/**
* 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 java.io.IOException;
import java.util.Collection;
import java.util.Set;
import org.openbel.framework.common.InvalidArgument;
import org.openbel.framework.common.index.ResourceIndex;
import org.openbel.framework.common.model.Document;
import org.openbel.framework.common.model.EquivalenceDataIndex;
import org.openbel.framework.common.protonetwork.model.ProtoNetwork;
import org.openbel.framework.core.equivalence.EquivalenceMapResolutionFailure;
import org.openbel.framework.core.protonetwork.ProtoNetworkDescriptor;
/**
* BEL compiler phase two interface.
* <p>
* Phase two compilation consists of:
* <ol>
* <li><b>Stage 1 -- Merge Proto Networks</b><br>
* Merge each {@link Document}'s Phase I {@link ProtoNetwork} representation.</li>
*
* <li><b>Stage 2 -- Load Namespace Equivalences</b><br>
* Load namespace equivalence indices.</li>
*
* <li><b>Stage 3 -- Equivalence Merged Proto Network</b><br>
* Equivalence the Phase II / Stage 1 merged {@link ProtoNetwork}. This stage
* only needs to execute if the user provided namespace equivalences in Stage 2.
* </li>
*
* <li><b>Stage 4 -- Externalize the Merged/Equivalenced Proto Network</b><br>
* Externalize the merged/equivalenced {@link ProtoNetwork}.</li>
* </ol>
* </p>
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public interface DefaultPhaseTwo {
/**
* Executes stage one merging of each phase I {@link ProtoNetwork}.
*
* @param protoNetworkDescriptors Collection of
* {@link ProtoNetworkDescriptor}, the proto network descriptors in order to
* load the {@link ProtoNetwork}s
* @return {@link ProtoNetwork}, the merged proto network, which cannot be
* null
*/
public ProtoNetwork stage1Merger(
Collection<ProtoNetworkDescriptor> protoNetworkDescriptors);
/**
* Executes stage two loading of namespace equivalence indices. The
* namespace equivalences are determined from the loaded
* {@link ResourceIndex}.
*
* @return {@link Set} of {@link EquivalenceDataIndex}, the set of
* equivalence data indices, which may by empty but not null
* @throws EquivalenceMapResolutionFailure Thrown if the equivalence map
* file could not be resolved
*/
public Set<EquivalenceDataIndex> stage2LoadNamespaceEquivalences()
throws EquivalenceMapResolutionFailure;
/**
* Executes stage three parameter equivalencing of the merged
* {@link ProtoNetwork}.
* <p>
* Note this method will modify the proto-network {@code protoNetwork}.
* </p>
*
* @param protoNetwork {@link ProtoNetwork}, the merged proto-network to
* equivalence
* @param indexes {@link Set} of {@link EquivalenceDataIndex} equivalence
* data indexes, which cannot be null
* @return int Number of parameters equivalenced
* @throws IOException Thrown if an I/O error occurred during equivalencing
* @throws InvalidArgument Thrown if <tt>indexes</tt> is null
*/
public int stage3EquivalenceParameters(ProtoNetwork protoNetwork,
Set<EquivalenceDataIndex> indexes) throws IOException;
/**
* Executes stage three equivalencing of the merged {@link ProtoNetwork}.
* <p>
* Note this method will modify the proto-network {@code protoNetwork}.
* </p>
*
* @param protoNetwork {@link ProtoNetwork}, the merged proto-network to
* equivalence
* @return int Number of terms equivalenced
*/
public int stage3EquivalenceTerms(ProtoNetwork protoNetwork);
/**
* Executes stage three equivalencing of the merged {@link ProtoNetwork}.
* <p>
* Note this method will modify the proto-network {@code protoNetwork}.
* </p>
*
* @param protoNetwork {@link ProtoNetwork}, the merged proto-network to
* equivalence
* @return int Number of statements equivalenced
*/
public int stage3EquivalenceStatements(ProtoNetwork protoNetwork);
/**
* Executes stage four externalization of the merged/equivalenced
* {@link ProtoNetwork}.
*
* @param protoNetwork {@link ProtoNetwork}, the proto network to
* externalize
* @param protoNetworkRoot {@link String}, the proto network root path to
* write to, which cannot be null
* @return {@link ProtoNetworkDescriptor}, the proto network descriptor,
* which cannot be null
*/
public ProtoNetworkDescriptor stage4WriteEquivalentProtoNetwork(
ProtoNetwork protoNetwork, String protoNetworkRoot);
}