is used
* when examining the proto-network.
* @param d BEL protein families document to be pruned
* @param p Input {@link ProtoNetwork proto-network}
* @return {@link DocumentModificationResult Prune result}
*/
public DocumentModificationResult pruneFamilies(boolean expand, Document d,
ProtoNetwork p);
/**
* Infer and add {@link Statement statements} for protein families and its
* members when
* {@link FunctionEnum#getActivities() molecular activity functions} are
* defined in the {@link ProtoNetwork proto network}.
*
* @param d {@link Document}, the protein family document, which cannot be
* null
* @param p {@link ProtoNetwork}, the proto network being compiled, which
* cannot be null
* @return the {@link DocumentModificationResult result} that indicates
* status and counts of statements added
* @throws InvalidArgument Thrown if the {@link Document d} or
* {@link ProtoNetwork p} is <tt>null</tt>
*/
public DocumentModificationResult inferFamilies(final Document d,
ProtoNetwork p);
/**
* Prunes the named complexes document of statements that are not relevant
* to the input proto-network.
* <p>
* Note: This method will modify the provided BEL document.
* </p>
*
* @param expand When {@code true}, components of a named complex found
* within the proto-network will result in named complex injection. Without
* expansion (i.e., {@code false}), only the named complex itself is used
* when examining the proto-network.
* @param d BEL named complexes document to be pruned
* @param p Input {@link ProtoNetwork proto-network}
* @return {@link DocumentModificationResult Prune result}
*/
public DocumentModificationResult pruneComplexes(boolean expand,
Document d,
ProtoNetwork p);
/**
* Prunes the gene {@link Document document} of {@link Statement statements}
* that are not relevant to the input {@link ProtoNetwork proto-network}.
* <p>
* Note: This method will modify the provided BEL document.
* </p>
*
* @param d document BEL gene scaffolding document to be pruned
* @param p Input {@link ProtoNetwork proto-network}
* @return {@link DocumentModificationResult Prune result}
*/
public DocumentModificationResult pruneGene(Document d, ProtoNetwork p);
/**
* Prunes orthology BEL {@link Document document} by:
* <p>
* Prune the {@link Document document}, relative to the
* {@link ProtoNetwork proto network} being compiled, using equivalencing
* to match up BEL terms.
* </p>
*
* @param d {@link Document} the orthology BEL document, which cannot be
* {@code null}
* @param pn {@link ProtoNetwork} the compiled proto network, which cannot
* be {@code null}
* @return {@link DocumentModificationResult} containing the pruning
* results
* @throws InvalidArgument Thrown if {@code d} or {@code pn} is
* {@code null}
*/
public DocumentModificationResult pruneOrthologyDocument(final Document d,
final ProtoNetwork pn);
/**
* Compiles {@link Document BEL common documents} to {@link ProtoNetwork
* proto-networks}.
*
* @param document {@link Document} the document to compile
* @return {@link ProtoNetwork} the compiled proto network
*/
public ProtoNetwork compile(final Document d);
/**
* Deserialize and merge the proto network in <tt>protoNetworkSource</tt>
* into the proto network in <tt>protoNetworkSource</tt>.
*
* @param destination {@link ProtoNetwork}, the proto-network containing the
* merged results
* @param source {@link ProtoNetwork}, the proto-network to merge into
* {@code destination}
* @throws ProtoNetworkError Thrown if an error occurred reading the proto-
* network from the {@code source} descriptor.
*/
public void merge(ProtoNetwork destination, ProtoNetwork source)
throws ProtoNetworkError;
/**
* Writes the {@link ProtoNetwork proto-network}.
*
* @param protoNetworkRootPath {@link String}, the proto network root path
* to write to
* @param protoNetwork {@link ProtoNetwork}, the proto network to write
*/
public ProtoNetworkDescriptor write(final String path,
final ProtoNetwork network) throws ProtoNetworkError;
/**
* XXX: njb
*/
public static class DocumentModificationResult {
private int totalStatements;
private int deltaStatements;
private boolean success;
private List<String> warnings;
private List<String> errors;
public boolean isSuccess() {
return success;
}
public boolean isFailure() {
return !success;
}
public int getRemainingStatements() {
return totalStatements + deltaStatements;
}
public int getTotalStatements() {
return totalStatements;
}
public void setTotalStatements(int i) {
totalStatements = i;
}
public int getDeltaStatements() {
return deltaStatements;
}
public void setDeltaStatements(int i) {
deltaStatements = i;
}
public void setSuccess(boolean b) {
success = b;
}
public void addWarning(String s) {
if (warnings == null) {
warnings = new ArrayList<String>();
}
warnings.add(s);
}
public List<String> getWarnings() {
if (warnings == null) {
return emptyList();
}
return warnings;
}
public void addError(String s) {
if (errors == null) {
errors = new ArrayList<String>();
}
errors.add(s);
}
public List<String> getErrors() {
if (errors == null) {
return emptyList();
}
return errors;
}
}
}