net.maizegenetics.dna.map.PositionArrayList Maven / Gradle / Ivy
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TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.
package net.maizegenetics.dna.map;
import com.google.common.collect.ArrayListMultimap;
import net.maizegenetics.dna.WHICH_ALLELE;
import java.nio.IntBuffer;
import java.util.*;
/**
* In memory immutable instance of {@link PositionList}. Use the {@link PositionListBuilder}
* to create the list. This list is sorted by position.
*
* @author Ed Buckler
*/
final class PositionArrayList implements PositionList {
private final List mySiteList;
private final int numPositions;
private final byte[][] alleles;
private final Map myChrOffPosTree;
private final Map myChrNameHash;
private final Chromosome firstChromosome; //null chromosome calls revert to the first chromosome
private final String genomeVersion;
private static class ChrOffPos {
final int startSiteOff;
final int endSiteOff;
final int[] position;
private ChrOffPos(int startSiteOff, int endSiteOff, int[] position) {
this.startSiteOff=startSiteOff;
this.endSiteOff=endSiteOff;
this.position=position;
}
}
PositionArrayList(ArrayList builderList, String genomeVersion) {
this.genomeVersion=genomeVersion;
this.numPositions=builderList.size();
alleles=new byte[WHICH_ALLELE.COUNT][numPositions];
ArrayListMultimap pTS=ArrayListMultimap.create();
mySiteList=new ArrayList(builderList.size());
myChrOffPosTree=new TreeMap();
myChrNameHash=new HashMap<>();
int currStart=0;
if(builderList.isEmpty()) {
firstChromosome=null;
return; //allows for the creation of an empty PositionArrayList
}
Chromosome currChr=builderList.get(0).getChromosome();
for (int i=0; i p=pTS.get(chr);
int[] intP=new int[p.size()];
for (int i=0; i)myChrOffPosTree).firstKey();
pTS=null;
}
@Override
public byte allele(WHICH_ALLELE alleleType, int site) {
return mySiteList.get(site).getAllele(alleleType);
}
@Override
public byte[] alleles(WHICH_ALLELE alleleType, int startSite, int endSite) {
byte[] result = new byte[endSite - startSite];
System.arraycopy(alleles[alleleType.index()],startSite,result,0, result.length);
return result;
}
@Override
public byte[] alleleForAllSites(WHICH_ALLELE alleleType) {
return Arrays.copyOf(alleles[alleleType.index()],alleles[alleleType.index()].length);
}
@Override
public boolean hasReference() {
if (genomeVersion == null) {
return false;
}
return true;
}
@Override
public String siteName(int site) {
return mySiteList.get(site).getSNPID();
}
@Override
public int numberOfSites() {
return numPositions;
}
@Override
public int chromosomeSiteCount(Chromosome chromosome) {
return myChrOffPosTree.get(chromosome).position.length;
}
@Override
public int[] startAndEndOfChromosome(Chromosome chromosome) {
if(chromosome==null) chromosome=firstChromosome;
ChrOffPos cop=myChrOffPosTree.get(chromosome);
if(cop==null) return null;
return new int[]{cop.startSiteOff,cop.endSiteOff};
}
@Override
public int chromosomalPosition(int site) {
return mySiteList.get(site).getPosition();
}
@Override
public int siteOfPhysicalPosition(int physicalPosition, Chromosome chromosome) {
if(chromosome==null) chromosome=firstChromosome;
ChrOffPos cop=myChrOffPosTree.get(chromosome);
if(cop==null) return Integer.MIN_VALUE;
int i=Arrays.binarySearch(cop.position, physicalPosition); //AvgPerObj:227.5715ns for 2million positions
while((i>0)&&(physicalPosition==cop.position[i-1])) {i--;} //backup to the first position if there are duplicates
i+=(i<0)?-cop.startSiteOff:cop.startSiteOff;
return i;
}
@Override
public int siteOfPhysicalPosition(int physicalPosition, Chromosome chromosome, String snpName) {
int result=siteOfPhysicalPosition(physicalPosition, chromosome);
if (result < 0) {return result;}
else {
if (snpName.equals(siteName(result))) {return result;
} else {
int index=result;
while ((index < numPositions) && (chromosomalPosition(index) == physicalPosition)) {
if (snpName.equals(siteName(index))) {return index;}
result++;
}
return -result - 1;
}
}
}
@Override
public int[] physicalPositions() {
int[] result=new int[numPositions];
IntBuffer ib=IntBuffer.wrap(result);
for (ChrOffPos cop: myChrOffPosTree.values()) {
ib.put(cop.position);
}
return result;
}
@Override
public String chromosomeName(int site) {
return mySiteList.get(site).getChromosome().getName();
}
@Override
public Chromosome chromosome(int site) {
