AdunTrajectory.h

/*
 Project:  AdunCore
 
 Copyright (C) 2007 Michael Johnston & Jordi Villà--Freixa
 
 Author: Michael Johnston
 
 This application is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public
 License as published by the Free Software Foundation; either
 version 2 of the License, or (at your option) any later version.
 
 This application 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
 Library General Public License for more details.
 
 You should have received a copy of the GNU General Public
 License along with this library; if not, write to the Free
 Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111 USA.
 */

#ifndef _AdTrajectory_H_
#define _AdTrajectory_H_

#include <Foundation/Foundation.h>
#include <AdunKernel/AdunDefinitions.h>
#include <AdunKernel/AdunModelObject.h>
#include <AdunKernel/AdunDataMatrix.h>
#include <AdunKernel/AdunDataSet.h>
#include <AdunKernel/AdunSystem.h>
#include <AdunKernel/AdunSystemCollection.h>
#include <AdunKernel/AdunForceFieldCollection.h>
#include <AdunKernel/AdunInteractionSystem.h>

typedef enum
{
        AdSimulationStorageWriteMode = 1, 
        AdSimulationStorageReadMode = 2, 
        AdSimulationStorageAppendMode = 5, 
        AdSimulationStorageUpdateMode = 6, 
}
AdSimulationStorageMode;

@protocol AdSimulationStorageReading <NSObject>
- (NSURL*) storagePath;
- (AdSimulationStorageMode) storageMode;
- (unsigned long long) sizeOfStore;
- (BOOL) isTemporary;
- (BOOL) isAccessible;
- (NSError*) accessError;
- (NSError*) dataError;
- (unsigned int) numberTrajectoryCheckpoints;
- (unsigned int) numberTopologyCheckpoints;
- (NSData*) trajectoryCheckpoint: (int) number;
- (NSData*) topologyCheckpoint: (int) number;
- (NSData*) energyData;
- (NSData*) systemData;
- (NSData*) frameData;
- (void) update;

@end

@protocol AdSimulationStorageWriting
- (void) setEnergyData: (NSData*) data;
- (void) setFrameData: (NSData*) data;
- (void) setSystemData: (NSData*) data;
- (void) addTrajectoryCheckpoint: (NSData*) data;
- (void) removeTrajectoryCheckpoints: (int) number;
- (void) addTopologyCheckpoint: (NSData*) data;
- (void) removeTopologyCheckpoints: (int) number;
- (void) synchronizeStore;
- (BOOL) destroyStoredData;
- (void) setIsTemporary: (BOOL) value;
@end

@protocol AdTrajectoryCheckpointRequestPreparation
- (void) prepareForCheckpointRequestsWithRange: (NSRange) range stepSize: (unsigned int) stepSize;
- (void) stopPreparingForCheckpointRequests;
@end

@interface AdTrajectory: NSObject <AdTrajectoryCheckpointRequestPreparation>
{
        BOOL checkDataStorageIdentification;
        unsigned int numberEnergyCheckpoints;
        AdDataSet* stateData;
        id systemCollection;
        id <AdSimulationStorageReading, AdTrajectoryCheckpointRequestPreparation> dataStorage;
        id frames;
}
+ (id) trajectoryFromLocation: (id) location;
+ (id) trajectoryFromLocation: (id) location error: (NSError**) error;
- (id) initWithLocation: (id) location error: (NSError**) error;
- (NSURL*) location;
- (id) dataStorage;
- (AdDataSet*) energies;
- (AdSystemCollection*) systemCollection;
- (NSArray*) systems;
- (AdDataSet*) frames;
- (id) mementoForSystem: (id) system inTrajectoryCheckpoint: (unsigned int) number;
- (id) dataSourceForSystem: (id) system inTopologyCheckpoint: (unsigned int) number;
- (AdDataMatrix*) coordinatesForSystem: (id) system inTrajectoryCheckpoint: (unsigned int) number;
- (void) coordinatesForSystem: (id) system inTrajectoryCheckpoint: (unsigned int) number usingBuffer: (AdMatrix*) buffer;
- (BOOL) compareCheckpointsForSystem: (id) aSystem 
                inTrajectory: (AdTrajectory*) aTrajectory 
                toSystem: (id) ourSystem 
                range: (NSRange) range;
- (unsigned int) numberTrajectoryCheckpoints;
- (unsigned int) numberTopologyCheckpoints;
- (unsigned int) numberOfFrames;
- (unsigned int) frameForTopologyCheckpoint: (unsigned int) number;
- (unsigned int) frameForEnergyCheckpoint: (unsigned int) number;
- (unsigned int) frameForTrajectoryCheckpoint: (unsigned int) number;
- (id) lastRecordedDataSourceForSystem: (id) system inRange: (NSRange) aRange;
- (NSArray*) dataRecordedInFrame: (unsigned int) frame;
- (void) update;
@end


