jpayne@68: package tax;
jpayne@68: 
jpayne@68: import java.io.Serializable;
jpayne@68: import java.util.Comparator;
jpayne@68: 
jpayne@68: import shared.Tools;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Represents a taxonomic identifier, such as a specific genus.
jpayne@68:  * Includes the name, NCBI numeric id, parent id, and taxonomic level.
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Mar 6, 2015
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class TaxNode implements Serializable{
jpayne@68: 
jpayne@68: 	/**
jpayne@68: 	 * 
jpayne@68: 	 */
jpayne@68: 	private static final long serialVersionUID = -4618526038942239246L;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Initialization        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public TaxNode(int id_, String name_){
jpayne@68: 		this(id_, -1, -1, -1, name_);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public TaxNode(int id_, int parent_, int level_, int levelExtended_, String name_){
jpayne@68: 		id=id_;
jpayne@68: 		pid=parent_;
jpayne@68: 		level=level_;
jpayne@68: 		levelExtended=levelExtended_;
jpayne@68: 		setOriginalLevel(levelExtended);
jpayne@68: 		name=name_;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------           Methods            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/**
jpayne@68: 	 * @param split
jpayne@68: 	 * @param idx
jpayne@68: 	 * @return True if the node's name matches the 
jpayne@68: 	 */
jpayne@68: 	public boolean matchesName(String[] split, int idx, TaxTree tree) {
jpayne@68: 		if(idx<0){return true;}
jpayne@68: 		if(!split[idx].equalsIgnoreCase(name)){return false;}
jpayne@68: 		return tree.getNode(pid).matchesName(split, idx-1, tree);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public String toString(){
jpayne@68: 		return "("+id+","+pid+","+countRaw+","+countSum+",'"+levelStringExtended(false)+"',"+(canonical() ? "T" : "F")+",'"+name+"')";
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean equals(TaxNode b){
jpayne@68: 		if(id!=b.id || pid!=b.pid || levelExtended!=b.levelExtended || flag!=b.flag){return false;}
jpayne@68: 		if(name==b.name){return true;}
jpayne@68: 		if((name==null) != (b.name==null)){return false;}
jpayne@68: 		return name.equals(b.name);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public long incrementRaw(long amt){
jpayne@68: 		if(amt==0){return countRaw;}
jpayne@68: 		if(verbose){System.err.println("incrementRaw("+amt+") node: "+this);}
jpayne@68: 		countRaw+=amt;
jpayne@68: 		assert(countRaw>=0) : "Overflow! "+countRaw+", "+amt;
jpayne@68: 		return countRaw;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public long incrementSum(long amt){
jpayne@68: 		if(amt==0){return countSum;}
jpayne@68: 		if(verbose){System.err.println("incrementSum("+amt+") node: "+this);}
jpayne@68: 		countSum+=amt;
jpayne@68: 		assert(countSum>=0 || amt<0) : "Overflow! "+countSum+", "+amt;
jpayne@68: 		return countSum;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean isSimple(){
jpayne@68: 		return TaxTree.isSimple(levelExtended);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean isSimple2(){
jpayne@68: 		return TaxTree.isSimple2(levelExtended);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: //	public String levelString(){return level<0 ? "unknown" : TaxTree.levelToString(level);}
jpayne@68: 	
jpayne@68: 	public String levelStringExtended(boolean original){
jpayne@68: 		int x=(original ? originalLevel() : levelExtended);
jpayne@68: 		return x<0 ? "unknown" : TaxTree.levelToStringExtended(x);
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public String levelToStringShort() {return level<0 ? "x" : TaxTree.levelToStringShort(level);}
jpayne@68: 	
jpayne@68: 
jpayne@68: 	
jpayne@68: 	public boolean isUnclassified(){
jpayne@68: 		return name.startsWith("unclassified");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean isEnvironmentalSample(){
jpayne@68: 		return name.startsWith("environmental");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Nested Classes        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public static class CountComparator implements Comparator<TaxNode>{
jpayne@68: 		
jpayne@68: 		@Override
jpayne@68: 		public int compare(TaxNode a, TaxNode b) {
jpayne@68: 			long x=b.countSum-a.countSum;
jpayne@68: //			System.err.println("x="+x+" -> "+Tools.longToInt(x));
jpayne@68: 			if(x!=0){return Tools.longToInt(x);}
