/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.symbol; import java.io.Serializable; import java.util.ArrayList; import java.util.Collections; import java.util.Iterator; import java.util.List; import org.biojava.bio.BioError; /** *
* A complex location. It is made up from multiple sub-locations and is essentially * the point-wise union of the child locations. *
* ** NOTE: It is no longer possible to directly construct * CompoundLocations. Use LocationTools.union instead. *
* * @author Matthew Pocock * @author Thomas Down * @author Greg Cox */ class CompoundLocation extends AbstractLocation implements Location, Serializable { /** * The list of child locations in order. Should contain only RangeLocation * instances. */ private List locations; /** * Minimum index contained. */ private int min = Integer.MAX_VALUE; /** * Maximum index contained. */ private int max = Integer.MIN_VALUE; /** ** Generate a new CompoundLocation from a list of locations. *
* ** You will nearly always want to generate these beasts using the * Location.union method. *
* ** The locations list should contain contiguous locations, sorted by getMin() * and guaranteed to be non-overlapping. *
* * @param locations a list of Location instances to combine into a single * compound location */ CompoundLocation(List locs) { this.locations = new ArrayList(locs); Collections.sort(locations, Location.naturalOrder); locations = Collections.unmodifiableList(locations); Location minL = (Location) locations.get(0); Location maxL = (Location) locations.get(locs.size() - 1); this.min = minL.getMin(); this.max = maxL.getMax(); } public int getMin() { return min; } public int getMax() { return max; } public boolean contains(int p) { if(p < min || p > max) return false; int m = locations.size(); int n = 0; while (m >= n) { int i = (m + n) / 2; Location l = (Location) locations.get(i); if (p < l.getMin()) { m = i - 1; } else if (p > l.getMax()) { n = i + 1; } else { return true; } } return false; } public boolean contains(Location l) { return LocationTools.contains(this, l); } public boolean overlaps(Location l) { return LocationTools.overlaps(this, l); } public Location union(Location loc) { return LocationTools.union(this, loc); } public Location intersection(Location loc) { return LocationTools.intersection(this, loc); } public boolean equals(Object o) { if(!(o instanceof Location)) { return false; } else { return LocationTools.areEqual(this, (Location) o); } } public SymbolList symbols(SymbolList seq) { if (isContiguous()) return seq.subList(min, max); List res = new ArrayList(); for (Iterator i = blockIterator(); i.hasNext(); ) { Location l = (Location) i.next(); res.addAll(l.symbols(seq).toList()); } try { return new SimpleSymbolList(seq.getAlphabet(), res); } catch (IllegalSymbolException ex) { throw new BioError(ex); } } public Location translate(int dist) { if (dist == 0) { return this; } List res = new ArrayList(); for(Iterator i = locations.iterator(); i.hasNext(); ) { res.add( ((Location) i.next()).translate(dist) ); } return new CompoundLocation(res); } public boolean isContiguous() { return locations.size() <= 1; } List getBlockList() { return locations; } public Iterator blockIterator() { return locations.iterator(); } public int hashCode() { return getMin() ^ getMax(); } public String toString() { StringBuffer sb = new StringBuffer(); sb.append(getMin() + ", " + getMax() + " {"); Iterator i = locations.iterator(); if(i.hasNext()) sb.append("(" + i.next() + ")"); while(i.hasNext()) sb.append(", (" + i.next() + ")"); sb.append("}"); return sb.substring(0); } }