return mySiteList.get(site).getChromosome();
}
@Override
public Chromosome chromosome(String name) {
return myChrNameHash.get(name);
}
@Override
public Chromosome[] chromosomes() {
return myChrOffPosTree.keySet().toArray(new Chromosome[0]);
}
@Override
public int numChromosomes() {
return myChrOffPosTree.size();
}
@Override
public int[] chromosomesOffsets() {
int[] result=new int[myChrOffPosTree.size()];
int index=0;
for (ChrOffPos cop: myChrOffPosTree.values()) {
result[index++]=cop.startSiteOff;
}
return result;
}
@Override
public int indelSize(int site) {
return mySiteList.get(site).getKnownVariants()[1].length();
}
@Override
public boolean isIndel(int site) {
return mySiteList.get(site).isIndel();
}
@Override
public String genomeVersion() {
return genomeVersion;
}
@Override
public boolean isPositiveStrand(int site) {
return (1==mySiteList.get(site).getStrand());
}
// List methods
@Override
public int size() {
return mySiteList.size();
}
@Override
public boolean isEmpty() {
return mySiteList.isEmpty();
}
@Override
public boolean contains(Object o) {
Position p=(Position)o;
return (siteOfPhysicalPosition(p.getPosition(),p.getChromosome())>-1);
}
@Override
public Iterator iterator() {
return mySiteList.iterator();
}
@Override
public Object[] toArray() {
return mySiteList.toArray();
}
@Override
public AnnotatedSite[] toArray(AnnotatedSite[] a) {
return mySiteList.toArray(a);
}
/**Not supported immutable class*/
@Override@Deprecated
public boolean add(Position e) {
throw new UnsupportedOperationException("This Class is Immutable.");
}
/**Not supported immutable class*/
@Override@Deprecated
public boolean remove(Object o) {
throw new UnsupportedOperationException("This Class is Immutable.");
}
@Override
public boolean containsAll(Collection c) {
for (Object e : c)
if (!contains(e))
return false;
return true;
}
/**Not supported immutable class*/
@Override@Deprecated
public boolean addAll(Collection c) {
throw new UnsupportedOperationException("This Class is Immutable.");
}
/**Not supported immutable class*/
@Override@Deprecated
public boolean addAll(int index, Collection c) {
throw new UnsupportedOperationException("This Class is Immutable.");
}
/**Not supported immutable class*/
@Override@Deprecated
public boolean removeAll(Collection c) {
throw new UnsupportedOperationException("This Class is Immutable.");
}
/**Not supported immutable class*/
@Override@Deprecated
public boolean retainAll(Collection c) {
throw new UnsupportedOperationException("This Class is Immutable.");
}
/**Not supported immutable class*/
@Override@Deprecated
public void clear() {
throw new UnsupportedOperationException("This Class is Immutable.");
}
@Override
public Position get(int index) {
return mySiteList.get(index);
}
/**Not supported immutable class*/
@Override@Deprecated
public Position set(int index, Position element) {
throw new UnsupportedOperationException("This Class is Immutable.");
}
/**Not supported immutable class*/
@Override@Deprecated
public void add(int index, Position element) {
throw new UnsupportedOperationException("This Class is Immutable.");
}
/**Not supported immutable class*/
@Override@Deprecated
public Position remove(int index) {
throw new UnsupportedOperationException("This Class is Immutable.");
}
@Override
public int indexOf(Object o) {
return Collections.binarySearch(mySiteList,(Position)o);
// return mySiteList.indexOf(o);
}
@Override
public int lastIndexOf(Object o) {
return mySiteList.lastIndexOf(o);
}
@Override
public ListIterator listIterator() {
return listIterator(0);
}
@Override
public ListIterator listIterator(final int index) {
return new ListIterator() {
private final ListIterator i= mySiteList.listIterator(index);
public boolean hasNext() {return i.hasNext();}
public Position next() {return i.next();}
public boolean hasPrevious() {return i.hasPrevious();}
public Position previous() {return i.previous();}
public int nextIndex() {return i.nextIndex();}
public int previousIndex() {return i.previousIndex();}
public void remove() {throw new UnsupportedOperationException();}
public void set(Position e) {throw new UnsupportedOperationException();}
public void add(Position e) {throw new UnsupportedOperationException();}
};
}
@Override
public List subList(int fromIndex, int toIndex) {
return Collections.unmodifiableList(mySiteList.subList(fromIndex, toIndex));
}
}