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package sketch;
import java.util.ArrayList;
import java.util.HashMap;
import fileIO.ByteStreamWriter;
import fileIO.ReadWrite;
import shared.Parse;
import shared.Tools;
import structures.FloatList;
import tax.TaxNode;
import tax.TaxTree;
class ResultLineParser {
ResultLineParser(int mode_, TaxTree tree_, ByteStreamWriter bswBad_, ArrayList<RecordSet> recordSets_, boolean keepText_){
mode=mode_;
tree=tree_;
bswBad=bswBad_;
recordSets=recordSets_;
keepText=keepText_ || bswBad!=null;
for(int i=0; i<AnalyzeSketchResults.taxLevels; i++){
aniLists[i]=new FloatList();
ssuLists[i]=new FloatList();
}
}
void parse(byte[] line){
if(keepText){text=line;}
if(line[0]!='#'){
if(mode==AnalyzeSketchResults.BBSKETCH_MODE){
parseData(line);
}else if(mode==AnalyzeSketchResults.MASH_MODE){
parseDataMash(line);
}else{
assert(false) : "Bad mode: "+mode;
}
}else{
parseHeader(line);
if(bswBad!=null){bswBad.println(line);}
}
}
private synchronized void parseHeader(byte[] line){
ArrayList<byte[]> split=Tools.split(line, 0, (byte)'\t');
for(int col=0; col<split.size(); col++){
byte[] array=split.get(col);
if(Tools.equals(array, "ANI") || Tools.equals(array, "AAI")){
aniColumn=col;
}else if(Tools.equals(array, "QTaxID")){
qTaxIDColumn=col;
}else if(Tools.equals(array, "RTaxID")){
rTaxIDColumn=col;
}else if(Tools.equals(array, "SSU")){
ssuColumn=col;
}else if(Tools.equals(array, "CALevel")){
caLevelColumn=col;
}
else if(Tools.equals(array, "QSize")){
qSizeColumn=col;
}else if(Tools.equals(array, "RefSize") || Tools.equals(array, "RSize")){
rSizeColumn=col;
}else if(Tools.equals(array, "QBases")){
qBasesColumn=col;
}else if(Tools.equals(array, "RBases")){
rBasesColumn=col;
}
}
}
private void parseData(byte[] line){
ArrayList<byte[]> split=Tools.split(line, 0, (byte)'\t');
qTaxID=Parse.parseInt(split.get(qTaxIDColumn), 0);
rTaxID=Parse.parseInt(split.get(rTaxIDColumn), 0);
qBases=Parse.parseLong(split.get(qBasesColumn), 0);
rBases=Parse.parseLong(split.get(rBasesColumn), 0);
qSize=Parse.parseLong(split.get(qSizeColumn), 0);
rSize=Parse.parseLong(split.get(rSizeColumn), 0);
ani=Parse.parseDouble(split.get(aniColumn), 0);
byte[] ssuArray=split.get(ssuColumn);
ssu=ssuArray.length==1 && ssuArray[0]=='.' ? -1 : Parse.parseDouble(ssuArray, 0);
taxLevelExtended=TaxTree.stringToLevelExtended(new String(split.get(caLevelColumn)));
if(taxLevelExtended<0) {
System.err.println(new String(split.get(caLevelColumn)));
taxLevelExtended=0;
}
processed=false;
}
private TaxNode getTaxNode(String fname){
String name=ReadWrite.stripToCore(fname);
if(name.startsWith("tid_")){
int idx2=fname.indexOf('_', 4);
int x=Parse.parseInt(fname, 4, idx2);
return x>0 ? tree.getNode(x) : null;
//name=name.substring(idx2+1); //This would allow fall-through to name parsing
}
try {
return tree.getNodeByName(name);
} catch (Throwable e) {
return null;
}
}
private void parseDataMash(byte[] line){
///dev/shm/tid_123_Zymomonas_mobilis.fna.gz /dev/shm/tid_456_bacterium_endosymbiont_of_Bathymodiolus_sp._5_South.fna.gz 0.43859 0.00515848 1/20000
String[] split=new String(line).split("\t");
String fraction=split[split.length-1];
int numerator=Integer.parseInt(fraction.split("/")[0]);
if(numerator<MIN_HITS){return;}
int denominator=Integer.parseInt(fraction.split("/")[1]);
//The default ordering is reversed since mash output is ordered first by ref, then query
//The normal ordering (as below) requires a linux sort
{
TaxNode qNode=getTaxNode(split[0]);
TaxNode rNode=getTaxNode(split[1]);
if(qNode==null || rNode==null){return;}
qTaxID=qNode.id;
rTaxID=rNode.id;
TaxNode ancestor=tree.commonAncestor(qNode, rNode);
taxLevelExtended=ancestor.levelExtended;
}
ani=numerator/(float)denominator;
ssu=-1;
if(taxLevelExtended<0){taxLevelExtended=0;}
processed=false;
}
//Returns a complete set when a new set is started
RecordSet processData(HashMap<Long, Float> map, boolean saveRecord){
RecordSet old=null;
if(processed){return null;}
levelAniSums[taxLevelExtended]+=ani;
levelCounts[taxLevelExtended]++;
aniLists[taxLevelExtended].add((float)ani);
if(ssu>0){
levelSSUSums[taxLevelExtended]+=ssu;
levelCountsSSU[taxLevelExtended]++;
ssuLists[taxLevelExtended].add((float)ssu);
}
if(map!=null){
long key=(((long)qTaxID)<<32)|rTaxID;
map.put(key, (float)ani);
}
if(saveRecord){
if(currentSet==null || currentSet.qID!=qTaxID){
old=currentSet;
currentSet=new RecordSet(qTaxID);
if(recordSets!=null){
recordSets.add(currentSet);
}
}
currentSet.records.add(new Record(this));
}
processed=true;
return old;
}
/*--------------------------------------------------------------*/
// final static int taxLevels=TaxTree.numTaxaNamesExtended;
final long[] levelCounts=new long[AnalyzeSketchResults.taxLevels];
final long[] levelCountsSSU=new long[AnalyzeSketchResults.taxLevels];
final double[] levelAniSums=new double[AnalyzeSketchResults.taxLevels];
final double[] levelSSUSums=new double[AnalyzeSketchResults.taxLevels];
final FloatList[] aniLists=new FloatList[AnalyzeSketchResults.taxLevels];
final FloatList[] ssuLists=new FloatList[AnalyzeSketchResults.taxLevels];
final ArrayList<RecordSet> recordSets;
final int mode;
final TaxTree tree;
final ByteStreamWriter bswBad;
int qTaxID=-1;
int rTaxID=-1;
long qBases;
long rBases;
long qSize;
long rSize;
double ani=-1;
double ssu=-1;
int taxLevelExtended=-1;
boolean processed=true;
RecordSet currentSet=null;
final boolean keepText;
byte[] text=null;
private static int qTaxIDColumn=7;
private static int rTaxIDColumn=8;
private static int qSizeColumn=3;
private static int rSizeColumn=4;
private static int qBasesColumn=5;
private static int rBasesColumn=6;
private static int aniColumn=2;
private static int ssuColumn=11;
private static int caLevelColumn=12;
static int MIN_HITS=3;
}
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