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package sketch;
import java.io.File;
import java.util.ArrayList;
import dna.Data;
import kmer.AbstractKmerTable;
import shared.PreParser;
public class Blacklist extends SketchObject {
public static boolean parseBlacklist(String arg, String a, String b) {
String x;
boolean force=false;
if(a.equals("bl") || a.equals("blacklist")){
force=true;
x=b;
}else{
x=a;
}
if(force || blacklist==null){
if(x.equalsIgnoreCase("nt")){
blacklist=Blacklist.ntBlacklist();
}else if(x.equalsIgnoreCase("silva") || x.equalsIgnoreCase("ribo")){
blacklist=Blacklist.silvaBlacklist();
}else if(x.equalsIgnoreCase("refseq") || x.equalsIgnoreCase("refseqbig")){
blacklist=Blacklist.refseqBlacklist();
}else if(x.equalsIgnoreCase("img")){
blacklist=Blacklist.imgBlacklist();
}else if(x.equalsIgnoreCase("nr")){
blacklist=Blacklist.nrBlacklist();
}else if(x.equalsIgnoreCase("refseqprot") || x.equalsIgnoreCase("prokprot") || x.equalsIgnoreCase("prokprotbig")
|| x.equalsIgnoreCase("protein") || x.equalsIgnoreCase("protien") || x.equalsIgnoreCase("prot")){
blacklist=Blacklist.prokProtBlacklist();
}else if(x.equalsIgnoreCase("mito")){
blacklist=Blacklist.mitoBlacklist();
}else if(x.equalsIgnoreCase("fungi")){
blacklist=Blacklist.fungiBlacklist();
}else if(force){
blacklist=b;
}else{
return false;
}
return true;
}
return false;
}
public static void addFiles(String fname){
if(fname==null){return;}
ArrayList<Sketch> sketches=new ArrayList<Sketch>();
if(fname.indexOf(',')<0 || new File(fname).exists()){
ArrayList<Sketch> temp=addFile(fname);
sketches.addAll(temp);
}else{
String[] split=fname.split(",");
for(String s : split){
if(s!=null && !"null".equalsIgnoreCase(s)){
ArrayList<Sketch> temp=addFile(s);
sketches.addAll(temp);
}
}
}
addSketches(sketches);
}
private static ArrayList<Sketch> addFile(String fname){
if(fname==null){return null;}
if(!new File(fname).exists()){
if("nt".equalsIgnoreCase(fname)){
fname=Blacklist.ntBlacklist();
}else if(("silva".equalsIgnoreCase(fname) || "ribo".equalsIgnoreCase(fname))){
fname=Blacklist.silvaBlacklist();
}else if("refseq".equalsIgnoreCase(fname)){
fname=Blacklist.refseqBlacklist();
}else if("img".equalsIgnoreCase(fname)){
fname=Blacklist.imgBlacklist();
}else if("prokprot".equalsIgnoreCase(fname) || "protein".equalsIgnoreCase(fname) || "protien".equalsIgnoreCase(fname) || "prot".equalsIgnoreCase(fname)){
fname=Blacklist.prokProtBlacklist();
}else if("fungi".equalsIgnoreCase(fname)){
fname=Blacklist.fungiBlacklist();
}else if("mito".equalsIgnoreCase(fname)){
fname=Blacklist.mitoBlacklist();
}
}
if(!PreParser.silent){System.err.println("Adding "+fname+" to blacklist.");}
assert(!added.contains(fname));
added.add(fname);
SketchTool tool=new SketchTool(1000000, 1, false, false, rcomp);
ArrayList<Sketch> sketches=tool.loadSketchesFromFile(fname, null, 1, -1, ONE_SKETCH, 1f, 0f, 0f, (byte)0, false);
return sketches;
}
private static void addSketches(ArrayList<Sketch> sketches){
if(sketches==null || sketches.isEmpty()){return;}
long size=0;
for(Sketch sk : sketches){
size+=sk.length();
}
long size2=(size*4)/3;
assert(size2>0 && size2+1000<Integer.MAX_VALUE) : size2;
if(keySets==null){
