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package org.rcsb.mmtf.encoder;

import java.util.ArrayList;
import java.util.List;

import org.rcsb.mmtf.api.StructureDataInterface;
import org.rcsb.mmtf.dataholders.BioAssemblyData;
import org.rcsb.mmtf.dataholders.BioAssemblyTransformation;
import org.rcsb.mmtf.dataholders.Entity;
import org.rcsb.mmtf.dataholders.Group;
import org.rcsb.mmtf.dataholders.MmtfStructure;
import org.rcsb.mmtf.utils.CodecUtils;

/**
 * A class of static utility functions to aid encoding of data.
 * Convert from {@link StructureDataInterface} into a format useable by
 * the {@link MmtfStructure}.
 * @author Anthony Bradley
 *
 */
public class EncoderUtils {

	/**
	 * Regenerate a group map from the {@link StructureDataInterface}.
	 * @param structureDataInterface the input interface
	 * @return a list of all the groups in the molecule
	 */
	public static Group[] generateGroupMap(StructureDataInterface structureDataInterface) {
		int[] groupTypeIndices = structureDataInterface.getGroupTypeIndices();
		int maxIndex = CodecUtils.findMaxInIntArray(groupTypeIndices);
		Group[] outGroupList = new Group[maxIndex+1];
		for (int i=0; i generateBioassemblies(StructureDataInterface structureDataInterface) {
		int numBioassemblies = structureDataInterface.getNumBioassemblies();
		List outList = new ArrayList<>();
		for (int i=0; i transformList = new ArrayList<>();
			bioAssemblyData.setTransformList(transformList);
			int numTrans = structureDataInterface.getNumTransInBioassembly(i);
			for (int j=0; j