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package dna;
import java.util.ArrayList;
import shared.Shared;
import shared.Tools;
public class GeneSet implements Comparable<GeneSet>{
public static void main(String[] args){
Data.getGeneIDTable();
}
public GeneSet(String n, ArrayList<Gene> g){
name=n;
id=g.get(0).id;
genes=g;
chrom=g.get(0).chromosome;
transcripts=genes.size();
assert(transcripts>0);
byte st=-1;
boolean pse=true, unt=true;
for(int i=0; i<transcripts; i++){
Gene gene=g.get(i);
assert(gene.id==id) : g;
pse=(pse&&gene.pseudo);
unt=(unt&&gene.untranslated);
minStart=min((int)gene.txStart, minStart);
maxEnd=max((int)gene.txStop, maxEnd);
// assert(st==-1 || st==gene.strand) : g;
if(st==-1){st=gene.strand;}
else if(st!=gene.strand){st=(byte) Tools.find("?", Shared.strandCodes);}
}
pseudo=pse;
untranslated=unt;
for(Gene gene : g){
assert(pseudo==gene.pseudo || (!pseudo && gene.pseudo)) : g;
assert(untranslated==gene.untranslated || (!untranslated && gene.untranslated)) : g;
// assert(untranslated==gene.untranslated) : g;
}
strand=st;
}
@Override
public String toString(){
StringBuilder sb=new StringBuilder();
sb.append(name);
while(sb.length()<10){sb.append(' ');}
sb.append('\t');
sb.append(padFront(transcripts+"",2)+" transcript"+(transcripts==1 ? " " : "s"));
sb.append("\tchr"+chrom+" ("+minStart+" - "+maxEnd+"), '"+Shared.strandCodes[strand]+"'");
return sb.toString();
}
private static final String padFront(String num, int width){
String r=num;
while(r.length()<width){r=" "+r;}
return r;
}
private static final String padBack(String num, int width){
String r=num;
while(r.length()<width){r=r+" ";}
return r;
}
public final String name;
public final int id;
public final byte chrom;
public final byte strand;
public final ArrayList<Gene> genes;
public final int transcripts;
/** True if all transcripts are untranslated */
public final boolean untranslated;
/** True if all transcripts are psuedogenes */
public final boolean pseudo;
public int minStart=Integer.MAX_VALUE;
public int maxEnd=0;
public boolean intersects(int point){
return point>=minStart && point<=maxEnd;
}
public boolean intersects(int point1, int point2){
return point2>=minStart && point1<=maxEnd;
}
@Override
public int compareTo(GeneSet other) {
if(chrom!=other.chrom){
return chrom>other.chrom ? 1 : -1;
}
int x=minStart<other.minStart ? -1 : minStart>other.minStart ? 1 : 0;
if(x!=0){return x;}
return x=name.compareTo(other.name);
}
@Override
public boolean equals(Object other){
return equals((GeneSet)other);
}
public boolean equals(GeneSet other){
return compareTo(other)==0;
}
@Override
public int hashCode(){
return Integer.rotateLeft(name.hashCode(), 5)^chrom;
}
private static final int min(int x, int y){return x<y ? x : y;}
private static final int max(int x, int y){return x>y ? x : y;}
private static final byte min(byte x, byte y){return x<y ? x : y;}
private static final byte max(byte x, byte y){return x>y ? x : y;}
private static final long min(long x, long y){return x<y ? x : y;}
private static final long max(long x, long y){return x>y ? x : y;}
private static final float min(float x, float y){return x<y ? x : y;}
private static final float max(float x, float y){return x>y ? x : y;}
}
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