keySets=AbstractKmerTable.preallocate(ways, AbstractKmerTable.ARRAY1D, new int[] {(int)size2}, -1L);
// keySets=AbstractKmerTable.preallocate(ways, AbstractKmerTable.ARRAY1D, (int)size2, -1L, true);
}
for(Sketch sk : sketches){
for(long key : sk.keys){
increment(Long.MAX_VALUE-key);
}
}
}
public static int increment(long key){
int way=0;//(int)(key%ways);
return keySets[way].increment(key, 1);
}
public static boolean contains(long key){
if(keySets==null){return false;}
int way=0;//(int)(key%ways);
return keySets[way].getValue(key)>0;
}
public static boolean exists(){
return keySets!=null;
}
public static final String toBlacklist(String b){
String blacklist=b;
if(b==null){
//do nothing
}else if(b.equalsIgnoreCase("nt")){
blacklist=ntBlacklist();
}else if(b.equalsIgnoreCase("refseq")){
blacklist=refseqBlacklist();
}else if(b.equalsIgnoreCase("silva") || b.equalsIgnoreCase("ribo")){
blacklist=silvaBlacklist();
}else if(b.equalsIgnoreCase("img")){
blacklist=imgBlacklist();
}else if(b.equalsIgnoreCase("refseqprot") || b.equalsIgnoreCase("prokprot")
|| b.equalsIgnoreCase("protein") || b.equalsIgnoreCase("protien") || b.equalsIgnoreCase("prot")){
blacklist=prokProtBlacklist();
}else if(b.equalsIgnoreCase("refseqmito") || b.equalsIgnoreCase("mito")){
blacklist=mitoBlacklist();
}else if(b.equalsIgnoreCase("refseqfungi") || b.equalsIgnoreCase("fungi")){
blacklist=fungiBlacklist();
}
return blacklist;
}
static synchronized String ntBlacklist(){return ntBlacklist!=null ? ntBlacklist : (ntBlacklist=Data.findPath("?blacklist_nt_merged.sketch"));}
static synchronized String silvaBlacklist(){return silvaBlacklist!=null ? silvaBlacklist : (silvaBlacklist=Data.findPath("?blacklist_silva_merged.sketch"));}
static synchronized String refseqBlacklist(){return refseqBlacklist!=null ? refseqBlacklist : (refseqBlacklist=Data.findPath("?blacklist_refseq_merged.sketch"));}
static synchronized String imgBlacklist(){return imgBlacklist!=null ? imgBlacklist : (imgBlacklist=Data.findPath("?blacklist_img_species_300.sketch"));}
static synchronized String nrBlacklist(){return null;}//Data.findPath("?blacklist_nr_species_1000.sketch");
static synchronized String prokProtBlacklist(){return prokProtBlacklist!=null ? prokProtBlacklist : (prokProtBlacklist=Data.findPath("?blacklist_prokprot_merged.sketch"));}
static synchronized String mitoBlacklist(){return mitoBlacklist!=null ? mitoBlacklist : (mitoBlacklist=Data.findPath("?blacklist_refseq_merged.sketch"));}
static synchronized String fungiBlacklist(){return fungiBlacklist!=null ? fungiBlacklist : (fungiBlacklist=Data.findPath("?blacklist_refseq_merged.sketch"));}
private static String ntBlacklist;
private static String silvaBlacklist;
private static String refseqBlacklist;
private static String imgBlacklist;
private static String prokProtBlacklist;
private static String nrBlacklist;
private static String mitoBlacklist;
private static String fungiBlacklist;
/** Hold kmers. A kmer X such that X%WAYS=Y will be stored in keySets[Y] */
static AbstractKmerTable[] keySets;
private static final int ways=1;
// private static final int initialSize=16000;
private static ArrayList<String> added=new ArrayList<String>();
}
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