package org.biojava.bio.annodb; import java.util.ArrayList; import java.util.Iterator; import java.util.List; import java.util.NoSuchElementException; import org.biojava.bio.AnnotationTools; import org.biojava.bio.AnnotationType; /** *
An AnnotationDB that provides a merged view of a list of underlying DBs.
* * @author Matthew Pocock * @since 1.3 */ public class MergingAnnotationDB implements AnnotationDB { private final String name; private final List merged; /** * Create a new MergingAnnotationDB with a name and no DBs to merge. * * @param name the name of this DB */ public MergingAnnotationDB(String name) { this.name = name; this.merged = new ArrayList(); } /** * Create a new MergingAnnotationDB with a name and a list of DBs to merge. * * @param name the name of this DB * @param merged a list of DBs to merge */ public MergingAnnotationDB(String name, List merged) { this.name = name; this.merged = new ArrayList(merged); } /** * Add a DB to be merged in this view. * * @param toAdd the AnnotationDB to add */ public void addAnnotationDB(AnnotationDB toAdd) { if(!merged.contains(toAdd)) { merged.add(toAdd); } } /** * Remove a DB from this view. * * @param toRemove the AnnotationDB to remove */ public void removeAnnotationDB(AnnotationDB toRemove) { merged.remove(toRemove); } /** * Return a list of merged DBs. This can be modified independantly of this DB. * * @return a List of merged DBs */ public List getMerged() { return new ArrayList(merged); } public String getName() { return name; } public AnnotationType getSchema() { AnnotationType schema = AnnotationType.NONE; for(Iterator i = merged.iterator(); i.hasNext(); ) { AnnotationDB db = (AnnotationDB) i.next(); schema = AnnotationTools.union(schema, db.getSchema()); } return schema; } public Iterator iterator() { return new Iterator() { Iterator ii; Iterator ci; Object item; { ii = merged.iterator(); EVERYTHING: while(item == null) { if(ii.hasNext()) { AnnotationDB adb = (AnnotationDB) ii.next(); ci = adb.iterator(); if(ci.hasNext()) { item = ci.next(); } } else { break EVERYTHING; } } } public boolean hasNext() { return item != null; } public Object next() { Object it = item; item = _next(); return it; } private Object _next() { while(!ci.hasNext()) { if(ii.hasNext()) { AnnotationDB adb = (AnnotationDB) ii.next(); ci = adb.iterator(); } else { return null; } } return ci.next(); } public void remove() { throw new NoSuchElementException(); } }; } public int size() { int size = 0; for(Iterator dbi = merged.iterator(); dbi.hasNext(); ) { size += ((AnnotationDB) dbi.next()).size(); } return size; } public AnnotationDB filter(AnnotationType at) { List anns = new ArrayList(); for(Iterator i = merged.iterator(); i.hasNext(); ) { AnnotationDB adb = (AnnotationDB) i.next(); AnnotationDB res = adb.filter(at); if(res.size() > 0) { anns.add(res); } } if(anns.isEmpty()) { return AnnotationDB.EMPTY; } else if(anns.size() == 1) { return (AnnotationDB) anns.get(0); } else { return new MergingAnnotationDB("", anns); } } public AnnotationDB search(AnnotationType at) { List anns = new ArrayList(); for(Iterator i = merged.iterator(); i.hasNext(); ) { AnnotationDB adb = (AnnotationDB) i.next(); AnnotationDB res = adb.search(at); if(res.size() > 0) { anns.add(res); } } if(anns.isEmpty()) { return AnnotationDB.EMPTY; } else if(anns.size() == 1) { return (AnnotationDB) anns.get(0); } else { return new MergingAnnotationDB("", anns); } } }