@protocol AdTrajectoryMethods
- (NSString*) location;
- (AdDataSet*) energies;
- (NSArray*) systems;
- (AdDataSet*) frames;
- (id) mementoForSystem: (id) system inTrajectoryCheckpoint: (unsigned int) number;
- (id) dataSourceForSystem: (id) system inTopologyCheckpoint: (unsigned int) number;
- (AdDataMatrix*) coordinatesForSystem: (id) system inTrajectoryCheckpoint: (unsigned int) number;
- (void) coordinatesForSystem: (id) system inTrajectoryCheckpoint: (unsigned int) number usingBuffer: (AdMatrix*) buffer;
- (unsigned int) numberTrajectoryCheckpoints;
- (unsigned int) numberTopologyCheckpoints;
- (unsigned int) numberOfFrames;
- (unsigned int) frameForTopologyCheckpoint: (unsigned int) number;
- (unsigned int) frameForEnergyCheckpoint: (unsigned int) number;
- (unsigned int) frameForTrajectoryCheckpoint: (unsigned int) number;
- (id) lastRecordedDataSourceForSystem: (id) system inRange: (NSRange) aRange;
- (NSArray*) dataRecordedInFrame: (unsigned int) frame;
- (void) update;
- (AdSystemCollection*) systemCollection;
@end

@interface AdMutableTrajectory: NSObject <AdTrajectoryMethods>
{
        BOOL needsUpdate;
        BOOL frameOpen;
        BOOL trajectoryCheckpoint;
        BOOL topologyCheckpoint;
        BOOL energyCheckpoint;
        int lastFrame;
        NSMutableData* trajectoryData;          
        NSMutableDictionary* energyData;        
        NSString* iterationHeader;
        NSNumber* iterationValue;
        NSMutableDictionary* topologyData; 
        AdForceFieldCollection* forceFieldCollection;
        AdSystemCollection* systemCollection;
        AdDataSet* stateData;
        AdMutableDataMatrix* frames;
        AdTrajectory* trajectoryReader;
        id dataStorage;
}
+ (id) trajectoryFromLocation: (NSString*) location;
+ (id) trajectoryFromLocation: (NSString*) location error: (NSError**) error;
- (id) initWithLocation: (NSString*) path error: (NSError**) error;
- (id) initWithLocation: (id) path
                systems: (AdSystemCollection*) aSystemCollection
            forceFields: (AdForceFieldCollection*) aForceFieldCollection
        iterationHeader: (NSString*) aString
                  error: (NSError**) error;
- (void) setForceFields: (AdForceFieldCollection*) aForceFieldCollection;                 
- (void) openFrame: (NSNumber*) iterationNumber;
- (BOOL) isOpenFrame;
- (void) closeFrame;
- (int)  lastFrame;
- (unsigned int) lastEnergyCheckpoint;
- (unsigned int) lastTrajectoryCheckpoint;
- (unsigned int) lastTopologyCheckpoint;
- (NSNumber*) lastIterationNumber;
- (void) addTopologyCheckpoint;
- (void) addTopologyCheckpointForSystem: (id) aSystem;
- (void) addTrajectoryCheckpoint;
- (void) addEnergyCheckpoint;
- (void) rollBackToFrame: (unsigned int) value;
- (void) synchToStore;
- (id) dataStorage; 
@end

#endif