jpayne@68: 			return a.levelExtended==b.levelExtended ? a.id-b.id : a.levelExtended-b.levelExtended;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------           Getters            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final int hashCode(){return id;}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public boolean canonical(){
jpayne@68: 		return (flag&CANON_MASK)==CANON_MASK;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean levelChanged(){
jpayne@68: 		return originalLevel()!=levelExtended;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public int originalLevel(){
jpayne@68: 		int x=(int)(flag&ORIGINAL_LEVEL_MASK);
jpayne@68: 		return x==ORIGINAL_LEVEL_MASK ? -1 : x;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean cellularOrganisms(){
jpayne@68: 		return id==TaxTree.CELLULAR_ORGANISMS_ID;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: //	public int numChildren(){
jpayne@68: //		return numChildren;
jpayne@68: //	}
jpayne@68: //
jpayne@68: //	public int minParentLevelExtended(){
jpayne@68: //		return minParentLevelExtended;
jpayne@68: //	}
jpayne@68: //
jpayne@68: //	public int maxChildLevelExtended(){
jpayne@68: //		return maxChildLevelExtended;
jpayne@68: //	}
jpayne@68: 	
jpayne@68: 	int minAncestorLevelIncludingSelf(){
jpayne@68: 		return levelExtended<1 ? minParentLevelExtended : levelExtended;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	int maxDescendantLevelIncludingSelf(){
jpayne@68: 		return levelExtended<1 ? maxChildLevelExtended : levelExtended;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public String simpleName(){
jpayne@68: 		if(name==null){return null;}
jpayne@68: 		StringBuilder sb=new StringBuilder();
jpayne@68: 		char last='?';
jpayne@68: 		for(int i=0; i<name.length(); i++){
jpayne@68: 			char c=name.charAt(i);
jpayne@68: 			if((c>='a' && c<='z') || (c>='A' && c<='Z') || (c>='1' && c<='0')){
jpayne@68: 				sb.append(c);
jpayne@68: 				last=c;
jpayne@68: 			}else{
jpayne@68: 				if(sb.length()>0 && last!=' '){sb.append(' ');}
jpayne@68: 				last=' ';
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		String s=sb.toString().trim();
jpayne@68: 		return s.replace(' ', '_');
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean isRanked() {return levelExtended!=TaxTree.NO_RANK_E;}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------           Setters            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public void setCanonical(boolean b){
jpayne@68: 		if(b){flag=flag|CANON_MASK;}
jpayne@68: 		else{flag=flag&~CANON_MASK;}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void setOriginalLevel(int x){
jpayne@68: 		flag=(flag&~ORIGINAL_LEVEL_MASK)|(x&ORIGINAL_LEVEL_MASK);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Return true if changed */
jpayne@68: 	boolean discussWithParent(TaxNode parent){
jpayne@68: 		final int oldChildLevel=parent.maxChildLevelExtended;
jpayne@68: 		final int oldParentLevel=minParentLevelExtended;
jpayne@68: 		parent.maxChildLevelExtended=Tools.max(parent.maxChildLevelExtended, maxDescendantLevelIncludingSelf());
jpayne@68: 		minParentLevelExtended=Tools.min(parent.minAncestorLevelIncludingSelf(), minParentLevelExtended);
jpayne@68: 		return oldChildLevel!=parent.maxChildLevelExtended || oldParentLevel!=minParentLevelExtended;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public final int id;
jpayne@68: 	public final String name;
jpayne@68: 	public int pid;
jpayne@68: 	public int level;
jpayne@68: 	public int levelExtended;
jpayne@68: 	
jpayne@68: 	public int numChildren=0;
jpayne@68: 	public int minParentLevelExtended=TaxTree.LIFE_E;
jpayne@68: 	public int maxChildLevelExtended=TaxTree.NO_RANK_E;
jpayne@68: 	
jpayne@68: 	private long flag=0;
jpayne@68: 	
jpayne@68: 	public long countRaw=0;
jpayne@68: 	public long countSum=0;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------          Constants           ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private static final long ORIGINAL_LEVEL_MASK=63; //bits 0-5
jpayne@68: 	private static final long CANON_MASK=64; //bit 6
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------           Statics            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public static final boolean verbose=false;
jpayne@68: 	public static final CountComparator countComparator=new CountComparator();
jpayne@68: 	
jpayne@68: 	
jpayne@68: }